Image interpolation used in three-dimensional range data compression.

PubMed

Zhang, Shaoze; Zhang, Jianqi; Huang, Xi; Liu, Delian

2016-05-20

Advances in the field of three-dimensional (3D) scanning have made the acquisition of 3D range data easier and easier. However, with the large size of 3D range data comes the challenge of storing and transmitting it. To address this challenge, this paper presents a framework to further compress 3D range data using image interpolation. We first use a virtual fringe-projection system to store 3D range data as images, and then apply the interpolation algorithm to the images to reduce their resolution to further reduce the data size. When the 3D range data are needed, the low-resolution image is scaled up to its original resolution by applying the interpolation algorithm, and then the scaled-up image is decoded and the 3D range data are recovered according to the decoded result. Experimental results show that the proposed method could further reduce the data size while maintaining a low rate of error.

Structured illumination microscopy for dual-modality 3D sub-diffraction resolution fluorescence and refractive-index reconstruction

PubMed Central

Chowdhury, Shwetadwip; Eldridge, Will J.; Wax, Adam; Izatt, Joseph A.

2017-01-01

Though structured illumination (SI) microscopy is a popular imaging technique conventionally associated with fluorescent super-resolution, recent works have suggested its applicability towards sub-diffraction resolution coherent imaging with quantitative endogenous biological contrast. Here, we demonstrate that SI can efficiently integrate together the principles of fluorescent super-resolution and coherent synthetic aperture to achieve 3D dual-modality sub-diffraction resolution, fluorescence and refractive-index (RI) visualizations of biological samples. We experimentally demonstrate this framework by introducing a SI microscope capable of 3D sub-diffraction resolution fluorescence and RI imaging, and verify its biological visualization capabilities by experimentally reconstructing 3D RI/fluorescence visualizations of fluorescent calibration microspheres as well as alveolar basal epithelial adenocarcinoma (A549) and human colorectal adenocarcinmoa (HT-29) cells, fluorescently stained for F-actin. This demonstration may suggest SI as an especially promising imaging technique to enable future biological studies that explore synergistically operating biophysical/biochemical and molecular mechanisms at sub-diffraction resolutions. PMID:29296504

3D laser imaging for ODOT interstate network at true 1-mm resolution.

DOT National Transportation Integrated Search

2014-12-01

With the development of 3D laser imaging technology, the latest iteration of : PaveVision3D Ultra can obtain true 1mm resolution 3D data at full-lane coverage in all : three directions at highway speed up to 60MPH. This project provides rapid survey ...

Projection x-space magnetic particle imaging.

PubMed

Goodwill, Patrick W; Konkle, Justin J; Zheng, Bo; Saritas, Emine U; Conolly, Steven M

2012-05-01

Projection magnetic particle imaging (MPI) can improve imaging speed by over 100-fold over traditional 3-D MPI. In this work, we derive the 2-D x-space signal equation, 2-D image equation, and introduce the concept of signal fading and resolution loss for a projection MPI imager. We then describe the design and construction of an x-space projection MPI scanner with a field gradient of 2.35 T/m across a 10 cm magnet free bore. The system has an expected resolution of 3.5 × 8.0 mm using Resovist tracer, and an experimental resolution of 3.8 × 8.4 mm resolution. The system images 2.5 cm × 5.0 cm partial field-of views (FOVs) at 10 frames/s, and acquires a full field-of-view of 10 cm × 5.0 cm in 4 s. We conclude by imaging a resolution phantom, a complex "Cal" phantom, mice injected with Resovist tracer, and experimentally confirm the theoretically predicted x-space spatial resolution.

4-D photoacoustic tomography.

PubMed

Xiang, Liangzhong; Wang, Bo; Ji, Lijun; Jiang, Huabei

2013-01-01

Photoacoustic tomography (PAT) offers three-dimensional (3D) structural and functional imaging of living biological tissue with label-free, optical absorption contrast. These attributes lend PAT imaging to a wide variety of applications in clinical medicine and preclinical research. Despite advances in live animal imaging with PAT, there is still a need for 3D imaging at centimeter depths in real-time. We report the development of four dimensional (4D) PAT, which integrates time resolutions with 3D spatial resolution, obtained using spherical arrays of ultrasonic detectors. The 4D PAT technique generates motion pictures of imaged tissue, enabling real time tracking of dynamic physiological and pathological processes at hundred micrometer-millisecond resolutions. The 4D PAT technique is used here to image needle-based drug delivery and pharmacokinetics. We also use this technique to monitor 1) fast hemodynamic changes during inter-ictal epileptic seizures and 2) temperature variations during tumor thermal therapy.

Computational-optical microscopy for 3D biological imaging beyond the diffraction limit

NASA Astrophysics Data System (ADS)

Grover, Ginni

In recent years, super-resolution imaging has become an important fluorescent microscopy tool. It has enabled imaging of structures smaller than the optical diffraction limit with resolution less than 50 nm. Extension to high-resolution volume imaging has been achieved by integration with various optical techniques. In this thesis, development of a fluorescent microscope to enable high resolution, extended depth, three dimensional (3D) imaging is discussed; which is achieved by integration of computational methods with optical systems. In the first part of the thesis, point spread function (PSF) engineering for volume imaging is discussed. A class of PSFs, referred to as double-helix (DH) PSFs, is generated. The PSFs exhibit two focused spots in the image plane which rotate about the optical axis, encoding depth in rotation of the image. These PSFs extend the depth-of-field up to a factor of ˜5. Precision performance of the DH-PSFs, based on an information theoretical analysis, is compared with other 3D methods with conclusion that the DH-PSFs provide the best precision and the longest depth-of-field. Out of various possible DH-PSFs, a suitable PSF is obtained for super-resolution microscopy. The DH-PSFs are implemented in imaging systems, such as a microscope, with a special phase modulation at the pupil plane. Surface-relief elements which are polarization-insensitive and ˜90% light efficient are developed for phase modulation. The photon-efficient DH-PSF microscopes thus developed are used, along with optimal position estimation algorithms, for tracking and super-resolution imaging in 3D. Imaging at depths-of-field of up to 2.5 microm is achieved without focus scanning. Microtubules were imaged with 3D resolution of (6, 9, 39) nm, which is in close agreement with the theoretical limit. A quantitative study of co-localization of two proteins in volume was conducted in live bacteria. In the last part of the thesis practical aspects of the DH-PSF microscope are discussed. A method to stabilize it, for extended periods of time, with 3-4 nm precision in 3D is developed. 3D Super-resolution is demonstrated without drift. A PSF correction algorithm is demonstrated to improve characteristics of the DH-PSF in an experiment, where it is implemented with a polarization-insensitive liquid crystal spatial light modulator.

Three-Dimensional Terahertz Coded-Aperture Imaging Based on Single Input Multiple Output Technology.

PubMed

Chen, Shuo; Luo, Chenggao; Deng, Bin; Wang, Hongqiang; Cheng, Yongqiang; Zhuang, Zhaowen

2018-01-19

As a promising radar imaging technique, terahertz coded-aperture imaging (TCAI) can achieve high-resolution, forward-looking, and staring imaging by producing spatiotemporal independent signals with coded apertures. In this paper, we propose a three-dimensional (3D) TCAI architecture based on single input multiple output (SIMO) technology, which can reduce the coding and sampling times sharply. The coded aperture applied in the proposed TCAI architecture loads either purposive or random phase modulation factor. In the transmitting process, the purposive phase modulation factor drives the terahertz beam to scan the divided 3D imaging cells. In the receiving process, the random phase modulation factor is adopted to modulate the terahertz wave to be spatiotemporally independent for high resolution. Considering human-scale targets, images of each 3D imaging cell are reconstructed one by one to decompose the global computational complexity, and then are synthesized together to obtain the complete high-resolution image. As for each imaging cell, the multi-resolution imaging method helps to reduce the computational burden on a large-scale reference-signal matrix. The experimental results demonstrate that the proposed architecture can achieve high-resolution imaging with much less time for 3D targets and has great potential in applications such as security screening, nondestructive detection, medical diagnosis, etc.

High-resolution 3D-constructive interference in steady-state MR imaging and 3D time-of-flight MR angiography in neurovascular compression: a comparison between 3T and 1.5T.

PubMed

Garcia, M; Naraghi, R; Zumbrunn, T; Rösch, J; Hastreiter, P; Dörfler, A

2012-08-01

High-resolution MR imaging is useful for diagnosis and preoperative planning in patients with NVC. Because high-field MR imaging promises higher SNR and resolution, the aim of this study was to determine the value of high-resolution 3D-CISS and 3D-TOF MRA at 3T compared with 1.5T in patients with NVC. Forty-seven patients with NVC, trigeminal neuralgia, hemifacial spasm, and glossopharyngeal neuralgia were examined at 1.5T and 3T, including high-resolution 3D-CISS and 3D-TOF MRA sequences. Delineation of anatomic structures, overall image quality, severity of artifacts, visibility of NVC, and assessment of the SNR and CNR were compared between field strengths. SNR and CNR were significantly higher at 3T (P < .001). Significantly better anatomic conspicuity, including delineation of CNs, nerve branches, and assessment of small vessels, was obtained at 3T (P < .02). Severity of artifacts was significantly lower at 3T (P < .001). Consequently, overall image quality was significantly higher at 3T. NVC was significantly better delineated at 3T (P < .001). Six patients in whom NVC was not with certainty identifiable at 1.5T were correctly diagnosed at 3T. Patients with NVC may benefit from the higher resolution and greater sensitivity of 3T for preoperative assessment of NVC, and 3T may be of particular value when 1.5T is equivocal.

High-resolution 3D imaging of polymerized photonic crystals by lab-based x-ray nanotomography with 50-nm resolution

NASA Astrophysics Data System (ADS)

Yin, Leilei; Chen, Ying-Chieh; Gelb, Jeff; Stevenson, Darren M.; Braun, Paul A.

2010-09-01

High resolution x-ray computed tomography is a powerful non-destructive 3-D imaging method. It can offer superior resolution on objects that are opaque or low contrast for optical microscopy. Synchrotron based x-ray computed tomography systems have been available for scientific research, but remain difficult to access for broader users. This work introduces a lab-based high-resolution x-ray nanotomography system with 50nm resolution in absorption and Zernike phase contrast modes. Using this system, we have demonstrated high quality 3-D images of polymerized photonic crystals which have been analyzed for band gap structures. The isotropic volumetric data shows excellent consistency with other characterization results.

Super long viewing distance light homogeneous emitting three-dimensional display

NASA Astrophysics Data System (ADS)

Liao, Hongen

2015-04-01

Three-dimensional (3D) display technology has continuously been attracting public attention with the progress in today's 3D television and mature display technologies. The primary characteristics of conventional glasses-free autostereoscopic displays, such as spatial resolution, image depths, and viewing angle, are often limited due to the use of optical lenses or optical gratings. We present a 3D display using MEMS-scanning-mechanism-based light homogeneous emitting (LHE) approach and demonstrate that the display can directly generate an autostereoscopic 3D image without the need for optical lenses or gratings. The generated 3D image has the advantages of non-aberration and a high-definition spatial resolution, making it the first to exhibit animated 3D images with image depth of six meters. Our LHE 3D display approach can be used to generate a natural flat-panel 3D display with super long viewing distance and alternative real-time image update.

CAIPIRINHA accelerated SPACE enables 10-min isotropic 3D TSE MRI of the ankle for optimized visualization of curved and oblique ligaments and tendons.

PubMed

Kalia, Vivek; Fritz, Benjamin; Johnson, Rory; Gilson, Wesley D; Raithel, Esther; Fritz, Jan

2017-09-01

To test the hypothesis that a fourfold CAIPIRINHA accelerated, 10-min, high-resolution, isotropic 3D TSE MRI prototype protocol of the ankle derives equal or better quality than a 20-min 2D TSE standard protocol. Following internal review board approval and informed consent, 3-Tesla MRI of the ankle was obtained in 24 asymptomatic subjects including 10-min 3D CAIPIRINHA SPACE TSE prototype and 20-min 2D TSE standard protocols. Outcome variables included image quality and visibility of anatomical structures using 5-point Likert scales. Non-parametric statistical testing was used. P values ≤0.001 were considered significant. Edge sharpness, contrast resolution, uniformity, noise, fat suppression and magic angle effects were without statistical difference on 2D and 3D TSE images (p > 0.035). Fluid was mildly brighter on intermediate-weighted 2D images (p < 0.001), whereas 3D images had substantially less partial volume, chemical shift and no pulsatile-flow artifacts (p < 0.001). Oblique and curved planar 3D images resulted in mildly-to-substantially improved visualization of joints, spring, bifurcate, syndesmotic, collateral and sinus tarsi ligaments, and tendons (p < 0.001, respectively). 3D TSE MRI with CAIPIRINHA acceleration enables high-spatial resolution oblique and curved planar MRI of the ankle and visualization of ligaments, tendons and joints equally well or better than a more time-consuming anisotropic 2D TSE MRI. • High-resolution 3D TSE MRI improves visualization of ankle structures. • Limitations of current 3D TSE MRI include long scan times. • 3D CAIPIRINHA SPACE allows now a fourfold-accelerated data acquisition. • 3D CAIPIRINHA SPACE enables high-spatial-resolution ankle MRI within 10 min. • 10-min 3D CAIPIRINHA SPACE produces equal-or-better quality than 20-min 2D TSE.

3D Imaging Millimeter Wave Circular Synthetic Aperture Radar

PubMed Central

Zhang, Renyuan; Cao, Siyang

2017-01-01

In this paper, a new millimeter wave 3D imaging radar is proposed. The user just needs to move the radar along a circular track, and high resolution 3D imaging can be generated. The proposed radar uses the movement of itself to synthesize a large aperture in both the azimuth and elevation directions. It can utilize inverse Radon transform to resolve 3D imaging. To improve the sensing result, the compressed sensing approach is further investigated. The simulation and experimental result further illustrated the design. Because a single transceiver circuit is needed, a light, affordable and high resolution 3D mmWave imaging radar is illustrated in the paper. PMID:28629140

Super-resolution photon-efficient imaging by nanometric double-helix point spread function localization of emitters (SPINDLE)

PubMed Central

Grover, Ginni; DeLuca, Keith; Quirin, Sean; DeLuca, Jennifer; Piestun, Rafael

2012-01-01

Super-resolution imaging with photo-activatable or photo-switchable probes is a promising tool in biological applications to reveal previously unresolved intra-cellular details with visible light. This field benefits from developments in the areas of molecular probes, optical systems, and computational post-processing of the data. The joint design of optics and reconstruction processes using double-helix point spread functions (DH-PSF) provides high resolution three-dimensional (3D) imaging over a long depth-of-field. We demonstrate for the first time a method integrating a Fisher information efficient DH-PSF design, a surface relief optical phase mask, and an optimal 3D localization estimator. 3D super-resolution imaging using photo-switchable dyes reveals the 3D microtubule network in mammalian cells with localization precision approaching the information theoretical limit over a depth of 1.2 µm. PMID:23187521

Imaging live cells at high spatiotemporal resolution for lab-on-a-chip applications.

PubMed

Chin, Lip Ket; Lee, Chau-Hwang; Chen, Bi-Chang

2016-05-24

Conventional optical imaging techniques are limited by the diffraction limit and difficult-to-image biomolecular and sub-cellular processes in living specimens. Novel optical imaging techniques are constantly evolving with the desire to innovate an imaging tool that is capable of seeing sub-cellular processes in a biological system, especially in three dimensions (3D) over time, i.e. 4D imaging. For fluorescence imaging on live cells, the trade-offs among imaging depth, spatial resolution, temporal resolution and photo-damage are constrained based on the limited photons of the emitters. The fundamental solution to solve this dilemma is to enlarge the photon bank such as the development of photostable and bright fluorophores, leading to the innovation in optical imaging techniques such as super-resolution microscopy and light sheet microscopy. With the synergy of microfluidic technology that is capable of manipulating biological cells and controlling their microenvironments to mimic in vivo physiological environments, studies of sub-cellular processes in various biological systems can be simplified and investigated systematically. In this review, we provide an overview of current state-of-the-art super-resolution and 3D live cell imaging techniques and their lab-on-a-chip applications, and finally discuss future research trends in new and breakthrough research areas of live specimen 4D imaging in controlled 3D microenvironments.

Hybrid-coded 3D structured illumination imaging with Bayesian estimation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Chen, Hsi-Hsun; Luo, Yuan; Singh, Vijay R.

2016-03-01

Light induced fluorescent microscopy has long been developed to observe and understand the object at microscale, such as cellular sample. However, the transfer function of lense-based imaging system limits the resolution so that the fine and detailed structure of sample cannot be identified clearly. The techniques of resolution enhancement are fascinated to break the limit of resolution for objective given. In the past decades, the resolution enhancement imaging has been investigated through variety of strategies, including photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), stimulated emission depletion (STED), and structure illuminated microscopy (SIM). In those methods, only SIM can intrinsically improve the resolution limit for a system without taking the structure properties of object into account. In this paper, we develop a SIM associated with Bayesian estimation, furthermore, with optical sectioning capability rendered from HiLo processing, resulting the high resolution through 3D volume. This 3D SIM can provide the optical sectioning and resolution enhancement performance, and be robust to noise owing to the Data driven Bayesian estimation reconstruction proposed. For validating the 3D SIM, we show our simulation result of algorithm, and the experimental result demonstrating the 3D resolution enhancement.

Intracranial arterial wall imaging using three-dimensional high isotropic resolution black blood MRI at 3.0 Tesla.

PubMed

Qiao, Ye; Steinman, David A; Qin, Qin; Etesami, Maryam; Schär, Michael; Astor, Brad C; Wasserman, Bruce A

2011-07-01

To develop a high isotropic-resolution sequence to evaluate intracranial vessels at 3.0 Tesla (T). Thirteen healthy volunteers and 4 patients with intracranial stenosis were imaged at 3.0T using 0.5-mm isotropic-resolution three-dimensional (3D) Volumetric ISotropic TSE Acquisition (VISTA; TSE, turbo spin echo), with conventional 2D-TSE for comparison. VISTA was repeated for 6 volunteers and 4 patients at 0.4-mm isotropic-resolution to explore the trade-off between SNR and voxel volume. Wall signal-to-noise-ratio (SNR(wall) ), wall-lumen contrast-to-noise-ratio (CNR(wall-lumen) ), lumen area (LA), wall area (WA), mean wall thickness (MWT), and maximum wall thickness (maxWT) were compared between 3D-VISTA and 2D-TSE sequences, as well as 3D images acquired at both resolutions. Reliability was assessed by intraclass correlations (ICC). Compared with 2D-TSE measurements, 3D-VISTA provided 58% and 74% improvement in SNR(wall) and CNR(wall-lumen) , respectively. LA, WA, MWT and maxWT from 3D and 2D techniques highly correlated (ICCs of 0.96, 0.95, 0.96, and 0.91, respectively). CNR(wall-lumen) using 0.4-mm resolution VISTA decreased by 27%, compared with 0.5-mm VISTA but with reduced partial-volume-based overestimation of wall thickness. Reliability for 3D measurements was good to excellent. The 3D-VISTA provides SNR-efficient, highly reliable measurements of intracranial vessels at high isotropic-resolution, enabling broad coverage in a clinically acceptable time. Copyright © 2011 Wiley-Liss, Inc.

Feasibility of Multiplane-Transmit Beamforming for Real-Time Volumetric Cardiac Imaging: A Simulation Study.

PubMed

Chen, Yinran; Tong, Ling; Ortega, Alejandra; Luo, Jianwen; D'hooge, Jan

2017-04-01

Today's 3-D cardiac ultrasound imaging systems suffer from relatively low spatial and temporal resolution, limiting their applicability in daily clinical practice. To address this problem, 3-D diverging wave imaging with spatial coherent compounding (DWC) as well as 3-D multiline-transmit (MLT) imaging have recently been proposed. Currently, the former improves the temporal resolution significantly at the expense of image quality and the risk of introducing motion artifacts, whereas the latter only provides a moderate gain in volume rate but mostly preserves quality. In this paper, a new technique for real-time volumetric cardiac imaging is proposed by combining the strengths of both approaches. Hereto, multiple planar (i.e., 2-D) diverging waves are simultaneously transmitted in order to scan the 3-D volume, i.e., multiplane transmit (MPT) beamforming. The performance of a 3MPT imaging system was contrasted to that of a 3-D DWC system and that of a 3-D MLT system by computer simulations during both static and moving conditions of the target structures while operating at similar volume rate. It was demonstrated that for stationary targets, the 3MPT imaging system was competitive with both the 3-D DWC and 3-D MLT systems in terms of spatial resolution and sidelobe levels (i.e., image quality). However, for moving targets, the image quality quickly deteriorated for the 3-D DWC systems while it remained stable for the 3MPT system while operating at twice the volume rate of the 3-D-MLT system. The proposed MPT beamforming approach was thus demonstrated to be feasible and competitive to state-of-the-art methodologies.

Thin polymer etalon arrays for high-resolution photoacoustic imaging

PubMed Central

Hou, Yang; Huang, Sheng-Wen; Ashkenazi, Shai; Witte, Russell; O’Donnell, Matthew

2009-01-01

Thin polymer etalons are demonstrated as high-frequency ultrasound sensors for three-dimensional (3-D) high-resolution photoacoustic imaging. The etalon, a Fabry-Perot optical resonator, consists of a thin polymer slab sandwiched between two gold layers. It is probed with a scanning continuous-wave (CW) laser for ultrasound array detection. Detection bandwidth of a 20-μm-diam array element exceeds 50 MHz, and the ultrasound sensitivity is comparable to polyvinylidene fluoride (PVDF) equivalents of similar size. In a typical photoacoustic imaging setup, a pulsed laser beam illuminates the imaging target, where optical energy is absorbed and acoustic waves are generated through the thermoelastic effect. An ultrasound detection array is formed by scanning the probing laser beam on the etalon surface in either a 1-D or a 2-D configuration, which produces 2-D or 3-D images, respectively. Axial and lateral resolutions have been demonstrated to be better than 20 μm. Detailed characterizations of the optical and acoustical properties of the etalon, as well as photoacoustic imaging results, suggest that thin polymer etalon arrays can be used as ultrasound detectors for 3-D high-resolution photoacoustic imaging applications. PMID:19123679

A resolution measure for three-dimensional microscopy

PubMed Central

Chao, Jerry; Ram, Sripad; Abraham, Anish V.; Ward, E. Sally; Ober, Raimund J.

2009-01-01

A three-dimensional (3D) resolution measure for the conventional optical microscope is introduced which overcomes the drawbacks of the classical 3D (axial) resolution limit. Formulated within the context of a parameter estimation problem and based on the Cramer-Rao lower bound, this 3D resolution measure indicates the accuracy with which a given distance between two objects in 3D space can be determined from the acquired image. It predicts that, given enough photons from the objects of interest, arbitrarily small distances of separation can be estimated with prespecified accuracy. Using simulated images of point source pairs, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure. We also demonstrate how different factors, such as extraneous noise sources and the spatial orientation of the imaged object pair, can affect the accuracy with which a given distance of separation can be determined. PMID:20161040

High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jianzhong; Cao, Yong; Wu, Tianding

2014-10-15

Purpose: Understanding the three-dimensional (3D) morphology of the spinal cord microvasculature has been limited by the lack of an effective high-resolution imaging technique. In this study, synchrotron radiation microcomputed tomography (SRµCT), a novel imaging technique based on absorption imaging, was evaluated with regard to the detection of the 3D morphology of the rat spinal cord microvasculature. Methods: Ten Sprague-Dawley rats were used in this ex vivo study. After contrast agent perfusion, their spinal cords were isolated and scanned using conventional x-rays, conventional micro-CT (CµCT), and SRµCT. Results: Based on contrast agent perfusion, the microvasculature of the rat spinal cord wasmore » clearly visualized for the first time ex vivo in 3D by means of SRµCT scanning. Compared to conventional imaging techniques, SRµCT achieved higher resolution 3D vascular imaging, with the smallest vessel that could be distinguished approximately 7.4 μm in diameter. Additionally, a 3D pseudocolored image of the spinal cord microvasculature was generated in a single session of SRµCT imaging, which was conducive to detailed observation of the vessel morphology. Conclusions: The results of this study indicated that SRµCT scanning could provide higher resolution images of the vascular network of the spinal cord. This modality also has the potential to serve as a powerful imaging tool for the investigation of morphology changes in the 3D angioarchitecture of the neurovasculature in preclinical research.« less

Retinal Structure of Birds of Prey Revealed by Ultra-High Resolution Spectral-Domain Optical Coherence Tomography

PubMed Central

Ruggeri, Marco; Major, James C.; McKeown, Craig; Knighton, Robert W.; Puliafito, Carmen A.

2010-01-01

Purpose. To reveal three-dimensional (3-D) information about the retinal structures of birds of prey in vivo. Methods. An ultra-high resolution spectral-domain optical coherence tomography (SD-OCT) system was built for in vivo imaging of retinas of birds of prey. The calibrated imaging depth and axial resolution of the system were 3.1 mm and 2.8 μm (in tissue), respectively. 3-D segmentation was performed for calculation of the retinal nerve fiber layer (RNFL) map. Results. High-resolution OCT images were obtained of the retinas of four species of birds of prey: two diurnal hawks (Buteo platypterus and Buteo brachyurus) and two nocturnal owls (Bubo virginianus and Strix varia). These images showed the detailed retinal anatomy, including the retinal layers and the structure of the deep and shallow foveae. The calculated thickness map showed the RNFL distribution. Traumatic injury to one bird's retina was also successfully imaged. Conclusions. Ultra-high resolution SD-OCT provides unprecedented high-quality 2-D and 3-D in vivo visualization of the retinal structures of birds of prey. SD-OCT is a powerful imaging tool for vision research in birds of prey. PMID:20554605

FIMic: design for ultimate 3D-integral microscopy of in-vivo biological samples

PubMed Central

Scrofani, G.; Sola-Pikabea, J.; Llavador, A.; Sanchez-Ortiga, E.; Barreiro, J. C.; Saavedra, G.; Garcia-Sucerquia, J.; Martínez-Corral, M.

2017-01-01

In this work, Fourier integral microscope (FIMic), an ultimate design of 3D-integral microscopy, is presented. By placing a multiplexing microlens array at the aperture stop of the microscope objective of the host microscope, FIMic shows extended depth of field and enhanced lateral resolution in comparison with regular integral microscopy. As FIMic directly produces a set of orthographic views of the 3D-micrometer-sized sample, it is suitable for real-time imaging. Following regular integral-imaging reconstruction algorithms, a 2.75-fold enhanced depth of field and 2-time better spatial resolution in comparison with conventional integral microscopy is reported. Our claims are supported by theoretical analysis and experimental images of a resolution test target, cotton fibers, and in-vivo 3D-imaging of biological specimens. PMID:29359107

Ultrahigh speed Spectral / Fourier domain OCT ophthalmic imaging at 70,000 to 312,500 axial scans per second

PubMed Central

Potsaid, Benjamin; Gorczynska, Iwona; Srinivasan, Vivek J.; Chen, Yueli; Jiang, James; Cable, Alex; Fujimoto, James G.

2009-01-01

We demonstrate ultrahigh speed spectral / Fourier domain optical coherence tomography (OCT) using an ultrahigh speed CMOS line scan camera at rates of 70,000 - 312,500 axial scans per second. Several design configurations are characterized to illustrate trade-offs between acquisition speed, resolution, imaging range, sensitivity and sensitivity roll-off performance. Ultrahigh resolution OCT with 2.5 - 3.0 micron axial image resolution is demonstrated at ∼ 100,000 axial scans per second. A high resolution spectrometer design improves sensitivity roll-off and imaging range performance, trading off imaging speed to 70,000 axial scans per second. Ultrahigh speed imaging at >300,000 axial scans per second with standard image resolution is also demonstrated. Ophthalmic OCT imaging of the normal human retina is investigated. The high acquisition speeds enable dense raster scanning to acquire densely sampled volumetric three dimensional OCT (3D-OCT) data sets of the macula and optic disc with minimal motion artifacts. Imaging with ∼ 8 - 9 micron axial resolution at 250,000 axial scans per second, a 512 × 512 × 400 voxel volumetric 3D-OCT data set can be acquired in only ∼ 1.3 seconds. Orthogonal registration scans are used to register OCT raster scans and remove residual axial eye motion, resulting in 3D-OCT data sets which preserve retinal topography. Rapid repetitive imaging over small volumes can visualize small retinal features without motion induced distortions and enables volume registration to remove eye motion. Cone photoreceptors in some regions of the retina can be visualized without adaptive optics or active eye tracking. Rapid repetitive imaging of 3D volumes also provides dynamic volumetric information (4D-OCT) which is shown to enhance visualization of retinal capillaries and should enable functional imaging. Improvements in the speed and performance of 3D-OCT volumetric imaging promise to enable earlier diagnosis and improved monitoring of disease progression and response to therapy in ophthalmology, as well as have a wide range of research and clinical applications in other areas. PMID:18795054

Three-dimensional coherent x-ray diffraction imaging of molten iron in mantle olivine at nanoscale resolution.

PubMed

Jiang, Huaidong; Xu, Rui; Chen, Chien-Chun; Yang, Wenge; Fan, Jiadong; Tao, Xutang; Song, Changyong; Kohmura, Yoshiki; Xiao, Tiqiao; Wang, Yong; Fei, Yingwei; Ishikawa, Tetsuya; Mao, Wendy L; Miao, Jianwei

2013-05-17

We report quantitative 3D coherent x-ray diffraction imaging of a molten Fe-rich alloy and crystalline olivine sample, synthesized at 6 GPa and 1800 °C, with nanoscale resolution. The 3D mass density map is determined and the 3D distribution of the Fe-rich and Fe-S phases in the olivine-Fe-S sample is observed. Our results indicate that the Fe-rich melt exhibits varied 3D shapes and sizes in the olivine matrix. This work has potential for not only improving our understanding of the complex interactions between Fe-rich core-forming melts and mantle silicate phases but also paves the way for quantitative 3D imaging of materials at nanoscale resolution under extreme pressures and temperatures.

3D Cryo-Imaging: A Very High-Resolution View of the Whole Mouse

PubMed Central

Roy, Debashish; Steyer, Grant J.; Gargesha, Madhusudhana; Stone, Meredith E.; Wilson, David L.

2009-01-01

We developed the Case Cryo-imaging system that provides information rich, very high-resolution, color brightfield, and molecular fluorescence images of a whole mouse using a section-and-image block-face imaging technology. The system consists of a mouse-sized, motorized cryo-microtome with special features for imaging, a modified, brightfield/ fluorescence microscope, and a robotic xyz imaging system positioner, all of which is fully automated by a control system. Using the robotic system, we acquired microscopic tiled images at a pixel size of 15.6 µm over the block face of a whole mouse sectioned at 40 µm, with a total data volume of 55 GB. Viewing 2D images at multiple resolutions, we identified small structures such as cardiac vessels, muscle layers, villi of the small intestine, the optic nerve, and layers of the eye. Cryo-imaging was also suitable for imaging embryo mutants in 3D. A mouse, in which enhanced green fluorescent protein was expressed under gamma actin promoter in smooth muscle cells, gave clear 3D views of smooth muscle in the urogenital and gastrointestinal tracts. With cryo-imaging, we could obtain 3D vasculature down to 10 µm, over very large regions of mouse brain. Software is fully automated with fully programmable imaging/sectioning protocols, email notifications, and automatic volume visualization. With a unique combination of field-of-view, depth of field, contrast, and resolution, the Case Cryo-imaging system fills the gap between whole animal in vivo imaging and histology. PMID:19248166

Enhanced labeling density and whole-cell 3D dSTORM imaging by repetitive labeling of target proteins.

PubMed

Venkataramani, Varun; Kardorff, Markus; Herrmannsdörfer, Frank; Wieneke, Ralph; Klein, Alina; Tampé, Robert; Heilemann, Mike; Kuner, Thomas

2018-04-03

With continuing advances in the resolving power of super-resolution microscopy, the inefficient labeling of proteins with suitable fluorophores becomes a limiting factor. For example, the low labeling density achieved with antibodies or small molecule tags limits attempts to reveal local protein nano-architecture of cellular compartments. On the other hand, high laser intensities cause photobleaching within and nearby an imaged region, thereby further reducing labeling density and impairing multi-plane whole-cell 3D super-resolution imaging. Here, we show that both labeling density and photobleaching can be addressed by repetitive application of trisNTA-fluorophore conjugates reversibly binding to a histidine-tagged protein by a novel approach called single-epitope repetitive imaging (SERI). For single-plane super-resolution microscopy, we demonstrate that, after multiple rounds of labeling and imaging, the signal density is increased. Using the same approach of repetitive imaging, washing and re-labeling, we demonstrate whole-cell 3D super-resolution imaging compensated for photobleaching above or below the imaging plane. This proof-of-principle study demonstrates that repetitive labeling of histidine-tagged proteins provides a versatile solution to break the 'labeling barrier' and to bypass photobleaching in multi-plane, whole-cell 3D experiments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beckingham, Lauren E.; Peters, Catherine A.; Um, Wooyong

Although the impact of subsurface geochemical reactions on porosity is relatively well understood, changes in permeability remain difficult to estimate. In this work, pore-network modeling was used to predict permeability based on pore- and pore-throat size distributions determined from analysis of 2D scanning electron microscopy (SEM) images of thin sections and 3D X-ray computed microtomography (CMT) data. The analyzed specimens were a Viking sandstone sample from the Alberta sedimentary basin and an experimental column of reacted Hanford sediments. For the column, a decrease in permeability due to mineral precipitation was estimated, but the permeability estimates were dependent on imaging techniquemore » and resolution. X-ray CT imaging has the advantage of reconstructing a 3D pore network while 2D SEM imaging can easily analyze sub-grain and intragranular variations in mineralogy. Pore network models informed by analyses of 2D and 3D images at comparable resolutions produced permeability esti- mates with relatively good agreement. Large discrepancies in predicted permeabilities resulted from small variations in image resolution. Images with resolutions 0.4 to 4 lm predicted permeabilities differ- ing by orders of magnitude. While lower-resolution scans can analyze larger specimens, small pore throats may be missed due to resolution limitations, which in turn overestimates permeability in a pore-network model in which pore-to-pore conductances are statistically assigned. Conversely, high-res- olution scans are capable of capturing small pore throats, but if they are not actually flow-conducting predicted permeabilities will be below expected values. In addition, permeability is underestimated due to misinterpreting surface-roughness features as small pore throats. Comparison of permeability pre- dictions with expected and measured permeability values showed that the largest discrepancies resulted from the highest resolution images and the best predictions of permeability will result from images between 2 and 4 lm resolution. To reduce permeability underestimation from analyses of high-resolu- tion images, a resolution threshold between 3 and 15 lm was found to be effective, but it is not known whether this range is applicable beyond the samples studied here.« less

A synchrotron radiation microtomography system for the analysis of trabecular bone samples.

PubMed

Salomé, M; Peyrin, F; Cloetens, P; Odet, C; Laval-Jeantet, A M; Baruchel, J; Spanne, P

1999-10-01

X-ray computed microtomography is particularly well suited for studying trabecular bone architecture, which requires three-dimensional (3-D) images with high spatial resolution. For this purpose, we describe a three-dimensional computed microtomography (microCT) system using synchrotron radiation, developed at ESRF. Since synchrotron radiation provides a monochromatic and high photon flux x-ray beam, it allows high resolution and a high signal-to-noise ratio imaging. The principle of the system is based on truly three-dimensional parallel tomographic acquisition. It uses a two-dimensional (2-D) CCD-based detector to record 2-D radiographs of the transmitted beam through the sample under different angles of view. The 3-D tomographic reconstruction, performed by an exact 3-D filtered backprojection algorithm, yields 3-D images with cubic voxels. The spatial resolution of the detector was experimentally measured. For the application to bone investigation, the voxel size was set to 6.65 microm, and the experimental spatial resolution was found to be 11 microm. The reconstructed linear attenuation coefficient was calibrated from hydroxyapatite phantoms. Image processing tools are being developed to extract structural parameters quantifying trabecular bone architecture from the 3-D microCT images. First results on human trabecular bone samples are presented.

Ames Lab 101: Real-Time 3D Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Song

2010-08-02

Ames Laboratory scientist Song Zhang explains his real-time 3-D imaging technology. The technique can be used to create high-resolution, real-time, precise, 3-D images for use in healthcare, security, and entertainment applications.

Ames Lab 101: Real-Time 3D Imaging

ScienceCinema

Zhang, Song

2017-12-22

Ames Laboratory scientist Song Zhang explains his real-time 3-D imaging technology. The technique can be used to create high-resolution, real-time, precise, 3-D images for use in healthcare, security, and entertainment applications.

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy.

PubMed

Chen, Shaoxia; McMullan, Greg; Faruqi, Abdul R; Murshudov, Garib N; Short, Judith M; Scheres, Sjors H W; Henderson, Richard

2013-12-01

Three-dimensional (3D) structure determination by single particle electron cryomicroscopy (cryoEM) involves the calculation of an initial 3D model, followed by extensive iterative improvement of the orientation determination of the individual particle images and the resulting 3D map. Because there is much more noise than signal at high resolution in the images, this creates the possibility of noise reinforcement in the 3D map, which can give a false impression of the resolution attained. The balance between signal and noise in the final map at its limiting resolution depends on the image processing procedure and is not easily predicted. There is a growing awareness in the cryoEM community of how to avoid such over-fitting and over-estimation of resolution. Equally, there has been a reluctance to use the two principal methods of avoidance because they give lower resolution estimates, which some people believe are too pessimistic. Here we describe a simple test that is compatible with any image processing protocol. The test allows measurement of the amount of signal and the amount of noise from overfitting that is present in the final 3D map. We have applied the method to two different sets of cryoEM images of the enzyme beta-galactosidase using several image processing packages. Our procedure involves substituting the Fourier components of the initial particle image stack beyond a chosen resolution by either the Fourier components from an adjacent area of background, or by simple randomisation of the phases of the particle structure factors. This substituted noise thus has the same spectral power distribution as the original data. Comparison of the Fourier Shell Correlation (FSC) plots from the 3D map obtained using the experimental data with that from the same data with high-resolution noise (HR-noise) substituted allows an unambiguous measurement of the amount of overfitting and an accompanying resolution assessment. A simple formula can be used to calculate an unbiased FSC from the two curves, even when a substantial amount of overfitting is present. The approach is software independent. The user is therefore completely free to use any established method or novel combination of methods, provided the HR-noise test is carried out in parallel. Applying this procedure to cryoEM images of beta-galactosidase shows how overfitting varies greatly depending on the procedure, but in the best case shows no overfitting and a resolution of ~6 Å. (382 words). © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Imaging system for creating 3D block-face cryo-images of whole mice

NASA Astrophysics Data System (ADS)

Roy, Debashish; Breen, Michael; Salvado, Olivier; Heinzel, Meredith; McKinley, Eliot; Wilson, David

2006-03-01

We developed a cryomicrotome/imaging system that provides high resolution, high sensitivity block-face images of whole mice or excised organs, and applied it to a variety of biological applications. With this cryo-imaging system, we sectioned cryo-preserved tissues at 2-40 μm thickness and acquired high resolution brightfield and fluorescence images with microscopic in-plane resolution (as good as 1.2 μm). Brightfield images of normal and pathological anatomy show exquisite detail, especially in the abdominal cavity. Multi-planar reformatting and 3D renderings allow one to interrogate 3D structures. In this report, we present brightfield images of mouse anatomy, as well as 3D renderings of organs. For BPK mice model of polycystic kidney disease, we compared brightfield cryo-images and kidney volumes to MRI. The color images provided greater contrast and resolution of cysts as compared to in vivo MRI. We note that color cryo-images are closer to what a researcher sees in dissection, making it easier for them to interpret image data. The combination of field of view, depth of field, ultra high resolution and color/fluorescence contrast enables cryo-image volumes to provide details that cannot be found through in vivo imaging or other ex vivo optical imaging approaches. We believe that this novel imaging system will have applications that include identification of mouse phenotypes, characterization of diseases like blood vessel disease, kidney disease, and cancer, assessment of drug and gene therapy delivery and efficacy and validation of other imaging modalities.

First steps towards dual-modality 3D photoacoustic and speed of sound imaging with optical ultrasound detection

NASA Astrophysics Data System (ADS)

Nuster, Robert; Wurzinger, Gerhild; Paltauf, Guenther

2017-03-01

CCD camera based optical ultrasound detection is a promising alternative approach for high resolution 3D photoacoustic imaging (PAI). To fully exploit its potential and to achieve an image resolution <50 μm, it is necessary to incorporate variations of the speed of sound (SOS) in the image reconstruction algorithm. Hence, in the proposed work the idea and a first implementation are shown how speed of sound imaging can be added to a previously developed camera based PAI setup. The current setup provides SOS-maps with a spatial resolution of 2 mm and an accuracy of the obtained absolute SOS values of about 1%. The proposed dual-modality setup has the potential to provide highly resolved and perfectly co-registered 3D photoacoustic and SOS images.

[High resolution reconstruction of PET images using the iterative OSEM algorithm].

PubMed

Doll, J; Henze, M; Bublitz, O; Werling, A; Adam, L E; Haberkorn, U; Semmler, W; Brix, G

2004-06-01

Improvement of the spatial resolution in positron emission tomography (PET) by incorporation of the image-forming characteristics of the scanner into the process of iterative image reconstruction. All measurements were performed at the whole-body PET system ECAT EXACT HR(+) in 3D mode. The acquired 3D sinograms were sorted into 2D sinograms by means of the Fourier rebinning (FORE) algorithm, which allows the usage of 2D algorithms for image reconstruction. The scanner characteristics were described by a spatially variant line-spread function (LSF), which was determined from activated copper-64 line sources. This information was used to model the physical degradation processes in PET measurements during the course of 2D image reconstruction with the iterative OSEM algorithm. To assess the performance of the high-resolution OSEM algorithm, phantom measurements performed at a cylinder phantom, the hotspot Jaszczack phantom, and the 3D Hoffmann brain phantom as well as different patient examinations were analyzed. Scanner characteristics could be described by a Gaussian-shaped LSF with a full-width at half-maximum increasing from 4.8 mm at the center to 5.5 mm at a radial distance of 10.5 cm. Incorporation of the LSF into the iteration formula resulted in a markedly improved resolution of 3.0 and 3.5 mm, respectively. The evaluation of phantom and patient studies showed that the high-resolution OSEM algorithm not only lead to a better contrast resolution in the reconstructed activity distributions but also to an improved accuracy in the quantification of activity concentrations in small structures without leading to an amplification of image noise or even the occurrence of image artifacts. The spatial and contrast resolution of PET scans can markedly be improved by the presented image restauration algorithm, which is of special interest for the examination of both patients with brain disorders and small animals.

Non Destructive 3D X-Ray Imaging of Nano Structures & Composites at Sub-30 NM Resolution, With a Novel Lab Based X-Ray Microscope

DTIC Science & Technology

2006-11-01

NON DESTRUCTIVE 3D X-RAY IMAGING OF NANO STRUCTURES & COMPOSITES AT SUB-30 NM RESOLUTION, WITH A NOVEL LAB BASED X- RAY MICROSCOPE S H Lau...article we describe a 3D x-ray microscope based on a laboratory x-ray source operating at 2.7, 5.4 or 8.0 keV hard x-ray energies. X-ray computed...tomography (XCT) is used to obtain detailed 3D structural information inside optically opaque materials with sub-30 nm resolution. Applications include

Looking inside the heart: a see-through view of the vascular tree

PubMed Central

Nehrhoff, Imke; Ripoll, Jorge; Samaniego, Rafael; Desco, Manuel; Gómez-Gaviro, Maria Victoria

2017-01-01

The ability to acquire 3D images of the heart and its vasculature at cellular resolution facilitates a more detailed study of many heart diseases. Here, we describe a novel technique to image in 3D the heart vasculature by combining the CUBIC clearing protocol combined with in vivo administration of fluorescent-labeled lectin. The use of these techniques in combination with Selective Plane Illumination Microscopy (SPIM) made it possible to obtain high resolution 3D images of the cardiac vascular tree. This methodological approach may enhance the visualization of 3D images of the cardiac vasculature remodeling associated with coronary disease. PMID:28663930

Sparse representation-based volumetric super-resolution algorithm for 3D CT images of reservoir rocks

NASA Astrophysics Data System (ADS)

Li, Zhengji; Teng, Qizhi; He, Xiaohai; Yue, Guihua; Wang, Zhengyong

2017-09-01

The parameter evaluation of reservoir rocks can help us to identify components and calculate the permeability and other parameters, and it plays an important role in the petroleum industry. Until now, computed tomography (CT) has remained an irreplaceable way to acquire the microstructure of reservoir rocks. During the evaluation and analysis, large samples and high-resolution images are required in order to obtain accurate results. Owing to the inherent limitations of CT, however, a large field of view results in low-resolution images, and high-resolution images entail a smaller field of view. Our method is a promising solution to these data collection limitations. In this study, a framework for sparse representation-based 3D volumetric super-resolution is proposed to enhance the resolution of 3D voxel images of reservoirs scanned with CT. A single reservoir structure and its downgraded model are divided into a large number of 3D cubes of voxel pairs and these cube pairs are used to calculate two overcomplete dictionaries and the sparse-representation coefficients in order to estimate the high frequency component. Future more, to better result, a new feature extract method with combine BM4D together with Laplacian filter are introduced. In addition, we conducted a visual evaluation of the method, and used the PSNR and FSIM to evaluate it qualitatively.

Three-dimensional retinal imaging with high-speed ultrahigh-resolution optical coherence tomography.

PubMed

Wojtkowski, Maciej; Srinivasan, Vivek; Fujimoto, James G; Ko, Tony; Schuman, Joel S; Kowalczyk, Andrzej; Duker, Jay S

2005-10-01

To demonstrate high-speed, ultrahigh-resolution, 3-dimensional optical coherence tomography (3D OCT) and new protocols for retinal imaging. Ultrahigh-resolution OCT using broadband light sources achieves axial image resolutions of approximately 2 microm compared with standard 10-microm-resolution OCT current commercial instruments. High-speed OCT using spectral/Fourier domain detection enables dramatic increases in imaging speeds. Three-dimensional OCT retinal imaging is performed in normal human subjects using high-speed ultrahigh-resolution OCT. Three-dimensional OCT data of the macula and optic disc are acquired using a dense raster scan pattern. New processing and display methods for generating virtual OCT fundus images; cross-sectional OCT images with arbitrary orientations; quantitative maps of retinal, nerve fiber layer, and other intraretinal layer thicknesses; and optic nerve head topographic parameters are demonstrated. Three-dimensional OCT imaging enables new imaging protocols that improve visualization and mapping of retinal microstructure. An OCT fundus image can be generated directly from the 3D OCT data, which enables precise and repeatable registration of cross-sectional OCT images and thickness maps with fundus features. Optical coherence tomography images with arbitrary orientations, such as circumpapillary scans, can be generated from 3D OCT data. Mapping of total retinal thickness and thicknesses of the nerve fiber layer, photoreceptor layer, and other intraretinal layers is demonstrated. Measurement of optic nerve head topography and disc parameters is also possible. Three-dimensional OCT enables measurements that are similar to those of standard instruments, including the StratusOCT, GDx, HRT, and RTA. Three-dimensional OCT imaging can be performed using high-speed ultrahigh-resolution OCT. Three-dimensional OCT provides comprehensive visualization and mapping of retinal microstructures. The high data acquisition speeds enable high-density data sets with large numbers of transverse positions on the retina, which reduces the possibility of missing focal pathologies. In addition to providing image information such as OCT cross-sectional images, OCT fundus images, and 3D rendering, quantitative measurement and mapping of intraretinal layer thickness and topographic features of the optic disc are possible. We hope that 3D OCT imaging may help to elucidate the structural changes associated with retinal disease as well as improve early diagnosis and monitoring of disease progression and response to treatment.

Simultaneous 3D localization of multiple MR-visible markers in fully reconstructed MR images: proof-of-concept for subsecond position tracking.

PubMed

Thörmer, Gregor; Garnov, Nikita; Moche, Michael; Haase, Jürgen; Kahn, Thomas; Busse, Harald

2012-04-01

To determine whether a greatly reduced spatial resolution of fully reconstructed projection MR images can be used for the simultaneous 3D localization of multiple MR-visible markers and to assess the feasibility of a subsecond position tracking for clinical purposes. Miniature, inductively coupled RF coils were imaged in three orthogonal planes with a balanced steady-state free precession (SSFP) sequence and automatically localized using a two-dimensional template fitting and a subsequent three-dimensional (3D) matching of the coordinates. Precision, accuracy, speed and robustness of 3D localization were assessed for decreasing in-plane resolutions (0.6-4.7 mm). The feasibility of marker tracking was evaluated at the lowest resolution by following a robotically driven needle on a complex 3D trajectory. Average 3D precision and accuracy, sensitivity and specificity of localization ranged between 0.1 and 0.4 mm, 0.5 and 1.0 mm, 100% and 95%, and 100% and 96%, respectively. At the lowest resolution, imaging and localization took ≈350 ms and provided an accuracy of ≈1.0 mm. In the tracking experiment, the needle was clearly depicted on the oblique scan planes defined by the markers. Image-based marker localization at a greatly reduced spatial resolution is considered a feasible approach to monitor reference points or rigid instruments at subsecond update rates. Copyright © 2012 Elsevier Inc. All rights reserved.

An efficient implementation of 3D high-resolution imaging for large-scale seismic data with GPU/CPU heterogeneous parallel computing

NASA Astrophysics Data System (ADS)

Xu, Jincheng; Liu, Wei; Wang, Jin; Liu, Linong; Zhang, Jianfeng

2018-02-01

De-absorption pre-stack time migration (QPSTM) compensates for the absorption and dispersion of seismic waves by introducing an effective Q parameter, thereby making it an effective tool for 3D, high-resolution imaging of seismic data. Although the optimal aperture obtained via stationary-phase migration reduces the computational cost of 3D QPSTM and yields 3D stationary-phase QPSTM, the associated computational efficiency is still the main problem in the processing of 3D, high-resolution images for real large-scale seismic data. In the current paper, we proposed a division method for large-scale, 3D seismic data to optimize the performance of stationary-phase QPSTM on clusters of graphics processing units (GPU). Then, we designed an imaging point parallel strategy to achieve an optimal parallel computing performance. Afterward, we adopted an asynchronous double buffering scheme for multi-stream to perform the GPU/CPU parallel computing. Moreover, several key optimization strategies of computation and storage based on the compute unified device architecture (CUDA) were adopted to accelerate the 3D stationary-phase QPSTM algorithm. Compared with the initial GPU code, the implementation of the key optimization steps, including thread optimization, shared memory optimization, register optimization and special function units (SFU), greatly improved the efficiency. A numerical example employing real large-scale, 3D seismic data showed that our scheme is nearly 80 times faster than the CPU-QPSTM algorithm. Our GPU/CPU heterogeneous parallel computing framework significant reduces the computational cost and facilitates 3D high-resolution imaging for large-scale seismic data.

SU-E-J-157: Improving the Quality of T2-Weighted 4D Magnetic Resonance Imaging for Clinical Evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, D; Mutic, S; Hu, Y

2014-06-01

Purpose: To develop an imaging technique that enables us to acquire T2- weighted 4D Magnetic Resonance Imaging (4DMRI) with sufficient spatial coverage, temporal resolution and spatial resolution for clinical evaluation. Methods: T2-weighed 4DMRI images were acquired from a healthy volunteer using a respiratory amplitude triggered T2-weighted Turbo Spin Echo sequence. 10 respiratory states were used to equally sample the respiratory range based on amplitude (0%, 20%i, 40%i, 60%i, 80%i, 100%, 80%e, 60%e, 40%e and 20%e). To avoid frequent scanning halts, a methodology was devised that split 10 respiratory states into two packages in an interleaved manner and packages were acquiredmore » separately. Sixty 3mm sagittal slices at 1.5mm in-plane spatial resolution were acquired to offer good spatial coverage and reasonable spatial resolution. The in-plane field of view was 375mm × 260mm with nominal scan time of 3 minutes 42 seconds. Acquired 2D images at the same respiratory state were combined to form the 3D image set corresponding to that respiratory state and reconstructed in the coronal view to evaluate whether all slices were at the same respiratory state. 3D image sets of 10 respiratory states represented a complete 4D MRI image set. Results: T2-weighted 4DMRI image were acquired in 10 minutes which was within clinical acceptable range. Qualitatively, the acquired MRI images had good image quality for delineation purposes. There were no abrupt position changes in reconstructed coronal images which confirmed that all sagittal slices were in the same respiratory state. Conclusion: We demonstrated it was feasible to acquire T2-weighted 4DMRI image set within a practical amount of time (10 minutes) that had good temporal resolution (10 respiratory states), spatial resolution (1.5mm × 1.5mm × 3.0mm) and spatial coverage (60 slices) for future clinical evaluation.« less

Synthesis and identification of three-dimensional faces from image(s) and three-dimensional generic models

NASA Astrophysics Data System (ADS)

Liu, Zexi; Cohen, Fernand

2017-11-01

We describe an approach for synthesizing a three-dimensional (3-D) face structure from an image or images of a human face taken at a priori unknown poses using gender and ethnicity specific 3-D generic models. The synthesis process starts with a generic model, which is personalized as images of the person become available using preselected landmark points that are tessellated to form a high-resolution triangular mesh. From a single image, two of the three coordinates of the model are reconstructed in accordance with the given image of the person, while the third coordinate is sampled from the generic model, and the appearance is made in accordance with the image. With multiple images, all coordinates and appearance are reconstructed in accordance with the observed images. This method allows for accurate pose estimation as well as face identification in 3-D rendering of a difficult two-dimensional (2-D) face recognition problem into a much simpler 3-D surface matching problem. The estimation of the unknown pose is achieved using the Levenberg-Marquardt optimization process. Encouraging experimental results are obtained in a controlled environment with high-resolution images under a good illumination condition, as well as for images taken in an uncontrolled environment under arbitrary illumination with low-resolution cameras.

SEM-microphotogrammetry, a new take on an old method for generating high-resolution 3D models from SEM images.

PubMed

Ball, A D; Job, P A; Walker, A E L

2017-08-01

The method we present here uses a scanning electron microscope programmed via macros to automatically capture dozens of images at suitable angles to generate accurate, detailed three-dimensional (3D) surface models with micron-scale resolution. We demonstrate that it is possible to use these Scanning Electron Microscope (SEM) images in conjunction with commercially available software originally developed for photogrammetry reconstructions from Digital Single Lens Reflex (DSLR) cameras and to reconstruct 3D models of the specimen. These 3D models can then be exported as polygon meshes and eventually 3D printed. This technique offers the potential to obtain data suitable to reconstruct very tiny features (e.g. diatoms, butterfly scales and mineral fabrics) at nanometre resolution. Ultimately, we foresee this as being a useful tool for better understanding spatial relationships at very high resolution. However, our motivation is also to use it to produce 3D models to be used in public outreach events and exhibitions, especially for the blind or partially sighted. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Nanoscale Photoacoustic Tomography (nPAT) for label-free super-resolution 3D imaging of red blood cells

NASA Astrophysics Data System (ADS)

Samant, Pratik; Hernandez, Armando; Conklin, Shelby; Xiang, Liangzhong

2017-08-01

We present our results in developing nanoscale photoacoustic tomography (nPAT) for label-free super-resolution imaging in 3D. We have made progress in the development of nPAT, and have acquired our first signal. We have also performed simulations that demonstrate that nPAT is a viable imaging modality for the visualization of malaria infected red blood cells (RBCs). Our results demonstrate that nPAT is both feasible and powerful for the high resolution labelfree imaging of RBCs.

Application of Curved MPR Algorithm to High Resolution 3 Dimensional T2 Weighted CISS Images for Virtual Uncoiling of Membranous Cochlea as an Aid for Cochlear Morphometry.

PubMed

Kumar, Joish Upendra; Kavitha, Y

2017-02-01

With the use of various surgical techniques, types of implants, the preoperative assessment of cochlear dimensions is becoming increasingly relevant prior to cochlear implantation. High resolution CISS protocol MRI gives a better assessment of membranous cochlea, cochlear nerve, and membranous labyrinth. Curved Multiplanar Reconstruction (MPR) algorithm provides better images that can be used for measuring dimensions of membranous cochlea. To ascertain the value of curved multiplanar reconstruction algorithm in high resolution 3-Dimensional T2 Weighted Gradient Echo Constructive Interference Steady State (3D T2W GRE CISS) imaging for accurate morphometry of membranous cochlea. Fourteen children underwent MRI for inner ear assessment. High resolution 3D T2W GRE CISS sequence was used to obtain images of cochlea. Curved MPR reconstruction algorithm was used to virtually uncoil the membranous cochlea on the volume images and cochlear measurements were done. Virtually uncoiled images of membranous cochlea of appropriate resolution were obtained from the volume data obtained from the high resolution 3D T2W GRE CISS images, after using curved MPR reconstruction algorithm mean membranous cochlear length in the children was 27.52 mm. Maximum apical turn diameter of membranous cochlea was 1.13 mm, mid turn diameter was 1.38 mm, basal turn diameter was 1.81 mm. Curved MPR reconstruction algorithm applied to CISS protocol images facilitates in getting appropriate quality images of membranous cochlea for accurate measurements.

Evaluation of prospective motion correction of high-resolution 3D-T2-FLAIR acquisitions in epilepsy patients.

PubMed

Vos, Sjoerd B; Micallef, Caroline; Barkhof, Frederik; Hill, Andrea; Winston, Gavin P; Ourselin, Sebastien; Duncan, John S

2018-03-02

T2-FLAIR is the single most sensitive MRI contrast to detect lesions underlying focal epilepsies but 3D sequences used to obtain isotropic high-resolution images are susceptible to motion artefacts. Prospective motion correction (PMC) - demonstrated to improve 3D-T1 image quality in a pediatric population - was applied to high-resolution 3D-T2-FLAIR scans in adult epilepsy patients to evaluate its clinical benefit. Coronal 3D-T2-FLAIR scans were acquired with a 1mm isotropic resolution on a 3T MRI scanner. Two expert neuroradiologists reviewed 40 scans without PMC and 40 with navigator-based PMC. Visual assessment addressed six criteria of image quality (resolution, SNR, WM-GM contrast, intensity homogeneity, lesion conspicuity, diagnostic confidence) on a seven-point Likert scale (from non-diagnostic to outstanding). SNR was also objectively quantified within the white matter. PMC scans had near-identical scores on the criteria of image quality to non-PMC scans, with the notable exception that intensity homogeneity was generally worse. Using PMC, the percentage of scans with bad image quality was substantially lower than without PMC (3.25% vs. 12.5%) on the other five criteria. Quantitative SNR estimates revealed that PMC and non-PMC had no significant difference in SNR (P=0.07). Application of prospective motion correction to 3D-T2-FLAIR sequences decreased the percentage of low-quality scans, reducing the number of scans that need to be repeated to obtain clinically useful data. Copyright © 2018 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins

PubMed Central

Tsai, Chun-Ying; Chang, Yuan-Chih; Lobato, Ivan; Van Dyck, Dirk; Chen, Fu-Rong

2016-01-01

The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images. PMID:27292544

Dual-modal three-dimensional imaging of single cells with isometric high resolution using an optical projection tomography microscope

NASA Astrophysics Data System (ADS)

Miao, Qin; Rahn, J. Richard; Tourovskaia, Anna; Meyer, Michael G.; Neumann, Thomas; Nelson, Alan C.; Seibel, Eric J.

2009-11-01

The practice of clinical cytology relies on bright-field microscopy using absorption dyes like hematoxylin and eosin in the transmission mode, while the practice of research microscopy relies on fluorescence microscopy in the epi-illumination mode. The optical projection tomography microscope is an optical microscope that can generate 3-D images of single cells with isometric high resolution both in absorption and fluorescence mode. Although the depth of field of the microscope objective is in the submicron range, it can be extended by scanning the objective's focal plane. The extended depth of field image is similar to a projection in a conventional x-ray computed tomography. Cells suspended in optical gel flow through a custom-designed microcapillary. Multiple pseudoprojection images are taken by rotating the microcapillary. After these pseudoprojection images are further aligned, computed tomography methods are applied to create 3-D reconstruction. 3-D reconstructed images of single cells are shown in both absorption and fluorescence mode. Fluorescence spatial resolution is measured at 0.35 μm in both axial and lateral dimensions. Since fluorescence and absorption images are taken in two different rotations, mechanical error may cause misalignment of 3-D images. This mechanical error is estimated to be within the resolution of the system.

Research on the underwater target imaging based on the streak tube laser lidar

NASA Astrophysics Data System (ADS)

Cui, Zihao; Tian, Zhaoshuo; Zhang, Yanchao; Bi, Zongjie; Yang, Gang; Gu, Erdan

2018-03-01

A high frame rate streak tube imaging lidar (STIL) for real-time 3D imaging of underwater targets is presented in this paper. The system uses 532nm pulse laser as the light source, the maximum repetition rate is 120Hz, and the pulse width is 8ns. LabVIEW platform is used in the system, the system control, synchronous image acquisition, 3D data processing and display are realized through PC. 3D imaging experiment of underwater target is carried out in a flume with attenuation coefficient of 0.2, and the images of different depth and different material targets are obtained, the imaging frame rate is 100Hz, and the maximum detection depth is 31m. For an underwater target with a distance of 22m, the high resolution 3D image real-time acquisition is realized with range resolution of 1cm and space resolution of 0.3cm, the spatial relationship of the targets can be clearly identified by the image. The experimental results show that STIL has a good application prospect in underwater terrain detection, underwater search and rescue, and other fields.

High-resolution high-sensitivity elemental imaging by secondary ion mass spectrometry: from traditional 2D and 3D imaging to correlative microscopy

NASA Astrophysics Data System (ADS)

Wirtz, T.; Philipp, P.; Audinot, J.-N.; Dowsett, D.; Eswara, S.

2015-10-01

Secondary ion mass spectrometry (SIMS) constitutes an extremely sensitive technique for imaging surfaces in 2D and 3D. Apart from its excellent sensitivity and high lateral resolution (50 nm on state-of-the-art SIMS instruments), advantages of SIMS include high dynamic range and the ability to differentiate between isotopes. This paper first reviews the underlying principles of SIMS as well as the performance and applications of 2D and 3D SIMS elemental imaging. The prospects for further improving the capabilities of SIMS imaging are discussed. The lateral resolution in SIMS imaging when using the microprobe mode is limited by (i) the ion probe size, which is dependent on the brightness of the primary ion source, the quality of the optics of the primary ion column and the electric fields in the near sample region used to extract secondary ions; (ii) the sensitivity of the analysis as a reasonable secondary ion signal, which must be detected from very tiny voxel sizes and thus from a very limited number of sputtered atoms; and (iii) the physical dimensions of the collision cascade determining the origin of the sputtered ions with respect to the impact site of the incident primary ion probe. One interesting prospect is the use of SIMS-based correlative microscopy. In this approach SIMS is combined with various high-resolution microscopy techniques, so that elemental/chemical information at the highest sensitivity can be obtained with SIMS, while excellent spatial resolution is provided by overlaying the SIMS images with high-resolution images obtained by these microscopy techniques. Examples of this approach are given by presenting in situ combinations of SIMS with transmission electron microscopy (TEM), helium ion microscopy (HIM) and scanning probe microscopy (SPM).

GPU acceleration towards real-time image reconstruction in 3D tomographic diffractive microscopy

NASA Astrophysics Data System (ADS)

Bailleul, J.; Simon, B.; Debailleul, M.; Liu, H.; Haeberlé, O.

2012-06-01

Phase microscopy techniques regained interest in allowing for the observation of unprepared specimens with excellent temporal resolution. Tomographic diffractive microscopy is an extension of holographic microscopy which permits 3D observations with a finer resolution than incoherent light microscopes. Specimens are imaged by a series of 2D holograms: their accumulation progressively fills the range of frequencies of the specimen in Fourier space. A 3D inverse FFT eventually provides a spatial image of the specimen. Consequently, acquisition then reconstruction are mandatory to produce an image that could prelude real-time control of the observed specimen. The MIPS Laboratory has built a tomographic diffractive microscope with an unsurpassed 130nm resolution but a low imaging speed - no less than one minute. Afterwards, a high-end PC reconstructs the 3D image in 20 seconds. We now expect an interactive system providing preview images during the acquisition for monitoring purposes. We first present a prototype implementing this solution on CPU: acquisition and reconstruction are tied in a producer-consumer scheme, sharing common data into CPU memory. Then we present a prototype dispatching some reconstruction tasks to GPU in order to take advantage of SIMDparallelization for FFT and higher bandwidth for filtering operations. The CPU scheme takes 6 seconds for a 3D image update while the GPU scheme can go down to 2 or > 1 seconds depending on the GPU class. This opens opportunities for 4D imaging of living organisms or crystallization processes. We also consider the relevance of GPU for 3D image interaction in our specific conditions.

Three-dimensional rotational micro-angiography

NASA Astrophysics Data System (ADS)

Patel, Vikas

Computed tomography (CT) is state-of-the-art for 3D imaging in which images are acquired about the patient and are used to reconstruct the data. But the commercial CT systems suffer from low spatial resolution (0.5-2 lp/mm). Micro-CT (microCT) systems have high resolution 3D reconstruction (>10 lp/mm), but are currently limited to small objects, e.g., small animals. To achieve artifact free reconstructions, geometric calibration of the rotating-object cone-beam microCT (CBmicroCT) system is performed using new techniques that use only the projection images of the object, i.e., no calibration objects are required. Translations (up to 0.2 mm) occurring during the acquisition in the horizontal direction are detected, quantified, and corrected based on sinogram analysis. The parameters describing the physical axis of rotation determined using our image-based method (aligning anti-posed images) agree well (within 0.1 mm and 0.3 degrees) with those determined using other techniques that use calibration objects. Geometric calibrations of the rotational angiography (RA) systems (clinical cone-beam CT systems with fluoroscopic capabilities provided by flat-panel detectors (FPD)) are performed using a simple single projection technique (SPT), which aligns a known 3D model of a calibration phantom with the projection data. The calibration parameters obtained by the SPT are found to be reproducible (angles within 0.2° and x- and y-translations less than 2 mm) for over 7 months. The spatial resolution of the RA systems is found to be virtually unaffected by such small geometric variations. Finally, using our understanding of the geometric calibrations, we have developed methods to combine relatively low-resolution RA acquisitions (2-3 lp/mm) with high resolution microCT acquisitions (using a high-resolution micro-angiographic fluoroscope (MAF) attached to the RA gantry) to produce the first-ever 3D rotational micro-angiography (3D-RmicroA) system on a clinical gantry. Images of a rabbit with a coronary stent placed in an artery were obtained and reconstructed. To eliminate artifacts due to image truncation, lower-dose (compared to the MAF acquisition) full-FOV (FFOV) FPD RA sequences are also obtained. To ensure high-quality high-resolution reconstruction, the high-resolution images from the MAF are aligned spatially with the lower-dose FPD images (average correlation coefficient before and after alignment: 0.65 and 0.97 respectively), and the pixel values in the FPD image data are scaled (using linear regression) to match those of the MAF. Greater details without any visible truncation artifacts are seen in 3D RmicroA (MAF-FPD) images than in those of the FPD alone. The FWHM of line profiles of stent struts (100 micron diameter) are approximately 192 +/- 21 and 313 +/- 38 microns for the 3D RmicroA and FPD data, respectively. Thus, with the RmicroA system, we have essentially developed a high resolution CBmicroCT system for clinical use.

Cell sheets image validation of phase-diversity homodyne OCT and effect of the light irradiation on cells

NASA Astrophysics Data System (ADS)

Senda, Naoko; Osawa, Kentaro

2016-04-01

Optical coherence tomography (OCT) is one of powerful 3D tissue imaging tools with no fluorescence staining. We have reported that Phase-Diversity Homodyne OCT developed in Hitachi could be useful for non-invasive regeneration tissue evaluation test. The OCT enables cell imaging because of high resolution (axial resolution; ~2.6 μm, lateral resolution; ~1 μm, in the air), whereas conventional OCT was not used for cell imaging because of low resolution (10~20 μm). Furthermore, the OCT has advantage over other 3D imaging devices in cost because the light source and the objective were originally used as an optical pickup of compact disc. In this report, we aimed to assess effectiveness and safety of Phase-Diversity Homodyne OCT cell imaging. Effectiveness of OCT was evaluated by imaging a living cell sheet of human oral mucosal epithelial cells. OCT images were compared with reflection confocal microscopy (RCM) images, because confocal optical system is the highest resolution (<1 μm) 3D in vivo imaging technique. Similar nuclei images were confirmed with OCT and RCM, which suggested the OCT has enough resolution to image nuclei inside a cell sheet. Degree of differentiation could be estimated using OCT images, which becomes possible because the size of cells depends on distribution of differentiation. Effect of the OCT light irradiation on cells was studied using NIH/3T3 cells. Light irradiation, the exposure amount of which is equivalent to OCT, had no impact on cell shape, cell viability, and proliferation rate. It suggested that the light irradiation has no cell damage under the condition.

Super-resolved Mirau digital holography by structured illumination

NASA Astrophysics Data System (ADS)

Ganjkhani, Yasaman; Charsooghi, Mohammad A.; Akhlaghi, Ehsan A.; Moradi, Ali-Reza

2017-12-01

In this paper, we apply structured illumination toward super-resolved 3D imaging in a common-path digital holography arrangement. Digital holographic microscopy (DHM) provides non-invasive 3D images of transparent samples as well as 3D profiles of reflective surfaces. A compact and vibration-immune arrangement for DHM may be obtained through the use of a Mirau microscope objective. However, high-magnification Mirau objectives have a low working distance and are expensive. Low-magnification ones, on the other hand, suffer from low lateral resolution. Structured illumination has been widely used for resolution improvement of intensity images, but the technique can also be readily applied to DHM. We apply structured illumination to Mirau DHM by implementing successive sinusoidal gratings with different orientations onto a spatial light modulator (SLM) and forming its image on the specimen. Moreover, we show that, instead of different orientations of 1D gratings, alternative single 2D gratings, e.g. checkerboard or hexagonal patterns, can provide resolution enhancement in multiple directions. Our results show a 35% improvement in the resolution power of the DHM. The presented arrangement has the potential to serve as a table-top device for high resolution holographic microscopy.

Non-model-based correction of respiratory motion using beat-to-beat 3D spiral fat-selective imaging.

PubMed

Keegan, Jennifer; Gatehouse, Peter D; Yang, Guang-Zhong; Firmin, David N

2007-09-01

To demonstrate the feasibility of retrospective beat-to-beat correction of respiratory motion, without the need for a respiratory motion model. A high-resolution three-dimensional (3D) spiral black-blood scan of the right coronary artery (RCA) of six healthy volunteers was acquired over 160 cardiac cycles without respiratory gating. One spiral interleaf was acquired per cardiac cycle, prior to each of which a complete low-resolution fat-selective 3D spiral dataset was acquired. The respiratory motion (3D translation) on each cardiac cycle was determined by cross-correlating a region of interest (ROI) in the fat around the artery in the low-resolution datasets with that on a reference end-expiratory dataset. The measured translations were used to correct the raw data of the high-resolution spiral interleaves. Beat-to-beat correction provided consistently good results, with the image quality being better than that obtained with a fixed superior-inferior tracking factor of 0.6 and better than (N = 5) or equal to (N = 1) that achieved using a subject-specific retrospective 3D translation motion model. Non-model-based correction of respiratory motion using 3D spiral fat-selective imaging is feasible, and in this small group of volunteers produced better-quality images than a subject-specific retrospective 3D translation motion model. (c) 2007 Wiley-Liss, Inc.

Positive contrast high-resolution 3D-cine imaging of the cardiovascular system in small animals using a UTE sequence and iron nanoparticles at 4.7, 7 and 9.4 T.

PubMed

Trotier, Aurélien J; Lefrançois, William; Van Renterghem, Kris; Franconi, Jean-Michel; Thiaudière, Eric; Miraux, Sylvain

2015-07-07

To show that 3D sequences with ultra-short echo times (UTEs) can generate a positive contrast whatever the magnetic field (4.7, 7 or 9.4 T) and whatever Ultra Small Particles of Iron Oxide (USPIO) concentration injected and to use it for 3D time-resolved imaging of the murine cardiovascular system with high spatial and temporal resolutions. Three different concentrations (50, 200 and 500 μmol Fe/kg) of USPIO were injected in mice and static images of the middle part of the animals were acquired at 4.7, 7 and 9.4 T pre and post-contrast with UTE (TE/TR = 0.05/4.5 ms) sequences. Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR) of blood and static tissus were evaluated before and after contrast agent injection. 3D-cine images (TE/TR = 0.05/3.5 ms, scan time < 12 min) at 156 μm isotropic resolution of the mouse cardiopulmonary system were acquired prospectively with the UTE sequence for the three magnetic fields and with an USPIO dose of 200 μmol Fe/kg. SNR, CNR and signal homogeneity of blood were measured. High spatial (104 μm) or temporal (3.5 ms) resolution 3D-cine imaging (scan time < 35 min) isotropic resolution were also performed at 7 T with a new sequence encoding scheme. UTE imaging generated positive contrast and higher SNR and CNR whatever the magnetic field and the USPIO concentration used compared to pre-contrast images. Time-resolved 3D acquisition enables high blood SNR (66.6 ± 4.5 at 7 T) and CNR (33.2 ± 4.2 at 7 T) without flow or motion artefact. Coronary arteries and aortic valve were visible on images acquired at 104 μm resolution. We have demonstrated that by combining the injection of iron nanoparticles with 3D-cine UTE sequences, it was possible to generate a strong positive contrast between blood and surrounding tissues. These properties were exploited to produce images of the cardiovascular system in small animals at high magnetic fields with a high spatial and temporal resolution. This approach might be useful to measure the functional cardiac parameters or to assess anatomical modifications to the blood vessels in cardio-vascular disease models.

High-resolution 3D laser imaging based on tunable fiber array link

NASA Astrophysics Data System (ADS)

Zhao, Sisi; Ruan, Ningjuan; Yang, Song

2017-10-01

Airborne photoelectric reconnaissance system with the bore sight down to the ground is an important battlefield situational awareness system, which can be used for reconnaissance and surveillance of complex ground scene. Airborne 3D imaging Lidar system is recognized as the most potential candidates for target detection under the complex background, and is progressing in the directions of high resolution, long distance detection, high sensitivity, low power consumption, high reliability, eye safe and multi-functional. However, the traditional 3D laser imaging system has the disadvantages of lower imaging resolutions because of the small size of the existing detector, and large volume. This paper proposes a high resolution laser 3D imaging technology based on the tunable optical fiber array link. The echo signal is modulated by a tunable optical fiber array link and then transmitted to the focal plane detector. The detector converts the optical signal into electrical signals which is given to the computer. Then, the computer accomplishes the signal calculation and image restoration based on modulation information, and then reconstructs the target image. This paper establishes the mathematical model of tunable optical fiber array signal receiving link, and proposes the simulation and analysis of the affect factors on high density multidimensional point cloud reconstruction.

High-resolution anatomy of the human brain stem using 7-T MRI: improved detection of inner structures and nerves?

PubMed

Gizewski, Elke R; Maderwald, Stefan; Linn, Jennifer; Dassinger, Benjamin; Bochmann, Katja; Forsting, Michael; Ladd, Mark E

2014-03-01

The purpose of this paper is to assess the value of 7 Tesla (7 T) MRI for the depiction of brain stem and cranial nerve (CN) anatomy. Six volunteers were examined at 7 T using high-resolution SWI, MPRAGE, MP2RAGE, 3D SPACE T2, T2, and PD images to establish scanning parameters targeted at optimizing spatial resolution. Direct comparisons between 3 and 7 T were performed in two additional subjects using the finalized sequences (3 T: T2, PD, MPRAGE, SWAN; 7 T: 3D T2, MPRAGE, SWI, MP2RAGE). Artifacts and the depiction of structures were evaluated by two neuroradiologists using a standardized score sheet. Sequences could be established for high-resolution 7 T imaging even in caudal cranial areas. High in-plane resolution T2, PD, and SWI images provided depiction of inner brain stem structures such as pons fibers, raphe, reticular formation, nerve roots, and periaqueductal gray. MPRAGE and MP2RAGE provided clear depiction of the CNs. 3D T2 images improved depiction of inner brain structure in comparison to T2 images at 3 T. Although the 7-T SWI sequence provided improved contrast to some inner structures, extended areas were influenced by artifacts due to image disturbances from susceptibility differences. Seven-tesla imaging of basal brain areas is feasible and might have significant impact on detection and diagnosis in patients with specific diseases, e.g., trigeminal pain related to affection of the nerve root. Some inner brain stem structures can be depicted at 3 T, but certain sequences at 7 T, in particular 3D SPACE T2, are superior in producing anatomical in vivo images of deep brain stem structures.

Three-dimensional wide-field pump-probe structured illumination microscopy

PubMed Central

Kim, Yang-Hyo; So, Peter T.C.

2017-01-01

We propose a new structured illumination scheme for achieving depth resolved wide-field pump-probe microscopy with sub-diffraction limit resolution. By acquiring coherent pump-probe images using a set of 3D structured light illumination patterns, a 3D super-resolution pump-probe image can be reconstructed. We derive the theoretical framework to describe the coherent image formation and reconstruction scheme for this structured illumination pump-probe imaging system and carry out numerical simulations to investigate its imaging performance. The results demonstrate a lateral resolution improvement by a factor of three and providing 0.5 µm level axial optical sectioning. PMID:28380860

Fusion and Visualization of HiRISE Super-Resolution, Shape-from-Shading DTM with MER Stereo 3D Reconstructions

NASA Astrophysics Data System (ADS)

Gupta, S.; Paar, G.; Muller, J. P.; Tao, Y.; Tyler, L.; Traxler, C.; Hesina, G.; Huber, B.; Nauschnegg, B.

2014-12-01

The FP7-SPACE project PRoViDE has assembled a major portion of the imaging data gathered so far from rover vehicles, landers and probes on extra-terrestrial planetary surfaces into a unique database, bringing them into a common planetary geospatial context and providing access to a complete set of 3D vision products. One major aim of PRoViDE is the fusion between orbiter and rover image products. To close the gap between HiRISE imaging resolution (down to 25cm for the OrthoRectified image (ORI), down to 1m for the DTM) and surface vision products, images from multiple HiRISE acquisitions are combined into a super resolution data set (Tao & Muller, 2014), increasing to 5cm resolution the Ortho images. Furthermore, shape-from-shading is applied to one of the ORIs at its original resolution for refinement of the HiRISE DTM, leading to DTM ground resolutions of up to 25 cm. After texture-based co-registration with these refined orbiter 3D products, MER PanCam and NavCam 3D image products can be smoothly pasted into a multi-resolution 3D data representation. Typical results from the MER mission are presented by a dedicated real-time rendering tool which is fed by a hierarchical 3D data structure that is able to cope with all involved scales from global planetary scale down to close-up reconstructions in the mm range. This allows us to explore and analyze the geological characteristics of rock outcrops, for example the detailed geometry and internal features of sedimentary rock layers, to aid paleoenvironmental interpretation. This integrated approach enables more efficient development of geological models of martian rock outcrops. The rendering tool also provides measurement tools to obtain geospatial data of surface points and distances between them. We report on novel scientific use cases and the added value potential of the resultant high-quality data set and presentation means to support further geologic investigations. The research leading to these results has received funding from the EC's 7th Framework Programme (FP7/2007-2013) under grant agreement n° 312377.

Joint estimation of high resolution images and depth maps from light field cameras

NASA Astrophysics Data System (ADS)

Ohashi, Kazuki; Takahashi, Keita; Fujii, Toshiaki

2014-03-01

Light field cameras are attracting much attention as tools for acquiring 3D information of a scene through a single camera. The main drawback of typical lenselet-based light field cameras is the limited resolution. This limitation comes from the structure where a microlens array is inserted between the sensor and the main lens. The microlens array projects 4D light field on a single 2D image sensor at the sacrifice of the resolution; the angular resolution and the position resolution trade-off under the fixed resolution of the image sensor. This fundamental trade-off remains after the raw light field image is converted to a set of sub-aperture images. The purpose of our study is to estimate a higher resolution image from low resolution sub-aperture images using a framework of super-resolution reconstruction. In this reconstruction, these sub-aperture images should be registered as accurately as possible. This registration is equivalent to depth estimation. Therefore, we propose a method where super-resolution and depth refinement are performed alternatively. Most of the process of our method is implemented by image processing operations. We present several experimental results using a Lytro camera, where we increased the resolution of a sub-aperture image by three times horizontally and vertically. Our method can produce clearer images compared to the original sub-aperture images and the case without depth refinement.

Enhanced FIB-SEM systems for large-volume 3D imaging.

PubMed

Xu, C Shan; Hayworth, Kenneth J; Lu, Zhiyuan; Grob, Patricia; Hassan, Ahmed M; García-Cerdán, José G; Niyogi, Krishna K; Nogales, Eva; Weinberg, Richard J; Hess, Harald F

2017-05-13

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 µm 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.

Rapid 3D bioprinting from medical images: an application to bone scaffolding

NASA Astrophysics Data System (ADS)

Lee, Daniel Z.; Peng, Matthew W.; Shinde, Rohit; Khalid, Arbab; Hong, Abigail; Pennacchi, Sara; Dawit, Abel; Sipzner, Daniel; Udupa, Jayaram K.; Rajapakse, Chamith S.

2018-03-01

Bioprinting of tissue has its applications throughout medicine. Recent advances in medical imaging allows the generation of 3-dimensional models that can then be 3D printed. However, the conventional method of converting medical images to 3D printable G-Code instructions has several limitations, namely significant processing time for large, high resolution images, and the loss of microstructural surface information from surface resolution and subsequent reslicing. We have overcome these issues by creating a JAVA program that skips the intermediate triangularization and reslicing steps and directly converts binary dicom images into G-Code. In this study, we tested the two methods of G-Code generation on the application of synthetic bone graft scaffold generation. We imaged human cadaveric proximal femurs at an isotropic resolution of 0.03mm using a high resolution peripheral quantitative computed tomography (HR-pQCT) scanner. These images, of the Digital Imaging and Communications in Medicine (DICOM) format, were then processed through two methods. In each method, slices and regions of print were selected, filtered to generate a smoothed image, and thresholded. In the conventional method, these processed images are converted to the STereoLithography (STL) format and then resliced to generate G-Code. In the new, direct method, these processed images are run through our JAVA program and directly converted to G-Code. File size, processing time, and print time were measured for each. We found that this new method produced a significant reduction in G-Code file size as well as processing time (92.23% reduction). This allows for more rapid 3D printing from medical images.

A new 4-dimensional imaging system for jaw tracking.

PubMed

Lauren, Mark

2014-01-01

A non-invasive 4D imaging system that produces high resolution time-based 3D surface data has been developed to capture jaw motion. Fluorescent microspheres are brushed onto both tooth and soft-tissue areas of the upper and lower arches to be imaged. An extraoral hand-held imaging device, operated about 12 cm from the mouth, captures a time-based set of perspective image triplets of the patch areas. Each triplet, containing both upper and lower arch data, is converted to a high-resolution 3D point mesh using photogrammetry, providing the instantaneous relative jaw position. Eight 3D positions per second are captured. Using one of the 3D frames as a reference, a 4D model can be constructed to describe the incremental free body motion of the mandible. The surface data produced by this system can be registered to conventional 3D models of the dentition, allowing them to be animated. Applications include integration into prosthetic CAD and CBCT data.

Three-dimensional imaging of sulfides in silicate rocks at submicron resolution with multiphoton microscopy.

PubMed

Bénard, Antoine; Palle, Sabine; Doucet, Luc Serge; Ionov, Dmitri A

2011-12-01

We report the first application of multiphoton microscopy (MPM) to generate three-dimensional (3D) images of natural minerals (micron-sized sulfides) in thick (∼120 μm) rock sections. First, reflection mode (RM) using confocal laser scanning microscopy (CLSM), combined with differential interference contrast (DIC), was tested on polished sections. Second, two-photon fluorescence (TPF) and second harmonic signal (SHG) images were generated using a femtosecond-laser on the same rock section without impregnation by a fluorescent dye. CSLM results show that the silicate matrix is revealed with DIC and RM, while sulfides can be imaged in 3D at low resolution by RM. Sulfides yield strong autofluorescence from 392 to 715 nm with TPF, while SHG is only produced by the embedding medium. Simultaneous recording of TPF and SHG images enables efficient discrimination between different components of silicate rocks. Image stacks obtained with MPM enable complete reconstruction of the 3D structure of a rock slice and of sulfide morphology at submicron resolution, which has not been previously reported for 3D imaging of minerals. Our work suggests that MPM is a highly efficient tool for 3D studies of microstructures and morphologies of minerals in silicate rocks, which may find other applications in geosciences.

High resolution multiplexed functional imaging in live embryos (Conference Presentation)

NASA Astrophysics Data System (ADS)

Xu, Dongli; Zhou, Weibin; Peng, Leilei

2017-02-01

Fourier multiplexed fluorescence lifetime imaging (FmFLIM) scanning laser optical tomography (FmFLIM-SLOT) combines FmFLIM and Scanning laser optical tomography (SLOT) to perform multiplexed 3D FLIM imaging of live embryos. The system had demonstrate multiplexed functional imaging of zebrafish embryos genetically express Foster Resonant Energy Transfer (FRET) sensors. However, previous system has a 20 micron resolution because the focused Gaussian beam diverges quickly from the focused plane, makes it difficult to achieve high resolution imaging over a long projection depth. Here, we present a high-resolution FmFLIM-SLOT system with achromatic Bessel beam, which achieves 3 micron resolution in 3D deep tissue imaging. In Bessel-FmFLIM-SLOT, multiple laser excitation lines are firstly intensity modulated by a Michelson interferometer with a spinning polygon mirror optical delay line, which enables Fourier multiplexed multi-channel lifetime measurements. Then, a spatial light modulator and a prism are used to transform the modulated Gaussian laser beam to an achromatic Bessel beam. The achromatic Bessel beam scans across the whole specimen with equal angular intervals as sample rotated. After tomography reconstruction and the frequency domain lifetime analysis method, both the 3D intensity and lifetime image of multiple excitation-emission can be obtained. Using Bessel-FmFLIM-SLOT system, we performed cellular-resolution FLIM tomography imaging of live zebrafish embryo. Genetically expressed FRET sensors in these embryo will allow non-invasive observation of multiple biochemical processes in vivo.

High-resolution imaging of the large non-human primate brain using microPET: a feasibility study

NASA Astrophysics Data System (ADS)

Naidoo-Variawa, S.; Hey-Cunningham, A. J.; Lehnert, W.; Kench, P. L.; Kassiou, M.; Banati, R.; Meikle, S. R.

2007-11-01

The neuroanatomy and physiology of the baboon brain closely resembles that of the human brain and is well suited for evaluating promising new radioligands in non-human primates by PET and SPECT prior to their use in humans. These studies are commonly performed on clinical scanners with 5 mm spatial resolution at best, resulting in sub-optimal images for quantitative analysis. This study assessed the feasibility of using a microPET animal scanner to image the brains of large non-human primates, i.e. papio hamadryas (baboon) at high resolution. Factors affecting image accuracy, including scatter, attenuation and spatial resolution, were measured under conditions approximating a baboon brain and using different reconstruction strategies. Scatter fraction measured 32% at the centre of a 10 cm diameter phantom. Scatter correction increased image contrast by up to 21% but reduced the signal-to-noise ratio. Volume resolution was superior and more uniform using maximum a posteriori (MAP) reconstructed images (3.2-3.6 mm3 FWHM from centre to 4 cm offset) compared to both 3D ordered subsets expectation maximization (OSEM) (5.6-8.3 mm3) and 3D reprojection (3DRP) (5.9-9.1 mm3). A pilot 18F-2-fluoro-2-deoxy-d-glucose ([18F]FDG) scan was performed on a healthy female adult baboon. The pilot study demonstrated the ability to adequately resolve cortical and sub-cortical grey matter structures in the baboon brain and improved contrast when images were corrected for attenuation and scatter and reconstructed by MAP. We conclude that high resolution imaging of the baboon brain with microPET is feasible with appropriate choices of reconstruction strategy and corrections for degrading physical effects. Further work to develop suitable correction algorithms for high-resolution large primate imaging is warranted.

Optimized 14 + 1 receive coil array and position system for 3D high-resolution MRI of dental and maxillomandibular structures.

PubMed

Sedlacik, Jan; Kutzner, Daniel; Khokale, Arun; Schulze, Dirk; Fiehler, Jens; Celik, Turgay; Gareis, Daniel; Smeets, Ralf; Friedrich, Reinhard E; Heiland, Max; Assaf, Alexandre T

2016-01-01

The purpose of this study was to design, build and test a multielement receive coil array and position system, which is optimized for three-dimensional (3D) high-resolution dental and maxillomandibular MRI with high patient comfort. A 14 + 1 coil array and positioning system, allowing easy handling by the technologists, reproducible positioning of the patients and high patient comfort, was tested with three healthy volunteers using a 3.0-T MRI machine (Siemens Skyra; Siemens Medical Solutions, Erlangen, Germany). High-resolution 3D T1 weighted, water excitation T1 weighted and fat-saturated T2 weighted imaging sequences were scanned, and 3D image data were reformatted in different orientations and curvatures to aid diagnosis. The high number of receiving coils and the comfortable positioning of the coil array close to the patient's face provided a high signal-to-noise ratio and allowed high quality, high resolution, 3D image data to be acquired within reasonable scan times owing to the possibility of parallel image acquisition acceleration. Reformatting the isotropic 3D image data in different views is helpful for diagnosis, e.g. panoramic reconstruction. The visibility of soft tissues such as the mandibular canal, nutritive canals and periodontal ligaments was exquisite. The optimized MRI receive coil array and positioning system for dental and oral-maxillofacial imaging provides a valuable tool for detecting and diagnosing pathologies in dental and oral-maxillofacial structures while avoiding radiation dose. The high patient comfort, as achieved by our design, is very crucial, since image artefacts due to movement or failing to complete the examination jeopardize the diagnostic value of MRI examinations.

Micro-optical system based 3D imaging for full HD depth image capturing

NASA Astrophysics Data System (ADS)

Park, Yong-Hwa; Cho, Yong-Chul; You, Jang-Woo; Park, Chang-Young; Yoon, Heesun; Lee, Sang-Hun; Kwon, Jong-Oh; Lee, Seung-Wan

2012-03-01

20 Mega-Hertz-switching high speed image shutter device for 3D image capturing and its application to system prototype are presented. For 3D image capturing, the system utilizes Time-of-Flight (TOF) principle by means of 20MHz high-speed micro-optical image modulator, so called 'optical shutter'. The high speed image modulation is obtained using the electro-optic operation of the multi-layer stacked structure having diffractive mirrors and optical resonance cavity which maximizes the magnitude of optical modulation. The optical shutter device is specially designed and fabricated realizing low resistance-capacitance cell structures having small RC-time constant. The optical shutter is positioned in front of a standard high resolution CMOS image sensor and modulates the IR image reflected from the object to capture a depth image. Suggested novel optical shutter device enables capturing of a full HD depth image with depth accuracy of mm-scale, which is the largest depth image resolution among the-state-of-the-arts, which have been limited up to VGA. The 3D camera prototype realizes color/depth concurrent sensing optical architecture to capture 14Mp color and full HD depth images, simultaneously. The resulting high definition color/depth image and its capturing device have crucial impact on 3D business eco-system in IT industry especially as 3D image sensing means in the fields of 3D camera, gesture recognition, user interface, and 3D display. This paper presents MEMS-based optical shutter design, fabrication, characterization, 3D camera system prototype and image test results.

Fusion of laser and image sensory data for 3-D modeling of the free navigation space

NASA Technical Reports Server (NTRS)

Mass, M.; Moghaddamzadeh, A.; Bourbakis, N.

1994-01-01

A fusion technique which combines two different types of sensory data for 3-D modeling of a navigation space is presented. The sensory data is generated by a vision camera and a laser scanner. The problem of different resolutions for these sensory data was solved by reduced image resolution, fusion of different data, and use of a fuzzy image segmentation technique.

Feasibility of fabricating personalized 3D-printed bone grafts guided by high-resolution imaging

NASA Astrophysics Data System (ADS)

Hong, Abigail L.; Newman, Benjamin T.; Khalid, Arbab; Teter, Olivia M.; Kobe, Elizabeth A.; Shukurova, Malika; Shinde, Rohit; Sipzner, Daniel; Pignolo, Robert J.; Udupa, Jayaram K.; Rajapakse, Chamith S.

2017-03-01

Current methods of bone graft treatment for critical size bone defects can give way to several clinical complications such as limited available bone for autografts, non-matching bone structure, lack of strength which can compromise a patient's skeletal system, and sterilization processes that can prevent osteogenesis in the case of allografts. We intend to overcome these disadvantages by generating a patient-specific 3D printed bone graft guided by high-resolution medical imaging. Our synthetic model allows us to customize the graft for the patients' macro- and microstructure and correct any structural deficiencies in the re-meshing process. These 3D-printed models can presumptively serve as the scaffolding for human mesenchymal stem cell (hMSC) engraftment in order to facilitate bone growth. We performed highresolution CT imaging of a cadaveric human proximal femur at 0.030-mm isotropic voxels. We used these images to generate a 3D computer model that mimics bone geometry from micro to macro scale represented by STereoLithography (STL) format. These models were then reformatted to a format that can be interpreted by the 3D printer. To assess how much of the microstructure was replicated, 3D-printed models were re-imaged using micro-CT at 0.025-mm isotropic voxels and compared to original high-resolution CT images used to generate the 3D model in 32 sub-regions. We found a strong correlation between 3D-printed bone volume and volume of bone in the original images used for 3D printing (R2 = 0.97). We expect to further refine our approach with additional testing to create a viable synthetic bone graft with clinical functionality.

Three-dimensional nanoscale molecular imaging by extreme ultraviolet laser ablation mass spectrometry

PubMed Central

Kuznetsov, Ilya; Filevich, Jorge; Dong, Feng; Woolston, Mark; Chao, Weilun; Anderson, Erik H.; Bernstein, Elliot R.; Crick, Dean C.; Rocca, Jorge J.; Menoni, Carmen S.

2015-01-01

Analytical probes capable of mapping molecular composition at the nanoscale are of critical importance to materials research, biology and medicine. Mass spectral imaging makes it possible to visualize the spatial organization of multiple molecular components at a sample's surface. However, it is challenging for mass spectral imaging to map molecular composition in three dimensions (3D) with submicron resolution. Here we describe a mass spectral imaging method that exploits the high 3D localization of absorbed extreme ultraviolet laser light and its fundamentally distinct interaction with matter to determine molecular composition from a volume as small as 50 zl in a single laser shot. Molecular imaging with a lateral resolution of 75 nm and a depth resolution of 20 nm is demonstrated. These results open opportunities to visualize chemical composition and chemical changes in 3D at the nanoscale. PMID:25903827

Near-isotropic 3D optical nanoscopy with photon-limited chromophores

PubMed Central

Tang, Jianyong; Akerboom, Jasper; Vaziri, Alipasha; Looger, Loren L.; Shank, Charles V.

2010-01-01

Imaging approaches based on single molecule localization break the diffraction barrier of conventional fluorescence microscopy, allowing for bioimaging with nanometer resolution. It remains a challenge, however, to precisely localize photon-limited single molecules in 3D. We have developed a new localization-based imaging technique achieving almost isotropic subdiffraction resolution in 3D. A tilted mirror is used to generate a side view in addition to the front view of activated single emitters, allowing their 3D localization to be precisely determined for superresolution imaging. Because both front and side views are in focus, this method is able to efficiently collect emitted photons. The technique is simple to implement on a commercial fluorescence microscope, and especially suitable for biological samples with photon-limited chromophores such as endogenously expressed photoactivatable fluorescent proteins. Moreover, this method is relatively resistant to optical aberration, as it requires only centroid determination for localization analysis. Here we demonstrate the application of this method to 3D imaging of bacterial protein distribution and neuron dendritic morphology with subdiffraction resolution. PMID:20472826

High axial resolution imaging system for large volume tissues using combination of inclined selective plane illumination and mechanical sectioning

PubMed Central

Zhang, Qi; Yang, Xiong; Hu, Qinglei; Bai, Ke; Yin, Fangfang; Li, Ning; Gang, Yadong; Wang, Xiaojun; Zeng, Shaoqun

2017-01-01

To resolve fine structures of biological systems like neurons, it is required to realize microscopic imaging with sufficient spatial resolution in three dimensional systems. With regular optical imaging systems, high lateral resolution is accessible while high axial resolution is hard to achieve in a large volume. We introduce an imaging system for high 3D resolution fluorescence imaging of large volume tissues. Selective plane illumination was adopted to provide high axial resolution. A scientific CMOS working in sub-array mode kept the imaging area in the sample surface, which restrained the adverse effect of aberrations caused by inclined illumination. Plastic embedding and precise mechanical sectioning extended the axial range and eliminated distortion during the whole imaging process. The combination of these techniques enabled 3D high resolution imaging of large tissues. Fluorescent bead imaging showed resolutions of 0.59 μm, 0.47μm, and 0.59 μm in the x, y, and z directions, respectively. Data acquired from the volume sample of brain tissue demonstrated the applicability of this imaging system. Imaging of different depths showed uniform performance where details could be recognized in either the near-soma area or terminal area, and fine structures of neurons could be seen in both the xy and xz sections. PMID:29296503

MRI of the hip at 7T: feasibility of bone microarchitecture, high-resolution cartilage, and clinical imaging.

PubMed

Chang, Gregory; Deniz, Cem M; Honig, Stephen; Egol, Kenneth; Regatte, Ravinder R; Zhu, Yudong; Sodickson, Daniel K; Brown, Ryan

2014-06-01

To demonstrate the feasibility of performing bone microarchitecture, high-resolution cartilage, and clinical imaging of the hip at 7T. This study had Institutional Review Board approval. Using an 8-channel coil constructed in-house, we imaged the hips of 15 subjects on a 7T magnetic resonance imaging (MRI) scanner. We applied: 1) a T1-weighted 3D fast low angle shot (3D FLASH) sequence (0.23 × 0.23 × 1-1.5 mm(3) ) for bone microarchitecture imaging; 2) T1-weighted 3D FLASH (water excitation) and volumetric interpolated breath-hold examination (VIBE) sequences (0.23 × 0.23 × 1.5 mm(3) ) with saturation or inversion recovery-based fat suppression for cartilage imaging; 3) 2D intermediate-weighted fast spin-echo (FSE) sequences without and with fat saturation (0.27 × 0.27 × 2 mm) for clinical imaging. Bone microarchitecture images allowed visualization of individual trabeculae within the proximal femur. Cartilage was well visualized and fat was well suppressed on FLASH and VIBE sequences. FSE sequences allowed visualization of cartilage, the labrum (including cartilage and labral pathology), joint capsule, and tendons. This is the first study to demonstrate the feasibility of performing a clinically comprehensive hip MRI protocol at 7T, including high-resolution imaging of bone microarchitecture and cartilage, as well as clinical imaging. Copyright © 2013 Wiley Periodicals, Inc.

[A study of the transport of three dimensional medical images to remote institutions for telediagnosis].

PubMed

Hayashi, Takashi; Iwai, Mitsuhiro; Takahashi, Katsuhiko; Takeda, Satoshi; Tateishi, Toshiki; Kaneko, Rumi; Ogasawara, Yoko; Yonezawa, Kazuya; Hanada, Akiko

2011-01-01

Using a 3D-imaging-create-function server and network services by IP-VPN, we began to deliver 3D images to the remote institution. An indication trial of the primary image, a rotary trial of a 3D image, and a reproducibility trial were studied in order to examine the practicality of using the system in a real network between Hakodate and Sapporo (communication distance of about 150 km). In these trials, basic data (time and receiving data volume) were measured for every variation of QF (quality factor) or monitor resolution. Analyzing the results of the system using a 3D image delivery server of our hospital with variations in the setting of QF and monitor resolutions, we concluded that this system has practicality in the remote interpretation-of-radiogram work, even if the access point of the region has a line speed of 6 Mbps.

A multi-directional backlight for a wide-angle, glasses-free three-dimensional display.

PubMed

Fattal, David; Peng, Zhen; Tran, Tho; Vo, Sonny; Fiorentino, Marco; Brug, Jim; Beausoleil, Raymond G

2013-03-21

Multiview three-dimensional (3D) displays can project the correct perspectives of a 3D image in many spatial directions simultaneously. They provide a 3D stereoscopic experience to many viewers at the same time with full motion parallax and do not require special glasses or eye tracking. None of the leading multiview 3D solutions is particularly well suited to mobile devices (watches, mobile phones or tablets), which require the combination of a thin, portable form factor, a high spatial resolution and a wide full-parallax view zone (for short viewing distance from potentially steep angles). Here we introduce a multi-directional diffractive backlight technology that permits the rendering of high-resolution, full-parallax 3D images in a very wide view zone (up to 180 degrees in principle) at an observation distance of up to a metre. The key to our design is a guided-wave illumination technique based on light-emitting diodes that produces wide-angle multiview images in colour from a thin planar transparent lightguide. Pixels associated with different views or colours are spatially multiplexed and can be independently addressed and modulated at video rate using an external shutter plane. To illustrate the capabilities of this technology, we use simple ink masks or a high-resolution commercial liquid-crystal display unit to demonstrate passive and active (30 frames per second) modulation of a 64-view backlight, producing 3D images with a spatial resolution of 88 pixels per inch and full-motion parallax in an unprecedented view zone of 90 degrees. We also present several transparent hand-held prototypes showing animated sequences of up to six different 200-view images at a resolution of 127 pixels per inch.

BLIPPED (BLIpped Pure Phase EncoDing) high resolution MRI with low amplitude gradients

NASA Astrophysics Data System (ADS)

Xiao, Dan; Balcom, Bruce J.

2017-12-01

MRI image resolution is proportional to the maximum k-space value, i.e. the temporal integral of the magnetic field gradient. High resolution imaging usually requires high gradient amplitudes and/or long spatial encoding times. Special gradient hardware is often required for high amplitudes and fast switching. We propose a high resolution imaging sequence that employs low amplitude gradients. This method was inspired by the previously proposed PEPI (π Echo Planar Imaging) sequence, which replaced EPI gradient reversals with multiple RF refocusing pulses. It has been shown that when the refocusing RF pulse is of high quality, i.e. sufficiently close to 180°, the magnetization phase introduced by the spatial encoding magnetic field gradient can be preserved and transferred to the following echo signal without phase rewinding. This phase encoding scheme requires blipped gradients that are identical for each echo, with low and constant amplitude, providing opportunities for high resolution imaging. We now extend the sequence to 3D pure phase encoding with low amplitude gradients. The method is compared with the Hybrid-SESPI (Spin Echo Single Point Imaging) technique to demonstrate the advantages in terms of low gradient duty cycle, compensation of concomitant magnetic field effects and minimal echo spacing, which lead to superior image quality and high resolution. The 3D imaging method was then applied with a parallel plate resonator RF probe, achieving a nominal spatial resolution of 17 μm in one dimension in the 3D image, requiring a maximum gradient amplitude of only 5.8 Gauss/cm.

Direct microCT imaging of non-mineralized connective tissues at high resolution.

PubMed

Naveh, Gili R S; Brumfeld, Vlad; Dean, Mason; Shahar, Ron; Weiner, Steve

2014-01-01

The 3D imaging of soft tissues in their native state is challenging, especially when high resolution is required. An X-ray-based microCT is, to date, the best choice for high resolution 3D imaging of soft tissues. However, since X-ray attenuation of soft tissues is very low, contrasting enhancement using different staining materials is needed. The staining procedure, which also usually involves tissue fixation, causes unwanted and to some extent unknown tissue alterations. Here, we demonstrate that a method that enables 3D imaging of soft tissues without fixing and staining using an X-ray-based bench-top microCT can be applied to a variety of different tissues. With the sample mounted in a custom-made loading device inside a humidity chamber, we obtained soft tissue contrast and generated 3D images of fresh, soft tissues with a resolution of 1 micron voxel size. We identified three critical conditions which make it possible to image soft tissues: humidified environment, mechanical stabilization of the sample and phase enhancement. We demonstrate the capability of the technique using different specimens: an intervertebral disc, the non-mineralized growth plate, stingray tessellated radials (calcified cartilage) and the collagenous network of the periodontal ligament. Since the scanned specimen is fresh an interesting advantage of this technique is the ability to scan a specimen under load and track the changes of the different structures. This method offers a unique opportunity for obtaining valuable insights into 3D structure-function relationships of soft tissues.

Comparison of three-dimensional visualization techniques for depicting the scala vestibuli and scala tympani of the cochlea by using high-resolution MR imaging.

PubMed

Hans, P; Grant, A J; Laitt, R D; Ramsden, R T; Kassner, A; Jackson, A

1999-08-01

Cochlear implantation requires introduction of a stimulating electrode array into the scala vestibuli or scala tympani. Although these structures can be separately identified on many high-resolution scans, it is often difficult to ascertain whether these channels are patent throughout their length. The aim of this study was to determine whether an optimized combination of an imaging protocol and a visualization technique allows routine 3D rendering of the scala vestibuli and scala tympani. A submillimeter T2 fast spin-echo imaging sequence was designed to optimize the performance of 3D visualization methods. The spatial resolution was determined experimentally using primary images and 3D surface and volume renderings from eight healthy subjects. These data were used to develop the imaging sequence and to compare the quality and signal-to-noise dependency of four data visualization algorithms: maximum intensity projection, ray casting with transparent voxels, ray casting with opaque voxels, and isosurface rendering. The ability of these methods to produce 3D renderings of the scala tympani and scala vestibuli was also examined. The imaging technique was used in five patients with sensorineural deafness. Visualization techniques produced optimal results in combination with an isotropic volume imaging sequence. Clinicians preferred the isosurface-rendered images to other 3D visualizations. Both isosurface and ray casting displayed the scala vestibuli and scala tympani throughout their length. Abnormalities were shown in three patients, and in one of these, a focal occlusion of the scala tympani was confirmed at surgery. Three-dimensional images of the scala vestibuli and scala tympani can be routinely produced. The combination of an MR sequence optimized for use with isosurface rendering or ray-casting algorithms can produce 3D images with greater spatial resolution and anatomic detail than has been possible previously.

High resolution NMR imaging using a high field yokeless permanent magnet.

PubMed

Kose, Katsumi; Haishi, Tomoyuki

2011-01-01

We measured the homogeneity and stability of the magnetic field of a high field (about 1.04 tesla) yokeless permanent magnet with 40-mm gap for high resolution nuclear magnetic resonance (NMR) imaging. Homogeneity was evaluated using a 3-dimensional (3D) lattice phantom and 3D spin-echo imaging sequences. In the central sphere (20-mm diameter), peak-to-peak magnetic field inhomogeneity was about 60 ppm, and the root-mean-square was 8 ppm. We measured room temperature, magnet temperature, and NMR frequency of the magnet simultaneously every minute for about 68 hours with and without the thermal insulator of the magnet. A simple mathematical model described the magnet's thermal property. Based on magnet performance, we performed high resolution (up to [20 µm](2)) imaging with internal NMR lock sequences of several biological samples. Our results demonstrated the usefulness of the high field small yokeless permanent magnet for high resolution NMR imaging.

A Novel Image Compression Algorithm for High Resolution 3D Reconstruction

NASA Astrophysics Data System (ADS)

Siddeq, M. M.; Rodrigues, M. A.

2014-06-01

This research presents a novel algorithm to compress high-resolution images for accurate structured light 3D reconstruction. Structured light images contain a pattern of light and shadows projected on the surface of the object, which are captured by the sensor at very high resolutions. Our algorithm is concerned with compressing such images to a high degree with minimum loss without adversely affecting 3D reconstruction. The Compression Algorithm starts with a single level discrete wavelet transform (DWT) for decomposing an image into four sub-bands. The sub-band LL is transformed by DCT yielding a DC-matrix and an AC-matrix. The Minimize-Matrix-Size Algorithm is used to compress the AC-matrix while a DWT is applied again to the DC-matrix resulting in LL2, HL2, LH2 and HH2 sub-bands. The LL2 sub-band is transformed by DCT, while the Minimize-Matrix-Size Algorithm is applied to the other sub-bands. The proposed algorithm has been tested with images of different sizes within a 3D reconstruction scenario. The algorithm is demonstrated to be more effective than JPEG2000 and JPEG concerning higher compression rates with equivalent perceived quality and the ability to more accurately reconstruct the 3D models.

Wavefront coding for fast, high-resolution light-sheet microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Olarte, Omar E.; Licea-Rodriguez, Jacob; Loza-Alvarez, Pablo

2017-02-01

Some biological experiments demand the observation of dynamics processes in 3D with high spatiotemporal resolution. The use of wavefront coding to extend the depth-of-field (DOF) of the collection arm of a light-sheet microscope is an interesting alternative for fast 3D imaging. Under this scheme, the 3D features of the sample are captured at high volumetric rates while the light sheet is swept rapidly within the extended DOF. The DOF is extended by coding the pupil function of the imaging lens by using a custom-designed phase mask. A posterior restoration step is required to decode the information of the captured images based on the applied phase mask [1]. This hybrid optical-digital approach is known as wavefront coding (WFC). Previously, we have demonstrated this method for performing fast 3D imaging of biological samples at medium resolution [2]. In this work, we present the extension of this approach for high-resolution microscopes. Under these conditions, the effective DOF of a standard high NA objective is of a few micrometers. Here we demonstrate that by the use of WFC, we can extend the DOF more than one order of magnitude keeping the high-resolution imaging. This is demonstrated for two designed phase masks using Zebrafish and C. elegans samples. [1] Olarte, O.E., Andilla, J., Artigas, D., and Loza-Alvarez, P., "Decoupled Illumination-Detection Microscopy. Selected Optics in Year 2105," in Optics and Photonics news 26, p. 41 (2015). [2] Olarte, O.E., Andilla, J., Artigas, D., and Loza-Alvarez, P., "Decoupled illumination detection in light sheet microscopy for fast volumetric imaging," Optica 2(8), 702 (2015).

[Depiction of the cranial nerves around the cavernous sinus by 3D reversed FISP with diffusion weighted imaging (3D PSIF-DWI)].

PubMed

Ishida, Go; Oishi, Makoto; Jinguji, Shinya; Yoneoka, Yuichiro; Sato, Mitsuya; Fujii, Yukihiko

2011-10-01

To evaluate the anatomy of cranial nerves running in and around the cavernous sinus, we employed three-dimensional reversed fast imaging with steady-state precession (FISP) with diffusion weighted imaging (3D PSIF-DWI) on 3-T magnetic resonance (MR) system. After determining the proper parameters to obtain sufficient resolution of 3D PSIF-DWI, we collected imaging data of 20-side cavernous regions in 10 normal subjects. 3D PSIF-DWI provided high contrast between the cranial nerves and other soft tissues, fluid, and blood in all subjects. We also created volume-rendered images of 3D PSIF-DWI and anatomically evaluated the reliability of visualizing optic, oculomotor, trochlear, trigeminal, and abducens nerves on 3D PSIF-DWI. All 20 sets of cranial nerves were visualized and 12 trochlear nerves and 6 abducens nerves were partially identified. We also presented preliminary clinical experiences in two cases with pituitary adenomas. The anatomical relationship between the tumor and cranial nerves running in and around the cavernous sinus could be three-dimensionally comprehended by 3D PSIF-DWI and the volume-rendered images. In conclusion, 3D PSIF-DWI has great potential to provide high resolution "cranial nerve imaging", which visualizes the whole length of the cranial nerves including the parts in the blood flow as in the cavernous sinus region.

Single-frame 3D fluorescence microscopy with ultraminiature lensless FlatScope

PubMed Central

Adams, Jesse K.; Boominathan, Vivek; Avants, Benjamin W.; Vercosa, Daniel G.; Ye, Fan; Baraniuk, Richard G.; Robinson, Jacob T.; Veeraraghavan, Ashok

2017-01-01

Modern biology increasingly relies on fluorescence microscopy, which is driving demand for smaller, lighter, and cheaper microscopes. However, traditional microscope architectures suffer from a fundamental trade-off: As lenses become smaller, they must either collect less light or image a smaller field of view. To break this fundamental trade-off between device size and performance, we present a new concept for three-dimensional (3D) fluorescence imaging that replaces lenses with an optimized amplitude mask placed a few hundred micrometers above the sensor and an efficient algorithm that can convert a single frame of captured sensor data into high-resolution 3D images. The result is FlatScope: perhaps the world’s tiniest and lightest microscope. FlatScope is a lensless microscope that is scarcely larger than an image sensor (roughly 0.2 g in weight and less than 1 mm thick) and yet able to produce micrometer-resolution, high–frame rate, 3D fluorescence movies covering a total volume of several cubic millimeters. The ability of FlatScope to reconstruct full 3D images from a single frame of captured sensor data allows us to image 3D volumes roughly 40,000 times faster than a laser scanning confocal microscope while providing comparable resolution. We envision that this new flat fluorescence microscopy paradigm will lead to implantable endoscopes that minimize tissue damage, arrays of imagers that cover large areas, and bendable, flexible microscopes that conform to complex topographies. PMID:29226243

High Efficiency, Low Distortion 3D Diffusion Tensor Imaging with Variable Density Spiral Fast Spin Echoes (3D DW VDS RARE)

PubMed Central

Frank, Lawrence R.; Jung, Youngkyoo; Inati, Souheil; Tyszka, J. Michael; Wong, Eric C.

2009-01-01

We present an acquisition and reconstruction method designed to acquire high resolution 3D fast spin echo diffusion tensor images while mitigating the major sources of artifacts in DTI - field distortions, eddy currents and motion. The resulting images, being 3D, are of high SNR, and being fast spin echoes, exhibit greatly reduced field distortions. This sequence utilizes variable density spiral acquisition gradients, which allow for the implementation of a self-navigation scheme by which both eddy current and motion artifacts are removed. The result is that high resolution 3D DTI images are produced without the need for eddy current compensating gradients or B0 field correction. In addition, a novel method for fast and accurate reconstruction of the non-Cartesian data is employed. Results are demonstrated in the brains of normal human volunteers. PMID:19778618

Use of High Resolution 3D Diffusion Tensor Imaging to Study Brain White Matter Development in Live Neonatal Rats

PubMed Central

Cai, Yu; McMurray, Matthew S.; Oguz, Ipek; Yuan, Hong; Styner, Martin A.; Lin, Weili; Johns, Josephine M.; An, Hongyu

2011-01-01

High resolution diffusion tensor imaging (DTI) can provide important information on brain development, yet it is challenging in live neonatal rats due to the small size of neonatal brain and motion-sensitive nature of DTI. Imaging in live neonatal rats has clear advantages over fixed brain scans, as longitudinal and functional studies would be feasible to understand neuro-developmental abnormalities. In this study, we developed imaging strategies that can be used to obtain high resolution 3D DTI images in live neonatal rats at postnatal day 5 (PND5) and PND14, using only 3 h of imaging acquisition time. An optimized 3D DTI pulse sequence and appropriate animal setup to minimize physiological motion artifacts are the keys to successful high resolution 3D DTI imaging. Thus, a 3D rapid acquisition relaxation enhancement DTI sequence with twin navigator echoes was implemented to accelerate imaging acquisition time and minimize motion artifacts. It has been suggested that neonatal mammals possess a unique ability to tolerate mild-to-moderate hypothermia and hypoxia without long term impact. Thus, we additionally utilized this ability to minimize motion artifacts in magnetic resonance images by carefully suppressing the respiratory rate to around 15/min for PND5 and 30/min for PND14 using mild-to-moderate hypothermia. These imaging strategies have been successfully implemented to study how the effect of cocaine exposure in dams might affect brain development in their rat pups. Image quality resulting from this in vivo DTI study was comparable to ex vivo scans. fractional anisotropy values were also similar between the live and fixed brain scans. The capability of acquiring high quality in vivo DTI imaging offers a valuable opportunity to study many neurological disorders in brain development in an authentic living environment. PMID:22013426

Three-Dimensional Terahertz Coded-Aperture Imaging Based on Matched Filtering and Convolutional Neural Network.

PubMed

Chen, Shuo; Luo, Chenggao; Wang, Hongqiang; Deng, Bin; Cheng, Yongqiang; Zhuang, Zhaowen

2018-04-26

As a promising radar imaging technique, terahertz coded-aperture imaging (TCAI) can achieve high-resolution, forward-looking, and staring imaging by producing spatiotemporal independent signals with coded apertures. However, there are still two problems in three-dimensional (3D) TCAI. Firstly, the large-scale reference-signal matrix based on meshing the 3D imaging area creates a heavy computational burden, thus leading to unsatisfactory efficiency. Secondly, it is difficult to resolve the target under low signal-to-noise ratio (SNR). In this paper, we propose a 3D imaging method based on matched filtering (MF) and convolutional neural network (CNN), which can reduce the computational burden and achieve high-resolution imaging for low SNR targets. In terms of the frequency-hopping (FH) signal, the original echo is processed with MF. By extracting the processed echo in different spike pulses separately, targets in different imaging planes are reconstructed simultaneously to decompose the global computational complexity, and then are synthesized together to reconstruct the 3D target. Based on the conventional TCAI model, we deduce and build a new TCAI model based on MF. Furthermore, the convolutional neural network (CNN) is designed to teach the MF-TCAI how to reconstruct the low SNR target better. The experimental results demonstrate that the MF-TCAI achieves impressive performance on imaging ability and efficiency under low SNR. Moreover, the MF-TCAI has learned to better resolve the low-SNR 3D target with the help of CNN. In summary, the proposed 3D TCAI can achieve: (1) low-SNR high-resolution imaging by using MF; (2) efficient 3D imaging by downsizing the large-scale reference-signal matrix; and (3) intelligent imaging with CNN. Therefore, the TCAI based on MF and CNN has great potential in applications such as security screening, nondestructive detection, medical diagnosis, etc.

Experimental study of sector and linear array ultrasound accuracy and the influence of navigated 3D-reconstruction as compared to MRI in a brain tumor model.

PubMed

Siekmann, Max; Lothes, Thomas; König, Ralph; Wirtz, Christian Rainer; Coburger, Jan

2018-03-01

Currently, intraoperative ultrasound in brain tumor surgery is a rapidly propagating option in imaging technology. We examined the accuracy and resolution limits of different ultrasound probes and the influence of 3D-reconstruction in a phantom and compared these results to MRI in an intraoperative setting (iMRI). An agarose gel phantom with predefined gel targets was examined with iMRI, a sector (SUS) and a linear (LUS) array probe with two-dimensional images. Additionally, 3D-reconstructed sweeps in perpendicular directions were made of every target with both probes, resulting in 392 measurements. Statistical calculations were performed, and comparative boxplots were generated. Every measurement of iMRI and LUS was more precise than SUS, while there was no apparent difference in height of iMRI and 3D-reconstructed LUS. Measurements with 3D-reconstructed LUS were always more accurate than in 2D-LUS, while 3D-reconstruction of SUS showed nearly no differences to 2D-SUS in some measurements. We found correlations of 3D-reconstructed SUS and LUS length and width measurements with 2D results in the same image orientation. LUS provides an accuracy and resolution comparable to iMRI, while SUS is less exact than LUS and iMRI. 3D-reconstruction showed the potential to distinctly improve accuracy and resolution of ultrasound images, although there is a strong correlation with the sweep direction during data acquisition.

3D nanometer images of biological fibers by directed motion of gold nanoparticles.

PubMed

Estrada, Laura C; Gratton, Enrico

2011-11-09

Using near-infrared femtosecond pulses, we move single gold nanoparticles (AuNPs) along biological fibers, such as collagen and actin filaments. While the AuNP is sliding on the fiber, its trajectory is measured in three dimensions (3D) with nanometer resolution providing a high-resolution image of the fiber. Here, we systematically moved a single AuNP along nanometer-size collagen fibers and actin filament inside chinese hamster ovary K1 living cells, mapping their 3D topography with high fidelity.

Computational microscopy: illumination coding and nonlinear optimization enables gigapixel 3D phase imaging

NASA Astrophysics Data System (ADS)

Tian, Lei; Waller, Laura

2017-05-01

Microscope lenses can have either large field of view (FOV) or high resolution, not both. Computational microscopy based on illumination coding circumvents this limit by fusing images from different illumination angles using nonlinear optimization algorithms. The result is a Gigapixel-scale image having both wide FOV and high resolution. We demonstrate an experimentally robust reconstruction algorithm based on a 2nd order quasi-Newton's method, combined with a novel phase initialization scheme. To further extend the Gigapixel imaging capability to 3D, we develop a reconstruction method to process the 4D light field measurements from sequential illumination scanning. The algorithm is based on a 'multislice' forward model that incorporates both 3D phase and diffraction effects, as well as multiple forward scatterings. To solve the inverse problem, an iterative update procedure that combines both phase retrieval and 'error back-propagation' is developed. To avoid local minimum solutions, we further develop a novel physical model-based initialization technique that accounts for both the geometric-optic and 1st order phase effects. The result is robust reconstructions of Gigapixel 3D phase images having both wide FOV and super resolution in all three dimensions. Experimental results from an LED array microscope were demonstrated.

Automatic correspondence detection in mammogram and breast tomosynthesis images

NASA Astrophysics Data System (ADS)

Ehrhardt, Jan; Krüger, Julia; Bischof, Arpad; Barkhausen, Jörg; Handels, Heinz

2012-02-01

Two-dimensional mammography is the major imaging modality in breast cancer detection. A disadvantage of mammography is the projective nature of this imaging technique. Tomosynthesis is an attractive modality with the potential to combine the high contrast and high resolution of digital mammography with the advantages of 3D imaging. In order to facilitate diagnostics and treatment in the current clinical work-flow, correspondences between tomosynthesis images and previous mammographic exams of the same women have to be determined. In this paper, we propose a method to detect correspondences in 2D mammograms and 3D tomosynthesis images automatically. In general, this 2D/3D correspondence problem is ill-posed, because a point in the 2D mammogram corresponds to a line in the 3D tomosynthesis image. The goal of our method is to detect the "most probable" 3D position in the tomosynthesis images corresponding to a selected point in the 2D mammogram. We present two alternative approaches to solve this 2D/3D correspondence problem: a 2D/3D registration method and a 2D/2D mapping between mammogram and tomosynthesis projection images with a following back projection. The advantages and limitations of both approaches are discussed and the performance of the methods is evaluated qualitatively and quantitatively using a software phantom and clinical breast image data. Although the proposed 2D/3D registration method can compensate for moderate breast deformations caused by different breast compressions, this approach is not suitable for clinical tomosynthesis data due to the limited resolution and blurring effects perpendicular to the direction of projection. The quantitative results show that the proposed 2D/2D mapping method is capable of detecting corresponding positions in mammograms and tomosynthesis images automatically for 61 out of 65 landmarks. The proposed method can facilitate diagnosis, visual inspection and comparison of 2D mammograms and 3D tomosynthesis images for the physician.

Visualization of Stereoscopic Anatomic Models of the Paranasal Sinuses and Cervical Vertebrae from the Surgical and Procedural Perspective

ERIC Educational Resources Information Center

Chen, Jian; Smith, Andrew D.; Khan, Majid A.; Sinning, Allan R.; Conway, Marianne L.; Cui, Dongmei

2017-01-01

Recent improvements in three-dimensional (3D) virtual modeling software allows anatomists to generate high-resolution, visually appealing, colored, anatomical 3D models from computed tomography (CT) images. In this study, high-resolution CT images of a cadaver were used to develop clinically relevant anatomic models including facial skull, nasal…

3D sensitivity encoded ellipsoidal MR spectroscopic imaging of gliomas at 3T☆

PubMed Central

Ozturk-Isik, Esin; Chen, Albert P.; Crane, Jason C.; Bian, Wei; Xu, Duan; Han, Eric T.; Chang, Susan M.; Vigneron, Daniel B.; Nelson, Sarah J.

2010-01-01

Purpose The goal of this study was to implement time efficient data acquisition and reconstruction methods for 3D magnetic resonance spectroscopic imaging (MRSI) of gliomas at a field strength of 3T using parallel imaging techniques. Methods The point spread functions, signal to noise ratio (SNR), spatial resolution, metabolite intensity distributions and Cho:NAA ratio of 3D ellipsoidal, 3D sensitivity encoding (SENSE) and 3D combined ellipsoidal and SENSE (e-SENSE) k-space sampling schemes were compared with conventional k-space data acquisition methods. Results The 3D SENSE and e-SENSE methods resulted in similar spectral patterns as the conventional MRSI methods. The Cho:NAA ratios were highly correlated (P<.05 for SENSE and P<.001 for e-SENSE) with the ellipsoidal method and all methods exhibited significantly different spectral patterns in tumor regions compared to normal appearing white matter. The geometry factors ranged between 1.2 and 1.3 for both the SENSE and e-SENSE spectra. When corrected for these factors and for differences in data acquisition times, the empirical SNRs were similar to values expected based upon theoretical grounds. The effective spatial resolution of the SENSE spectra was estimated to be same as the corresponding fully sampled k-space data, while the spectra acquired with ellipsoidal and e-SENSE k-space samplings were estimated to have a 2.36–2.47-fold loss in spatial resolution due to the differences in their point spread functions. Conclusion The 3D SENSE method retained the same spatial resolution as full k-space sampling but with a 4-fold reduction in scan time and an acquisition time of 9.28 min. The 3D e-SENSE method had a similar spatial resolution as the corresponding ellipsoidal sampling with a scan time of 4:36 min. Both parallel imaging methods provided clinically interpretable spectra with volumetric coverage and adequate SNR for evaluating Cho, Cr and NAA. PMID:19766422

Iodine and freeze-drying enhanced high-resolution MicroCT imaging for reconstructing 3D intraneural topography of human peripheral nerve fascicles.

PubMed

Yan, Liwei; Guo, Yongze; Qi, Jian; Zhu, Qingtang; Gu, Liqiang; Zheng, Canbin; Lin, Tao; Lu, Yutong; Zeng, Zitao; Yu, Sha; Zhu, Shuang; Zhou, Xiang; Zhang, Xi; Du, Yunfei; Yao, Zhi; Lu, Yao; Liu, Xiaolin

2017-08-01

The precise annotation and accurate identification of the topography of fascicles to the end organs are prerequisites for studying human peripheral nerves. In this study, we present a feasible imaging method that acquires 3D high-resolution (HR) topography of peripheral nerve fascicles using an iodine and freeze-drying (IFD) micro-computed tomography (microCT) method to greatly increase the contrast of fascicle images. The enhanced microCT imaging method can facilitate the reconstruction of high-contrast HR fascicle images, fascicle segmentation and extraction, feature analysis, and the tracing of fascicle topography to end organs, which define fascicle functions. The complex intraneural aggregation and distribution of fascicles is typically assessed using histological techniques or MR imaging to acquire coarse axial three-dimensional (3D) maps. However, the disadvantages of histological techniques (static, axial manual registration, and data instability) and MR imaging (low-resolution) limit these applications in reconstructing the topography of nerve fascicles. Thus, enhanced microCT is a new technique for acquiring 3D intraneural topography of the human peripheral nerve fascicles both to improve our understanding of neurobiological principles and to guide accurate repair in the clinic. Additionally, 3D microstructure data can be used as a biofabrication model, which in turn can be used to fabricate scaffolds to repair long nerve gaps. Copyright © 2017 Elsevier B.V. All rights reserved.

3D in vivo imaging with extended-focus optical coherence microscopy.

PubMed

Chen, Yu; Trinh, Le A; Fingler, Jeff; Fraser, Scott E

2017-11-01

Optical coherence microscopy (OCM) has unique advantages of non-invasive 3D imaging without the need of exogenous labels for studying biological samples. However, the imaging depth of this technique is limited by the tradeoff between the depth of focus (DOF) and high lateral resolution in Gaussian optics. To overcome this limitation, we have developed an extended-focus OCM (xf-OCM) imaging system using quasi-Bessel beam illumination to extend the DOF to ∼100 μm, about 3-fold greater than standard OCM. High lateral resolution of 1.6 μm ensured detailed identification of structures within live animal samples. The insensitivity to spherical aberrations strengthened the capability of our xf-OCM system in 3D biological imaging. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels.

PubMed

Si, Dong; He, Jing

2014-01-01

Electron cryo-microscopy (Cryo-EM) technique produces 3-dimensional (3D) density images of proteins. When resolution of the images is not high enough to resolve the molecular details, it is challenging for image processing methods to enhance the molecular features. β-barrel is a particular structure feature that is formed by multiple β-strands in a barrel shape. There is no existing method to derive β-strands from the 3D image of a β-barrel at medium resolutions. We propose a new method, StrandRoller, to generate a small set of possible β-traces from the density images at medium resolutions of 5-10Å. StrandRoller has been tested using eleven β-barrel images simulated to 10Å resolution and one image isolated from the experimentally derived cryo-EM density image at 6.7Å resolution. StrandRoller was able to detect 81.84% of the β-strands with an overall 1.5Å 2-way distance between the detected and the observed β-traces, if the best of fifteen detections is considered. Our results suggest that it is possible to derive a small set of possible β-traces from the β-barrel cryo-EM image at medium resolutions even when no separation of the β-strands is visible in the images.

Diffusion-prepared stimulated-echo turbo spin echo (DPsti-TSE): An eddy current-insensitive sequence for three-dimensional high-resolution and undistorted diffusion-weighted imaging.

PubMed

Zhang, Qinwei; Coolen, Bram F; Versluis, Maarten J; Strijkers, Gustav J; Nederveen, Aart J

2017-07-01

In this study, we present a new three-dimensional (3D), diffusion-prepared turbo spin echo sequence based on a stimulated-echo read-out (DPsti-TSE) enabling high-resolution and undistorted diffusion-weighted imaging (DWI). A dephasing gradient in the diffusion preparation module and rephasing gradients in the turbo spin echo module create stimulated echoes, which prevent signal loss caused by eddy currents. Near to perfect agreement of apparent diffusion coefficient (ADC) values between DPsti-TSE and diffusion-weighted echo planar imaging (DW-EPI) was demonstrated in both phantom transient signal experiments and phantom imaging experiments. High-resolution and undistorted DPsti-TSE was demonstrated in vivo in prostate and carotid vessel wall. 3D whole-prostate DWI was achieved with four b values in only 6 min. Undistorted ADC maps of the prostate peripheral zone were obtained at low and high imaging resolutions with no change in mean ADC values [(1.60 ± 0.10) × 10 -3 versus (1.60 ± 0.02) × 10 -3  mm 2 /s]. High-resolution 3D DWI of the carotid vessel wall was achieved in 12 min, with consistent ADC values [(1.40 ± 0.23) × 10 -3  mm 2 /s] across different subjects, as well as slice locations through the imaging volume. This study shows that DPsti-TSE can serve as a robust 3D diffusion-weighted sequence and is an attractive alternative to the traditional two-dimensional DW-EPI approaches. Copyright © 2017 John Wiley & Sons, Ltd.

High-Resolution 3T MR Imaging of the Triangular Fibrocartilage Complex

PubMed Central

von Borstel, Donald; Wang, Michael; Small, Kirstin; Nozaki, Taiki; Yoshioka, Hiroshi

2017-01-01

This study is intended as a review of 3Tesla (T) magnetic resonance (MR) imaging of the triangular fibrocartilage complex (TFCC). The recent advances in MR imaging, which includes high field strength magnets, multi-channel coils, and isotropic 3-dimensional (3D) sequences have enabled the visualization of precise TFCC anatomy with high spatial and contrast resolution. In addition to the routine wrist protocol, there are specific techniques used to optimize 3T imaging of the wrist; including driven equilibrium sequence (DRIVE), parallel imaging, and 3D imaging. The coil choice for 3T imaging of the wrist depends on a number of variables, and the proper coil design selection is critical for high-resolution wrist imaging with high signal and contrast-to-noise ratio. The TFCC is a complex structure and is composed of the articular disc (disc proper), the triangular ligament, the dorsal and volar radioulnar ligaments, the meniscus homologue, the ulnar collateral ligament (UCL), the extensor carpi ulnaris (ECU) tendon sheath, and the ulnolunate and ulnotriquetral ligaments. The Palmer classification categorizes TFCC lesions as traumatic (type 1) or degenerative (type 2). In this review article, we present clinical high-resolution MR images of normal TFCC anatomy and TFCC injuries with this classification system. PMID:27535592

High-Resolution 3T MR Imaging of the Triangular Fibrocartilage Complex.

PubMed

von Borstel, Donald; Wang, Michael; Small, Kirstin; Nozaki, Taiki; Yoshioka, Hiroshi

2017-01-10

This study is intended as a review of 3Tesla (T) magnetic resonance (MR) imaging of the triangular fibrocartilage complex (TFCC). The recent advances in MR imaging, which includes high field strength magnets, multi-channel coils, and isotropic 3-dimensional (3D) sequences have enabled the visualization of precise TFCC anatomy with high spatial and contrast resolution. In addition to the routine wrist protocol, there are specific techniques used to optimize 3T imaging of the wrist; including driven equilibrium sequence (DRIVE), parallel imaging, and 3D imaging. The coil choice for 3T imaging of the wrist depends on a number of variables, and the proper coil design selection is critical for high-resolution wrist imaging with high signal and contrast-to-noise ratio. The TFCC is a complex structure and is composed of the articular disc (disc proper), the triangular ligament, the dorsal and volar radioulnar ligaments, the meniscus homologue, the ulnar collateral ligament (UCL), the extensor carpi ulnaris (ECU) tendon sheath, and the ulnolunate and ulnotriquetral ligaments. The Palmer classification categorizes TFCC lesions as traumatic (type 1) or degenerative (type 2). In this review article, we present clinical high-resolution MR images of normal TFCC anatomy and TFCC injuries with this classification system.

Enhanced FIB-SEM systems for large-volume 3D imaging

PubMed Central

Xu, C Shan; Hayworth, Kenneth J; Lu, Zhiyuan; Grob, Patricia; Hassan, Ahmed M; García-Cerdán, José G; Niyogi, Krishna K; Nogales, Eva; Weinberg, Richard J; Hess, Harald F

2017-01-01

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 106 µm3. These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processes and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology. DOI: http://dx.doi.org/10.7554/eLife.25916.001 PMID:28500755

Enhanced FIB-SEM systems for large-volume 3D imaging

DOE PAGES

Xu, C. Shan; Hayworth, Kenneth J.; Lu, Zhiyuan; ...

2017-05-13

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 ?m 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processesmore » and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.« less

Efficient fabrication method of nano-grating for 3D holographic display with full parallax views.

PubMed

Wan, Wenqiang; Qiao, Wen; Huang, Wenbin; Zhu, Ming; Fang, Zongbao; Pu, Donglin; Ye, Yan; Liu, Yanhua; Chen, Linsen

2016-03-21

Without any special glasses, multiview 3D displays based on the diffractive optics can present high resolution, full-parallax 3D images in an ultra-wide viewing angle. The enabling optical component, namely the phase plate, can produce arbitrarily distributed view zones by carefully designing the orientation and the period of each nano-grating pixel. However, such 3D display screen is restricted to a limited size due to the time-consuming fabricating process of nano-gratings on the phase plate. In this paper, we proposed and developed a lithography system that can fabricate the phase plate efficiently. Here we made two phase plates with full nano-grating pixel coverage at a speed of 20 mm²/mins, a 500 fold increment in the efficiency when compared to the method of E-beam lithography. One 2.5-inch phase plate generated 9-view 3D images with horizontal-parallax, while the other 6-inch phase plate produced 64-view 3D images with full-parallax. The angular divergence in horizontal axis and vertical axis was 1.5 degrees, and 1.25 degrees, respectively, slightly larger than the simulated value of 1.2 degrees by Finite Difference Time Domain (FDTD). The intensity variation was less than 10% for each viewpoint, in consistency with the simulation results. On top of each phase plate, a high-resolution binary masking pattern containing amplitude information of all viewing zone was well aligned. We achieved a resolution of 400 pixels/inch and a viewing angle of 40 degrees for 9-view 3D images with horizontal parallax. In another prototype, the resolution of each view was 160 pixels/inch and the view angle was 50 degrees for 64-view 3D images with full parallax. As demonstrated in the experiments, the homemade lithography system provided the key fabricating technology for multiview 3D holographic display.

Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME.

PubMed

Reboul, Cyril F; Eager, Michael; Elmlund, Dominika; Elmlund, Hans

2018-01-01

Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated. © 2017 The Protein Society.

Protein secondary structure determination by constrained single-particle cryo-electron tomography.

PubMed

Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

2012-12-05

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

Time-Resolved 3D Quantitative Flow MRI of the Major Intracranial Vessels: Initial Experience and Comparative Evaluation at 1.5T and 3.0T in Combination With Parallel Imaging

PubMed Central

Bammer, Roland; Hope, Thomas A.; Aksoy, Murat; Alley, Marcus T.

2012-01-01

Exact knowledge of blood flow characteristics in the major cerebral vessels is of great relevance for diagnosing cerebrovascular abnormalities. This involves the assessment of hemodynamically critical areas as well as the derivation of biomechanical parameters such as wall shear stress and pressure gradients. A time-resolved, 3D phase-contrast (PC) MRI method using parallel imaging was implemented to measure blood flow in three dimensions at multiple instances over the cardiac cycle. The 4D velocity data obtained from 14 healthy volunteers were used to investigate dynamic blood flow with the use of multiplanar reformatting, 3D streamlines, and 4D particle tracing. In addition, the effects of magnetic field strength, parallel imaging, and temporal resolution on the data were investigated in a comparative evaluation at 1.5T and 3T using three different parallel imaging reduction factors and three different temporal resolutions in eight of the 14 subjects. Studies were consistently performed faster at 3T than at 1.5T because of better parallel imaging performance. A high temporal resolution (65 ms) was required to follow dynamic processes in the intracranial vessels. The 4D flow measurements provided a high degree of vascular conspicuity. Time-resolved streamline analysis provided features that have not been reported previously for the intracranial vasculature. PMID:17195166

SU-F-J-158: Respiratory Motion Resolved, Self-Gated 4D-MRI Using Rotating Cartesian K-Space Sampling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, F; Zhou, Z; Yang, Y

Purpose: Dynamic MRI has been used to quantify respiratory motion of abdominal organs in radiation treatment planning. Many existing 4D-MRI methods based on 2D acquisitions suffer from limited slice resolution and additional stitching artifacts when evaluated in 3D{sup 1}. To address these issues, we developed a 4D-MRI (3D dynamic) technique with true 3D k-space encoding and respiratory motion self-gating. Methods: The 3D k-space was acquired using a Rotating Cartesian K-space (ROCK) pattern, where the Cartesian grid was reordered in a quasi-spiral fashion with each spiral arm rotated using golden angle{sup 2}. Each quasi-spiral arm started with the k-space center-line, whichmore » were used as self-gating{sup 3} signal for respiratory motion estimation. The acquired k-space data was then binned into 8 respiratory phases and the golden angle ensures a near-uniform k-space sampling in each phase. Finally, dynamic 3D images were reconstructed using the ESPIRiT technique{sup 4}. 4D-MRI was performed on 6 healthy volunteers, using the following parameters (bSSFP, Fat-Sat, TE/TR=2ms/4ms, matrix size=500×350×120, resolution=1×1×1.2mm, TA=5min, 8 respiratory phases). Supplemental 2D real-time images were acquired in 9 different planes. Dynamic locations of the diaphragm dome and left kidney were measured from both 4D and 2D images. The same protocol was also performed on a MRI-compatible motion phantom where the motion was programmed with different amplitude (10–30mm) and frequency (3–10/min). Results: High resolution 4D-MRI were obtained successfully in 5 minutes. Quantitative motion measurements from 4D-MRI agree with the ones from 2D CINE (<5% error). The 4D images are free of the stitching artifacts and their near-isotropic resolution facilitates 3D visualization and segmentation of abdominal organs such as the liver, kidney and pancreas. Conclusion: Our preliminary studies demonstrated a novel ROCK 4D-MRI technique with true 3D k-space encoding and respiratory motion self-gating. The technique leads to high-resolution and artifacts-free 4D images for improved abdominal organ motion studies. K.S acknowledges funding support from NIH R01CA188300.« less

Single Anisotropic 3-D MR Image Upsampling via Overcomplete Dictionary Trained From In-Plane High Resolution Slices.

PubMed

Jia, Yuanyuan; He, Zhongshi; Gholipour, Ali; Warfield, Simon K

2016-11-01

In magnetic resonance (MR), hardware limitation, scanning time, and patient comfort often result in the acquisition of anisotropic 3-D MR images. Enhancing image resolution is desired but has been very challenging in medical image processing. Super resolution reconstruction based on sparse representation and overcomplete dictionary has been lately employed to address this problem; however, these methods require extra training sets, which may not be always available. This paper proposes a novel single anisotropic 3-D MR image upsampling method via sparse representation and overcomplete dictionary that is trained from in-plane high resolution slices to upsample in the out-of-plane dimensions. The proposed method, therefore, does not require extra training sets. Abundant experiments, conducted on simulated and clinical brain MR images, show that the proposed method is more accurate than classical interpolation. When compared to a recent upsampling method based on the nonlocal means approach, the proposed method did not show improved results at low upsampling factors with simulated images, but generated comparable results with much better computational efficiency in clinical cases. Therefore, the proposed approach can be efficiently implemented and routinely used to upsample MR images in the out-of-planes views for radiologic assessment and postacquisition processing.

Spheroid imaging of phase-diversity homodyne OCT

NASA Astrophysics Data System (ADS)

Senda, Naoko; Osawa, Kentaro

2017-02-01

Non-invasive 3D imaging technique is essential for regenerative tissues evaluation. Optical coherence tomography (OCT) is one of 3D imaging tools with no staining and is used extensively for fundus examination. We have developed Phase-Diversity Homodyne OCT which enables cell imaging because of high resolution, whereas conventional OCT was not used for cell imaging because of low resolution. We demonstrated non-invasive imaging inside living spheroids with Phase-Diversity Homodyne OCT. Spheroids are spheroidal cell aggregates and used as regenerative tissues. Cartilage cells were cultured in low-adhesion 96-well plates and spheroids were manufactured. Cell membrane and cytoplasm of spheroid were imaged with OCT.

Sodium 3D COncentration MApping (COMA 3D) using 23Na and proton MRI

NASA Astrophysics Data System (ADS)

Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

2014-10-01

Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8 × 0.8 × 0.8 mm3 and imaging matrices of 60 × 60 × 60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/ truongm/COMA3D/.

3D imaging by serial block face scanning electron microscopy for materials science using ultramicrotomy.

PubMed

Hashimoto, Teruo; Thompson, George E; Zhou, Xiaorong; Withers, Philip J

2016-04-01

Mechanical serial block face scanning electron microscopy (SBFSEM) has emerged as a means of obtaining three dimensional (3D) electron images over volumes much larger than possible by focused ion beam (FIB) serial sectioning and at higher spatial resolution than achievable with conventional X-ray computed tomography (CT). Such high resolution 3D electron images can be employed for precisely determining the shape, volume fraction, distribution and connectivity of important microstructural features. While soft (fixed or frozen) biological samples are particularly well suited for nanoscale sectioning using an ultramicrotome, the technique can also produce excellent 3D images at electron microscope resolution in a time and resource-efficient manner for engineering materials. Currently, a lack of appreciation of the capabilities of ultramicrotomy and the operational challenges associated with minimising artefacts for different materials is limiting its wider application to engineering materials. Consequently, this paper outlines the current state of the art for SBFSEM examining in detail how damage is introduced during slicing and highlighting strategies for minimising such damage. A particular focus of the study is the acquisition of 3D images for a variety of metallic and coated systems. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Speed of sound and photoacoustic imaging with an optical camera based ultrasound detection system

NASA Astrophysics Data System (ADS)

Nuster, Robert; Paltauf, Guenther

2017-07-01

CCD camera based optical ultrasound detection is a promising alternative approach for high resolution 3D photoacoustic imaging (PAI). To fully exploit its potential and to achieve an image resolution <50 μm, it is necessary to incorporate variations of the speed of sound (SOS) in the image reconstruction algorithm. Hence, in the proposed work the idea and a first implementation are shown how speed of sound imaging can be added to a previously developed camera based PAI setup. The current setup provides SOS-maps with a spatial resolution of 2 mm and an accuracy of the obtained absolute SOS values of about 1%. The proposed dual-modality setup has the potential to provide highly resolved and perfectly co-registered 3D photoacoustic and SOS images.

2D-3D registration using gradient-based MI for image guided surgery systems

NASA Astrophysics Data System (ADS)

Yim, Yeny; Chen, Xuanyi; Wakid, Mike; Bielamowicz, Steve; Hahn, James

2011-03-01

Registration of preoperative CT data to intra-operative video images is necessary not only to compare the outcome of the vocal fold after surgery with the preplanned shape but also to provide the image guidance for fusion of all imaging modalities. We propose a 2D-3D registration method using gradient-based mutual information. The 3D CT scan is aligned to 2D endoscopic images by finding the corresponding viewpoint between the real camera for endoscopic images and the virtual camera for CT scans. Even though mutual information has been successfully used to register different imaging modalities, it is difficult to robustly register the CT rendered image to the endoscopic image due to varying light patterns and shape of the vocal fold. The proposed method calculates the mutual information in the gradient images as well as original images, assigning more weight to the high gradient regions. The proposed method can emphasize the effect of vocal fold and allow a robust matching regardless of the surface illumination. To find the viewpoint with maximum mutual information, a downhill simplex method is applied in a conditional multi-resolution scheme which leads to a less-sensitive result to local maxima. To validate the registration accuracy, we evaluated the sensitivity to initial viewpoint of preoperative CT. Experimental results showed that gradient-based mutual information provided robust matching not only for two identical images with different viewpoints but also for different images acquired before and after surgery. The results also showed that conditional multi-resolution scheme led to a more accurate registration than single-resolution.

Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging

DTIC Science & Technology

2009-10-01

molecular breast imaging, with the ability to dynamically contour any sized breast, will improve detection and potentially in vivo characterization of...Having flexible 3D positioning about the breast yielded minimal RMSD differences, which is important for high resolution molecular emission imaging. This...TITLE: Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging PRINCIPAL

Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy

NASA Astrophysics Data System (ADS)

Stemkens, Bjorn; Tijssen, Rob H. N.; de Senneville, Baudouin Denis; Lagendijk, Jan J. W.; van den Berg, Cornelis A. T.

2016-07-01

Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0-1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy.

Image-driven, model-based 3D abdominal motion estimation for MR-guided radiotherapy.

PubMed

Stemkens, Bjorn; Tijssen, Rob H N; de Senneville, Baudouin Denis; Lagendijk, Jan J W; van den Berg, Cornelis A T

2016-07-21

Respiratory motion introduces substantial uncertainties in abdominal radiotherapy for which traditionally large margins are used. The MR-Linac will open up the opportunity to acquire high resolution MR images just prior to radiation and during treatment. However, volumetric MRI time series are not able to characterize 3D tumor and organ-at-risk motion with sufficient temporal resolution. In this study we propose a method to estimate 3D deformation vector fields (DVFs) with high spatial and temporal resolution based on fast 2D imaging and a subject-specific motion model based on respiratory correlated MRI. In a pre-beam phase, a retrospectively sorted 4D-MRI is acquired, from which the motion is parameterized using a principal component analysis. This motion model is used in combination with fast 2D cine-MR images, which are acquired during radiation, to generate full field-of-view 3D DVFs with a temporal resolution of 476 ms. The geometrical accuracies of the input data (4D-MRI and 2D multi-slice acquisitions) and the fitting procedure were determined using an MR-compatible motion phantom and found to be 1.0-1.5 mm on average. The framework was tested on seven healthy volunteers for both the pancreas and the kidney. The calculated motion was independently validated using one of the 2D slices, with an average error of 1.45 mm. The calculated 3D DVFs can be used retrospectively for treatment simulations, plan evaluations, or to determine the accumulated dose for both the tumor and organs-at-risk on a subject-specific basis in MR-guided radiotherapy.

Interactive Volume Exploration of Petascale Microscopy Data Streams Using a Visualization-Driven Virtual Memory Approach.

PubMed

Hadwiger, M; Beyer, J; Jeong, Won-Ki; Pfister, H

2012-12-01

This paper presents the first volume visualization system that scales to petascale volumes imaged as a continuous stream of high-resolution electron microscopy images. Our architecture scales to dense, anisotropic petascale volumes because it: (1) decouples construction of the 3D multi-resolution representation required for visualization from data acquisition, and (2) decouples sample access time during ray-casting from the size of the multi-resolution hierarchy. Our system is designed around a scalable multi-resolution virtual memory architecture that handles missing data naturally, does not pre-compute any 3D multi-resolution representation such as an octree, and can accept a constant stream of 2D image tiles from the microscopes. A novelty of our system design is that it is visualization-driven: we restrict most computations to the visible volume data. Leveraging the virtual memory architecture, missing data are detected during volume ray-casting as cache misses, which are propagated backwards for on-demand out-of-core processing. 3D blocks of volume data are only constructed from 2D microscope image tiles when they have actually been accessed during ray-casting. We extensively evaluate our system design choices with respect to scalability and performance, compare to previous best-of-breed systems, and illustrate the effectiveness of our system for real microscopy data from neuroscience.

TU-F-17A-04: Respiratory Phase-Resolved 3D MRI with Isotropic High Spatial Resolution: Determination of the Average Breathing Motion Pattern for Abdominal Radiotherapy Planning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Z; Pang, J; Yang, W

Purpose: To develop a retrospective 4D-MRI technique (respiratory phase-resolved 3D-MRI) for providing an accurate assessment of tumor motion secondary to respiration. Methods: A 3D projection reconstruction (PR) sequence with self-gating (SG) was developed for 4D-MRI on a 3.0T MRI scanner. The respiration-induced shift of the imaging target was recorded by SG signals acquired in the superior-inferior direction every 15 radial projections (i.e. temporal resolution 98 ms). A total of 73000 radial projections obtained in 8-min were retrospectively sorted into 10 time-domain evenly distributed respiratory phases based on the SG information. Ten 3D image sets were then reconstructed offline. The techniquemore » was validated on a motion phantom (gadolinium-doped water-filled box, frequency of 10 and 18 cycles/min) and humans (4 healthy and 2 patients with liver tumors). Imaging protocol included 8-min 4D-MRI followed by 1-min 2D-realtime (498 ms/frame) MRI as a reference. Results: The multiphase 3D image sets with isotropic high spatial resolution (1.56 mm) permits flexible image reformatting and visualization. No intra-phase motion-induced blurring was observed. Comparing to 2D-realtime, 4D-MRI yielded similar motion range (phantom: 10.46 vs. 11.27 mm; healthy subject: 25.20 vs. 17.9 mm; patient: 11.38 vs. 9.30 mm), reasonable displacement difference averaged over the 10 phases (0.74mm; 3.63mm; 1.65mm), and excellent cross-correlation (0.98; 0.96; 0.94) between the two displacement series. Conclusion: Our preliminary study has demonstrated that the 4D-MRI technique can provide high-quality respiratory phase-resolved 3D images that feature: a) isotropic high spatial resolution, b) a fixed scan time of 8 minutes, c) an accurate estimate of average motion pattern, and d) minimal intra-phase motion artifact. This approach has the potential to become a viable alternative solution to assess the impact of breathing on tumor motion and determine appropriate treatment margins. Comparison with 4D-CT in a clinical setting is warranted to assess the value of 4D-MRI in radiotherapy planning. This work supported in part by grant 1R03CA173273-01.« less

Three-dimensional refractive index and fluorescence tomography using structured illumination (Conference Presentation)

NASA Astrophysics Data System (ADS)

Park, GwangSik; Shin, SeungWoo; Kim, Kyoohyun; Park, YongKeun

2017-02-01

Optical diffraction tomography (ODT) has been an emerging optical technique for label-free imaging of three-dimensional (3-D) refractive index (RI) distribution of biological samples. ODT employs interferometric microscopy for measuring multiple holograms of samples with various incident angles, from which the Fourier diffraction theorem reconstructs the 3-D RI distribution of samples from retrieved complex optical fields. Since the RI value is linearly proportional to the protein concentration of biological samples where the proportional coefficient is called as refractive index increment (RII), reconstructed 3-D RI tomograms provide precise structural and biochemical information of individual biological samples. Because most proteins have similar RII value, however, ODT has limited molecular specificity, especially for imaging eukaryotic cells having various types of proteins and subcellular organelles. Here, we present an ODT system combined with structured illumination microscopy which can measure the 3-D RI distribution of biological samples as well as 3-D super-resolution fluorescent images in the same optical setup. A digital micromirror device (DMD) controls the incident angle of the illumination beam for tomogram reconstruction, and the same DMD modulates the structured illumination pattern of the excitation beam for super-resolution fluorescent imaging. We first validate the proposed method for simultaneous optical diffraction tomographic imaging and super-resolution fluorescent imaging of fluorescent beads. The proposed method is also exploited for various biological samples.

Technique development of 3D dynamic CS-EPSI for hyperpolarized 13 C pyruvate MR molecular imaging of human prostate cancer.

PubMed

Chen, Hsin-Yu; Larson, Peder E Z; Gordon, Jeremy W; Bok, Robert A; Ferrone, Marcus; van Criekinge, Mark; Carvajal, Lucas; Cao, Peng; Pauly, John M; Kerr, Adam B; Park, Ilwoo; Slater, James B; Nelson, Sarah J; Munster, Pamela N; Aggarwal, Rahul; Kurhanewicz, John; Vigneron, Daniel B

2018-03-25

The purpose of this study was to develop a new 3D dynamic carbon-13 compressed sensing echoplanar spectroscopic imaging (EPSI) MR sequence and test it in phantoms, animal models, and then in prostate cancer patients to image the metabolic conversion of hyperpolarized [1- 13 C]pyruvate to [1- 13 C]lactate with whole gland coverage at high spatial and temporal resolution. A 3D dynamic compressed sensing (CS)-EPSI sequence with spectral-spatial excitation was designed to meet the required spatial coverage, time and spatial resolution, and RF limitations of the 3T MR scanner for its clinical translation for prostate cancer patient imaging. After phantom testing, animal studies were performed in rats and transgenic mice with prostate cancers. For patient studies, a GE SPINlab polarizer (GE Healthcare, Waukesha, WI) was used to produce hyperpolarized sterile GMP [1- 13 C]pyruvate. 3D dynamic 13 C CS-EPSI data were acquired starting 5 s after injection throughout the gland with a spatial resolution of 0.5 cm 3 , 18 time frames, 2-s temporal resolution, and 36 s total acquisition time. Through preclinical testing, the 3D CS-EPSI sequence developed in this project was shown to provide the desired spectral, temporal, and spatial 5D HP 13 C MR data. In human studies, the 3D dynamic HP CS-EPSI approach provided first-ever simultaneously volumetric and dynamic images of the LDH-catalyzed conversion of [1- 13 C]pyruvate to [1- 13 C]lactate in a biopsy-proven prostate cancer patient with full gland coverage. The results demonstrate the feasibility to characterize prostate cancer metabolism in animals, and now patients using this new 3D dynamic HP MR technique to measure k PL , the kinetic rate constant of [1- 13 C]pyruvate to [1- 13 C]lactate conversion. © 2018 International Society for Magnetic Resonance in Medicine.

Coregistration of high-resolution Mars orbital images

NASA Astrophysics Data System (ADS)

Sidiropoulos, Panagiotis; Muller, Jan-Peter

2015-04-01

The systematic orbital imaging of the Martian surface started 4 decades ago from NASA's Viking Orbiter 1 & 2 missions, which were launched in August 1975, and acquired orbital images of the planet between 1976 and 1980. The result of this reconnaissance was the first medium-resolution (i.e. ≤ 300m/pixel) global map of Mars, as well as a variety of high-resolution images (reaching up to 8m/pixel) of special regions of interest. Over the last two decades NASA has sent 3 more spacecraft with onboard instruments for high-resolution orbital imaging: Mars Global Surveyor (MGS) having onboard the Mars Orbital Camera - Narrow Angle (MOC-NA), Mars Odyssey having onboard the Thermal Emission Imaging System - Visual (THEMIS-VIS) and the Mars Reconnaissance Orbiter (MRO) having on board two distinct high-resolution cameras, Context Camera (CTX) and High-Resolution Imaging Science Experiment (HiRISE). Moreover, ESA has the multispectral High resolution Stereo Camera (HRSC) onboard ESA's Mars Express with resolution up to 12.5m since 2004. Overall, this set of cameras have acquired more than 400,000 high-resolution images, i.e. with resolution better than 100m and as fine as 25 cm/pixel. Notwithstanding the high spatial resolution of the available NASA orbital products, their accuracy of areo-referencing is often very poor. As a matter of fact, due to pointing inconsistencies, usually form errors in roll attitude, the acquired products may actually image areas tens of kilometers far away from the point that they are supposed to be looking at. On the other hand, since 2004, the ESA Mars Express has been acquiring stereo images through the High Resolution Stereo Camera (HRSC), with resolution that is usually 12.5-25 metres per pixel. The achieved coverage is more than 64% for images with resolution finer than 20 m/pixel, while for ~40% of Mars, Digital Terrain Models (DTMs) have been produced with are co-registered with MOLA [Gwinner et al., 2010]. The HRSC images and DTMs represent the best available 3D reference frame for Mars showing co-registration with MOLA<25m (loc.cit.). In our work, the reference generated by HRSC terrain corrected orthorectified images is used as a common reference frame to co-register all available high-resolution orbital NASA products into a common 3D coordinate system, thus allowing the examination of the changes that happen on the surface of Mars over time (such as seasonal flows [McEwen et al., 2011] or new impact craters [Byrne, et al., 2009]). In order to accomplish such a tedious manual task, we have developed an automatic co-registration pipeline that produces orthorectified versions of the NASA images in realistic time (i.e. from ~15 minutes to 10 hours per image depending on size). In the first step of this pipeline, tie-points are extracted from the target NASA image and the reference HRSC image or image mosaic. Subsequently, the HRSC areo-reference information is used to transform the HRSC tie-points pixel coordinates into 3D "world" coordinates. This way, a correspondence between the pixel coordinates of the target NASA image and the 3D "world" coordinates is established for each tie-point. This set of correspondences is used to estimate a non-rigid, 3D to 2D transformation model, which transforms the target image into the HRSC reference coordinate system. Finally, correlation of the transformed target image and the HRSC image is employed to fine-tune the orthorectification results, thus generating results with sub-pixel accuracy. This method, which has been proven to be accurate, robust to resolution differences and reliable when dealing with partially degraded data and fast, will be presented, along with some example co-registration results that have been achieved by using it. Acknowledgements: The research leading to these results has received partial funding from the STFC "MSSL Consolidated Grant" ST/K000977/1 and partial support from the European Union's Seventh Framework Programme (FP7/2007-2013) under iMars grant agreement n° 607379. References: [1] K. F. Gwinner, et al. (2010) Topography of Mars from global mapping by HRSC high-resolution digital terrain models and orthoimages: characteristics and performance. Earth and Planetary Science Letters 294, 506-519, doi:10.1016/j.epsl.2009.11.007. [2] A. McEwen, et al. (2011) Seasonal flows on warm martian slopes. Science , 333 (6043): 740-743. [3] S. Byrne, et al. (2009) Distribution of mid-latitude ground ice on mars from new impact craters. Science, 325(5948):1674-1676.

Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking

PubMed Central

von Diezmann, Alex; Shechtman, Yoav; Moerner, W. E.

2017-01-01

Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers, or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information of single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field-dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems. PMID:28151646

Optimal resolution in Fresnel incoherent correlation holographic fluorescence microscopy

PubMed Central

Brooker, Gary; Siegel, Nisan; Wang, Victor; Rosen, Joseph

2011-01-01

Fresnel Incoherent Correlation Holography (FINCH) enables holograms and 3D images to be created from incoherent light with just a camera and spatial light modulator (SLM). We previously described its application to microscopic incoherent fluorescence wherein one complex hologram contains all the 3D information in the microscope field, obviating the need for scanning or serial sectioning. We now report experiments which have led to the optimal optical, electro-optic, and computational conditions necessary to produce holograms which yield high quality 3D images from fluorescent microscopic specimens. An important improvement from our previous FINCH configurations capitalizes on the polarization sensitivity of the SLM so that the same SLM pixels which create the spherical wave simulating the microscope tube lens, also pass the plane waves from the infinity corrected microscope objective, so that interference between the two wave types at the camera creates a hologram. This advance dramatically improves the resolution of the FINCH system. Results from imaging a fluorescent USAF pattern and a pollen grain slide reveal resolution which approaches the Rayleigh limit by this simple method for 3D fluorescent microscopic imaging. PMID:21445140

Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy

PubMed Central

Fu, Qinyi; Martin, Benjamin L.; Matus, David Q.; Gao, Liang

2016-01-01

Despite the progress made in selective plane illumination microscopy, high-resolution 3D live imaging of multicellular specimens remains challenging. Tiling light-sheet selective plane illumination microscopy (TLS-SPIM) with real-time light-sheet optimization was developed to respond to the challenge. It improves the 3D imaging ability of SPIM in resolving complex structures and optimizes SPIM live imaging performance by using a real-time adjustable tiling light sheet and creating a flexible compromise between spatial and temporal resolution. We demonstrate the 3D live imaging ability of TLS-SPIM by imaging cellular and subcellular behaviours in live C. elegans and zebrafish embryos, and show how TLS-SPIM can facilitate cell biology research in multicellular specimens by studying left-right symmetry breaking behaviour of C. elegans embryos. PMID:27004937

First Human Brain Imaging by the jPET-D4 Prototype With a Pre-Computed System Matrix

NASA Astrophysics Data System (ADS)

Yamaya, Taiga; Yoshida, Eiji; Obi, Takashi; Ito, Hiroshi; Yoshikawa, Kyosan; Murayama, Hideo

2008-10-01

The jPET-D4 is a novel brain PET scanner which aims to achieve not only high spatial resolution but also high scanner sensitivity by using 4-layer depth-of-interaction (DOI) information. The dimensions of a system matrix for the jPET-D4 are 3.3 billion (lines-of-response) times 5 million (image elements) when a standard field-of-view (FOV) of 25 cm diameter is sampled with a (1.5 mm)3 voxel . The size of the system matrix is estimated as 117 petabytes (PB) with the accuracy of 8 bytes per element. An on-the-fly calculation is usually used to deal with such a huge system matrix. However we cannot avoid extension of the calculation time when we improve the accuracy of system modeling. In this work, we implemented an alternative approach based on pre-calculation of the system matrix. A histogram-based 3D OS-EM algorithm was implemented on a desktop workstation with 32 GB memory installed. The 117 PB system matrix was compressed under the limited amount of computer memory by (1) eliminating zero elements, (2) applying the DOI compression (DOIC) method and (3) applying rotational symmetry and an axial shift property of the crystal arrangement. Spanning, which degrades axial resolution, was not applied. The system modeling and the DOIC method, which had been validated in 2D image reconstruction, were expanded into 3D implementation. In particular, a new system model including the DOIC transformation was introduced to suppress resolution loss caused by the DOIC method. Experimental results showed that the jPET-D4 has almost uniform spatial resolution of better than 3 mm over the FOV. Finally the first human brain images were obtained with the jPET-D4.

Mapping detailed 3D information onto high resolution SAR signatures

NASA Astrophysics Data System (ADS)

Anglberger, H.; Speck, R.

2017-05-01

Due to challenges in the visual interpretation of radar signatures or in the subsequent information extraction, a fusion with other data sources can be beneficial. The most accurate basis for a fusion of any kind of remote sensing data is the mapping of the acquired 2D image space onto the true 3D geometry of the scenery. In the case of radar images this is a challenging task because the coordinate system is based on the measured range which causes ambiguous regions due to layover effects. This paper describes a method that accurately maps the detailed 3D information of a scene to the slantrange-based coordinate system of imaging radars. Due to this mapping all the contributing geometrical parts of one resolution cell can be determined in 3D space. The proposed method is highly efficient, because computationally expensive operations can be directly performed on graphics card hardware. The described approach builds a perfect basis for sophisticated methods to extract data from multiple complimentary sensors like from radar and optical images, especially because true 3D information from whole cities will be available in the near future. The performance of the developed methods will be demonstrated with high resolution radar data acquired by the space-borne SAR-sensor TerraSAR-X.

Evaluation of a 3D local multiresolution algorithm for the correction of partial volume effects in positron emission tomography

PubMed Central

Le Pogam, Adrien; Hatt, Mathieu; Descourt, Patrice; Boussion, Nicolas; Tsoumpas, Charalampos; Turkheimer, Federico E.; Prunier-Aesch, Caroline; Baulieu, Jean-Louis; Guilloteau, Denis; Visvikis, Dimitris

2011-01-01

Purpose Partial volume effects (PVE) are consequences of the limited spatial resolution in emission tomography leading to under-estimation of uptake in tissues of size similar to the point spread function (PSF) of the scanner as well as activity spillover between adjacent structures. Among PVE correction methodologies, a voxel-wise mutual multi-resolution analysis (MMA) was recently introduced. MMA is based on the extraction and transformation of high resolution details from an anatomical image (MR/CT) and their subsequent incorporation into a low resolution PET image using wavelet decompositions. Although this method allows creating PVE corrected images, it is based on a 2D global correlation model which may introduce artefacts in regions where no significant correlation exists between anatomical and functional details. Methods A new model was designed to overcome these two issues (2D only and global correlation) using a 3D wavelet decomposition process combined with a local analysis. The algorithm was evaluated on synthetic, simulated and patient images, and its performance was compared to the original approach as well as the geometric transfer matrix (GTM) method. Results Quantitative performance was similar to the 2D global model and GTM in correlated cases. In cases where mismatches between anatomical and functional information were present the new model outperformed the 2D global approach, avoiding artefacts and significantly improving quality of the corrected images and their quantitative accuracy. Conclusions A new 3D local model was proposed for a voxel-wise PVE correction based on the original mutual multi-resolution analysis approach. Its evaluation demonstrated an improved and more robust qualitative and quantitative accuracy compared to the original MMA methodology, particularly in the absence of full correlation between anatomical and functional information. PMID:21978037

Imaging of cellular spread on a three-dimensional scaffold by means of a novel cell-labeling technique for high-resolution computed tomography.

PubMed

Thimm, Benjamin W; Hofmann, Sandra; Schneider, Philipp; Carretta, Roberto; Müller, Ralph

2012-03-01

Computed tomography (CT) represents a truly three-dimensional (3D) imaging technique that can provide high-resolution images on the cellular level. Thus, one approach to detect single cells is X-ray absorption-based CT, where cells are labeled with a dense, opaque material providing the required contrast for CT imaging. Within the present work, a novel cell-labeling method has been developed showing the feasibility of labeling fixed cells with iron oxide (FeO) particles for subsequent CT imaging and quantitative morphometry. A biotin-streptavidin detection system was exploited to bind FeO particles to its target endothelial cells. The binding of the particles was predominantly close to the cell centers on 2D surfaces as shown by light microscopy, scanning electron microscopy, and CT. When cells were cultured on porous, 3D polyurethane surfaces, significantly more FeO particles were detected compared with surfaces without cells and FeO particle labeling using CT. Here, we report on the implementation and evaluation of a novel cell detection method based on high-resolution CT. This system has potential in cell tracking for 3D in vitro imaging in the future.

High spatial resolution diffusion weighted imaging on clinical 3 T MRI scanners using multislab spiral acquisitions

PubMed Central

Holtrop, Joseph L.; Sutton, Bradley P.

2016-01-01

Abstract. A diffusion weighted imaging (DWI) approach that is signal-to-noise ratio (SNR) efficient and can be applied to achieve sub-mm resolutions on clinical 3 T systems was developed. The sequence combined a multislab, multishot pulsed gradient spin echo diffusion scheme with spiral readouts for imaging data and navigators. Long data readouts were used to keep the number of shots, and hence total imaging time, for the three-dimensional acquisition short. Image quality was maintained by incorporating a field-inhomogeneity-corrected image reconstruction to remove distortions associated with long data readouts. Additionally, multiple shots were required for the high-resolution images, necessitating motion induced phase correction through the use of efficiently integrated navigator data. The proposed approach is compared with two-dimensional (2-D) acquisitions that use either a spiral or a typical echo-planar imaging (EPI) acquisition to demonstrate the improved SNR efficiency. The proposed technique provided 71% higher SNR efficiency than the standard 2-D EPI approach. The adaptability of the technique to achieve high spatial resolutions is demonstrated by acquiring diffusion tensor imaging data sets with isotropic resolutions of 1.25 and 0.8 mm. The proposed approach allows for SNR-efficient sub-mm acquisitions of DWI data on clinical 3 T systems. PMID:27088107

Phased Array 3D MR Spectroscopic Imaging of the Brain at 7 Tesla

PubMed Central

Xu, Duan; Cunningham, Charles H; Chen, Albert P.; Li, Yan; Kelley, Douglas AC; Mukherjee, Pratik; Pauly, John M.; Nelson, Sarah J.; Vigneron, Daniel B.

2008-01-01

Ultrahigh field 7T MR scanners offer the potential for greatly improved MR spectroscopic imaging due to increased sensitivity and spectral resolution. Prior 7T human single-voxel MRS studies have shown significant increases in SNR and spectral resolution as compared to lower magnetic fields, but have not demonstrated the increase in spatial resolution and multivoxel coverage possible with 7T MR spectroscopic imaging. The goal of this study was to develop specialized rf pulses and sequences for 3D MRSI at 7T to address the challenges of increased chemical shift misregistration, B1 power limitations, and increased spectral bandwidth. The new 7T MRSI sequence was tested in volunteer studies and demonstrated the feasibility of obtaining high SNR phased-array 3D MRSI from the human brain. PMID:18486386

All-optical endoscopic probe for high resolution 3D photoacoustic tomography

NASA Astrophysics Data System (ADS)

Ansari, R.; Zhang, E.; Desjardins, A. E.; Beard, P. C.

2017-03-01

A novel all-optical forward-viewing photoacoustic probe using a flexible coherent fibre-optic bundle and a Fabry- Perot (FP) ultrasound sensor has been developed. The fibre bundle, along with the FP sensor at its distal end, synthesizes a high density 2D array of wideband ultrasound detectors. Photoacoustic waves arriving at the sensor are spatially mapped by optically scanning the proximal end face of the bundle in 2D with a CW wavelength-tunable interrogation laser. 3D images are formed from the detected signals using a time-reversal image reconstruction algorithm. The system has been characterized in terms of its PSF, noise-equivalent pressure and field of view. Finally, the high resolution 3D imaging capability has been demonstrated using arbitrary shaped phantoms and duck embryo.

Pseudo-shading technique in the two-dimensional domain: a post-processing algorithm for enhancing the Z-buffer of a three-dimensional binary image.

PubMed

Tan, A C; Richards, R

1989-01-01

Three-dimensional (3D) medical graphics is becoming popular in clinical use on tomographic scanners. Research work in 3D reconstructive display of computerized tomography (CT) and magnetic resonance imaging (MRI) scans on conventional computers has produced many so-called pseudo-3D images. The quality of these images depends on the rendering algorithm, the coarseness of the digitized object, the number of grey levels and the image screen resolution. CT and MRI data are fundamentally voxel based and they produce images that are coarse because of the resolution of the data acquisition system. 3D images produced by the Z-buffer depth shading technique suffer loss of detail when complex objects with fine textural detail need to be displayed. Attempts have been made to improve the display of voxel objects, and existing techniques have shown the improvement possible using these post-processing algorithms. The improved rendering technique works on the Z-buffer image to generate a shaded image using a single light source in any direction. The effectiveness of the technique in generating a shaded image has been shown to be a useful means of presenting 3D information for clinical use.

EIT image reconstruction with four dimensional regularization.

PubMed

Dai, Tao; Soleimani, Manuchehr; Adler, Andy

2008-09-01

Electrical impedance tomography (EIT) reconstructs internal impedance images of the body from electrical measurements on body surface. The temporal resolution of EIT data can be very high, although the spatial resolution of the images is relatively low. Most EIT reconstruction algorithms calculate images from data frames independently, although data are actually highly correlated especially in high speed EIT systems. This paper proposes a 4-D EIT image reconstruction for functional EIT. The new approach is developed to directly use prior models of the temporal correlations among images and 3-D spatial correlations among image elements. A fast algorithm is also developed to reconstruct the regularized images. Image reconstruction is posed in terms of an augmented image and measurement vector which are concatenated from a specific number of previous and future frames. The reconstruction is then based on an augmented regularization matrix which reflects the a priori constraints on temporal and 3-D spatial correlations of image elements. A temporal factor reflecting the relative strength of the image correlation is objectively calculated from measurement data. Results show that image reconstruction models which account for inter-element correlations, in both space and time, show improved resolution and noise performance, in comparison to simpler image models.

Dedicated mobile high resolution prostate PET imager with an insertable transrectal probe

DOEpatents

Majewski, Stanislaw; Proffitt, James

2010-12-28

A dedicated mobile PET imaging system to image the prostate and surrounding organs. The imaging system includes an outside high resolution PET imager placed close to the patient's torso and an insertable and compact transrectal probe that is placed in close proximity to the prostate and operates in conjunction with the outside imager. The two detector systems are spatially co-registered to each other. The outside imager is mounted on an open rotating gantry to provide torso-wide 3D images of the prostate and surrounding tissue and organs. The insertable probe provides closer imaging, high sensitivity, and very high resolution predominately 2D view of the prostate and immediate surroundings. The probe is operated in conjunction with the outside imager and a fast data acquisition system to provide very high resolution reconstruction of the prostate and surrounding tissue and organs.

High-resolution imaging of craniofacial sutures: new tools for understanding the origins of craniosynostoses.

PubMed

Khonsari, R H; Di Rocco, F; Arnaud, E; Sanchez, S; Tafforeau, P

2012-09-01

The developmental genetics and the biomechanics of sutures are well-studied topics, while their microanatomy is still imperfectly known. Here, we aim to investigate the structure of skull vault sutures using a high-resolution imaging device. We used synchrotron X-ray microtomography in order to obtain high-resolution images of skull vault sutures from an extant mammal (the mouse Mus musculus) and from an extinct fish (the placoderm Compagopiscis croucheri). We used segmentation and 3D reconstruction softwares in order to reveal the microanatomy of sutures in these species. The high-resolution images allowed us to study the distribution of osteocytes, the organisation of vascular canals, the shapes of the suture borders, the insertion of Sharpey's fibres, the bone growth lines and the structure of the soft tissues surrounding the sutures. Synchrotron imaging provides new perspectives for the study of the normal microanatomy of sutures. The submicronic resolution of the synchrotron scans gives access to the 3D organisation of structures that were previously only known in 2D, even in normal sutures. The description of anatomical entities such as vascular canals and Sharpey's fibres in abnormally fused sutures would be of interest in the understanding of craniosynostoses.

Rapid brain MRI acquisition techniques at ultra-high fields

PubMed Central

Setsompop, Kawin; Feinberg, David A.; Polimeni, Jonathan R.

2017-01-01

Ultra-high-field MRI provides large increases in signal-to-noise ratio as well as enhancement of several contrast mechanisms in both structural and functional imaging. Combined, these gains result in a substantial boost in contrast-to-noise ratio that can be exploited for higher spatial resolution imaging to extract finer-scale information about the brain. With increased spatial resolution, however, is a concurrent increased image encoding burden that can cause unacceptably long scan times for structural imaging and slow temporal sampling of the hemodynamic response in functional MRI—particularly when whole-brain imaging is desired. To address this issue, new directions of imaging technology development—such as the move from conventional 2D slice-by-slice imaging to more efficient Simultaneous MultiSlice (SMS) or MultiBand imaging (which can be viewed as “pseudo-3D” encoding) as well as full 3D imaging—have provided dramatic improvements in acquisition speed. Such imaging paradigms provide higher SNR efficiency as well as improved encoding efficiency. Moreover, SMS and 3D imaging can make better use of coil sensitivity information in multi-channel receiver arrays used for parallel imaging acquisitions through controlled aliasing in multiple spatial directions. This has enabled unprecedented acceleration factors of an order of magnitude or higher in these imaging acquisition schemes, with low image artifact levels and high SNR. Here we review the latest developments of SMS and 3D imaging methods and related technologies at ultra-high field for rapid high-resolution functional and structural imaging of the brain. PMID:26835884

High-resolution gadolinium-enhanced 3D MRA of the infrapopliteal arteries. Lessons for improving bolus-chase peripheral MRA.

PubMed

Hood, Maureen N; Ho, Vincent B; Foo, Thomas K F; Marcos, Hani B; Hess, Sandra L; Choyke, Peter L

2002-09-01

Peripheral magnetic resonance angiography (MRA) is growing in use. However, methods of performing peripheral MRA vary widely and continue to be optimized, especially for improvement in illustration of infrapopliteal arteries. The main purpose of this project was to identify imaging factors that can improve arterial visualization in the lower leg using bolus chase peripheral MRA. Eighteen healthy adults were imaged on a 1.5T MR scanner. The calf was imaged using conventional three-station bolus chase three-dimensional (3D) MRA, two dimensional (2D) time-of-flight (TOF) MRA and single-station Gadolinium (Gd)-enhanced 3D MRA. Observer comparisons of vessel visualization, signal to noise ratios (SNR), contrast to noise ratios (CNR) and spatial resolution comparisons were performed. Arterial SNR and CNR were similar for all three techniques. However, arterial visualization was dramatically improved on dedicated, arterial-phase Gd-enhanced 3D MRA compared with the multi-station bolus chase MRA and 2D TOF MRA. This improvement was related to optimization of Gd-enhanced 3D MRA parameters (fast injection rate of 2 mL/sec, high spatial resolution imaging, the use of dedicated phased array coils, elliptical centric k-space sampling and accurate arterial phase timing for image acquisition). The visualization of the infrapopliteal arteries can be substantially improved in bolus chase peripheral MRA if voxel size, contrast delivery, and central k-space data acquisition for arterial enhancement are optimized. Improvements in peripheral MRA should be directed at these parameters.

Single-frequency 3D synthetic aperture imaging with dynamic metasurface antennas.

PubMed

Boyarsky, Michael; Sleasman, Timothy; Pulido-Mancera, Laura; Diebold, Aaron V; Imani, Mohammadreza F; Smith, David R

2018-05-20

Through aperture synthesis, an electrically small antenna can be used to form a high-resolution imaging system capable of reconstructing three-dimensional (3D) scenes. However, the large spectral bandwidth typically required in synthetic aperture radar systems to resolve objects in range often requires costly and complex RF components. We present here an alternative approach based on a hybrid imaging system that combines a dynamically reconfigurable aperture with synthetic aperture techniques, demonstrating the capability to resolve objects in three dimensions (3D), with measurements taken at a single frequency. At the core of our imaging system are two metasurface apertures, both of which consist of a linear array of metamaterial irises that couple to a common waveguide feed. Each metamaterial iris has integrated within it a diode that can be biased so as to switch the element on (radiating) or off (non-radiating), such that the metasurface antenna can produce distinct radiation profiles corresponding to different on/off patterns of the metamaterial element array. The electrically large size of the metasurface apertures enables resolution in range and one cross-range dimension, while aperture synthesis provides resolution in the other cross-range dimension. The demonstrated imaging capabilities of this system represent a step forward in the development of low-cost, high-performance 3D microwave imaging systems.

3D quantitative phase imaging of neural networks using WDT

NASA Astrophysics Data System (ADS)

Kim, Taewoo; Liu, S. C.; Iyer, Raj; Gillette, Martha U.; Popescu, Gabriel

2015-03-01

White-light diffraction tomography (WDT) is a recently developed 3D imaging technique based on a quantitative phase imaging system called spatial light interference microscopy (SLIM). The technique has achieved a sub-micron resolution in all three directions with high sensitivity granted by the low-coherence of a white-light source. Demonstrations of the technique on single cell imaging have been presented previously; however, imaging on any larger sample, including a cluster of cells, has not been demonstrated using the technique. Neurons in an animal body form a highly complex and spatially organized 3D structure, which can be characterized by neuronal networks or circuits. Currently, the most common method of studying the 3D structure of neuron networks is by using a confocal fluorescence microscope, which requires fluorescence tagging with either transient membrane dyes or after fixation of the cells. Therefore, studies on neurons are often limited to samples that are chemically treated and/or dead. WDT presents a solution for imaging live neuron networks with a high spatial and temporal resolution, because it is a 3D imaging method that is label-free and non-invasive. Using this method, a mouse or rat hippocampal neuron culture and a mouse dorsal root ganglion (DRG) neuron culture have been imaged in order to see the extension of processes between the cells in 3D. Furthermore, the tomogram is compared with a confocal fluorescence image in order to investigate the 3D structure at synapses.

The high resolution stereo camera (HRSC): acquisition of multi-spectral 3D-data and photogrammetric processing

NASA Astrophysics Data System (ADS)

Neukum, Gerhard; Jaumann, Ralf; Scholten, Frank; Gwinner, Klaus

2017-11-01

At the Institute of Space Sensor Technology and Planetary Exploration of the German Aerospace Center (DLR) the High Resolution Stereo Camera (HRSC) has been designed for international missions to planet Mars. For more than three years an airborne version of this camera, the HRSC-A, has been successfully applied in many flight campaigns and in a variety of different applications. It combines 3D-capabilities and high resolution with multispectral data acquisition. Variable resolutions depending on the camera control settings can be generated. A high-end GPS/INS system in combination with the multi-angle image information yields precise and high-frequent orientation data for the acquired image lines. In order to handle these data a completely automated photogrammetric processing system has been developed, and allows to generate multispectral 3D-image products for large areas and with accuracies for planimetry and height in the decimeter range. This accuracy has been confirmed by detailed investigations.

High-resolution, time-resolved MRA provides superior definition of lower-extremity arterial segments compared to 2D time-of-flight imaging.

PubMed

Thornton, F J; Du, J; Suleiman, S A; Dieter, R; Tefera, G; Pillai, K R; Korosec, F R; Mistretta, C A; Grist, T M

2006-08-01

To evaluate a novel time-resolved contrast-enhanced (CE) projection reconstruction (PR) magnetic resonance angiography (MRA) method for identifying potential bypass graft target vessels in patients with Class II-IV peripheral vascular disease. Twenty patients (M:F = 15:5, mean age = 58 years, range = 48-83 years), were recruited from routine MRA referrals. All imaging was performed on a 1.5 T MRI system with fast gradients (Signa LX; GE Healthcare, Waukesha, WI). Images were acquired with a novel technique that combined undersampled PR with a time-resolved acquisition to yield an MRA method with high temporal and spatial resolution. The method is called PR hyper time-resolved imaging of contrast kinetics (PR-hyperTRICKS). Quantitative and qualitative analyses were used to compare two-dimensional (2D) time-of-flight (TOF) and PR-hyperTRICKS in 13 arterial segments per lower extremity. Statistical analysis was performed with the Wilcoxon signed-rank test. Fifteen percent (77/517) of the vessels were scored as missing or nondiagnostic with 2D TOF, but were scored as diagnostic with PR-hyperTRICKS. Image quality was superior with PR-hyperTRICKS vs. 2D TOF (on a four-point scale, mean rank = 3.3 +/- 1.2 vs. 2.9 +/- 1.2, P < 0.0001). PR-hyperTRICKS produced images with high contrast-to-noise ratios (CNR) and high spatial and temporal resolution. 2D TOF images were of inferior quality due to moderate spatial resolution, inferior CNR, greater flow-related artifacts, and absence of temporal resolution. PR-hyperTRICKS provides superior preoperative assessment of lower limb ischemia compared to 2D TOF.

Volumetric Arterial Spin-labeled Perfusion Imaging of the Kidneys with a Three-dimensional Fast Spin Echo Acquisition.

PubMed

Robson, Philip M; Madhuranthakam, Ananth J; Smith, Martin P; Sun, Maryellen R M; Dai, Weiying; Rofsky, Neil M; Pedrosa, Ivan; Alsop, David C

2016-02-01

Renal perfusion measurements using noninvasive arterial spin-labeled (ASL) magnetic resonance imaging techniques are gaining interest. Currently, focus has been on perfusion in the context of renal transplant. Our objectives were to explore the use of ASL in patients with renal cancer, and to evaluate three-dimensional (3D) fast spin echo (FSE) acquisition, a robust volumetric imaging method for abdominal applications. We evaluate 3D ASL perfusion magnetic resonance imaging in the kidneys compared to two-dimensional (2D) ASL in patients and healthy subjects. Isotropic resolution (2.6 × 2.6 × 2.8 mm(3)) 3D ASL using segmented FSE was compared to 2D single-shot FSE. ASL used pseudo-continuous labeling, suppression of background signal, and synchronized breathing. Quantitative perfusion values and signal-to-noise ratio (SNR) were compared between 3D and 2D ASL in four healthy volunteers and semiquantitative assessments were made by four radiologists in four patients with known renal masses (primary renal cell carcinoma). Renal cortex perfusion in healthy subjects was 284 ± 21 mL/100 g/min, with test-retest repeatability of 8.8%. No significant differences were found between the quantitative perfusion value and SNR in volunteers between 3D ASL and 2D ASL, or in 3D ASL with synchronized or free breathing. In patients, semiquantitative assessment by radiologists showed no significant difference in image quality between 2D ASL and 3D ASL. In one case, 2D ASL missed a high perfusion focus in a mass that was seen by 3D ASL. 3D ASL renal perfusion imaging provides isotropic-resolution images, with comparable quantitative perfusion values and image SNR in similar imaging time to single-slice 2D ASL. Copyright © 2015 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Automatic 3D Segmentation and Quantification of Lenticulostriate Arteries from High-Resolution 7 Tesla MRA Images.

PubMed

Wei Liao; Rohr, Karl; Chang-Ki Kang; Zang-Hee Cho; Worz, Stefan

2016-01-01

We propose a novel hybrid approach for automatic 3D segmentation and quantification of high-resolution 7 Tesla magnetic resonance angiography (MRA) images of the human cerebral vasculature. Our approach consists of two main steps. First, a 3D model-based approach is used to segment and quantify thick vessels and most parts of thin vessels. Second, remaining vessel gaps of the first step in low-contrast and noisy regions are completed using a 3D minimal path approach, which exploits directional information. We present two novel minimal path approaches. The first is an explicit approach based on energy minimization using probabilistic sampling, and the second is an implicit approach based on fast marching with anisotropic directional prior. We conducted an extensive evaluation with over 2300 3D synthetic images and 40 real 3D 7 Tesla MRA images. Quantitative and qualitative evaluation shows that our approach achieves superior results compared with a previous minimal path approach. Furthermore, our approach was successfully used in two clinical studies on stroke and vascular dementia.

Multiple-aperture optical design for micro-level cameras using 3D-printing method

NASA Astrophysics Data System (ADS)

Peng, Wei-Jei; Hsu, Wei-Yao; Cheng, Yuan-Chieh; Lin, Wen-Lung; Yu, Zong-Ru; Chou, Hsiao-Yu; Chen, Fong-Zhi; Fu, Chien-Chung; Wu, Chong-Syuan; Huang, Chao-Tsung

2018-02-01

The design of the ultra miniaturized camera using 3D-printing technology directly printed on to the complementary metal-oxide semiconductor (CMOS) imaging sensor is presented in this paper. The 3D printed micro-optics is manufactured using the femtosecond two-photon direct laser writing, and the figure error which could achieve submicron accuracy is suitable for the optical system. Because the size of the micro-level camera is approximately several hundreds of micrometers, the resolution is reduced much and highly limited by the Nyquist frequency of the pixel pitch. For improving the reduced resolution, one single-lens can be replaced by multiple-aperture lenses with dissimilar field of view (FOV), and then stitching sub-images with different FOV can achieve a high resolution within the central region of the image. The reason is that the angular resolution of the lens with smaller FOV is higher than that with larger FOV, and then the angular resolution of the central area can be several times than that of the outer area after stitching. For the same image circle, the image quality of the central area of the multi-lens system is significantly superior to that of a single-lens. The foveated image using stitching FOV breaks the limitation of the resolution for the ultra miniaturized imaging system, and then it can be applied such as biomedical endoscopy, optical sensing, and machine vision, et al. In this study, the ultra miniaturized camera with multi-aperture optics is designed and simulated for the optimum optical performance.

3D printing in X-ray and Gamma-Ray Imaging: A novel method for fabricating high-density imaging apertures☆

PubMed Central

Miller, Brian W.; Moore, Jared W.; Barrett, Harrison H.; Fryé, Teresa; Adler, Steven; Sery, Joe; Furenlid, Lars R.

2011-01-01

Advances in 3D rapid-prototyping printers, 3D modeling software, and casting techniques allow for cost-effective fabrication of custom components in gamma-ray and X-ray imaging systems. Applications extend to new fabrication methods for custom collimators, pinholes, calibration and resolution phantoms, mounting and shielding components, and imaging apertures. Details of the fabrication process for these components, specifically the 3D printing process, cold casting with a tungsten epoxy, and lost-wax casting in platinum are presented. PMID:22199414

3D super-resolution imaging with blinking quantum dots

PubMed Central

Wang, Yong; Fruhwirth, Gilbert; Cai, En; Ng, Tony; Selvin, Paul R.

2013-01-01

Quantum dots are promising candidates for single molecule imaging due to their exceptional photophysical properties, including their intense brightness and resistance to photobleaching. They are also notorious for their blinking. Here we report a novel way to take advantage of quantum dot blinking to develop an imaging technique in three-dimensions with nanometric resolution. We first applied this method to simulated images of quantum dots, and then to quantum dots immobilized on microspheres. We achieved imaging resolutions (FWHM) of 8–17 nm in the x-y plane and 58 nm (on coverslip) or 81 nm (deep in solution) in the z-direction, approximately 3–7 times better than what has been achieved previously with quantum dots. This approach was applied to resolve the 3D distribution of epidermal growth factor receptor (EGFR) molecules at, and inside of, the plasma membrane of resting basal breast cancer cells. PMID:24093439

A Comparison of Four-Image Reconstruction Algorithms for 3-D PET Imaging of MDAPET Camera Using Phantom Data

NASA Astrophysics Data System (ADS)

Baghaei, H.; Wong, Wai-Hoi; Uribe, J.; Li, Hongdi; Wang, Yu; Liu, Yaqiang; Xing, Tao; Ramirez, R.; Xie, Shuping; Kim, Soonseok

2004-10-01

We compared two fully three-dimensional (3-D) image reconstruction algorithms and two 3-D rebinning algorithms followed by reconstruction with a two-dimensional (2-D) filtered-backprojection algorithm for 3-D positron emission tomography (PET) imaging. The two 3-D image reconstruction algorithms were ordered-subsets expectation-maximization (3D-OSEM) and 3-D reprojection (3DRP) algorithms. The two rebinning algorithms were Fourier rebinning (FORE) and single slice rebinning (SSRB). The 3-D projection data used for this work were acquired with a high-resolution PET scanner (MDAPET) with an intrinsic transaxial resolution of 2.8 mm. The scanner has 14 detector rings covering an axial field-of-view of 38.5 mm. We scanned three phantoms: 1) a uniform cylindrical phantom with inner diameter of 21.5 cm; 2) a uniform 11.5-cm cylindrical phantom with four embedded small hot lesions with diameters of 3, 4, 5, and 6 mm; and 3) the 3-D Hoffman brain phantom with three embedded small hot lesion phantoms with diameters of 3, 5, and 8.6 mm in a warm background. Lesions were placed at different radial and axial distances. We evaluated the different reconstruction methods for MDAPET camera by comparing the noise level of images, contrast recovery, and hot lesion detection, and visually compared images. We found that overall the 3D-OSEM algorithm, especially when images post filtered with the Metz filter, produced the best results in terms of contrast-noise tradeoff, and detection of hot spots, and reproduction of brain phantom structures. Even though the MDAPET camera has a relatively small maximum axial acceptance (/spl plusmn/5 deg), images produced with the 3DRP algorithm had slightly better contrast recovery and reproduced the structures of the brain phantom slightly better than the faster 2-D rebinning methods.

Improving the visualization of 3D ultrasound data with 3D filtering

NASA Astrophysics Data System (ADS)

Shamdasani, Vijay; Bae, Unmin; Managuli, Ravi; Kim, Yongmin

2005-04-01

3D ultrasound imaging is quickly gaining widespread clinical acceptance as a visualization tool that allows clinicians to obtain unique views not available with traditional 2D ultrasound imaging and an accurate understanding of patient anatomy. The ability to acquire, manipulate and interact with the 3D data in real time is an important feature of 3D ultrasound imaging. Volume rendering is often used to transform the 3D volume into 2D images for visualization. Unlike computed tomography (CT) and magnetic resonance imaging (MRI), volume rendering of 3D ultrasound data creates noisy images in which surfaces cannot be readily discerned due to speckles and low signal-to-noise ratio. The degrading effect of speckles is especially severe when gradient shading is performed to add depth cues to the image. Several researchers have reported that smoothing the pre-rendered volume with a 3D convolution kernel, such as 5x5x5, can significantly improve the image quality, but at the cost of decreased resolution. In this paper, we have analyzed the reasons for the improvement in image quality with 3D filtering and determined that the improvement is due to two effects. The filtering reduces speckles in the volume data, which leads to (1) more accurate gradient computation and better shading and (2) decreased noise during compositing. We have found that applying a moderate-size smoothing kernel (e.g., 7x7x7) to the volume data before gradient computation combined with some smoothing of the volume data (e.g., with a 3x3x3 lowpass filter) before compositing yielded images with good depth perception and no appreciable loss in resolution. Providing the clinician with the flexibility to control both of these effects (i.e., shading and compositing) independently could improve the visualization of the 3D ultrasound data. Introducing this flexibility into the ultrasound machine requires 3D filtering to be performed twice on the volume data, once before gradient computation and again before compositing. 3D filtering of an ultrasound volume containing millions of voxels requires a large amount of computation, and doing it twice decreases the number of frames that can be visualized per second. To address this, we have developed several techniques to make computation efficient. For example, we have used the moving average method to filter a 128x128x128 volume with a 3x3x3 boxcar kernel in 17 ms on a single MAP processor running at 400 MHz. The same methods reduced the computing time on a Pentium 4 running at 3 GHz from 110 ms to 62 ms. We believe that our proposed method can improve 3D ultrasound visualization without sacrificing resolution and incurring an excessive computing time.

Single-shot three-dimensional reconstruction based on structured light line pattern

NASA Astrophysics Data System (ADS)

Wang, ZhenZhou; Yang, YongMing

2018-07-01

Reconstruction of the object by single-shot is of great importance in many applications, in which the object is moving or its shape is non-rigid and changes irregularly. In this paper, we propose a single-shot structured light 3D imaging technique that calculates the phase map from the distorted line pattern. This technique makes use of the image processing techniques to segment and cluster the projected structured light line pattern from one single captured image. The coordinates of the clustered lines are extracted to form a low-resolution phase matrix which is then transformed to full-resolution phase map by spline interpolation. The 3D shape of the object is computed from the full-resolution phase map and the 2D camera coordinates. Experimental results show that the proposed method was able to reconstruct the three-dimensional shape of the object robustly from one single image.

High-resolution three-dimensional magnetic resonance imaging of mouse lung in situ.

PubMed

Scadeng, Miriam; Rossiter, Harry B; Dubowitz, David J; Breen, Ellen C

2007-01-01

This study establishes a method for high-resolution isotropic magnetic resonance (MR) imaging of mouse lungs using tracheal liquid-instillation to remove MR susceptibility artifacts. C57BL/6J mice were instilled sequentially with perfluorocarbon and phosphate-buffered saline to an airway pressure of 10, 20, or 30 cm H2O. Imaging was performed in a 7T MR scanner using a 2.5-cm Quadrature volume coil and a 3-dimensional (3D) FLASH imaging sequence. Liquid-instillation removed magnetic susceptibility artifacts and allowed lung structure to be viewed at an isotropic resolution of 78-90 microm. Instilled liquid and modeled lung volumes were well correlated (R = 0.92; P < 0.05) and differed by a constant tissue volume (220 +/- 92 microL). 3D image renderings allowed differences in structural dimensions (volumes and areas) to be accurately measured at each inflation pressure. These data demonstrate the efficacy of pulmonary liquid instillation for in situ high-resolution MR imaging of mouse lungs for accurate measurement of pulmonary airway, parenchymal, and vascular structures.

Employing unmanned aerial vehicle to monitor the health condition of wind turbines

NASA Astrophysics Data System (ADS)

Huang, Yishuo; Chiang, Chih-Hung; Hsu, Keng-Tsang; Cheng, Chia-Chi

2018-04-01

Unmanned aerial vehicle (UAV) can gather the spatial information of huge structures, such as wind turbines, that can be difficult to obtain with traditional approaches. In this paper, the UAV used in the experiments is equipped with high resolution camera and thermal infrared camera. The high resolution camera can provide a series of images with resolution up to 10 Megapixels. Those images can be used to form the 3D model using the digital photogrammetry technique. By comparing the 3D scenes of the same wind turbine at different times, possible displacement of the supporting tower of the wind turbine, caused by ground movement or foundation deterioration may be determined. The recorded thermal images are analyzed by applying the image segmentation methods to the surface temperature distribution. A series of sub-regions are separated by the differences of the surface temperature. The high-resolution optical image and the segmented thermal image are fused such that the surface anomalies are more easily identified for wind turbines.

Dynamic integral imaging technology for 3D applications (Conference Presentation)

NASA Astrophysics Data System (ADS)

Huang, Yi-Pai; Javidi, Bahram; Martínez-Corral, Manuel; Shieh, Han-Ping D.; Jen, Tai-Hsiang; Hsieh, Po-Yuan; Hassanfiroozi, Amir

2017-05-01

Depth and resolution are always the trade-off in integral imaging technology. With the dynamic adjustable devices, the two factors of integral imaging can be fully compensated with time-multiplexed addressing. Those dynamic devices can be mechanical or electrical driven. In this presentation, we will mainly focused on discussing various Liquid Crystal devices which can change the focal length, scan and shift the image position, or switched in between 2D/3D mode. By using the Liquid Crystal devices, dynamic integral imaging have been successfully applied on 3D Display, capturing, and bio-imaging applications.

Optical bench performance of a novel trifocal intraocular lens compared with a multifocal intraocular lens

PubMed Central

Lee, Shinwook; Choi, Myoung; Xu, Zaiwei; Zhao, Zeyu; Alexander, Elsinore; Liu, Yueai

2016-01-01

Purpose The purpose of this study is to compare the optical characteristics of the novel PanOptix presbyopia-correcting trifocal intraocular lens (IOL) and the multifocal ReSTOR +3.0 D IOL, through in vitro bench investigations. Methods The optical characteristics of AcrySof® IQ PanOptix™ (PanOptix) and AcrySof® IQ ReSTOR +3.0 D (ReSTOR +3.0 D) IOLs were evaluated by through-focus Badal images, simulated headlight images, and modulation transfer function (MTF) measurements which determine resolution, photic phenomena, and image quality. Through-focus Badal images of an Early Treatment of Diabetic Retinopathy Study chart were recorded at both photopic and mesopic pupil sizes. Simulated headlight images were taken on an MTF bench with a 50-μm pinhole target and a 5.0 mm pupil at the distance focus of the IOL. MTF curves were measured with a 3.0 mm pupil, and spatial frequencies equivalent to 20/40 and 20/20 visual acuities were recorded to illustrate the through-focus MTF curves. Far-, intermediate-, and near-focus MTF values were obtained. Results Bench Badal image testing and MTF measurements showed that PanOptix has a near focus at a distance of 42 cm and an additional intermediate focus at a distance of about 60 cm. The near focus for ReSTOR +3.0 D is at 45 cm. PanOptix and ReSTOR +3.0 D have comparable photopic distances and near MTF values. Additionally, PanOptix provided a substantial continuous range of vision from distance to intermediate and to near compared with ReSTOR +3.0 D. The halo propensity for PanOptix was slightly higher than that for ReSTOR +3.0 D. Conclusion Laboratory-based in vitro simulations showed that PanOptix trifocal IOL has comparable resolution and image quality performance in distance and near foci compared with ReSTOR +3.0 D IOL. PanOptix showed better resolution and image quality performance at the intermediate focus than ReSTOR +3.0 D IOL. PMID:27330273

Compact three-dimensional super-resolution system based on fluorescence emission difference microscopy

NASA Astrophysics Data System (ADS)

Zhu, Dazhao; Chen, Youhua; Fang, Yue; Hussain, Anwar; Kuang, Cuifang; Zhou, Xiaoxu; Xu, Yingke; Liu, Xu

2017-12-01

A compact microscope system for three-dimensional (3-D) super-resolution imaging is presented. The super-resolution capability of the system is based on a size-reduced effective 3-D point spread function generated through the fluorescence emission difference (FED) method. The appropriate polarization direction distribution and manipulation allows the panel active area of the spatial light modulator to be fully utilized. This allows simultaneous modulation of the incident light by two kinds of phase masks to be performed with a single spatial light modulator in order to generate a 3-D negative spot. The system is more compact than standard 3-D FED systems while maintaining all the advantages of 3-D FED microscopy. The experimental results demonstrated the improvement in 3-D resolution by nearly 1.7 times and 1.6 times compared to the classic confocal resolution in the lateral and axial directions, respectively.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

NASA Astrophysics Data System (ADS)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

High resolution three-dimensional photoacoustic imaging of human finger joints in vivo

NASA Astrophysics Data System (ADS)

Xi, Lei; Jiang, Huabei

2015-08-01

We present a method for noninvasively imaging the hand joints using a three-dimensional (3D) photoacoustic imaging (PAI) system. This 3D PAI system utilizes cylindrical scanning in data collection and virtual-detector concept in image reconstruction. The maximum lateral and axial resolutions of the PAI system are 70 μm and 240 μm. The cross-sectional photoacoustic images of a healthy joint clearly exhibited major internal structures including phalanx and tendons, which are not available from the current photoacoustic imaging methods. The in vivo PAI results obtained are comparable with the corresponding 3.0 T MRI images of the finger joint. This study suggests that the proposed method has the potential to be used in early detection of joint diseases such as osteoarthritis.

3D high- and super-resolution imaging using single-objective SPIM.

PubMed

Galland, Remi; Grenci, Gianluca; Aravind, Ajay; Viasnoff, Virgile; Studer, Vincent; Sibarita, Jean-Baptiste

2015-07-01

Single-objective selective-plane illumination microscopy (soSPIM) is achieved with micromirrored cavities combined with a laser beam-steering unit installed on a standard inverted microscope. The illumination and detection are done through the same objective. soSPIM can be used with standard sample preparations and features high background rejection and efficient photon collection, allowing for 3D single-molecule-based super-resolution imaging of whole cells or cell aggregates. Using larger mirrors enabled us to broaden the capabilities of our system to image Drosophila embryos.

Technical Note: Characterization of custom 3D printed multimodality imaging phantoms.

PubMed

Bieniosek, Matthew F; Lee, Brian J; Levin, Craig S

2015-10-01

Imaging phantoms are important tools for researchers and technicians, but they can be costly and difficult to customize. Three dimensional (3D) printing is a widely available rapid prototyping technique that enables the fabrication of objects with 3D computer generated geometries. It is ideal for quickly producing customized, low cost, multimodal, reusable imaging phantoms. This work validates the use of 3D printed phantoms by comparing CT and PET scans of a 3D printed phantom and a commercial "Micro Deluxe" phantom. This report also presents results from a customized 3D printed PET/MRI phantom, and a customized high resolution imaging phantom with sub-mm features. CT and PET scans of a 3D printed phantom and a commercial Micro Deluxe (Data Spectrum Corporation, USA) phantom with 1.2, 1.6, 2.4, 3.2, 4.0, and 4.8 mm diameter hot rods were acquired. The measured PET and CT rod sizes, activities, and attenuation coefficients were compared. A PET/MRI scan of a custom 3D printed phantom with hot and cold rods was performed, with photon attenuation and normalization measurements performed with a separate 3D printed normalization phantom. X-ray transmission scans of a customized two level high resolution 3D printed phantom with sub-mm features were also performed. Results show very good agreement between commercial and 3D printed micro deluxe phantoms with less than 3% difference in CT measured rod diameter, less than 5% difference in PET measured rod diameter, and a maximum of 6.2% difference in average rod activity from a 10 min, 333 kBq/ml (9 μCi/ml) Siemens Inveon (Siemens Healthcare, Germany) PET scan. In all cases, these differences were within the measurement uncertainties of our setups. PET/MRI scans successfully identified 3D printed hot and cold rods on PET and MRI modalities. X-ray projection images of a 3D printed high resolution phantom identified features as small as 350 μm wide. This work shows that 3D printed phantoms can be functionally equivalent to commercially available phantoms. They are a viable option for quickly distributing and fabricating low cost, customized phantoms.

Photogrammetric Point Clouds Generation in Urban Areas from Integrated Image Matching and Segmentation

NASA Astrophysics Data System (ADS)

Ye, L.; Wu, B.

2017-09-01

High-resolution imagery is an attractive option for surveying and mapping applications due to the advantages of high quality imaging, short revisit time, and lower cost. Automated reliable and dense image matching is essential for photogrammetric 3D data derivation. Such matching, in urban areas, however, is extremely difficult, owing to the complexity of urban textures and severe occlusion problems on the images caused by tall buildings. Aimed at exploiting high-resolution imagery for 3D urban modelling applications, this paper presents an integrated image matching and segmentation approach for reliable dense matching of high-resolution imagery in urban areas. The approach is based on the framework of our existing self-adaptive triangulation constrained image matching (SATM), but incorporates three novel aspects to tackle the image matching difficulties in urban areas: 1) occlusion filtering based on image segmentation, 2) segment-adaptive similarity correlation to reduce the similarity ambiguity, 3) improved dense matching propagation to provide more reliable matches in urban areas. Experimental analyses were conducted using aerial images of Vaihingen, Germany and high-resolution satellite images in Hong Kong. The photogrammetric point clouds were generated, from which digital surface models (DSMs) were derived. They were compared with the corresponding airborne laser scanning data and the DSMs generated from the Semi-Global matching (SGM) method. The experimental results show that the proposed approach is able to produce dense and reliable matches comparable to SGM in flat areas, while for densely built-up areas, the proposed method performs better than SGM. The proposed method offers an alternative solution for 3D surface reconstruction in urban areas.

Large depth of focus dynamic micro integral imaging for optical see-through augmented reality display using a focus-tunable lens.

PubMed

Shen, Xin; Javidi, Bahram

2018-03-01

We have developed a three-dimensional (3D) dynamic integral-imaging (InIm)-system-based optical see-through augmented reality display with enhanced depth range of a 3D augmented image. A focus-tunable lens is adopted in the 3D display unit to relay the elemental images with various positions to the micro lens array. Based on resolution priority integral imaging, multiple lenslet image planes are generated to enhance the depth range of the 3D image. The depth range is further increased by utilizing both the real and virtual 3D imaging fields. The 3D reconstructed image and the real-world scene are overlaid using an optical see-through display for augmented reality. The proposed system can significantly enhance the depth range of a 3D reconstructed image with high image quality in the micro InIm unit. This approach provides enhanced functionality for augmented information and adjusts the vergence-accommodation conflict of a traditional augmented reality display.

Three-dimensional nanoscale imaging by plasmonic Brownian microscopy

NASA Astrophysics Data System (ADS)

Labno, Anna; Gladden, Christopher; Kim, Jeongmin; Lu, Dylan; Yin, Xiaobo; Wang, Yuan; Liu, Zhaowei; Zhang, Xiang

2017-12-01

Three-dimensional (3D) imaging at the nanoscale is a key to understanding of nanomaterials and complex systems. While scanning probe microscopy (SPM) has been the workhorse of nanoscale metrology, its slow scanning speed by a single probe tip can limit the application of SPM to wide-field imaging of 3D complex nanostructures. Both electron microscopy and optical tomography allow 3D imaging, but are limited to the use in vacuum environment due to electron scattering and to optical resolution in micron scales, respectively. Here we demonstrate plasmonic Brownian microscopy (PBM) as a way to improve the imaging speed of SPM. Unlike photonic force microscopy where a single trapped particle is used for a serial scanning, PBM utilizes a massive number of plasmonic nanoparticles (NPs) under Brownian diffusion in solution to scan in parallel around the unlabeled sample object. The motion of NPs under an evanescent field is three-dimensionally localized to reconstruct the super-resolution topology of 3D dielectric objects. Our method allows high throughput imaging of complex 3D structures over a large field of view, even with internal structures such as cavities that cannot be accessed by conventional mechanical tips in SPM.

Acquisition of multiple image stacks with a confocal laser scanning microscope

NASA Astrophysics Data System (ADS)

Zuschratter, Werner; Steffen, Thomas; Braun, Katharina; Herzog, Andreas; Michaelis, Bernd; Scheich, Henning

1998-06-01

Image acquisition at high magnification is inevitably correlated with a limited view over the entire tissue section. To overcome this limitation we designed software for multiple image-stack acquisition (3D-MISA) in confocal laser scanning microscopy (CLSM). The system consists of a 4 channel Leica CLSM equipped with a high resolution z- scanning stage mounted on a xy-monitorized stage. The 3D- MISA software is implemented into the microscope scanning software and uses the microscope settings for the movements of the xy-stage. It allows storage and recall of 70 xyz- positions and the automatic 3D-scanning of image arrays between selected xyz-coordinates. The number of images within one array is limited only by the amount of disk space or memory available. Although for most applications the accuracy of the xy-scanning stage is sufficient for a precise alignment of tiled views, the software provides the possibility of an adjustable overlap between two image stacks by shifting the moving steps of the xy-scanning stage. After scanning a tiled image gallery of the extended focus-images of each channel will be displayed on a graphic monitor. In addition, a tiled image gallery of individual focal planes can be created. In summary, the 3D-MISA allows 3D-image acquisition of coherent regions in combination with high resolution of single images.

High energy near- and far-field ptychographic tomography at the ESRF

NASA Astrophysics Data System (ADS)

da Silva, Julio C.; Haubrich, Jan; Requena, Guillermo; Hubert, Maxime; Pacureanu, Alexandra; Bloch, Leonid; Yang, Yang; Cloetens, Peter

2017-09-01

In high-resolution tomography, one needs high-resolved projections in order to reconstruct a high-quality 3D map of a sample. X-ray ptychography is a robust technique which can provide such high-resolution 2D projections taking advantage of coherent X-rays. This technique was used in the far-field regime for a fair amount of time, but it can now also be implemented in the near-field regime. In both regimes, the technique enables not only high-resolution imaging, but also high sensitivity to the electron density of the sample. The combination with tomography makes 3D imaging possible via ptychographic X-ray computed tomography (PXCT), which can provide a 3D map of the complex-valued refractive index of the sample. The extension of PXCT to X-ray energies above 15 keV is challenging, but it can allow the imaging of object opaque to lower energy. We present here the implementation and developments of high-energy near- and far-field PXCT at the ESRF.

Development of a Dedicated Radiotherapy Unit with Real-Time Image Guidance and Motion Management for Accelerated Partial Breast Irradiation

DTIC Science & Technology

2012-08-01

respiratory motions using 4D tagged magnetic resonance imaging ( MRI ) data and 4D high-resolution respiratory-gated CT data respectively. Both...dimensional segmented human anatomy. Medical Physics, 1994. 21(2): p. 299-302. 6. Zubal, I.G., et al. High resolution, MRI -based, segmented...the beam direction. T2-weighted images were acquired after 24 hours with a 3T- MRI scanner using a turbo spin-echo sequence. Imaging parameters were

Functional cardiac magnetic resonance microscopy

NASA Astrophysics Data System (ADS)

Brau, Anja Christina Sophie

2003-07-01

The study of small animal models of human cardiovascular disease is critical to our understanding of the origin, progression, and treatment of this pervasive disease. Complete analysis of disease pathophysiology in these animal models requires measuring structural and functional changes at the level of the whole heart---a task for which an appropriate non-invasive imaging method is needed. The purpose of this work was thus to develop an imaging technique to support in vivo characterization of cardiac structure and function in rat and mouse models of cardiovascular disease. Whereas clinical cardiac magnetic resonance imaging (MRI) provides accurate assessment of the human heart, the extension of cardiac MRI from humans to rodents presents several formidable scaling challenges. Acquiring images of the mouse heart with organ definition and fluidity of contraction comparable to that achieved in humans requires an increase in spatial resolution by a factor of 3000 and an increase in temporal resolution by a factor of ten. No single technical innovation can meet the demanding imaging requirements imposed by the small animal. A functional cardiac magnetic resonance microscopy technique was developed by integrating improvements in physiological control, imaging hardware, biological synchronization of imaging, and pulse sequence design to achieve high-quality images of the murine heart with high spatial and temporal resolution. The specific methods and results from three different sets of imaging experiments are presented: (1) 2D functional imaging in the rat with spatial resolution of 175 mum2 x 1 mm and temporal resolution of 10 ms; (2) 3D functional imaging in the rat with spatial resolution of 100 mum 2 x 500 mum and temporal resolution of 30 ms; and (3) 2D functional imaging in the mouse with spatial resolution down to 100 mum2 x 1 mm and temporal resolution of 10 ms. The cardiac microscopy technique presented here represents a novel collection of technologies capable of acquiring routine high-quality images of murine cardiac structure and function with minimal artifacts and markedly higher spatial resolution compared to conventional techniques. This work is poised to serve a valuable role in the evaluation of cardiovascular disease and should find broad application in studies ranging from basic pathophysiology to drug discovery.

3D wide field-of-view Gabor-domain optical coherence microscopy advancing real-time in-vivo imaging and metrology

NASA Astrophysics Data System (ADS)

Canavesi, Cristina; Cogliati, Andrea; Hayes, Adam; Tankam, Patrice; Santhanam, Anand; Rolland, Jannick P.

2017-02-01

Real-time volumetric high-definition wide-field-of-view in-vivo cellular imaging requires micron-scale resolution in 3D. Compactness of the handheld device and distortion-free images with cellular resolution are also critically required for onsite use in clinical applications. By integrating a custom liquid lens-based microscope and a dual-axis MEMS scanner in a compact handheld probe, Gabor-domain optical coherence microscopy (GD-OCM) breaks the lateral resolution limit of optical coherence tomography through depth, overcoming the tradeoff between numerical aperture and depth of focus, enabling advances in biotechnology. Furthermore, distortion-free imaging with no post-processing is achieved with a compact, lightweight handheld MEMS scanner that obtained a 12-fold reduction in volume and 17-fold reduction in weight over a previous dual-mirror galvanometer-based scanner. Approaching the holy grail of medical imaging - noninvasive real-time imaging with histologic resolution - GD-OCM demonstrates invariant resolution of 2 μm throughout a volume of 1 x 1 x 0.6 mm3, acquired and visualized in less than 2 minutes with parallel processing on graphics processing units. Results on the metrology of manufactured materials and imaging of human tissue with GD-OCM are presented.

Focused ion beam assisted three-dimensional rock imaging at submicron scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomutsa, Liviu; Radmilovic, Velimir

2003-05-09

Computation of effective flow properties of fluids in porous media based on three dimensional (3D) pore structure information has become more successful in the last few years, due to both improvements in the input data and the network models. Computed X-ray microtomography has been successful in 3D pore imaging at micron scale, which is adequate for many sandstones. For other rocks of economic interest, such as chalk and diatomite, submicron resolution is needed in order to resolve the 3D-pore structure. To achieve submicron resolution, a new method of sample serial sectioning and imaging using Focused Ion Beam (FIB) technology hasmore » been developed and 3D pore images of the pore system for diatomite and chalk have been obtained. FIB was used in the milling of layers as wide as 50 micrometers and as thin as 100 nanometers by sputtering of atoms from the sample surface. The focused ion beam, consisting of gallium ions (Ga+) accelerated by potentials of up to 30 kV and currents up to 20,000 pA, yields very clean, flat surfaces in which the pore-grain boundaries appear in high contrast. No distortion of the pore boundaries due to the ion milling is apparent. After each milling step, as a new surface is exposed, an image of the surface is generated. Using secondary electrons or ions, resolutions as high as 10 nm can be obtained. Afterwards, the series of 2D images can be stacked in the computer and, using appropriate interpolation and surface rendering algorithms, the 3D pore structure is reconstructed.« less

Nanometer-scale imaging and pore-scale fluid flow modeling inchalk

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomutsa, Liviu; Silin, Dmitriy; Radmilovich, Velimir

2005-08-23

For many rocks of high economic interest such as chalk,diatomite, tight gas sands or coal, nanometer scale resolution is neededto resolve the 3D-pore structure, which controls the flow and trapping offluids in the rocks. Such resolutions cannot be achieved with existingtomographic technologies. A new 3D imaging method, based on serialsectioning and using the Focused Ion Beam (FIB) technology has beendeveloped. FIB allows for the milling of layers as thin as 10 nanometersby using accelerated Ga+ ions to sputter atoms from the sample surface.After each milling step, as a new surface is exposed, a 2D image of thissurface is generated. Next,more » the 2D images are stacked to reconstruct the3D pore or grain structure. Resolutions as high as 10 nm are achievableusing this technique. A new image processing method uses directmorphological analysis of the pore space to characterize thepetrophysical properties of diverse formations. In addition to estimationof the petrophysical properties (porosity, permeability, relativepermeability and capillary pressures), the method is used for simulationof fluid displacement processes, such as those encountered in variousimproved oil recovery (IOR) approaches. Computed with the new methodcapillary pressure curves are in good agreement with laboratory data. Themethod has also been applied for visualization of the fluid distributionat various saturations from the new FIB data.« less

SU-E-J-237: Real-Time 3D Anatomy Estimation From Undersampled MR Acquisitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glitzner, M; Lagendijk, J; Raaymakers, B

Recent developments made MRI guided radiotherapy feasible. Performing simultaneous imaging during fractions can provide information about changing anatomy by means of deformable image registration for either immediate plan adaptations or accurate dose accumulation on the changing anatomy. In 3D MRI, however, acquisition time is considerable and scales with resolution. Furthermore, intra-scan motion degrades image quality.In this work, we investigate the sensitivity of registration quality on imageresolution: potentially, by employing spatial undersampling, the acquisition timeof MR images for the purpose of deformable image registration can be reducedsignificantly.On a volunteer, 3D-MR imaging data was sampled in a navigator-gated manner, acquiring one axialmore » volume (360×260×100mm{sup 3}) per 3s during exhale phase. A T1-weighted FFE sequence was used with an acquired voxel size of (2.5mm{sup 3}) for a duration of 17min. Deformation vector fields were evaluated for 100 imaging cycles with respect to the initial anatomy using deformable image registration based on optical flow. Subsequently, the imaging data was downsampled by a factor of 2, simulating a fourfold acquisition speed. Displacements of the downsampled volumes were then calculated by the same process.In kidneyliver boundaries and the region around stomach/duodenum, prominent organ drifts could be observed in both the original and the downsampled imaging data. An increasing displacement of approximately 2mm was observed for the kidney, while an area around the stomach showed sudden displacements of 4mm. Comparison of the motile points over time showed high reproducibility between the displacements of high-resolution and downsampled volumes: over a 17min acquisition, the componentwise RMS error was not more than 0.38mm.Based on the synthetic experiments, 3D nonrigid image registration shows little sensitivity to image resolution and the displacement information is preserved even when halving the resolution. This can be employed to greatly reduce image acquisition times for interventional applications in real-time. This work was funded by the SoRTS consortium, which includes the industry partners Elekta, Philips and Technolution.« less

Structured illumination multimodal 3D-resolved quantitative phase and fluorescence sub-diffraction microscopy

PubMed Central

Chowdhury, Shwetadwip; Eldridge, Will J.; Wax, Adam; Izatt, Joseph A.

2017-01-01

Sub-diffraction resolution imaging has played a pivotal role in biological research by visualizing key, but previously unresolvable, sub-cellular structures. Unfortunately, applications of far-field sub-diffraction resolution are currently divided between fluorescent and coherent-diffraction regimes, and a multimodal sub-diffraction technique that bridges this gap has not yet been demonstrated. Here we report that structured illumination (SI) allows multimodal sub-diffraction imaging of both coherent quantitative-phase (QP) and fluorescence. Due to SI’s conventionally fluorescent applications, we first demonstrate the principle of SI-enabled three-dimensional (3D) QP sub-diffraction imaging with calibration microspheres. Image analysis confirmed enhanced lateral and axial resolutions over diffraction-limited QP imaging, and established striking parallels between coherent SI and conventional optical diffraction tomography. We next introduce an optical system utilizing SI to achieve 3D sub-diffraction, multimodal QP/fluorescent visualization of A549 biological cells fluorescently tagged for F-actin. Our results suggest that SI has a unique utility in studying biological phenomena with significant molecular, biophysical, and biochemical components. PMID:28663887

Efficient Use of Video for 3d Modelling of Cultural Heritage Objects

NASA Astrophysics Data System (ADS)

Alsadik, B.; Gerke, M.; Vosselman, G.

2015-03-01

Currently, there is a rapid development in the techniques of the automated image based modelling (IBM), especially in advanced structure-from-motion (SFM) and dense image matching methods, and camera technology. One possibility is to use video imaging to create 3D reality based models of cultural heritage architectures and monuments. Practically, video imaging is much easier to apply when compared to still image shooting in IBM techniques because the latter needs a thorough planning and proficiency. However, one is faced with mainly three problems when video image sequences are used for highly detailed modelling and dimensional survey of cultural heritage objects. These problems are: the low resolution of video images, the need to process a large number of short baseline video images and blur effects due to camera shake on a significant number of images. In this research, the feasibility of using video images for efficient 3D modelling is investigated. A method is developed to find the minimal significant number of video images in terms of object coverage and blur effect. This reduction in video images is convenient to decrease the processing time and to create a reliable textured 3D model compared with models produced by still imaging. Two experiments for modelling a building and a monument are tested using a video image resolution of 1920×1080 pixels. Internal and external validations of the produced models are applied to find out the final predicted accuracy and the model level of details. Related to the object complexity and video imaging resolution, the tests show an achievable average accuracy between 1 - 5 cm when using video imaging, which is suitable for visualization, virtual museums and low detailed documentation.

Automated detection, 3D segmentation and analysis of high resolution spine MR images using statistical shape models

NASA Astrophysics Data System (ADS)

Neubert, A.; Fripp, J.; Engstrom, C.; Schwarz, R.; Lauer, L.; Salvado, O.; Crozier, S.

2012-12-01

Recent advances in high resolution magnetic resonance (MR) imaging of the spine provide a basis for the automated assessment of intervertebral disc (IVD) and vertebral body (VB) anatomy. High resolution three-dimensional (3D) morphological information contained in these images may be useful for early detection and monitoring of common spine disorders, such as disc degeneration. This work proposes an automated approach to extract the 3D segmentations of lumbar and thoracic IVDs and VBs from MR images using statistical shape analysis and registration of grey level intensity profiles. The algorithm was validated on a dataset of volumetric scans of the thoracolumbar spine of asymptomatic volunteers obtained on a 3T scanner using the relatively new 3D T2-weighted SPACE pulse sequence. Manual segmentations and expert radiological findings of early signs of disc degeneration were used in the validation. There was good agreement between manual and automated segmentation of the IVD and VB volumes with the mean Dice scores of 0.89 ± 0.04 and 0.91 ± 0.02 and mean absolute surface distances of 0.55 ± 0.18 mm and 0.67 ± 0.17 mm respectively. The method compares favourably to existing 3D MR segmentation techniques for VBs. This is the first time IVDs have been automatically segmented from 3D volumetric scans and shape parameters obtained were used in preliminary analyses to accurately classify (100% sensitivity, 98.3% specificity) disc abnormalities associated with early degenerative changes.

Culturing of avian embryos for time-lapse imaging.

PubMed

Rupp, Paul A; Rongish, Brenda J; Czirok, Andras; Little, Charles D

2003-02-01

Monitoring morphogenetic processes, at high resolution over time, has been a long-standing goal of many developmental cell biologists. It is critical to image cells in their natural environment whenever possible; however, imaging many warm-blooded vertebrates, especially mammals, is problematic. At early stages of development, birds are ideal for imaging, since the avian body plan is very similar to that of mammals. We have devised a culturing technique that allows for the acquisition of high-resolution differential interference contrast and epifluorescence images of developing avian embryos in a 4-D (3-D + time) system. The resulting information, from intact embryos, is derived from an area encompassing several millimeters, at micrometer resolution for up to 30 h.

The application of paramagnetic contrast-based T2 effect to 3D heavily T2W high-resolution MR imaging of the brachial plexus and its branches.

PubMed

Wang, Lixia; Niu, Yanfeng; Kong, Xiangquan; Yu, Qun; Kong, Xiangchuang; Lv, Yinzhang; Shi, Heshui; Li, Chungao; Wu, Wenjun; Wang, Bing; Liu, Dingxi

2016-03-01

To introduce a new 3D magnetic resonance neurography (MRN) method involving a paramagnetic contrast-based T2 effect coupled with an advanced 3D heavily T2W SPACE-STIR high resolution imaging sequence that would enhance the contrast between nervous tissue and surrounding tissues. Thirty subjects (average age, 39.6±17.0 years; 18 male and 12 female) were enrolled, including three patients with brachial plexopathy and 27 healthy volunteers. Subjective scores from two neuroradiologists, evaluating noncontrast MRN (cMRN) and 3D SPACE-STIR contrast enhanced MRN (ceMRN) 3D data using a 3-point scoring system, were compared using Wilcoxon signed-rank test. Contrast-to-noise ratios (CNRs), SNRs, and contrast ratios within the brachial plexus on cMRN vs. ceMRN MIP and source images were also compared using the paired t-test. The average score for cMRN (0.77±0.43) was significantly lower than ceMRN (1.73±0.45) (p<0.001). Lower nerve vs. vein CNRs were found on cMRN vs. ceMRN, respectively (p<0.001 for both source and MIP images). All nerve-to-surrounding tissue contrast ratios (i.e., fat, muscle, veins, and bone) were higher for ceMRN compared with cMRN for both source and MIP images (all p<0.05). The improved 3D visualization of the brachial plexus and its branches, using this new contrast-enhanced MRN method, can provide high resolution imaging which may be of significant value in the assessment of brachial plexopathy. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Evaluation of the influence of acquisition parameters of microtomography in image quality applied by carbonate rocks

NASA Astrophysics Data System (ADS)

Santos, T. M. P.; Machado, A. S.; Araújo, O. M. O.; Ferreira, C. G.; Lopes, R. T.

2018-03-01

X-ray computed microtomography is a powerful nondestructive technique for 2D and 3D structure analysis. However, parameters used in acquisition promote directs influence in qualitative and quantitative results in characterization of samples, due image resolution. The aim of this study is value the influence of theses parameters in results through of tests changing these parameters in different situations and system characterization. Results demonstrate those pixel size and detector matrixes are the main parameters that influence in resolution and image quality. Microtomography was considered an excellent technique for characterization using the best image resolution possible.

The effect on surgical skills of expert surgeons using 3D/HD and 2D/4K resolution monitors in laparoscopic phantom tasks.

PubMed

Harada, Hitoshi; Kanaji, Shingo; Hasegawa, Hiroshi; Yamamoto, Masashi; Matsuda, Yoshiko; Yamashita, Kimihiro; Matsuda, Takeru; Oshikiri, Taro; Sumi, Yasuo; Nakamura, Tetsu; Suzuki, Satoshi; Kakeji, Yoshihiro

2018-03-30

Recently, several new imaging technologies, such as three-dimensional (3D)/high-definition (HD) stereovision and high-resolution two-dimensional (2D)/4K monitors, have been introduced in laparoscopic surgery. However, it is still unclear whether these technologies actually improve surgical performance. Participants were 11 expert laparoscopic surgeons. We designed three laparoscopic suturing tasks (task 1: simple suturing, task 2: knotting thread in a small box, and task 3: suturing in a narrow space) in training boxes. Performances were recorded by an optical position tracker. All participants first performed each task five times consecutively using a conventional 2D/HD monitor. Then they were randomly divided into two groups: six participants performed the tasks using 3D/HD before using 2D/4K; the other five participants performed the tasks using a 2D/4K monitor before the 3D/HD monitor. After the trials, we evaluated the performance scores (operative time, path length of forceps, and technical errors) and compared performance scores across all monitors. Surgical performances of participants were ranked in decreasing order: 3D/HD, 2D/4K, and 2D/HD using the total scores for each task. In task 1 (simple suturing), some surgical performances using 3D/HD were significantly better than those using 2D/4K (P = 0.017, P = 0.033, P = 0.492 for operative time, path length, and technical errors, respectively). On the other hand, with operation in narrow spaces such as in tasks 2 and 3, performances using 2D/4K were not inferior to 3D/HD performances. The high-resolution images from the 2D/4K monitor may enhance depth perception in narrow spaces and may complement stereoscopic vision almost as well as using 3D/HD. Compared to a 2D/HD monitor, a 3D/HD monitor improved the laparoscopic surgical technique of expert surgeons more than a 2D/4K monitor. However, the advantage of 2D/4K high-resolution images may be comparable to a 3D/HD monitor especially in narrow spaces.

Highly accelerated intracranial 4D flow MRI: evaluation of healthy volunteers and patients with intracranial aneurysms.

PubMed

Liu, Jing; Koskas, Louise; Faraji, Farshid; Kao, Evan; Wang, Yan; Haraldsson, Henrik; Kefayati, Sarah; Zhu, Chengcheng; Ahn, Sinyeob; Laub, Gerhard; Saloner, David

2018-04-01

To evaluate an accelerated 4D flow MRI method that provides high temporal resolution in a clinically feasible acquisition time for intracranial velocity imaging. Accelerated 4D flow MRI was developed by using a pseudo-random variable-density Cartesian undersampling strategy (CIRCUS) with the combination of k-t, parallel imaging and compressed sensing image reconstruction techniques (k-t SPARSE-SENSE). Four-dimensional flow data were acquired on five healthy volunteers and eight patients with intracranial aneurysms using CIRCUS (acceleration factor of R = 4, termed CIRCUS4) and GRAPPA (R = 2, termed GRAPPA2) as the reference method. Images with three times higher temporal resolution (R = 12, CIRCUS12) were also reconstructed from the same acquisition as CIRCUS4. Qualitative and quantitative image assessment was performed on the images acquired with different methods, and complex flow patterns in the aneurysms were identified and compared. Four-dimensional flow MRI with CIRCUS was achieved in 5 min and allowed further improved temporal resolution of <30 ms. Volunteer studies showed similar qualitative and quantitative evaluation obtained with the proposed approach compared to the reference (overall image scores: GRAPPA2 3.2 ± 0.6; CIRCUS4 3.1 ± 0.7; CIRCUS12 3.3 ± 0.4; difference of the peak velocities: -3.83 ± 7.72 cm/s between CIRCUS4 and GRAPPA2, -1.72 ± 8.41 cm/s between CIRCUS12 and GRAPPA2). In patients with intracranial aneurysms, the higher temporal resolution improved capturing of the flow features in intracranial aneurysms (pathline visualization scores: GRAPPA2 2.2 ± 0.2; CIRCUS4 2.5 ± 0.5; CIRCUS12 2.7 ± 0.6). The proposed rapid 4D flow MRI with a high temporal resolution is a promising tool for evaluating intracranial aneurysms in a clinically feasible acquisition time.

Comparing an accelerated 3D fast spin-echo sequence (CS-SPACE) for knee 3-T magnetic resonance imaging with traditional 3D fast spin-echo (SPACE) and routine 2D sequences.

PubMed

Altahawi, Faysal F; Blount, Kevin J; Morley, Nicholas P; Raithel, Esther; Omar, Imran M

2017-01-01

To compare a faster, new, high-resolution accelerated 3D-fast-spin-echo (3D-FSE) acquisition sequence (CS-SPACE) to traditional 2D and high-resolution 3D sequences for knee 3-T magnetic resonance imaging (MRI). Twenty patients received knee MRIs that included routine 2D (T1, PD ± FS, T2-FS; 0.5 × 0.5 × 3 mm 3 ; ∼10 min), traditional 3D FSE (SPACE-PD-FS; 0.5 × 0.5 × 0.5 mm 3 ; ∼7.5 min), and accelerated 3D-FSE prototype (CS-SPACE-PD-FS; 0.5 × 0.5 × 0.5 mm 3 ; ∼5 min) acquisitions on a 3-T MRI system (Siemens MAGNETOM Skyra). Three musculoskeletal radiologists (MSKRs) prospectively and independently reviewed the studies with graded surveys comparing image and diagnostic quality. Tissue-specific signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) were also compared. MSKR-perceived diagnostic quality of cartilage was significantly higher for CS-SPACE than for SPACE and 2D sequences (p < 0.001). Assessment of diagnostic quality of menisci and synovial fluid was higher for CS-SPACE than for SPACE (p < 0.001). CS-SPACE was not significantly different from SPACE but had lower assessments than 2D sequences for evaluation of bones, ligaments, muscles, and fat (p ≤ 0.004). 3D sequences had higher spatial resolution, but lower overall assessed contrast (p < 0.001). Overall image quality from CS-SPACE was assessed as higher than SPACE (p = 0.007), but lower than 2D sequences (p < 0.001). Compared to SPACE, CS-SPACE had higher fluid SNR and CNR against all other tissues (all p < 0.001). The CS-SPACE prototype allows for faster isotropic acquisitions of knee MRIs over currently used protocols. High fluid-to-cartilage CNR and higher spatial resolution over routine 2D sequences may present a valuable role for CS-SPACE in the evaluation of cartilage and menisci.

Correlative 3D imaging of Whole Mammalian Cells with Light and Electron Microscopy

PubMed Central

Murphy, Gavin E.; Narayan, Kedar; Lowekamp, Bradley C.; Hartnell, Lisa M.; Heymann, Jurgen A. W.; Fu, Jing; Subramaniam, Sriram

2011-01-01

We report methodological advances that extend the current capabilities of ion-abrasion scanning electron microscopy (IA–SEM), also known as focused ion beam scanning electron microscopy, a newly emerging technology for high resolution imaging of large biological specimens in 3D. We establish protocols that enable the routine generation of 3D image stacks of entire plastic-embedded mammalian cells by IA-SEM at resolutions of ~10 to 20 nm at high contrast and with minimal artifacts from the focused ion beam. We build on these advances by describing a detailed approach for carrying out correlative live confocal microscopy and IA–SEM on the same cells. Finally, we demonstrate that by combining correlative imaging with newly developed tools for automated image processing, small 100 nm-sized entities such as HIV-1 or gold beads can be localized in SEM image stacks of whole mammalian cells. We anticipate that these methods will add to the arsenal of tools available for investigating mechanisms underlying host-pathogen interactions, and more generally, the 3D subcellular architecture of mammalian cells and tissues. PMID:21907806

High resolution, wide field of view, real time 340GHz 3D imaging radar for security screening

NASA Astrophysics Data System (ADS)

Robertson, Duncan A.; Macfarlane, David G.; Hunter, Robert I.; Cassidy, Scott L.; Llombart, Nuria; Gandini, Erio; Bryllert, Tomas; Ferndahl, Mattias; Lindström, Hannu; Tenhunen, Jussi; Vasama, Hannu; Huopana, Jouni; Selkälä, Timo; Vuotikka, Antti-Jussi

2017-05-01

The EU FP7 project CONSORTIS (Concealed Object Stand-Off Real-Time Imaging for Security) is developing a demonstrator system for next generation airport security screening which will combine passive and active submillimeter wave imaging sensors. We report on the development of the 340 GHz 3D imaging radar which achieves high volumetric resolution over a wide field of view with high dynamic range and a high frame rate. A sparse array of 16 radar transceivers is coupled with high speed mechanical beam scanning to achieve a field of view of 1 x 1 x 1 m3 and a 10 Hz frame rate.

Extremely high resolution 3D electrical resistivity tomography to depict archaeological subsurface structures

NASA Astrophysics Data System (ADS)

Al-Saadi, Osamah; Schmidt, Volkmar; Becken, Michael; Fritsch, Thomas

2017-04-01

Electrical resistivity tomography (ERT) methods have been increasingly used in various shallow depth archaeological prospections in the last few decades. These non-invasive techniques are very useful in saving time, costs, and efforts. Both 2D and 3D ERT techniques are used to obtain detailed images of subsurface anomalies. In two surveyed areas near Nonnweiler (Germany), we present the results of the full 3D setup with a roll-along technique and of the quasi-3D setup (parallel and orthogonal profiles in dipole-dipole configuration). In area A, a dipole-dipole array with 96 electrodes in a uniform rectangular survey grid has been used in full 3D to investigate a presumed Roman building. A roll-along technique has been utilized to cover a large part of the archaeological site with an electrode spacing of 1 meter and with 0.5 meter for a more detailed image. Additional dense parallel 2D profiles have been carried out in dipole-dipole array with 0.25 meter electrode spacing and 0.25 meter between adjacent profiles in both direction for higher- resolution subsurface images. We have designed a new field procedure, which used an electrode array fixed in a frame. This facilitates efficient field operation, which comprised 2376 electrode positions. With the quasi 3D imaging, we confirmed the full 3D inversion model but at a much better resolution. In area B, dense parallel 2D profiles were directly used to survey the second target with also 0.25 meter electrode spacing and profiles separation respectively. The same field measurement design has been utilized and comprised 9648 electrode positions in total. The quasi-3D inversion results clearly revealed the main structures of the Roman construction. These ERT inversion results coincided well with the archaeological excavation, which has been done in some parts of this area. The ERT result successfully images parts from the walls and also smaller internal structures of the Roman building.

Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution

PubMed Central

Meddens, Marjolein B. M.; Liu, Sheng; Finnegan, Patrick S.; Edwards, Thayne L.; James, Conrad D.; Lidke, Keith A.

2016-01-01

We have developed a method for performing light-sheet microscopy with a single high numerical aperture lens by integrating reflective side walls into a microfluidic chip. These 45° side walls generate light-sheet illumination by reflecting a vertical light-sheet into the focal plane of the objective. Light-sheet illumination of cells loaded in the channels increases image quality in diffraction limited imaging via reduction of out-of-focus background light. Single molecule super-resolution is also improved by the decreased background resulting in better localization precision and decreased photo-bleaching, leading to more accepted localizations overall and higher quality images. Moreover, 2D and 3D single molecule super-resolution data can be acquired faster by taking advantage of the increased illumination intensities as compared to wide field, in the focused light-sheet. PMID:27375939

A 360-degree floating 3D display based on light field regeneration.

PubMed

Xia, Xinxing; Liu, Xu; Li, Haifeng; Zheng, Zhenrong; Wang, Han; Peng, Yifan; Shen, Weidong

2013-05-06

Using light field reconstruction technique, we can display a floating 3D scene in the air, which is 360-degree surrounding viewable with correct occlusion effect. A high-frame-rate color projector and flat light field scanning screen are used in the system to create the light field of real 3D scene in the air above the spinning screen. The principle and display performance of this approach are investigated in this paper. The image synthesis method for all the surrounding viewpoints is analyzed, and the 3D spatial resolution and angular resolution of the common display zone are employed to evaluate display performance. The prototype is achieved and the real 3D color animation image has been presented vividly. The experimental results verified the representability of this method.

Dual-view inverted selective plane illumination microscopy (diSPIM) with improved background rejection for accurate 3D digital pathology

NASA Astrophysics Data System (ADS)

Hu, Bihe; Bolus, Daniel; Brown, J. Quincy

2018-02-01

Current gold-standard histopathology for cancerous biopsies is destructive, time consuming, and limited to 2D slices, which do not faithfully represent true 3D tumor micro-morphology. Light sheet microscopy has emerged as a powerful tool for 3D imaging of cancer biospecimens. Here, we utilize the versatile dual-view inverted selective plane illumination microscopy (diSPIM) to render digital histological images of cancer biopsies. Dual-view architecture enabled more isotropic resolution in X, Y, and Z; and different imaging modes, such as adding electronic confocal slit detection (eCSD) or structured illumination (SI), can be used to improve degraded image quality caused by background signal of large, scattering samples. To obtain traditional H&E-like images, we used DRAQ5 and eosin (D&E) staining, with 488nm and 647nm laser illumination, and multi-band filter sets. Here, phantom beads and a D&E stained buccal cell sample have been used to verify our dual-view method. We also show that via dual view imaging and deconvolution, more isotropic resolution has been achieved for optical cleared human prostate sample, providing more accurate quantitation of 3D tumor architecture than was possible with single-view SPIM methods. We demonstrate that the optimized diSPIM delivers more precise analysis of 3D cancer microarchitecture in human prostate biopsy than simpler light sheet microscopy arrangements.

Accommodation response measurements for integral 3D image

NASA Astrophysics Data System (ADS)

Hiura, H.; Mishina, T.; Arai, J.; Iwadate, Y.

2014-03-01

We measured accommodation responses under integral photography (IP), binocular stereoscopic, and real object display conditions, and viewing conditions of binocular and monocular viewing conditions. The equipment we used was an optometric device and a 3D display. We developed the 3D display for IP and binocular stereoscopic images that comprises a high-resolution liquid crystal display (LCD) and a high-density lens array. The LCD has a resolution of 468 dpi and a diagonal size of 4.8 inches. The high-density lens array comprises 106 x 69 micro lenses that have a focal length of 3 mm and diameter of 1 mm. The lenses are arranged in a honeycomb pattern. The 3D display was positioned 60 cm from an observer under IP and binocular stereoscopic display conditions. The target was presented at eight depth positions relative to the 3D display: 15, 10, and 5 cm in front of the 3D display, on the 3D display panel, and 5, 10, 15 and 30 cm behind the 3D display under the IP and binocular stereoscopic display conditions. Under the real object display condition, the target was displayed on the 3D display panel, and the 3D display was placed at the eight positions. The results suggest that the IP image induced more natural accommodation responses compared to the binocular stereoscopic image. The accommodation responses of the IP image were weaker than those of a real object; however, they showed a similar tendency with those of the real object under the two viewing conditions. Therefore, IP can induce accommodation to the depth positions of 3D images.

A high-resolution 3D ultrasonic system for rapid evaluation of the anterior and posterior segment.

PubMed

Peyman, Gholam A; Ingram, Charles P; Montilla, Leonardo G; Witte, Russell S

2012-01-01

Traditional ultrasound imaging systems for ophthalmology employ slow, mechanical scanning of a single-element ultrasound transducer. The goal was to demonstrate rapid examination of the anterior and posterior segment with a three-dimensional (3D) commercial ultrasound system incorporating high-resolution linear probe arrays. The 3D images of the porcine eye were generated in approximately 10 seconds by scanning one of two commercial linear arrays (25- and 50-MHz). Healthy enucleated pig eyes were compared with those with induced injury or placement of a foreign material (eg, metal). Rapid, volumetric imaging was also demonstrated in one human eye in vivo. The 50-MHz probe provided exquisite volumetric images of the anterior segment at a depth up to 15 mm and axial resolution of 30 μm. The 25-MHz probe provided a larger field of view (lateral X depth: 20 × 30 mm), sufficient for capturing the entire anterior and posterior segments of the pig eye, at a resolution of 60 μm. A 50-MHz scan through the human eyelid illustrated detailed structures of the Meibomian glands, cilia, cornea, and anterior segment back to the posterior capsule. The 3D system with its high-frequency ultrasound arrays, fast data acquisition, and volume rendering capability shows promise for investigating anterior and posterior structures of the eye. Copyright 2012, SLACK Incorporated.

Neurologic 3D MR Spectroscopic Imaging with Low-Power Adiabatic Pulses and Fast Spiral Acquisition

PubMed Central

Gagoski, Borjan A.; Sorensen, A. Gregory

2012-01-01

Purpose: To improve clinical three-dimensional (3D) MR spectroscopic imaging with more accurate localization and faster acquisition schemes. Materials and Methods: Institutional review board approval and patient informed consent were obtained. Data were acquired with a 3-T MR imager and a 32-channel head coil in phantoms, five healthy volunteers, and five patients with glioblastoma. Excitation was performed with localized adiabatic spin-echo refocusing (LASER) by using adiabatic gradient-offset independent adiabaticity wideband uniform rate and smooth truncation (GOIA-W[16,4]) pulses with 3.5-msec duration, 20-kHz bandwidth, 0.81-kHz amplitude, and 45-msec echo time. Interleaved constant-density spirals simultaneously encoded one frequency and two spatial dimensions. Conventional phase encoding (PE) (1-cm3 voxels) was performed after LASER excitation and was the reference standard. Spectra acquired with spiral encoding at similar and higher spatial resolution and with shorter imaging time were compared with those acquired with PE. Metabolite levels were fitted with software, and Bland-Altman analysis was performed. Results: Clinical 3D MR spectroscopic images were acquired four times faster with spiral protocols than with the elliptical PE protocol at low spatial resolution (1 cm3). Higher-spatial-resolution images (0.39 cm3) were acquired twice as fast with spiral protocols compared with the low-spatial-resolution elliptical PE protocol. A minimum signal-to-noise ratio (SNR) of 5 was obtained with spiral protocols under these conditions and was considered clinically adequate to reliably distinguish metabolites from noise. The apparent SNR loss was not linear with decreasing voxel sizes because of longer local T2* times. Improvement of spectral line width from 4.8 Hz to 3.5 Hz was observed at high spatial resolution. The Bland-Altman agreement between spiral and PE data is characterized by narrow 95% confidence intervals for their differences (0.12, 0.18 of their means). GOIA-W(16,4) pulses minimize chemical-shift displacement error to 2.1%, reduce nonuniformity of excitation to 5%, and eliminate the need for outer volume suppression. Conclusion: The proposed adiabatic spiral 3D MR spectroscopic imaging sequence can be performed in a standard clinical MR environment. Improvements in image quality and imaging time could enable more routine acquisition of spectroscopic data than is possible with current pulse sequences. © RSNA, 2011 PMID:22187628

[Reproducibility and accuracy in the morphometric and mechanical quantification of trabecular bone from 3 Tesla magnetic resonance images].

PubMed

Alberich-Bayarri, A; Martí-Bonmatí, L; Sanz-Requena, R; Sánchez-González, J; Hervás Briz, V; García-Martí, G; Pérez, M Á

2014-01-01

We used an animal model to analyze the reproducibility and accuracy of certain biomarkers of bone image quality in comparison to a gold standard of computed microtomography (μCT). We used magnetic resonance (MR) imaging and μCT to study the metaphyses of 5 sheep tibiae. The MR images (3 Teslas) were acquired with a T1-weighted gradient echo sequence and an isotropic spatial resolution of 180μm. The μCT images were acquired using a scanner with a spatial resolution of 7.5μm isotropic voxels. In the preparation of the images, we applied equalization, interpolation, and thresholding algorithms. In the quantitative analysis, we calculated the percentage of bone volume (BV/TV), the trabecular thickness (Tb.Th), the trabecular separation (Tb.Sp), the trabecular index (Tb.N), the 2D fractal dimension (D(2D)), the 3D fractal dimension (D(3D)), and the elastic module in the three spatial directions (Ex, Ey and Ez). The morphometric and mechanical quantification of trabecular bone by MR was very reproducible, with percentages of variation below 9% for all the parameters. Its accuracy compared to the gold standard (μCT) was high, with errors less than 15% for BV/TV, D(2D), D(3D), and E(app)x, E(app)y and E(app)z. Our experimental results in animals confirm that the parameters of BV/TV, D(2D), D(3D), and E(app)x, E(app)y and E(app)z obtained by MR have excellent reproducibility and accuracy and can be used as imaging biomarkers for the quality of trabecular bone. Copyright © 2013 SERAM. Published by Elsevier Espana. All rights reserved.

4D imaging of transient structures and morphologies in ultrafast electron microscopy.

PubMed

Barwick, Brett; Park, Hyun Soon; Kwon, Oh-Hoon; Baskin, J Spencer; Zewail, Ahmed H

2008-11-21

With advances in spatial resolution reaching the atomic scale, two-dimensional (2D) and 3D imaging in electron microscopy has become an essential methodology in various fields of study. Here, we report 4D imaging, with in situ spatiotemporal resolutions, in ultrafast electron microscopy (UEM). The ability to capture selected-area-image dynamics with pixel resolution and to control the time separation between pulses for temporal cooling of the specimen made possible studies of fleeting structures and morphologies. We demonstrate the potential for applications with two examples, gold and graphite. For gold, after thermally induced stress, we determined the atomic structural expansion, the nonthermal lattice temperature, and the ultrafast transients of warping/bulging. In contrast, in graphite, striking coherent transients of the structure were observed in both image and diffraction, directly measuring, on the nanoscale, the longitudinal resonance period governed by Young's elastic modulus. The success of these studies demonstrates the promise of UEM in real-space imaging of dynamics.

A volumetric three-dimensional digital light photoactivatable dye display

NASA Astrophysics Data System (ADS)

Patel, Shreya K.; Cao, Jian; Lippert, Alexander R.

2017-07-01

Volumetric three-dimensional displays offer spatially accurate representations of images with a 360° view, but have been difficult to implement due to complex fabrication requirements. Herein, a chemically enabled volumetric 3D digital light photoactivatable dye display (3D Light PAD) is reported. The operating principle relies on photoactivatable dyes that become reversibly fluorescent upon illumination with ultraviolet light. Proper tuning of kinetics and emission wavelengths enables the generation of a spatial pattern of fluorescent emission at the intersection of two structured light beams. A first-generation 3D Light PAD was fabricated using the photoactivatable dye N-phenyl spirolactam rhodamine B, a commercial picoprojector, an ultraviolet projector and a custom quartz imaging chamber. The system displays a minimum voxel size of 0.68 mm3, 200 μm resolution and good stability over repeated `on-off' cycles. A range of high-resolution 3D images and animations can be projected, setting the foundation for widely accessible volumetric 3D displays.

A volumetric three-dimensional digital light photoactivatable dye display

PubMed Central

Patel, Shreya K.; Cao, Jian; Lippert, Alexander R.

2017-01-01

Volumetric three-dimensional displays offer spatially accurate representations of images with a 360° view, but have been difficult to implement due to complex fabrication requirements. Herein, a chemically enabled volumetric 3D digital light photoactivatable dye display (3D Light PAD) is reported. The operating principle relies on photoactivatable dyes that become reversibly fluorescent upon illumination with ultraviolet light. Proper tuning of kinetics and emission wavelengths enables the generation of a spatial pattern of fluorescent emission at the intersection of two structured light beams. A first-generation 3D Light PAD was fabricated using the photoactivatable dye N-phenyl spirolactam rhodamine B, a commercial picoprojector, an ultraviolet projector and a custom quartz imaging chamber. The system displays a minimum voxel size of 0.68 mm3, 200 μm resolution and good stability over repeated ‘on-off’ cycles. A range of high-resolution 3D images and animations can be projected, setting the foundation for widely accessible volumetric 3D displays. PMID:28695887

5D-intravital tomography as a novel tool for non-invasive in-vivo analysis of human skin

NASA Astrophysics Data System (ADS)

König, Karsten; Weinigel, Martin; Breunig, Hans G.; Gregory, Axel; Fischer, Peter; Kellner-Höfer, Marcel; Bückle, Rainer; Schwarz, Martin; Riemann, Iris; Stracke, Frank; Huck, Volker; Gorzelanny, Christian; Schneider, Stefan W.

2010-02-01

Some years ago, CE-marked clinical multiphoton systems for 3D imaging of human skin with subcellular resolution have been launched. These tomographs provide optical biopsies with submicron resolution based on two-photon excited autofluorescence (NAD(P)H, flavoproteins, keratin, elastin, melanin, porphyrins) and second harmonic generation by collagen. The 3D tomograph was now transferred into a 5D imaging system by the additional detection of the emission spectrum and the fluorescence lifetime based on spatially and spectrally resolved time-resolved single photon counting. The novel 5D intravital tomograph (5D-IVT) was employed for the early detection of atopic dermatitis and the analysis of treatment effects.

Multispectral high-resolution hologram generation using orthographic projection images

NASA Astrophysics Data System (ADS)

Muniraj, I.; Guo, C.; Sheridan, J. T.

2016-08-01

We present a new method of synthesizing a digital hologram of three-dimensional (3D) real-world objects from multiple orthographic projection images (OPI). A high-resolution multiple perspectives of 3D objects (i.e., two dimensional elemental image array) are captured under incoherent white light using synthetic aperture integral imaging (SAII) technique and their OPIs are obtained respectively. The reference beam is then multiplied with the corresponding OPI and integrated to form a Fourier hologram. Eventually, a modified phase retrieval algorithm (GS/HIO) is applied to reconstruct the hologram. The principle is validated experimentally and the results support the feasibility of the proposed method.

Depth image super-resolution via semi self-taught learning framework

NASA Astrophysics Data System (ADS)

Zhao, Furong; Cao, Zhiguo; Xiao, Yang; Zhang, Xiaodi; Xian, Ke; Li, Ruibo

2017-06-01

Depth images have recently attracted much attention in computer vision and high-quality 3D content for 3DTV and 3D movies. In this paper, we present a new semi self-taught learning application framework for enhancing resolution of depth maps without making use of ancillary color images data at the target resolution, or multiple aligned depth maps. Our framework consists of cascade random forests reaching from coarse to fine results. We learn the surface information and structure transformations both from a small high-quality depth exemplars and the input depth map itself across different scales. Considering that edge plays an important role in depth map quality, we optimize an effective regularized objective that calculates on output image space and input edge space in random forests. Experiments show the effectiveness and superiority of our method against other techniques with or without applying aligned RGB information

High Resolution PET Imaging Probe for the Detection, Molecular Characterization, and Treatment Monitoring of Prostate cancer

DTIC Science & Technology

2011-07-01

impact on overall probe performance, including spatial resolution, energy resolution and timing resolution. We will show that 1 mm3 voxels will...ring, description of a strategy to remove scattered events, followed by characterization of impact of timing properties of the probe. In summary, the...described by the total distance d¼d1+d2 and a¼ d1=ðd1þd2Þ. We also want to account for impact angles, y1 and y2, defined versus line perpendicular to

Computational optical tomography using 3-D deep convolutional neural networks

NASA Astrophysics Data System (ADS)

Nguyen, Thanh; Bui, Vy; Nehmetallah, George

2018-04-01

Deep convolutional neural networks (DCNNs) offer a promising performance for many image processing areas, such as super-resolution, deconvolution, image classification, denoising, and segmentation, with outstanding results. Here, we develop for the first time, to our knowledge, a method to perform 3-D computational optical tomography using 3-D DCNN. A simulated 3-D phantom dataset was first constructed and converted to a dataset of phase objects imaged on a spatial light modulator. For each phase image in the dataset, the corresponding diffracted intensity image was experimentally recorded on a CCD. We then experimentally demonstrate the ability of the developed 3-D DCNN algorithm to solve the inverse problem by reconstructing the 3-D index of refraction distributions of test phantoms from the dataset from their corresponding diffraction patterns.

Overview of Three-Dimensional Atomic-Resolution Holography and Imaging Techniques: Recent Advances in Local-Structure Science

NASA Astrophysics Data System (ADS)

Daimon, Hiroshi

2018-06-01

Local three-dimensional (3D) atomic arrangements without periodicity have not been able to be studied until recently. Recently, several holographies and related techniques have been developed to reveal the 3D atomic arrangement around specific atoms with no translational symmetry. This review gives an overview of these new local 3D atomic imaging techniques.

Three-dimensional cascaded system analysis of a 50 µm pixel pitch wafer-scale CMOS active pixel sensor x-ray detector for digital breast tomosynthesis.

PubMed

Zhao, C; Vassiljev, N; Konstantinidis, A C; Speller, R D; Kanicki, J

2017-03-07

High-resolution, low-noise x-ray detectors based on the complementary metal-oxide-semiconductor (CMOS) active pixel sensor (APS) technology have been developed and proposed for digital breast tomosynthesis (DBT). In this study, we evaluated the three-dimensional (3D) imaging performance of a 50 µm pixel pitch CMOS APS x-ray detector named DynAMITe (Dynamic Range Adjustable for Medical Imaging Technology). The two-dimensional (2D) angle-dependent modulation transfer function (MTF), normalized noise power spectrum (NNPS), and detective quantum efficiency (DQE) were experimentally characterized and modeled using the cascaded system analysis at oblique incident angles up to 30°. The cascaded system model was extended to the 3D spatial frequency space in combination with the filtered back-projection (FBP) reconstruction method to calculate the 3D and in-plane MTF, NNPS and DQE parameters. The results demonstrate that the beam obliquity blurs the 2D MTF and DQE in the high spatial frequency range. However, this effect can be eliminated after FBP image reconstruction. In addition, impacts of the image acquisition geometry and detector parameters were evaluated using the 3D cascaded system analysis for DBT. The result shows that a wider projection angle range (e.g.  ±30°) improves the low spatial frequency (below 5 mm -1 ) performance of the CMOS APS detector. In addition, to maintain a high spatial resolution for DBT, a focal spot size of smaller than 0.3 mm should be used. Theoretical analysis suggests that a pixelated scintillator in combination with the 50 µm pixel pitch CMOS APS detector could further improve the 3D image resolution. Finally, the 3D imaging performance of the CMOS APS and an indirect amorphous silicon (a-Si:H) thin-film transistor (TFT) passive pixel sensor (PPS) detector was simulated and compared.

Three-dimensional cascaded system analysis of a 50 µm pixel pitch wafer-scale CMOS active pixel sensor x-ray detector for digital breast tomosynthesis

NASA Astrophysics Data System (ADS)

Zhao, C.; Vassiljev, N.; Konstantinidis, A. C.; Speller, R. D.; Kanicki, J.

2017-03-01

High-resolution, low-noise x-ray detectors based on the complementary metal-oxide-semiconductor (CMOS) active pixel sensor (APS) technology have been developed and proposed for digital breast tomosynthesis (DBT). In this study, we evaluated the three-dimensional (3D) imaging performance of a 50 µm pixel pitch CMOS APS x-ray detector named DynAMITe (Dynamic Range Adjustable for Medical Imaging Technology). The two-dimensional (2D) angle-dependent modulation transfer function (MTF), normalized noise power spectrum (NNPS), and detective quantum efficiency (DQE) were experimentally characterized and modeled using the cascaded system analysis at oblique incident angles up to 30°. The cascaded system model was extended to the 3D spatial frequency space in combination with the filtered back-projection (FBP) reconstruction method to calculate the 3D and in-plane MTF, NNPS and DQE parameters. The results demonstrate that the beam obliquity blurs the 2D MTF and DQE in the high spatial frequency range. However, this effect can be eliminated after FBP image reconstruction. In addition, impacts of the image acquisition geometry and detector parameters were evaluated using the 3D cascaded system analysis for DBT. The result shows that a wider projection angle range (e.g.  ±30°) improves the low spatial frequency (below 5 mm-1) performance of the CMOS APS detector. In addition, to maintain a high spatial resolution for DBT, a focal spot size of smaller than 0.3 mm should be used. Theoretical analysis suggests that a pixelated scintillator in combination with the 50 µm pixel pitch CMOS APS detector could further improve the 3D image resolution. Finally, the 3D imaging performance of the CMOS APS and an indirect amorphous silicon (a-Si:H) thin-film transistor (TFT) passive pixel sensor (PPS) detector was simulated and compared.

Conductive resins improve charging and resolution of acquired images in electron microscopic volume imaging

PubMed Central

Nguyen, Huy Bang; Thai, Truc Quynh; Saitoh, Sei; Wu, Bao; Saitoh, Yurika; Shimo, Satoshi; Fujitani, Hiroshi; Otobe, Hirohide; Ohno, Nobuhiko

2016-01-01

Recent advances in serial block-face imaging using scanning electron microscopy (SEM) have enabled the rapid and efficient acquisition of 3-dimensional (3D) ultrastructural information from a large volume of biological specimens including brain tissues. However, volume imaging under SEM is often hampered by sample charging, and typically requires specific sample preparation to reduce charging and increase image contrast. In the present study, we introduced carbon-based conductive resins for 3D analyses of subcellular ultrastructures, using serial block-face SEM (SBF-SEM) to image samples. Conductive resins were produced by adding the carbon black filler, Ketjen black, to resins commonly used for electron microscopic observations of biological specimens. Carbon black mostly localized around tissues and did not penetrate cells, whereas the conductive resins significantly reduced the charging of samples during SBF-SEM imaging. When serial images were acquired, embedding into the conductive resins improved the resolution of images by facilitating the successful cutting of samples in SBF-SEM. These results suggest that improving the conductivities of resins with a carbon black filler is a simple and useful option for reducing charging and enhancing the resolution of images obtained for volume imaging with SEM. PMID:27020327

The role of digital sample information within the digital geoscience infrastructure: a pragmatic approach

NASA Astrophysics Data System (ADS)

Howe, Michael

2014-05-01

Much of the digital geological information on the composition, properties and dynamics of the subsurface is based ultimately on physical samples, many of which are archived to provide a basis for the information. Online metadata catalogues of these collections have now been available for many years. Many of these are institutional and tightly focussed, with UK examples including the British Geological Survey's (BGS) palaeontological samples database, PalaeoSaurus (http://www.bgs.ac.uk/palaeosaurus/), and mineralogical and petrological sample database, Britrocks (http://www.bgs.ac.uk/data/britrocks.html) . There are now a growing number of international sample metadata databases, including The Palaeobiology Database (http://paleobiodb.org/) and SESAR, the IGSN (International Geo Sample Number) database (http://www.geosamples.org/catalogsearch/ ). More recently the emphasis has moved beyond metadata (locality, identification, age, citations, etc) to digital imagery, with the intention of providing the user with at least enough information to determine whether viewing the sample would be worthwhile. Recent BGS examples include high resolution (e.g. 7216 x 5412 pixel) hydrocarbon well core images (http://www.bgs.ac.uk/data/offshoreWells/wells.cfc?method=searchWells) , high resolution rock thin section images (e.g. http://www.largeimages.bgs.ac.uk/iip/britrocks.html?id=290000/291739 ) and building stone images (http://geoscenic.bgs.ac.uk/asset-bank/action/browseItems?categoryId=1547&categoryTypeId=1) . This has been developed further with high resolution stereo images. The Jisc funded GB3D type fossils online project delivers these as red-cyan anaglyphs (http://www.3d-fossils.ac.uk/). More innovatively, the GB3D type fossils project has laser scanned several thousand type fossils and the resulting 3d-digital models are now being delivered through the online portal. Importantly, this project also represents collaboration between the BGS, Oxford and Cambridge Universities, the National Museums of Wales, and numerous other national, local and regional museums. The lack of currently accepted international standards and infrastructures for the delivery of high resolution images and 3d-digital models has necessitated the BGS in developing or selecting its own. Most high resolution images have been delivered using the JPEG 2000 format because of its quality and speed. Digital models have been made available in both .PLY and .OBJ format because of their respective efficient file size, and flexibility. Consideration must now be given to European and international standards and infrastructures for the delivery of high resolution images and 3d-digital models.

Automated dynamic feature tracking of RSLs on the Martian surface through HiRISE super-resolution restoration and 3D reconstruction techniques

NASA Astrophysics Data System (ADS)

Tao, Y.; Muller, J.-P.

2017-09-01

In this paper, we demonstrate novel Super-resolution restoration and 3D reconstruction tools developed within the EU FP7 projects and their applications to advanced dynamic feature tracking through HiRISE repeat stereo. We show an example with one of the RSL sites in the Palikir Crater took 8 repeat-pass 25cm HiRISE images from which a 5cm RSL-free SRR image is generated using GPT-SRR. Together with repeat 3D modelling of the same area, it allows us to overlay tracked dynamic features onto the reconstructed "original" surface, providing a much more comprehensive interpretation of the surface formation processes in 3D.

Fast and background-free three-dimensional (3D) live-cell imaging with lanthanide-doped upconverting nanoparticles.

PubMed

Jo, Hong Li; Song, Yo Han; Park, Jinho; Jo, Eun-Jung; Goh, Yeongchang; Shin, Kyujin; Kim, Min-Gon; Lee, Kang Taek

2015-12-14

We report on the development of a three-dimensional (3D) live-cell imaging technique with high spatiotemporal resolution using lanthanide-doped upconverting nanoparticles (UCNPs). It employs the sectioning capability of confocal microscopy except that the two-dimensional (2D) section images are acquired by wide-field epi-fluorescence microscopy. Although epi-fluorescence images are contaminated with the out-of-focus background in general, the near-infrared (NIR) excitation used for the excitation of UCNPs does not generate any autofluorescence, which helps to lower the background. Moreover, the image blurring due to defocusing was naturally eliminated in the image reconstruction process. The 3D images were used to investigate the cellular dynamics such as nuclear uptake and single-particle tracking that require 3D description.

A low-cost microwell device for high-resolution imaging of neurite outgrowth in 3D

NASA Astrophysics Data System (ADS)

Ren, Yuan; Mlodzianoski, Michael J.; Cheun Lee, Aih; Huang, Fang; Suter, Daniel M.

2018-06-01

Objective. Current neuronal cell culture is mostly performed on two-dimensional (2D) surfaces, which lack many of the important features of the native environment of neurons, including topographical cues, deformable extracellular matrix, and spatial isotropy or anisotropy in three dimensions. Although three-dimensional (3D) cell culture systems provide a more physiologically relevant environment than 2D systems, their popularity is greatly hampered by the lack of easy-to-make-and-use devices. We aim to develop a widely applicable 3D culture procedure to facilitate the transition of neuronal cultures from 2D to 3D. Approach. We made a simple microwell device for 3D neuronal cell culture that is inexpensive, easy to assemble, and fully compatible with commonly used imaging techniques, including super-resolution microscopy. Main results. We developed a novel gel mixture to support 3D neurite regeneration of Aplysia bag cell neurons, a system that has been extensively used for quantitative analysis of growth cone dynamics in 2D. We found that the morphology and growth pattern of bag cell growth cones in 3D culture closely resemble the ones of growth cones observed in vivo. We demonstrated the capability of our device for high-resolution imaging of cytoskeletal and signaling proteins as well as organelles. Significance. Neuronal cell culture has been a valuable tool for neuroscientists to study the behavior of neurons in a controlled environment. Compared to 2D, neurons cultured in 3D retain the majority of their native characteristics, while offering higher accessibility, control, and repeatability. We expect that our microwell device will facilitate a wider adoption of 3D neuronal cultures to study the mechanisms of neurite regeneration.

Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology

PubMed Central

Ukwatta, Eranga; Arevalo, Hermenegild; Rajchl, Martin; White, James; Pashakhanloo, Farhad; Prakosa, Adityo; Herzka, Daniel A.; McVeigh, Elliot; Lardo, Albert C.; Trayanova, Natalia A.; Vadakkumpadan, Fijoy

2015-01-01

Purpose: Accurate three-dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient-specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two-dimensional (2D) late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE-CMR images has been lacking. The purpose of this study was to address this need. Methods: The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low-resolution (Lo-res) clinical LGE-CMR images. Their methodology employed the so-called logarithm of odds (LogOdds) function to implicitly represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high-resolution (Hi-res) LGE-CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi-res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method. Results: The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo-ECGs. Conclusions: The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo-res clinical 2D LGE-CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations. PMID:26233186

Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ukwatta, Eranga, E-mail: eukwatt1@jhu.edu; Arevalo, Hermenegild; Pashakhanloo, Farhad

Purpose: Accurate three-dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient-specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two-dimensional (2D) late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE-CMR images has been lacking. The purpose of this study was to address this need. Methods: The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low-resolution (Lo-res) clinical LGE-CMR images. Their methodology employed the so-called logarithm of odds (LogOdds) function to implicitlymore » represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high-resolution (Hi-res) LGE-CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi-res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method. Results: The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo-ECGs. Conclusions: The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo-res clinical 2D LGE-CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations.« less

Enhancement of digital radiography image quality using a convolutional neural network.

PubMed

Sun, Yuewen; Li, Litao; Cong, Peng; Wang, Zhentao; Guo, Xiaojing

2017-01-01

Digital radiography system is widely used for noninvasive security check and medical imaging examination. However, the system has a limitation of lower image quality in spatial resolution and signal to noise ratio. In this study, we explored whether the image quality acquired by the digital radiography system can be improved with a modified convolutional neural network to generate high-resolution images with reduced noise from the original low-quality images. The experiment evaluated on a test dataset, which contains 5 X-ray images, showed that the proposed method outperformed the traditional methods (i.e., bicubic interpolation and 3D block-matching approach) as measured by peak signal to noise ratio (PSNR) about 1.3 dB while kept highly efficient processing time within one second. Experimental results demonstrated that a residual to residual (RTR) convolutional neural network remarkably improved the image quality of object structural details by increasing the image resolution and reducing image noise. Thus, this study indicated that applying this RTR convolutional neural network system was useful to improve image quality acquired by the digital radiography system.

3D ultrasound computer tomography: Hardware setup, reconstruction methods and first clinical results

NASA Astrophysics Data System (ADS)

Gemmeke, Hartmut; Hopp, Torsten; Zapf, Michael; Kaiser, Clemens; Ruiter, Nicole V.

2017-11-01

A promising candidate for improved imaging of breast cancer is ultrasound computer tomography (USCT). Current experimental USCT systems are still focused in elevation dimension resulting in a large slice thickness, limited depth of field, loss of out-of-plane reflections, and a large number of movement steps to acquire a stack of images. 3D USCT emitting and receiving spherical wave fronts overcomes these limitations. We built an optimized 3D USCT, realizing for the first time the full benefits of a 3D system. The point spread function could be shown to be nearly isotropic in 3D, to have very low spatial variability and fit the predicted values. The contrast of the phantom images is very satisfactory in spite of imaging with a sparse aperture. The resolution and imaged details of the reflectivity reconstruction are comparable to a 3 T MRI volume. Important for the obtained resolution are the simultaneously obtained results of the transmission tomography. The KIT 3D USCT was then tested in a pilot study on ten patients. The primary goals of the pilot study were to test the USCT device, the data acquisition protocols, the image reconstruction methods and the image fusion techniques in a clinical environment. The study was conducted successfully; the data acquisition could be carried out for all patients with an average imaging time of six minutes per breast. The reconstructions provide promising images. Overlaid volumes of the modalities show qualitative and quantitative information at a glance. This paper gives a summary of the involved techniques, methods, and first results.

Soft x-ray holographic tomography for biological specimens

NASA Astrophysics Data System (ADS)

Gao, Hongyi; Chen, Jianwen; Xie, Honglan; Li, Ruxin; Xu, Zhizhan; Jiang, Shiping; Zhang, Yuxuan

2003-10-01

In this paper, we present some experimental results on X -ray holography, holographic tomography, and a new holographic tomography method called pre-amplified holographic tomography is proposed. Due to the shorter wavelength and the larger penetration depths, X-rays provide the potential of higher resolution in imaging techniques, and have the ability to image intact, living, hydrated cells w ithout slicing, dehydration, chemical fixation or stain. Recently, using X-ray source in National Synchrotron Radiation Laboratory in Hefei, we have successfully performed some soft X-ray holography experiments on biological specimen. The specimens used in the experiments was the garlic clove epidermis, we got their X-ray hologram, and then reconstructed them by computer programs, the feature of the cell walls, the nuclei and some cytoplasm were clearly resolved. However, there still exist some problems in realization of practical 3D microscopic imaging due to the near-unity refractive index of the matter. There is no X-ray optics having a sufficient high numerical aperture to achieve a depth resolution that is comparable to the transverse resolution. On the other hand, computer tomography needs a record of hundreds of views of the test object at different angles for high resolution. This is because the number of views required for a densely packed object is equal to the object radius divided by the desired depth resolution. Clearly, it is impractical for a radiation-sensitive biological specimen. Moreover, the X-ray diffraction effect makes projection data blur, this badly degrades the resolution of the reconstructed image. In order to observe 3D structure of the biological specimens, McNulty proposed a new method for 3D imaging called "holographic tomography (HT)" in which several holograms of the specimen are recorded from various illumination directions and combined in the reconstruction step. This permits the specimens to be sampled over a wide range of spatial frequencies to improve the depth resolution. In NSRL, we performed soft X-ray holographic tomography experiments. The specimen was the spider filaments and PM M A as recording medium. By 3D CT reconstruction of the projection data, three dimensional density distribution of the specimen was obtained. Also, we developed a new X-ray holographic tomography m ethod called pre-amplified holographic tomography. The method permits a digital real-time 3D reconstruction with high-resolution and a simple and compact experimental setup as well.

Integrated light-sheet imaging and flow-based enquiry (iLIFE) system for 3D in-vivo imaging of multicellular organism

NASA Astrophysics Data System (ADS)

Rasmi, Chelur K.; Padmanabhan, Sreedevi; Shirlekar, Kalyanee; Rajan, Kanhirodan; Manjithaya, Ravi; Singh, Varsha; Mondal, Partha Pratim

2017-12-01

We propose and demonstrate a light-sheet-based 3D interrogation system on a microfluidic platform for screening biological specimens during flow. To achieve this, a diffraction-limited light-sheet (with a large field-of-view) is employed to optically section the specimens flowing through the microfluidic channel. This necessitates optimization of the parameters for the illumination sub-system (illumination intensity, light-sheet width, and thickness), microfluidic specimen platform (channel-width and flow-rate), and detection sub-system (camera exposure time and frame rate). Once optimized, these parameters facilitate cross-sectional imaging and 3D reconstruction of biological specimens. The proposed integrated light-sheet imaging and flow-based enquiry (iLIFE) imaging technique enables single-shot sectional imaging of a range of specimens of varying dimensions, ranging from a single cell (HeLa cell) to a multicellular organism (C. elegans). 3D reconstruction of the entire C. elegans is achieved in real-time and with an exposure time of few hundred micro-seconds. A maximum likelihood technique is developed and optimized for the iLIFE imaging system. We observed an intracellular resolution for mitochondria-labeled HeLa cells, which demonstrates the dynamic resolution of the iLIFE system. The proposed technique is a step towards achieving flow-based 3D imaging. We expect potential applications in diverse fields such as structural biology and biophysics.

In vivo 3D PIXE-micron-CT imaging of Drosophila melanogaster using a contrast agent

NASA Astrophysics Data System (ADS)

Matsuyama, Shigeo; Hamada, Naoki; Ishii, Keizo; Nozawa, Yuichiro; Ohkura, Satoru; Terakawa, Atsuki; Hatori, Yoshinobu; Fujiki, Kota; Fujiwara, Mitsuhiro; Toyama, Sho

2015-04-01

In this study, we developed a three-dimensional (3D) computed tomography (CT) in vivo imaging system for imaging small insects with micrometer resolution. The 3D CT imaging system, referred to as 3D PIXE-micron-CT (PIXEμCT), uses characteristic X-rays produced by ion microbeam bombardment of a metal target. PIXEμCT was used to observe the body organs and internal structure of a living Drosophila melanogaster. Although the organs of the thorax were clearly imaged, the digestive organs in the abdominal cavity could not be clearly discerned initially, with the exception of the rectum and the Malpighian tubule. To enhance the abdominal images, a barium sulfate powder radiocontrast agent was added. For the first time, 3D images of the ventriculus of a living D. melanogaster were obtained. Our results showed that PIXEμCT can provide in vivo 3D-CT images that reflect correctly the structure of individual living organs, which is expected to be very useful in biological research.

Three-dimensional micro-scale strain mapping in living biological soft tissues.

PubMed

Moo, Eng Kuan; Sibole, Scott C; Han, Sang Kuy; Herzog, Walter

2018-04-01

Non-invasive characterization of the mechanical micro-environment surrounding cells in biological tissues at multiple length scales is important for the understanding of the role of mechanics in regulating the biosynthesis and phenotype of cells. However, there is a lack of imaging methods that allow for characterization of the cell micro-environment in three-dimensional (3D) space. The aims of this study were (i) to develop a multi-photon laser microscopy protocol capable of imprinting 3D grid lines onto living tissue at a high spatial resolution, and (ii) to develop image processing software capable of analyzing the resulting microscopic images and performing high resolution 3D strain analyses. Using articular cartilage as the biological tissue of interest, we present a novel two-photon excitation imaging technique for measuring the internal 3D kinematics in intact cartilage at sub-micrometer resolution, spanning length scales from the tissue to the cell level. Using custom image processing software, we provide accurate and robust 3D micro-strain analysis that allows for detailed qualitative and quantitative assessment of the 3D tissue kinematics. This novel technique preserves tissue structural integrity post-scanning, therefore allowing for multiple strain measurements at different time points in the same specimen. The proposed technique is versatile and opens doors for experimental and theoretical investigations on the relationship between tissue deformation and cell biosynthesis. Studies of this nature may enhance our understanding of the mechanisms underlying cell mechano-transduction, and thus, adaptation and degeneration of soft connective tissues. We presented a novel two-photon excitation imaging technique for measuring the internal 3D kinematics in intact cartilage at sub-micrometer resolution, spanning from tissue length scale to cellular length scale. Using a custom image processing software (lsmgridtrack), we provide accurate and robust micro-strain analysis that allowed for detailed qualitative and quantitative assessment of the 3D tissue kinematics. The approach presented here can also be applied to other biological tissues such as meniscus and annulus fibrosus, as well as tissue-engineered tissues for the characterization of their mechanical properties. This imaging technique opens doors for experimental and theoretical investigation on the relationship between tissue deformation and cell biosynthesis. Studies of this nature may enhance our understanding of the mechanisms underlying cell mechano-transduction, and thus, adaptation and degeneration of soft connective tissues. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution

DOE PAGES

Meddens, Marjolein B. M.; Liu, Sheng; Finnegan, Patrick S.; ...

2016-01-01

Here, we have developed a method for performing light-sheet microscopy with a single high numerical aperture lens by integrating reflective side walls into a microfluidic chip. These 45° side walls generate light-sheet illumination by reflecting a vertical light-sheet into the focal plane of the objective. Light-sheet illumination of cells loaded in the channels increases image quality in diffraction limited imaging via reduction of out-of-focus background light. Single molecule super-resolution is also improved by the decreased background resulting in better localization precision and decreased photo-bleaching, leading to more accepted localizations overall and higher quality images. Moreover, 2D and 3D single moleculemore » super-resolution data can be acquired faster by taking advantage of the increased illumination intensities as compared to wide field, in the focused light-sheet.« less

Automatic Building Damage Detection Method Using High-Resolution Remote Sensing Images and 3d GIS Model

NASA Astrophysics Data System (ADS)

Tu, Jihui; Sui, Haigang; Feng, Wenqing; Song, Zhina

2016-06-01

In this paper, a novel approach of building damaged detection is proposed using high resolution remote sensing images and 3D GIS-Model data. Traditional building damage detection method considers to detect damaged building due to earthquake, but little attention has been paid to analyze various building damaged types(e.g., trivial damaged, severely damaged and totally collapsed.) Therefore, we want to detect the different building damaged type using 2D and 3D feature of scenes because the real world we live in is a 3D space. The proposed method generalizes that the image geometric correction method firstly corrects the post-disasters remote sensing image using the 3D GIS model or RPC parameters, then detects the different building damaged types using the change of the height and area between the pre- and post-disasters and the texture feature of post-disasters. The results, evaluated on a selected study site of the Beichuan earthquake ruins, Sichuan, show that this method is feasible and effective in building damage detection. It has also shown that the proposed method is easily applicable and well suited for rapid damage assessment after natural disasters.

Nanoparticle imaging. 3D structure of individual nanocrystals in solution by electron microscopy.

PubMed

Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A; Zettl, A; Alivisatos, A Paul

2015-07-17

Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale. Copyright © 2015, American Association for the Advancement of Science.

A compact high-resolution 3-D imaging spectrometer for discovering Oases on Mars

USGS Publications Warehouse

Ge, J.; Ren, D.; Lunine, J.I.; Brown, R.H.; Yelle, R.V.; Soderblom, L.A.; ,

2002-01-01

A new design for a very lightweight, very high throughput reflectance sectrometer enabled by two new technologies being developed is presented. These new technologies include integral field unit optics to enable simultaneous imaging and spectroscopy at high spatial resolution with an infrared (IR) array, and silicon grisms to enable compact and high-resolution spectroscopy.

Utilization of high resolution computed tomography to visualize the three dimensional structure and function of plant vasculature

USDA-ARS?s Scientific Manuscript database

High resolution x-ray computed tomography (HRCT) is a non-destructive diagnostic imaging technique with sub-micron resolution capability that is now being used to evaluate the structure and function of plant xylem network in three dimensions (3D). HRCT imaging is based on the same principles as medi...

Fluid Lensing, Applications to High-Resolution 3D Subaqueous Imaging & Automated Remote Biosphere Assessment from Airborne and Space-borne Platforms

NASA Astrophysics Data System (ADS)

Chirayath, V.

2014-12-01

Fluid Lensing is a theoretical model and algorithm I present for fluid-optical interactions in turbulent flows as well as two-fluid surface boundaries that, when coupled with an unique computer vision and image-processing pipeline, may be used to significantly enhance the angular resolution of a remote sensing optical system with applicability to high-resolution 3D imaging of subaqueous regions and through turbulent fluid flows. This novel remote sensing technology has recently been implemented on a quadcopter-based UAS for imaging shallow benthic systems to create the first dataset of a biosphere with unprecedented sub-cm-level imagery in 3D over areas as large as 15 square kilometers. Perturbed two-fluid boundaries with different refractive indices, such as the surface between the ocean and air, may be exploited for use as lensing elements for imaging targets on either side of the interface with enhanced angular resolution. I present theoretical developments behind Fluid Lensing and experimental results from its recent implementation for the Reactive Reefs project to image shallow reef ecosystems at cm scales. Preliminary results from petabyte-scale aerial survey efforts using Fluid Lensing to image at-risk coral reefs in American Samoa (August, 2013) show broad applicability to large-scale automated species identification, morphology studies and reef ecosystem characterization for shallow marine environments and terrestrial biospheres, of crucial importance to understanding climate change's impact on coastal zones, global oxygen production and carbon sequestration.

Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging.

PubMed

Nolte-Ernsting, C C; Tacke, J; Adam, G B; Haage, P; Jung, P; Jakse, G; Günther, R W

2001-01-01

The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p < 0.0001). Susceptibility effects were more pronounced on GRE EPI MR urograms and calculi measured 0.8-21.7% greater in diameter compared with conventional GRE sequences. Increased spatial resolution degraded the image quality only in GRE-EPI urograms. In projection MR urography, the entire pelvicaliceal system was imaged by acquisition of a fast single-slice sequence and the conventional 2D GRE technique provided superior morphological accuracy than 2D GRE EPI projection images (p < 0.0003). Fast 3D GRE EPI sequences improve the clinical practicability of excretory MR urography especially in old or critically ill patients unable to suspend breathing for more than 20 s. Conventional GRE sequences are superior to EPI in high-resolution detail MR urograms and in projection imaging.

Super-resolution for everybody: An image processing workflow to obtain high-resolution images with a standard confocal microscope.

PubMed

Lam, France; Cladière, Damien; Guillaume, Cyndélia; Wassmann, Katja; Bolte, Susanne

2017-02-15

In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure. We validate our workflow by imaging sub resolution fluorescent beads and measuring the maximum lateral and axial resolution of the confocal system. Subsequently, we apply the parameters to the imaging and data restoration of fluorescently labelled meiotic spindles of mouse oocytes. We measure a resolution increase of approximately 2-fold in the lateral and 3-fold in the axial direction throughout a depth of 60μm. This demonstrates that with our optimized workflow we reach a resolution that is comparable to 3D-SIM-imaging, but with better depth penetration for confocal images of beads and the biological sample. Copyright © 2016 Elsevier Inc. All rights reserved.

Real-time three-dimensional optical coherence tomography image-guided core-needle biopsy system.

PubMed

Kuo, Wei-Cheng; Kim, Jongsik; Shemonski, Nathan D; Chaney, Eric J; Spillman, Darold R; Boppart, Stephen A

2012-06-01

Advances in optical imaging modalities, such as optical coherence tomography (OCT), enable us to observe tissue microstructure at high resolution and in real time. Currently, core-needle biopsies are guided by external imaging modalities such as ultrasound imaging and x-ray computed tomography (CT) for breast and lung masses, respectively. These image-guided procedures are frequently limited by spatial resolution when using ultrasound imaging, or by temporal resolution (rapid real-time feedback capabilities) when using x-ray CT. One feasible approach is to perform OCT within small gauge needles to optically image tissue microstructure. However, to date, no system or core-needle device has been developed that incorporates both three-dimensional OCT imaging and tissue biopsy within the same needle for true OCT-guided core-needle biopsy. We have developed and demonstrate an integrated core-needle biopsy system that utilizes catheter-based 3-D OCT for real-time image-guidance for target tissue localization, imaging of tissue immediately prior to physical biopsy, and subsequent OCT imaging of the biopsied specimen for immediate assessment at the point-of-care. OCT images of biopsied ex vivo tumor specimens acquired during core-needle placement are correlated with corresponding histology, and computational visualization of arbitrary planes within the 3-D OCT volumes enables feedback on specimen tissue type and biopsy quality. These results demonstrate the potential for using real-time 3-D OCT for needle biopsy guidance by imaging within the needle and tissue during biopsy procedures.

Performance tests for ray-scan 64 PET/CT based on NEMA NU-2 2007

NASA Astrophysics Data System (ADS)

Li, Suying; Zhou, Kun; Zhang, Qiushi; Zhang, Jinming; Yang, Kun; Xu, Baixuan; Ren, Qiushi

2015-03-01

This paper focuses on evaluating the performance of the Ray-Scan 64 PET/CT system, a newly developed PET/CT in China. It combines a 64 slice helical CT scanner with a high resolution PET scanner based on BGO crystals assembled in 36 rings. The energy window is 350~ 650 keV, and the coincidence window is set at 12 ns in both 2D and 3D mode. The transaxial field of view (FOV) is 600 mm in diameter, and the axial FOV is 163 mm. Method: Performance measurements were conducted focusing on PET scanners based on NEMA NU-2 2007 standard. We reported the full characterization (spatial resolution, sensitivity, count rate performance, scatter fraction, accuracy of correction, and image quality) in both 2D and 3D mode. In addition, the clinical images from two patients of different types of tumor were presented to further demonstrate this PET/CT system performance in clinical application. Results: using the NEMA NU-2 2007 standard, the main results: (1) the transaxial resolution at 1cm from the gantry center for 2D and 3D was both 4.5mm (FWHM), and at 10cm from the gantry center, the radial (tangential) resolution were 5.6mm (5.3mm) and 5.4mm (5.2mm) in 2D and 3D mode respectively. The axial resolution at 1cm and 10cm off axis was 3.4mm (4.8mm) and 5.5mm (5.8mm) in 2D (3D) mode respectively; (2) the sensitivity for the radial position R0(r=0mm) and R100(r=100mm) were 1.741 kcps/MBq and 1.767 kcps/MBq respectively in 2D mode and 7.157 kcps/MBq and 7.513 kcps/MBq in 3D mode; (3) the scatter fraction was calculated as 18.36% and 42.92% in 2D and 3D mode, respectively; (4) contrast of hot spheres in the image quality phantom in 2D mode was 50.33% (52.87%), 33.34% (40.86%), 20.64% (26.36%), and 10.99% (15.82%), respectively, in N=4 (N=8). Besides, in clinical study, the diameter of lymph tumor was about 2.4 cm, and the diameter of lung cancer was 4.2 cm. This PET/CT system can distinguish the position of cancer easily. Conclusion: The results show that the performance of the newly developed PET/CT system is of high resolution, and low scatter characteristics, and is suitable for clinical applications.

Articular cartilage grading of the knee: diagnostic performance of fat-suppressed 3D volume isotropic turbo spin-echo acquisition (VISTA) compared with 3D T1 high-resolution isovolumetric examination (THRIVE).

PubMed

Lee, Young Han; Hahn, Seok; Lim, Daekeon; Suh, Jin-Suck

2017-02-01

Background Conventionally, two-dimensional (2D) fast spin-echo (FSE) sequences have been widely used for clinical cartilage imaging as well as gradient (GRE) sequences. Recently, three-dimensional (3D) volumetric magnetic resonance imaging (MRI) has been introduced with one 3D volumetric scan, and this is replacing slice-by-slice 2D MR scans. Purpose To evaluate the image quality and diagnostic performance of two 3D sequences for abnormalities of knee cartilage: fat-suppressed (FS) FSE-based 3D volume isotropic turbo spin-echo acquisition (VISTA) and GRE-based 3D T1 high-resolution isovolumetric examination (THRIVE). Material and Methods The institutional review board approved the protocol of this retrospective review. This study enrolled 40 patients (41 knees) with arthroscopically confirmed abnormalities of cartilage. All patients underwent isovoxel 3D-VISTA and 3D-THRIVE MR sequences on 3T MRI. We assessed the cartilage grade on the two 3D sequences using arthroscopy as a gold standard. Inter-observer agreement for each technique was evaluated with the intraclass correlation coefficient (ICC). Differences in the area under the curve (AUC) were compared between the 3D-THRIVE and 3D-VISTA. Results Although inter-observer agreement for both sequences was excellent, the inter-observer agreement for 3D-VISTA was higher than for 3D-THRIVE for cartilage grading in all regions of the knee. There was no significant difference in the diagnostic performance ( P > 0.05) between the two sequences for detecting cartilage grade. Conclusion FSE-based 3D-VISTA images had good diagnostic performance that was comparable to GRE-based 3D-THRIVE images in the evaluation of knee cartilage, and can be used in routine knee MR protocols for the evaluation of cartilage.

Research in Image Understanding as Applied to 3-D Microwave Tomographic Imaging with Near Optical Resolution.

DTIC Science & Technology

1987-03-01

Oct. 1985. 28. D.L. Jaggard, K. Schultz, Y. Kim and P. Frangos , "Inverse Scattering for Dielectric Media", Annual OSA Meeting, Wash. D.C., Oct. 1985...T.H. Chu - Graduate Student (50%) C.Y. Ho - Graduate Student (50%) Y. Kim - Graduate Student (50%) K S. Lee - Graduate Student (50%) P. Frangos ...1982. 3. P. Frangos (Ph.D.) - "One-Dimensional Inverse Scattering: Exact Methods and Applications". 4. C.L. Werner (Ph.D.) - ŗ-D Imaging of Coherent and

Semantic Building FAÇADE Segmentation from Airborne Oblique Images

NASA Astrophysics Data System (ADS)

Lin, Y.; Nex, F.; Yang, M. Y.

2018-05-01

With the introduction of airborne oblique camera systems and the improvement of photogrammetric techniques, high-resolution 2D and 3D data can be acquired in urban areas. This high-resolution data allows us to perform detailed investigations on building roofs and façades which can contribute to LoD3 city modeling. Normally, façade segmentation is achieved from terrestrial views. In this paper, we address the problem from aerial views by using high resolution oblique aerial images as the data source in urban areas. In addition to traditional image features, such as RGB and SIFT, normal vector and planarity are also extracted from dense matching point clouds. Then, these 3D geometrical features are projected back to 2D space to assist façade interpretation. Random forest is trained and applied to label façade pixels. Fully connected conditional random field (CRF), capturing long-range spatial interactions, is used as a post-processing to refine our classification results. Its pairwise potential is defined by a linear combination of Gaussian kernels and the CRF model is efficiently solved by mean field approximation. Experiments show that 3D features can significantly improve classification results. Also, fully connected CRF performs well in correcting noisy pixels.

PSF Rotation with Changing Defocus and Applications to 3D Imaging for Space Situational Awareness

NASA Astrophysics Data System (ADS)

Prasad, S.; Kumar, R.

2013-09-01

For a clear, well corrected imaging aperture in space, the point-spread function (PSF) in its Gaussian image plane has the conventional, diffraction-limited, tightly focused Airy form. Away from that plane, the PSF broadens rapidly, however, resulting in a loss of sensitivity and transverse resolution that makes such a traditional best-optics approach untenable for rapid 3D image acquisition. One must scan in focus to maintain high sensitivity and resolution as one acquires image data, slice by slice, from a 3D volume with reduced efficiency. In this paper we describe a computational-imaging approach to overcome this limitation, one that uses pupil-phase engineering to fashion a PSF that, although not as tight as the Airy spot, maintains its shape and size while rotating uniformly with changing defocus over many waves of defocus phase at the pupil edge. As one of us has shown recently [1], the subdivision of a circular pupil aperture into M Fresnel zones, with the mth zone having an outer radius proportional to m and impressing a spiral phase profile of form m? on the light wave, where ? is the azimuthal angle coordinate measured from a fixed x axis (the dislocation line), yields a PSF that rotates with defocus while keeping its shape and size. Physically speaking, a nonzero defocus of a point source means a quadratic optical phase in the pupil that, because of the square-root dependence of the zone radius on the zone number, increases on average by the same amount from one zone to the next. This uniformly incrementing phase yields, in effect, a rotation of the dislocation line, and thus a rotated PSF. Since the zone-to-zone phase increment depends linearly on defocus to first order, the PSF rotates uniformly with changing defocus. For an M-zone pupil, a complete rotation of the PSF occurs when the defocus-induced phase at the pupil edge changes by M waves. Our recent simulations of reconstructions from image data for 3D image scenes comprised of point sources at different focal depths have shown remarkable robustness of our rotating-PSF approach to achieve good transverse and longitudinal resolution even for moderate SNR. Additionally, the work seeks to clarify an important theoretical issue about 3D imaging, namely the detailed nature of the interplay between transverse and longitudinal resolutions, including 3D generalizations of the space-bandwidth product (SBP) and its dependence on image noise. An underlying transport equation, which we shall derive and analyze, describes the trade-off between the transverse and longitudinal blur processes in a manner analogous to the diffractive spreading of a light beam that is transversely confined. This work has immediate applications for space-based surveillance, particularly for 3D mapping and tracking of space debris flying in the vicinity of important AF space assets. Working with a well corrected conventional imager, our 3D computational imager can acquire with high sensitivity and speed an extended focal volume in which individual objects of interest can be subsequently probed and imaged with high resolution over smaller 2D field segments. [1] S. Prasad, Rotating Point Spread Function by Pupil Phase Engineering, Opt. Lett., vol. 38, pp. 585-587 (2013)

Analysis on the 3D crosstalk in stereoscopic display

NASA Astrophysics Data System (ADS)

Choi, Hee-Jin

2010-11-01

Nowadays, with the rapid progresses in flat panel display (FPD) technologies, the three-dimensional (3D) display is now becoming a next mainstream of display market. Among the various 3D display techniques, the stereoscopic 3D display shows different left/right images for each eye of observer using special glasses and is the most popular 3D technique with the advantages of low price and high 3D resolution. However, current stereoscopic 3D displays suffer with the 3D crosstalk which means the interference between the left eye mage and right eye images since it degrades the quality of 3D image severely. In this paper, the meaning and causes of the 3D crosstalk in stereoscopic 3D display are introduced and the pre-proposed methods of 3D crosstalk measurement vision science are reviewed. Based on them The threshold of 3D crosstalk to realize a 3D display with no degradation is analyzed.

Technical Note: Characterization of custom 3D printed multimodality imaging phantoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bieniosek, Matthew F.; Lee, Brian J.; Levin, Craig S., E-mail: cslevin@stanford.edu

Purpose: Imaging phantoms are important tools for researchers and technicians, but they can be costly and difficult to customize. Three dimensional (3D) printing is a widely available rapid prototyping technique that enables the fabrication of objects with 3D computer generated geometries. It is ideal for quickly producing customized, low cost, multimodal, reusable imaging phantoms. This work validates the use of 3D printed phantoms by comparing CT and PET scans of a 3D printed phantom and a commercial “Micro Deluxe” phantom. This report also presents results from a customized 3D printed PET/MRI phantom, and a customized high resolution imaging phantom withmore » sub-mm features. Methods: CT and PET scans of a 3D printed phantom and a commercial Micro Deluxe (Data Spectrum Corporation, USA) phantom with 1.2, 1.6, 2.4, 3.2, 4.0, and 4.8 mm diameter hot rods were acquired. The measured PET and CT rod sizes, activities, and attenuation coefficients were compared. A PET/MRI scan of a custom 3D printed phantom with hot and cold rods was performed, with photon attenuation and normalization measurements performed with a separate 3D printed normalization phantom. X-ray transmission scans of a customized two level high resolution 3D printed phantom with sub-mm features were also performed. Results: Results show very good agreement between commercial and 3D printed micro deluxe phantoms with less than 3% difference in CT measured rod diameter, less than 5% difference in PET measured rod diameter, and a maximum of 6.2% difference in average rod activity from a 10 min, 333 kBq/ml (9 μCi/ml) Siemens Inveon (Siemens Healthcare, Germany) PET scan. In all cases, these differences were within the measurement uncertainties of our setups. PET/MRI scans successfully identified 3D printed hot and cold rods on PET and MRI modalities. X-ray projection images of a 3D printed high resolution phantom identified features as small as 350 μm wide. Conclusions: This work shows that 3D printed phantoms can be functionally equivalent to commercially available phantoms. They are a viable option for quickly distributing and fabricating low cost, customized phantoms.« less

Dual-dimensional microscopy: real-time in vivo three-dimensional observation method using high-resolution light-field microscopy and light-field display.

PubMed

Kim, Jonghyun; Moon, Seokil; Jeong, Youngmo; Jang, Changwon; Kim, Youngmin; Lee, Byoungho

2018-06-01

Here, we present dual-dimensional microscopy that captures both two-dimensional (2-D) and light-field images of an in-vivo sample simultaneously, synthesizes an upsampled light-field image in real time, and visualizes it with a computational light-field display system in real time. Compared with conventional light-field microscopy, the additional 2-D image greatly enhances the lateral resolution at the native object plane up to the diffraction limit and compensates for the image degradation at the native object plane. The whole process from capturing to displaying is done in real time with the parallel computation algorithm, which enables the observation of the sample's three-dimensional (3-D) movement and direct interaction with the in-vivo sample. We demonstrate a real-time 3-D interactive experiment with Caenorhabditis elegans. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Gray matter segmentation of the spinal cord with active contours in MR images.

PubMed

Datta, Esha; Papinutto, Nico; Schlaeger, Regina; Zhu, Alyssa; Carballido-Gamio, Julio; Henry, Roland G

2017-02-15

Fully or partially automated spinal cord gray matter segmentation techniques for spinal cord gray matter segmentation will allow for pivotal spinal cord gray matter measurements in the study of various neurological disorders. The objective of this work was multi-fold: (1) to develop a gray matter segmentation technique that uses registration methods with an existing delineation of the cord edge along with Morphological Geodesic Active Contour (MGAC) models; (2) to assess the accuracy and reproducibility of the newly developed technique on 2D PSIR T1 weighted images; (3) to test how the algorithm performs on different resolutions and other contrasts; (4) to demonstrate how the algorithm can be extended to 3D scans; and (5) to show the clinical potential for multiple sclerosis patients. The MGAC algorithm was developed using a publicly available implementation of a morphological geodesic active contour model and the spinal cord segmentation tool of the software Jim (Xinapse Systems) for initial estimate of the cord boundary. The MGAC algorithm was demonstrated on 2D PSIR images of the C2/C3 level with two different resolutions, 2D T2* weighted images of the C2/C3 level, and a 3D PSIR image. These images were acquired from 45 healthy controls and 58 multiple sclerosis patients selected for the absence of evident lesions at the C2/C3 level. Accuracy was assessed though visual assessment, Hausdorff distances, and Dice similarity coefficients. Reproducibility was assessed through interclass correlation coefficients. Validity was assessed through comparison of segmented gray matter areas in images with different resolution for both manual and MGAC segmentations. Between MGAC and manual segmentations in healthy controls, the mean Dice similarity coefficient was 0.88 (0.82-0.93) and the mean Hausdorff distance was 0.61 (0.46-0.76) mm. The interclass correlation coefficient from test and retest scans of healthy controls was 0.88. The percent change between the manual segmentations from high and low-resolution images was 25%, while the percent change between the MGAC segmentations from high and low resolution images was 13%. Between MGAC and manual segmentations in MS patients, the average Dice similarity coefficient was 0.86 (0.8-0.92) and the average Hausdorff distance was 0.83 (0.29-1.37) mm. We demonstrate that an automatic segmentation technique, based on a morphometric geodesic active contours algorithm, can provide accurate and precise spinal cord gray matter segmentations on 2D PSIR images. We have also shown how this automated technique can potentially be extended to other imaging protocols. Copyright © 2016 Elsevier Inc. All rights reserved.

Left ventricular function assessment using a fast 3D gradient echo pulse sequence: comparison to standard multi-breath hold 2D steady state free precession imaging and accounting for papillary muscles and trabeculations.

PubMed

Sievers, Burkhard; Schrader, Sebastian; Rehwald, Wolfgang; Hunold, Peter; Barkhausen, Joerg; Erbel, Raimund

2011-06-01

Papillary muscles and trabeculae for ventricular function analysis are known to significantly contribute to accurate volume and mass measurements. Fast imaging techniques such as three-dimensional steady-state free precession (3D SSFP) are increasingly being used to speed up imaging time, but sacrifice spatial resolution. It is unknown whether 3D SSFP, despite its reduced spatial resolution, allows for exact delineation of papillary muscles and trabeculations. We therefore compared 3D SSFP ventricular function measurements to those measured from standard multi-breath hold two-dimensional steady-state free precession cine images (standard 2D SSFP). 14 healthy subjects and 14 patients with impaired left ventricularfunction underwent 1.5 Tesla cine imaging. A stack of short axis images covering the left ventricle was acquired with 2D SSFP and 3D SSFP. Left ventricular volumes, ejection fraction, and mass were determined. Analysis was performed by substracting papillary muscles and trabeculae from left ventricular volumes. In addition, reproducibility was assessed. EDV, ESV, EF, and mass were not significantly different between 2D SSFP and 3D SSFP (mean difference healthy subjects: -0.06 +/- 3.2 ml, 0.54 +/- 2.2 ml, -0.45 +/- 1.8%, and 1.13 +/- 0.8 g, respectively; patients: 1.36 +/- 2.8 ml, -0.15 3.5 ml, 0.86 +/- 2.5%, and 0.91 +/- 0.9 g, respectively; P > or = 0.095). Intra- and interobserver variability was not different for 2D SSFP (P > or = 0.64 and P > or = 0.397) and 3D SSFP (P > or = 0.53 and P > or = 0.47). Differences in volumes, EF, and mass measurements between 3D SSFP and standard 2D SSFP are very small, and not statistically significant. 3D SSFP may be used for accurate ventricular function assessment when papillary muscles and trabeculations are to be taken into account.

Laboratory-based x-ray phase-contrast tomography enables 3D virtual histology

NASA Astrophysics Data System (ADS)

Töpperwien, Mareike; Krenkel, Martin; Quade, Felix; Salditt, Tim

2016-09-01

Due to the large penetration depth and small wavelength hard x-rays offer a unique potential for 3D biomedical and biological imaging, combining capabilities of high resolution and large sample volume. However, in classical absorption-based computed tomography, soft tissue only shows a weak contrast, limiting the actual resolution. With the advent of phase-contrast methods, the much stronger phase shift induced by the sample can now be exploited. For high resolution, free space propagation behind the sample is particularly well suited to make the phase shift visible. Contrast formation is based on the self-interference of the transmitted beam, resulting in object-induced intensity modulations in the detector plane. As this method requires a sufficiently high degree of spatial coherence, it was since long perceived as a synchrotron-based imaging technique. In this contribution we show that by combination of high brightness liquid-metal jet microfocus sources and suitable sample preparation techniques, as well as optimized geometry, detection and phase retrieval, excellent three-dimensional image quality can be obtained, revealing the anatomy of a cobweb spider in high detail. This opens up new opportunities for 3D virtual histology of small organisms. Importantly, the image quality is finally augmented to a level accessible to automatic 3D segmentation.

A range/depth modulation transfer function (RMTF) framework for characterizing 3D imaging LADAR performance

NASA Astrophysics Data System (ADS)

Staple, Bevan; Earhart, R. P.; Slaymaker, Philip A.; Drouillard, Thomas F., II; Mahony, Thomas

2005-05-01

3D imaging LADARs have emerged as the key technology for producing high-resolution imagery of targets in 3-dimensions (X and Y spatial, and Z in the range/depth dimension). Ball Aerospace & Technologies Corp. continues to make significant investments in this technology to enable critical NASA, Department of Defense, and national security missions. As a consequence of rapid technology developments, two issues have emerged that need resolution. First, the terminology used to rate LADAR performance (e.g., range resolution) is inconsistently defined, is improperly used, and thus has become misleading. Second, the terminology does not include a metric of the system"s ability to resolve the 3D depth features of targets. These two issues create confusion when translating customer requirements into hardware. This paper presents a candidate framework for addressing these issues. To address the consistency issue, the framework utilizes only those terminologies proposed and tested by leading LADAR research and standards institutions. We also provide suggestions for strengthening these definitions by linking them to the well-known Rayleigh criterion extended into the range dimension. To address the inadequate 3D image quality metrics, the framework introduces the concept of a Range/Depth Modulation Transfer Function (RMTF). The RMTF measures the impact of the spatial frequencies of a 3D target on its measured modulation in range/depth. It is determined using a new, Range-Based, Slanted Knife-Edge test. We present simulated results for two LADAR pulse detection techniques and compare them to a baseline centroid technique. Consistency in terminology plus a 3D image quality metric enable improved system standardization.

Quantitative comparison of 2D and 3D late gadolinium enhancement MR imaging in patients with Fabry disease and hypertrophic cardiomyopathy.

PubMed

Morsbach, F; Gordic, S; Gruner, C; Niemann, M; Goetti, R; Gotschy, A; Kozerke, S; Alkadhi, H; Manka, R

2016-08-15

This study aims to determine whether the quantification of myocardial fibrosis in patients with Fabry disease (FD) and hypertrophic cardiomyopathy (HCM) using a late gadolinium enhancement (LGE) singlebreath-hold three-dimensional (3D) inversion recovery magnetic resonance (MR) imaging sequence is comparable with a clinically established two-dimensional (2D) multi-breath-hold sequence. In this retrospective, IRB-approved study, 40 consecutive patients (18 male; mean age 50±17years) with Fabry disease (n=18) and HCM (n=22) underwent MR imaging at 1.5T. Spatial resolution was the same for 3D and 2D images (field-of-view, 350×350mm(2); in-plane-resolution, 1.2×1.2mm(2); section-thickness, 8mm). Datasets were analyzed for subjective image quality; myocardial and fibrotic mass, and total fibrotic tissue percentage were quantified. There was no significant difference in subjective image quality between 3D and 2D acquisitions (P=0.1 and P=0.3) for either disease. In patients with Fabry disease there were no significant differences between 3D and 2D acquisitions for myocardial mass (P=0.55), fibrous tissue mass (P=0.89), and total fibrous percentage (P=0.67), with good agreement between acquisitions according to Bland-Altman analyses. In patients with HCM there were also no significant differences between acquisitions for myocardial mass (P=0.48), fibrous tissue mass (P=0.56), and total fibrous percentage (P=0.67), with good agreement according to Bland-Altman analyses. Acquisition time was significantly shorter for 3D (25±5s) as compared to the 2D sequence (349±62s, P<0.001). In patients with Fabry disease and HCM, 3D LGE imaging provides equivalent diagnostic information in regard to quantification of myocardial fibrosis as compared with a standard 2D sequence, but at superior acquisition speed. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Multicolor 4D Fluorescence Microscopy using Ultrathin Bessel Light Sheets

PubMed Central

Zhao, Teng; Lau, Sze Cheung; Wang, Ying; Su, Yumian; Wang, Hao; Cheng, Aifang; Herrup, Karl; Ip, Nancy Y.; Du, Shengwang; Loy, M. M. T.

2016-01-01

We demonstrate a simple and efficient method for producing ultrathin Bessel (‘non-diffracting’) light sheets of any color using a line-shaped beam and an annulus filter. With this robust and cost-effective technology, we obtained two-color, 3D images of biological samples with lateral/axial resolution of 250 nm/400 nm, and high-speed, 4D volume imaging of 20 μm sized live sample at 1 Hz temporal resolution. PMID:27189786

Advances in high-resolution imaging--techniques for three-dimensional imaging of cellular structures.

PubMed

Lidke, Diane S; Lidke, Keith A

2012-06-01

A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques.

Bessel beam fluorescence lifetime tomography of live embryos (Conference Presentation)

NASA Astrophysics Data System (ADS)

Xu, Dongli; Peng, Leilei

2016-03-01

Optical tomography allows isotropic 3D imaging of embryos. Scanning-laser optical tomography (SLOT) has superior light collecting efficiency than wide-field optical tomography, making it ideal for fluorescence imaging of live embryos. We previously reported an imaging system that combines SLOT with a novel Fourier-multiplexed fluorescence lifetime imaging (FmFLIM) technique named FmFLIM-SLOT. FmFLIM-SLOT performs multiplexed FLIM-FRET readout of multiple FRET sensors in live embryos. Here we report a recent effort on improving the spatial resolution of the FmFLIM-SLOT system in order to image complex biochemical processes in live embryos at the cellular level. Optical tomography has to compromise between resolution and the depth of view. In SLOT, the commonly-used focused Gaussian beam diverges quickly from the focal plane, making it impossible to achieve high resolution imaging in a large volume specimen. We thus introduce Bessel beam laser-scanning tomography, which illuminates the sample with a spatial-light-modulator-generated Bessel beam that has an extended focal depth. The Bessel beam is scanned across the whole specimen. Fluorescence projection images are acquired at equal angular intervals as the sample rotates. Reconstruction artifacts due to annular-rings of the Bessel beam are removed by a modified 3D filtered back projection algorithm. Furthermore, in combination of Fourier-multiplexing fluorescence lifetime imaging (FmFLIM) method, the Bessel FmFLIM-SLOT system is capable of perform 3D lifetime imaging of live embryos at cellular resolution. The system is applied to in-vivo imaging of transgenic Zebrafish embryos. Results prove that Bessel FmFLIM-SLOT is a promising imaging method in development biology research.

Imaging whole mouse brains with a dual resolution serial swept-source optical coherence tomography scanner

NASA Astrophysics Data System (ADS)

Lefebvre, Joël.; Castonguay, Alexandre; Lesage, Frédéric

2018-02-01

High resolution imaging of whole rodent brains using serial OCT scanners is a promising method to investigate microstructural changes in tissue related to the evolution of neuropathologies. Although micron to sub-micron sampling resolution can be obtained by using high numerical aperture objectives and dynamic focusing, such an imaging system is not adapted to whole brain imaging. This is due to the large amount of data it generates and the significant computational resources required for reconstructing such volumes. To address this limitation, a dual resolution serial OCT scanner was developed. The optical setup consists in a swept-source OCT made of two sample and reference arms, each arm being coupled with different microscope objectives (3X / 40X). Motorized flip mirrors were used to switch between each OCT arm, thus allowing low and high resolution acquisitions within the same sample. The low resolution OCT volumes acquired with the 3X arm were stitched together, providing a 3D map of the whole mouse brain. This brain can be registered to an OCT brain template to enable neurological structures localization. The high resolution volumes acquired with the 40X arm were also stitched together to create local high resolution 3D maps of the tissue microstructure. The 40X data can be acquired at any arbitrary location in the sample, thus limiting storage-heavy high resolution data to application restricted to specific regions of interest. By providing dual-resolution OCT data, this setup can be used to validate diffusion MRI with tissue microstructure derived metrics measured at any location in ex vivo brains.

Conception and realization of a semiconductor based 240 GHz full 3D MIMO imaging system

NASA Astrophysics Data System (ADS)

Weisenstein, Christian; Kahl, Matthias; Friederich, Fabian; Haring Bolívar, Peter

2017-02-01

Multiple-input multiple-output (MIMO) imaging systems in the terahertz frequency range have a high potential in the field of non-destructive testing (NDT). With such systems it is possible to detect defects in composite materials, for example cracks or delaminations in fiber composites. To investigate mass-produced products it is necessary to study the objects in close to real-time on a conveyor without affecting the production cycle time. In this work we present the conception and realization of a 3D MIMO imaging system for in-line investigation of composite materials and structures. To achieve a lateral resolution of 1 mm, in order to detect such small defects in composite materials with a moderate number of elements, precise sensor design is crucial. In our approach we use the effective aperture concept. The designed sparse array consists of 32 transmitters and 30 receivers based on planar semiconductor components. High range resolution is achieved by an operating frequency between 220 GHz and 260 GHz in a stepped frequency continuous wave (SFCW) setup. A matched filter approach is used to simulate the reconstructed 3D image through the array. This allows the evaluation of the designed array geometry in regard of resolution and side lobe level. In contrast to earlier demonstrations, in which synthetic reconstruction is only performed in a 2D plane, an optics-free full 3D recon- struction has been implemented in our concept. Based on this simulation we designed an array geometry that enables to resolve objects with a resolution smaller than 1mm and moderate side lobe level.

Novel Applications of Rapid Prototyping in Gamma-ray and X-ray Imaging

PubMed Central

Miller, Brian W.; Moore, Jared W.; Gehm, Michael E.; Furenlid, Lars R.; Barrett, Harrison H.

2010-01-01

Advances in 3D rapid-prototyping printers, 3D modeling software, and casting techniques allow for the fabrication of cost-effective, custom components in gamma-ray and x-ray imaging systems. Applications extend to new fabrication methods for custom collimators, pinholes, calibration and resolution phantoms, mounting and shielding components, and imaging apertures. Details of the fabrication process for these components are presented, specifically the 3D printing process, cold casting with a tungsten epoxy, and lost-wax casting in platinum. PMID:22984341

Twin robotic x-ray system for 2D radiographic and 3D cone-beam CT imaging

NASA Astrophysics Data System (ADS)

Fieselmann, Andreas; Steinbrener, Jan; Jerebko, Anna K.; Voigt, Johannes M.; Scholz, Rosemarie; Ritschl, Ludwig; Mertelmeier, Thomas

2016-03-01

In this work, we provide an initial characterization of a novel twin robotic X-ray system. This system is equipped with two motor-driven telescopic arms carrying X-ray tube and flat-panel detector, respectively. 2D radiographs and fluoroscopic image sequences can be obtained from different viewing angles. Projection data for 3D cone-beam CT reconstruction can be acquired during simultaneous movement of the arms along dedicated scanning trajectories. We provide an initial evaluation of the 3D image quality based on phantom scans and clinical images. Furthermore, initial evaluation of patient dose is conducted. The results show that the system delivers high image quality for a range of medical applications. In particular, high spatial resolution enables adequate visualization of bone structures. This system allows 3D X-ray scanning of patients in standing and weight-bearing position. It could enable new 2D/3D imaging workflows in musculoskeletal imaging and improve diagnosis of musculoskeletal disorders.

0.125 mm(3) spatial resolution steady-state MR angiography of the thighs with a blood pool contrast agent using the quadrature body coil only at 1.5 Tesla.

PubMed

Boschewitz, Jack M; Hadizadeh, Dariusch R; Kukuk, Guido M; Meyer, Carsten; Wilhelm, Kai; Koscielny, Arne; Verrel, Frauke; Gieseke, Jürgen; Schild, Hans H; Willinek, Winfried A

2014-10-01

To implement and evaluate high spatial resolution three-dimensional MR contrast-enhanced angiography (3D-CEMRA) of the thighs using a blood pool contrast agent (BPCA) using the quadrature body coil only in patients with peripheral arterial occlusive disease (PAOD) in cases receiver coils cannot be used at 1.5 Tesla (T). Nineteen patients (mean age: 68.7 ± 11.2 years; range, 38-83 years) with known PAOD (Fontaine stages; III: 16, IV: 3) prospectively underwent 3D-CEMRA at 1.5T with a noninterpolated voxel size of 0.49 × 0.49 × 0.48 mm(3) . Digital subtraction angiography (DSA) was available for comparison in all patients. Two readers independently evaluated movement artifacts, overall image quality of 3D-CEMRA, and grade of stenosis as compared to DSA. SNR and CNR levels were quantified. The 3D-CEMRA was successfully completed in all patients. Patient movement artifacts that affected stenosis grading occurred in 3/38 thighs. Overall image quality was rated excellent in 15/38, good in 12/38, and diagnostic in 8/38 thighs. Stenosis grading matched with that in DSA in 35/38 thighs. High SNR and CNR were measured in all vessels. The 0.125 mm(3) spatial resolution 3D-CEMRA of the thighs with a BPCA is feasible using a quadrature body coil exclusively with excellent image quality despite long acquisition times. J. Magn. Reson. Imaging 2014;40:996-1001. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.

Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord

PubMed Central

Fratini, Michela; Bukreeva, Inna; Campi, Gaetano; Brun, Francesco; Tromba, Giuliana; Modregger, Peter; Bucci, Domenico; Battaglia, Giuseppe; Spanò, Raffaele; Mastrogiacomo, Maddalena; Requardt, Herwig; Giove, Federico; Bravin, Alberto; Cedola, Alessia

2015-01-01

Faults in vascular (VN) and neuronal networks of spinal cord are responsible for serious neurodegenerative pathologies. Because of inadequate investigation tools, the lacking knowledge of the complete fine structure of VN and neuronal system represents a crucial problem. Conventional 2D imaging yields incomplete spatial coverage leading to possible data misinterpretation, whereas standard 3D computed tomography imaging achieves insufficient resolution and contrast. We show that X-ray high-resolution phase-contrast tomography allows the simultaneous visualization of three-dimensional VN and neuronal systems of ex-vivo mouse spinal cord at scales spanning from millimeters to hundreds of nanometers, with nor contrast agent nor sectioning and neither destructive sample-preparation. We image both the 3D distribution of micro-capillary network and the micrometric nerve fibers, axon-bundles and neuron soma. Our approach is very suitable for pre-clinical investigation of neurodegenerative pathologies and spinal-cord-injuries, in particular to resolve the entangled relationship between VN and neuronal system. PMID:25686728

High resolution three-dimensional robotic synthetic tracked aperture ultrasound imaging: feasibility study

NASA Astrophysics Data System (ADS)

Zhang, Haichong K.; Fang, Ting Yun; Finocchi, Rodolfo; Boctor, Emad M.

2017-03-01

Three dimensional (3D) ultrasound imaging is becoming a standard mode for medical ultrasound diagnoses. Conventional 3D ultrasound imaging is mostly scanned either by using a two dimensional matrix array or by motorizing a one dimensional array in the elevation direction. However, the former system is not widely assessable due to its cost, and the latter one has limited resolution and field-of-view in the elevation axis. Here, we propose a 3D ultrasound imaging system based on the synthetic tracked aperture approach, in which a robotic arm is used to provide accurate tracking and motion. While the ultrasound probe is moved by a robotic arm, each probe position is tracked and can be used to reconstruct a wider field-of-view as there are no physical barriers that restrict the elevational scanning. At the same time, synthetic aperture beamforming provides a better resolution in the elevation axis. To synthesize the elevational information, the single focal point is regarded as the virtual element, and forward and backward delay-andsum are applied to the radio-frequency (RF) data collected through the volume. The concept is experimentally validated using a general ultrasound phantom, and the elevational resolution improvement of 2.54 and 2.13 times was measured at the target depths of 20 mm and 110 mm, respectively.

LC-lens array with light field algorithm for 3D biomedical applications

NASA Astrophysics Data System (ADS)

Huang, Yi-Pai; Hsieh, Po-Yuan; Hassanfiroozi, Amir; Martinez, Manuel; Javidi, Bahram; Chu, Chao-Yu; Hsuan, Yun; Chu, Wen-Chun

2016-03-01

In this paper, liquid crystal lens (LC-lens) array was utilized in 3D bio-medical applications including 3D endoscope and light field microscope. Comparing with conventional plastic lens array, which was usually placed in 3D endoscope or light field microscope system to record image disparity, our LC-lens array has higher flexibility of electrically changing its focal length. By using LC-lens array, the working distance and image quality of 3D endoscope and microscope could be enhanced. Furthermore, the 2D/3D switching ability could be achieved if we turn off/on the electrical power on LClens array. In 3D endoscope case, a hexagonal micro LC-lens array with 350um diameter was placed at the front end of a 1mm diameter endoscope. With applying electric field on LC-lens array, the 3D specimen would be recorded as from seven micro-cameras with different disparity. We could calculate 3D construction of specimen with those micro images. In the other hand, if we turn off the electric field on LC-lens array, the conventional high resolution 2D endoscope image would be recorded. In light field microscope case, the LC-lens array was placed in front of the CMOS sensor. The main purpose of LC-lens array is to extend the refocusing distance of light field microscope, which is usually very narrow in focused light field microscope system, by montaging many light field images sequentially focusing on different depth. With adjusting focal length of LC-lens array from 2.4mm to 2.9mm, the refocusing distance was extended from 1mm to 11.3mm. Moreover, we could use a LC wedge to electrically shift the optics axis and increase the resolution of light field.

An instrument for 3D x-ray nano-imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holler, M.; Raabe, J.; Diaz, A.

We present an instrument dedicated to 3D scanning x-ray microscopy, allowing a sample to be precisely scanned through a beam while the angle of x-ray incidence can be changed. The position of the sample is controlled with respect to the beam-defining optics by laser interferometry. The instrument achieves a position stability better than 10 nm standard deviation. The instrument performance is assessed using scanning x-ray diffraction microscopy and we demonstrate a resolution of 18 nm in 2D imaging of a lithographic test pattern while the beam was defined by a pinhole of 3 {mu}m in diameter. In 3D on amore » test object of copper interconnects of a microprocessor, a resolution of 53 nm is achieved.« less

A hybrid approach for fusing 4D-MRI temporal information with 3D-CT for the study of lung and lung tumor motion.

PubMed

Yang, Y X; Teo, S-K; Van Reeth, E; Tan, C H; Tham, I W K; Poh, C L

2015-08-01

Accurate visualization of lung motion is important in many clinical applications, such as radiotherapy of lung cancer. Advancement in imaging modalities [e.g., computed tomography (CT) and MRI] has allowed dynamic imaging of lung and lung tumor motion. However, each imaging modality has its advantages and disadvantages. The study presented in this paper aims at generating synthetic 4D-CT dataset for lung cancer patients by combining both continuous three-dimensional (3D) motion captured by 4D-MRI and the high spatial resolution captured by CT using the authors' proposed approach. A novel hybrid approach based on deformable image registration (DIR) and finite element method simulation was developed to fuse a static 3D-CT volume (acquired under breath-hold) and the 3D motion information extracted from 4D-MRI dataset, creating a synthetic 4D-CT dataset. The study focuses on imaging of lung and lung tumor. Comparing the synthetic 4D-CT dataset with the acquired 4D-CT dataset of six lung cancer patients based on 420 landmarks, accurate results (average error <2 mm) were achieved using the authors' proposed approach. Their hybrid approach achieved a 40% error reduction (based on landmarks assessment) over using only DIR techniques. The synthetic 4D-CT dataset generated has high spatial resolution, has excellent lung details, and is able to show movement of lung and lung tumor over multiple breathing cycles.

Imaging and reconstruction of cell cortex structures near the cell surface

NASA Astrophysics Data System (ADS)

Jin, Luhong; Zhou, Xiaoxu; Xiu, Peng; Luo, Wei; Huang, Yujia; Yu, Feng; Kuang, Cuifang; Sun, Yonghong; Liu, Xu; Xu, Yingke

2017-11-01

Total internal reflection fluorescence microscopy (TIRFM) provides high optical sectioning capability and superb signal-to-noise ratio for imaging of cell cortex structures. The development of multi-angle (MA)-TIRFM permits high axial resolution imaging and reconstruction of cellular structures near the cell surface. Cytoskeleton is composed of a network of filaments, which are important for maintenance of cell function. The high-resolution imaging and quantitative analysis of filament organization would contribute to our understanding of cytoskeleton regulation in cell. Here, we used a custom-developed MA-TIRFM setup, together with stochastic photobleaching and single molecule localization method, to enhance the lateral resolution of TIRFM imaging to about 100 nm. In addition, we proposed novel methods to perform filament segmentation and 3D reconstruction from MA-TIRFM images. Furthermore, we applied these methods to study the 3D localization of cortical actin and microtubule structures in U373 cancer cells. Our results showed that cortical actins localize ∼ 27 nm closer to the plasma membrane when compared with microtubules. We found that treatment of cells with chemotherapy drugs nocodazole and cytochalasin B disassembles cytoskeletal network and induces the reorganization of filaments towards the cell periphery. In summary, this study provides feasible approaches for 3D imaging and analyzing cell surface distribution of cytoskeletal network. Our established microscopy platform and image analysis toolkits would facilitate the study of cytoskeletal network in cells.

Dual-color 3D superresolution microscopy by combined spectral-demixing and biplane imaging.

PubMed

Winterflood, Christian M; Platonova, Evgenia; Albrecht, David; Ewers, Helge

2015-07-07

Multicolor three-dimensional (3D) superresolution techniques allow important insight into the relative organization of cellular structures. While a number of innovative solutions have emerged, multicolor 3D techniques still face significant technical challenges. In this Letter we provide a straightforward approach to single-molecule localization microscopy imaging in three dimensions and two colors. We combine biplane imaging and spectral-demixing, which eliminates a number of problems, including color cross-talk, chromatic aberration effects, and problems with color registration. We present 3D dual-color images of nanoscopic structures in hippocampal neurons with a 3D compound resolution routinely achieved only in a single color. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

High-Resolution Surface Reconstruction from Imagery for Close Range Cultural Heritage Applications

NASA Astrophysics Data System (ADS)

Wenzel, K.; Abdel-Wahab, M.; Cefalu, A.; Fritsch, D.

2012-07-01

The recording of high resolution point clouds with sub-mm resolution is a demanding and cost intensive task, especially with current equipment like handheld laser scanners. We present an image based approached, where techniques of image matching and dense surface reconstruction are combined with a compact and affordable rig of off-the-shelf industry cameras. Such cameras provide high spatial resolution with low radiometric noise, which enables a one-shot solution and thus an efficient data acquisition while satisfying high accuracy requirements. However, the largest drawback of image based solutions is often the acquisition of surfaces with low texture where the image matching process might fail. Thus, an additional structured light projector is employed, represented here by the pseudo-random pattern projector of the Microsoft Kinect. Its strong infrared-laser projects speckles of different sizes. By using dense image matching techniques on the acquired images, a 3D point can be derived for almost each pixel. The use of multiple cameras enables the acquisition of a high resolution point cloud with high accuracy for each shot. For the proposed system up to 3.5 Mio. 3D points with sub-mm accuracy can be derived per shot. The registration of multiple shots is performed by Structure and Motion reconstruction techniques, where feature points are used to derive the camera positions and rotations automatically without initial information.

A 3D MR-acquisition scheme for nonrigid bulk motion correction in simultaneous PET-MR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolbitsch, Christoph, E-mail: christoph.1.kolbitsch@kcl.ac.uk; Prieto, Claudia; Schaeffter, Tobias

Purpose: Positron emission tomography (PET) is a highly sensitive medical imaging technique commonly used to detect and assess tumor lesions. Magnetic resonance imaging (MRI) provides high resolution anatomical images with different contrasts and a range of additional information important for cancer diagnosis. Recently, simultaneous PET-MR systems have been released with the promise to provide complementary information from both modalities in a single examination. Due to long scan times, subject nonrigid bulk motion, i.e., changes of the patient's position on the scanner table leading to nonrigid changes of the patient's anatomy, during data acquisition can negatively impair image quality and tracermore » uptake quantification. A 3D MR-acquisition scheme is proposed to detect and correct for nonrigid bulk motion in simultaneously acquired PET-MR data. Methods: A respiratory navigated three dimensional (3D) MR-acquisition with Radial Phase Encoding (RPE) is used to obtain T1- and T2-weighted data with an isotropic resolution of 1.5 mm. Healthy volunteers are asked to move the abdomen two to three times during data acquisition resulting in overall 19 movements at arbitrary time points. The acquisition scheme is used to retrospectively reconstruct dynamic 3D MR images with different temporal resolutions. Nonrigid bulk motion is detected and corrected in this image data. A simultaneous PET acquisition is simulated and the effect of motion correction is assessed on image quality and standardized uptake values (SUV) for lesions with different diameters. Results: Six respiratory gated 3D data sets with T1- and T2-weighted contrast have been obtained in healthy volunteers. All bulk motion shifts have successfully been detected and motion fields describing the transformation between the different motion states could be obtained with an accuracy of 1.71 ± 0.29 mm. The PET simulation showed errors of up to 67% in measured SUV due to bulk motion which could be reduced to less than 10% with the proposed motion compensation approach. Conclusions: A MR acquisition scheme which yields both high resolution 3D anatomical data and highly accurate nonrigid motion information without an increase in scan time is presented. The proposed method leads to a strong improvement in both MR and PET image quality and ensures an accurate assessment of tracer uptake.« less

Brain single-photon emission CT physics principles.

PubMed

Accorsi, R

2008-08-01

The basic principles of scintigraphy are reviewed and extended to 3D imaging. Single-photon emission computed tomography (SPECT) is a sensitive and specific 3D technique to monitor in vivo functional processes in both clinical and preclinical studies. SPECT/CT systems are becoming increasingly common and can provide accurately registered anatomic information as well. In general, SPECT is affected by low photon-collection efficiency, but in brain imaging, not all of the large FOV of clinical gamma cameras is needed: The use of fan- and cone-beam collimation trades off the unused FOV for increased sensitivity and resolution. The design of dedicated cameras aims at increased angular coverage and resolution by minimizing the distance from the patient. The corrections needed for quantitative imaging are challenging but can take advantage of the relative spatial uniformity of attenuation and scatter. Preclinical systems can provide submillimeter resolution in small animal brain imaging with workable sensitivity.

Thermoacoustic imaging over large field of view for three-dimensional breast tumor localization: a phantom study.

PubMed

Fu, Yong; Ji, Zhong; Ding, Wenzheng; Ye, Fanghao; Lou, Cunguang

2014-11-01

Previous studies demonstrated that thermoacoustic imaging (TAI) has great potential for breast tumor detection. However, large field of view (FOV) imaging remains a long-standing challenge for three-dimensional (3D) breast tumor localization. Here, the authors propose a practical TAI system for noninvasive 3D localization of breast tumors with large FOV through the use of ultrashort microwave pulse (USMP). A USMP generator was employed for TAI. The energy density required for quality imaging and the corresponding microwave-to-acoustic conversion efficiency were compared with that of conventional TAI. The microwave energy distribution, imaging depth, resolution, and 3D imaging capabilities were then investigated. Finally, a breast phantom embedded with a laboratory-grown tumor was imaged to evaluate the FOV performance of the USMP TAI system, under a simulated clinical situation. A radiation energy density equivalent to just 1.6%-2.2% of that for conventional submicrosecond microwave TAI was sufficient to obtain a thermoacoustic signal with the required signal-to-noise ratio. This result clearly demonstrated a significantly higher microwave-to-acoustic conversion efficiency of USMP TAI compared to that of conventional TAI. The USMP TAI system achieved 61 mm imaging depth and 12 × 12 cm(2) microwave radiation area. The volumetric image of a copper target measured at depth of 4-6 cm matched well with the actual shape and the resolution reaches 230 μm. The TAI of the breast phantom was precisely localized to an accuracy of 0.1 cm over an 8 × 8 cm(2) FOV. The experimental results demonstrated that the USMP TAI system offered significant potential for noninvasive clinical detection and 3D localization of deep breast tumors, with low microwave radiation dose and high spatial resolution over a sufficiently large FOV.

A comparison of needle tip localization accuracy using 2D and 3D trans-rectal ultrasound for high-dose-rate prostate cancer brachytherapy treatment planning

NASA Astrophysics Data System (ADS)

Hrinivich, W. Thomas; Hoover, Douglas A.; Surry, Kathleen; Edirisinghe, Chandima; Montreuil, Jacques; D'Souza, David; Fenster, Aaron; Wong, Eugene

2016-03-01

Background: High-dose-rate brachytherapy (HDR-BT) is a prostate cancer treatment option involving the insertion of hollow needles into the gland through the perineum to deliver a radioactive source. Conventional needle imaging involves indexing a trans-rectal ultrasound (TRUS) probe in the superior/inferior (S/I) direction, using the axial transducer to produce an image set for organ segmentation. These images have limited resolution in the needle insertion direction (S/I), so the sagittal transducer is used to identify needle tips, requiring a manual registration with the axial view. This registration introduces a source of uncertainty in the final segmentations and subsequent treatment plan. Our lab has developed a device enabling 3D-TRUS guided insertions with high S/I spatial resolution, eliminating the need to align axial and sagittal views. Purpose: To compare HDR-BT needle tip localization accuracy between 2D and 3D-TRUS. Methods: 5 prostate cancer patients underwent conventional 2D TRUS guided HDR-BT, during which 3D images were also acquired for post-operative registration and segmentation. Needle end-length measurements were taken, providing a gold standard for insertion depths. Results: 73 needles were analyzed from all 5 patients. Needle tip position differences between imaging techniques was found to be largest in the S/I direction with mean+/-SD of -2.5+/-4.0 mm. End-length measurements indicated that 3D TRUS provided statistically significantly lower mean+/-SD insertion depth error of -0.2+/-3.4 mm versus 2.3+/-3.7 mm with 2D guidance (p < .001). Conclusions: 3D TRUS may provide more accurate HDR-BT needle localization than conventional 2D TRUS guidance for the majority of HDR-BT needles.

Spatially encoded phase-contrast MRI-3D MRI movies of 1D and 2D structures at millisecond resolution.

PubMed

Merboldt, Klaus-Dietmar; Uecker, Martin; Voit, Dirk; Frahm, Jens

2011-10-01

This work demonstrates that the principles underlying phase-contrast MRI may be used to encode spatial rather than flow information along a perpendicular dimension, if this dimension contains an MRI-visible object at only one spatial location. In particular, the situation applies to 3D mapping of curved 2D structures which requires only two projection images with different spatial phase-encoding gradients. These phase-contrast gradients define the field of view and mean spin-density positions of the object in the perpendicular dimension by respective phase differences. When combined with highly undersampled radial fast low angle shot (FLASH) and image reconstruction by regularized nonlinear inversion, spatial phase-contrast MRI allows for dynamic 3D mapping of 2D structures in real time. First examples include 3D MRI movies of the acting human hand at a temporal resolution of 50 ms. With an even simpler technique, 3D maps of curved 1D structures may be obtained from only three acquisitions of a frequency-encoded MRI signal with two perpendicular phase encodings. Here, 3D MRI movies of a rapidly rotating banana were obtained at 5 ms resolution or 200 frames per second. In conclusion, spatial phase-contrast 3D MRI of 2D or 1D structures is respective two or four orders of magnitude faster than conventional 3D MRI. Copyright © 2011 Wiley-Liss, Inc.

Assessing the intrinsic precision of 3D/3D rigid image registration results for patient setup in the absence of a ground truth.

PubMed

Wu, Jian; Murphy, Martin J

2010-06-01

To assess the precision and robustness of patient setup corrections computed from 3D/3D rigid registration methods using image intensity, when no ground truth validation is possible. Fifteen pairs of male pelvic CTs were rigidly registered using four different in-house registration methods. Registration results were compared for different resolutions and image content by varying the image down-sampling ratio and by thresholding out soft tissue to isolate bony landmarks. Intrinsic registration precision was investigated by comparing the different methods and by reversing the source and the target roles of the two images being registered. The translational reversibility errors for successful registrations ranged from 0.0 to 1.69 mm. Rotations were less than 1 degrees. Mutual information failed in most registrations that used only bony landmarks. The magnitude of the reversibility error was strongly correlated with the success/ failure of each algorithm to find the global minimum. Rigid image registrations have an intrinsic uncertainty and robustness that depends on the imaging modality, the registration algorithm, the image resolution, and the image content. In the absence of an absolute ground truth, the variation in the shifts calculated by several different methods provides a useful estimate of that uncertainty. The difference observed by reversing the source and target images can be used as an indication of robust convergence.

High-Resolution Large-Field-of-View Three-Dimensional Hologram Display System and Method Thereof

NASA Technical Reports Server (NTRS)

Chao, Tien-Hsin (Inventor); Mintz, Frederick W. (Inventor); Tsou, Peter (Inventor); Bryant, Nevin A. (Inventor)

2001-01-01

A real-time, dynamic, free space-virtual reality, 3-D image display system is enabled by using a unique form of Aerogel as the primary display media. A preferred embodiment of this system comprises a 3-D mosaic topographic map which is displayed by fusing four projected hologram images. In this embodiment, four holographic images are projected from four separate holograms. Each holographic image subtends a quadrant of the 4(pi) solid angle. By fusing these four holographic images, a static 3-D image such as a featured terrain map would be visible for 360 deg in the horizontal plane and 180 deg in the vertical plane. An input, either acquired by 3-D image sensor or generated by computer animation, is first converted into a 2-D computer generated hologram (CGH). This CGH is then downloaded into large liquid crystal (LC) panel. A laser projector illuminates the CGH-filled LC panel and generates and displays a real 3-D image in the Aerogel matrix.

Restoring 2D content from distorted documents.

PubMed

Brown, Michael S; Sun, Mingxuan; Yang, Ruigang; Yun, Lin; Seales, W Brent

2007-11-01

This paper presents a framework to restore the 2D content printed on documents in the presence of geometric distortion and non-uniform illumination. Compared with textbased document imaging approaches that correct distortion to a level necessary to obtain sufficiently readable text or to facilitate optical character recognition (OCR), our work targets nontextual documents where the original printed content is desired. To achieve this goal, our framework acquires a 3D scan of the document's surface together with a high-resolution image. Conformal mapping is used to rectify geometric distortion by mapping the 3D surface back to a plane while minimizing angular distortion. This conformal "deskewing" assumes no parametric model of the document's surface and is suitable for arbitrary distortions. Illumination correction is performed by using the 3D shape to distinguish content gradient edges from illumination gradient edges in the high-resolution image. Integration is performed using only the content edges to obtain a reflectance image with significantly less illumination artifacts. This approach makes no assumptions about light sources and their positions. The results from the geometric and photometric correction are combined to produce the final output.

Enhancing the performance of the light field microscope using wavefront coding

PubMed Central

Cohen, Noy; Yang, Samuel; Andalman, Aaron; Broxton, Michael; Grosenick, Logan; Deisseroth, Karl; Horowitz, Mark; Levoy, Marc

2014-01-01

Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective’s back focal plane and at the microscope’s native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain. PMID:25322056

Enhancing the performance of the light field microscope using wavefront coding.

PubMed

Cohen, Noy; Yang, Samuel; Andalman, Aaron; Broxton, Michael; Grosenick, Logan; Deisseroth, Karl; Horowitz, Mark; Levoy, Marc

2014-10-06

Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective's back focal plane and at the microscope's native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain.

Novel low-cost 2D/3D switchable autostereoscopic system for notebook computers and other portable devices

NASA Astrophysics Data System (ADS)

Eichenlaub, Jesse B.

1995-03-01

Mounting a lenticular lens in front of a flat panel display is a well known, inexpensive, and easy way to create an autostereoscopic system. Such a lens produces half resolution 3D images because half the pixels on the LCD are seen by the left eye and half by the right eye. This may be acceptable for graphics, but it makes full resolution text, as displayed by common software, nearly unreadable. Very fine alignment tolerances normally preclude the possibility of removing and replacing the lens in order to switch between 2D and 3D applications. Lenticular lens based displays are therefore limited to use as dedicated 3D devices. DTI has devised a technique which removes this limitation, allowing switching between full resolution 2D and half resolution 3D imaging modes. A second element, in the form of a concave lenticular lens array whose shape is exactly the negative of the first lens, is mounted on a hinge so that it can be swung down over the first lens array. When so positioned the two lenses cancel optically, allowing the user to see full resolution 2D for text or numerical applications. The two lenses, having complementary shapes, naturally tend to nestle together and snap into perfect alignment when pressed together--thus obviating any need for user operated alignment mechanisms. This system represents an ideal solution for laptop and notebook computer applications. It was devised to meet the stringent requirements of a laptop computer manufacturer including very compact size, very low cost, little impact on existing manufacturing or assembly procedures, and compatibility with existing full resolution 2D text- oriented software as well as 3D graphics. Similar requirements apply to high and electronic calculators, several models of which now use LCDs for the display of graphics.

Comparison of two structured illumination techniques based on different 3D illumination patterns

NASA Astrophysics Data System (ADS)

Shabani, H.; Patwary, N.; Doblas, A.; Saavedra, G.; Preza, C.

2017-02-01

Manipulating the excitation pattern in optical microscopy has led to several super-resolution techniques. Among different patterns, the lateral sinusoidal excitation was used for the first demonstration of structured illumination microscopy (SIM), which provides the fastest SIM acquisition system (based on the number of raw images required) compared to the multi-spot illumination approach. Moreover, 3D patterns that include lateral and axial variations in the illumination have attracted more attention recently as they address resolution enhancement in three dimensions. A threewave (3W) interference technique based on coherent illumination has already been shown to provide super-resolution and optical sectioning in 3D-SIM. In this paper, we investigate a novel tunable technique that creates a 3D pattern from a set of multiple incoherently illuminated parallel slits that act as light sources for a Fresnel biprism. This setup is able to modulate the illumination pattern in the object space both axially and laterally with adjustable modulation frequencies. The 3D forward model for the new system is developed here to consider the effect of the axial modulation due to the 3D patterned illumination. The performance of 3D-SIM based on 3W interference and the tunable system are investigated in simulation and compared based on two different criteria. First, restored images obtained for both 3D-SIM systems using a generalized Wiener filter are compared to determine the effect of the illumination pattern on the reconstruction. Second, the effective frequency response of both systems is studied to determine the axial and lateral resolution enhancement that is obtained in each case.

Portable optical-resolution photoacoustic microscopy for volumetric imaging of multiscale organisms.

PubMed

Jin, Tian; Guo, Heng; Yao, Lei; Xie, Huikai; Jiang, Huabei; Xi, Lei

2018-04-01

Photoacoustic microscopy (PAM) provides a fundamentally new tool for a broad range of studies of biological structures and functions. However, the use of PAM has been largely limited to small vertebrates due to the large size/weight and the inconvenience of the equipment. Here, we describe a portable optical-resolution photoacoustic microscopy (pORPAM) system for 3-dimensional (3D) imaging of small-to-large rodents and humans with a high spatiotemporal resolution and a large field of view. We show extensive applications of pORPAM to multiscale animals including mice and rabbits. In addition, we image the 3D vascular networks of human lips, and demonstrate the feasibility of pORPAM to observe the recovery process of oral ulcer and cancer-associated capillary loops in human oral cavities. This technology is promising for broad biomedical studies from fundamental biology to clinical diseases. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-Dimensional Photoactivated Localization Microscopy with Genetically Expressed Probes

PubMed Central

Temprine, Kelsey; York, Andrew G.; Shroff, Hari

2017-01-01

Photoactivated localization microscopy (PALM) and related single-molecule imaging techniques enable biological image acquisition at ~20 nm lateral and ~50–100 nm axial resolution. Although such techniques were originally demonstrated on single imaging planes close to the coverslip surface, recent technical developments now enable the 3D imaging of whole fixed cells. We describe methods for converting a 2D PALM into a system capable of acquiring such 3D images, with a particular emphasis on instrumentation that is compatible with choosing relatively dim, genetically expressed photoactivatable fluorescent proteins (PA-FPs) as PALM probes. After reviewing the basics of 2D PALM, we detail astigmatic and multiphoton imaging approaches well suited to working with PA-FPs. We also discuss the use of open-source localization software appropriate for 3D PALM. PMID:25391803

Optimized Deconvolution for Maximum Axial Resolution in Three-Dimensional Aberration-Corrected Scanning Transmission Electron Microscopy

PubMed Central

Ramachandra, Ranjan; de Jonge, Niels

2012-01-01

Three-dimensional (3D) data sets were recorded of gold nanoparticles placed on both sides of silicon nitride membranes using focal series aberration-corrected scanning transmission electron microscopy (STEM). The deconvolution of the 3D datasets was optimized to obtain the highest possible axial resolution. The deconvolution involved two different point spread function (PSF)s, each calculated iteratively via blind deconvolution.. Supporting membranes of different thicknesses were tested to study the effect of beam broadening on the deconvolution. It was found that several iterations of deconvolution was efficient in reducing the imaging noise. With an increasing number of iterations, the axial resolution was increased, and most of the structural information was preserved. Additional iterations improved the axial resolution by maximal a factor of 4 to 6, depending on the particular dataset, and up to 8 nm maximal, but at the cost of a reduction of the lateral size of the nanoparticles in the image. Thus, the deconvolution procedure optimized for highest axial resolution is best suited for applications where one is interested in the 3D locations of nanoparticles only. PMID:22152090

3D resolved mapping of optical aberrations in thick tissues

PubMed Central

Zeng, Jun; Mahou, Pierre; Schanne-Klein, Marie-Claire; Beaurepaire, Emmanuel; Débarre, Delphine

2012-01-01

We demonstrate a simple method for mapping optical aberrations with 3D resolution within thick samples. The method relies on the local measurement of the variation in image quality with externally applied aberrations. We discuss the accuracy of the method as a function of the signal strength and of the aberration amplitude and we derive the achievable resolution for the resulting measurements. We then report on measured 3D aberration maps in human skin biopsies and mouse brain slices. From these data, we analyse the consequences of tissue structure and refractive index distribution on aberrations and imaging depth in normal and cleared tissue samples. The aberration maps allow the estimation of the typical aplanetism region size over which aberrations can be uniformly corrected. This method and data pave the way towards efficient correction strategies for tissue imaging applications. PMID:22876353

Cardiac muscle organization revealed in 3-D by imaging whole-mount mouse hearts using two-photon fluorescence and confocal microscopy.

PubMed

Sivaguru, Mayandi; Fried, Glenn; Sivaguru, Barghav S; Sivaguru, Vignesh A; Lu, Xiaochen; Choi, Kyung Hwa; Saif, M Taher A; Lin, Brian; Sadayappan, Sakthivel

2015-11-01

The ability to image the entire adult mouse heart at high resolution in 3-D would provide enormous advantages in the study of heart disease. However, a technique for imaging nuclear/cellular detail as well as the overall structure of the entire heart in 3-D with minimal effort is lacking. To solve this problem, we modified the benzyl alcohol:benzyl benzoate (BABB) clearing technique by labeling mouse hearts with periodic acid Schiff (PAS) stain. We then imaged the hearts with a combination of two-photon fluorescence microscopy and automated tile-scan imaging/stitching. Utilizing the differential spectral properties of PAS, we could identify muscle and nuclear compartments in the heart. We were also able to visualize the differences between a 3-month-old normal mouse heart and a mouse heart that had undergone heart failure due to the expression of cardiac myosin binding protein-C (cMyBP-C) gene mutation (t/t). Using 2-D and 3-D morphometric analysis, we found that the t/t heart had anomalous ventricular shape, volume, and wall thickness, as well as a disrupted sarcomere pattern. We further validated our approach using decellularized hearts that had been cultured with 3T3 fibroblasts, which were tracked using a nuclear label. We were able to detect the 3T3 cells inside the decellularized intact heart tissue, achieving nuclear/cellular resolution in 3-D. The combination of labeling, clearing, and two-photon microscopy together with tiling eliminates laborious and time-consuming physical sectioning, alignment, and 3-D reconstruction.

Phantom studies investigating extravascular density imaging for partial volume correction of 3-D PET /sup 18/FDG studies

NASA Astrophysics Data System (ADS)

Wassenaar, R. W.; Beanlands, R. S. B.; deKemp, R. A.

2004-02-01

Limited scanner resolution and cardiac motion contribute to partial volume (PV) averaging of cardiac PET images. An extravascular (EV) density image, created from the subtraction of a blood pool scan from a transmission image, has been used to correct for PV averaging in H/sub 2//sup 15/O studies using 2-D imaging but not with 3-D imaging of other tracers such as /sup 18/FDG. A cardiac phantom emulating the left ventricle was used to characterize the method for use in 3-D PET studies. Measurement of the average myocardial activity showed PV losses of 32% below the true activity (p<0.001). Initial application of the EV density correction still yielded a myocardial activity 13% below the true value (p<0.001). This failure of the EV density image was due to the 1.66 mm thick plastic barrier separating the myocardial and ventricular chambers within the phantom. Upon removal of this artifact by morphological dilation of the blood pool, the corrected myocardial value was within 2% of the true value (p=ns). Spherical ROIs (diameter of 2 to 10 mm), evenly distributed about the myocardium, were also used to calculate the average activity. The EV density image was able to account for PV averaging throughout the range of diameters to within a 5% accuracy, however, a small bias was seen as the size of the ROIs increased. This indicated a slight mismatch between the emission and transmission image resolutions, a result of the difference in data acquisitions (i.e., span and ring difference) and default smoothing. These results show that the use of EV density image to correct for PV averaging is possible with 3-D PET. A method of correcting barrier effects in phantoms has been presented, as well as a process for evaluating resolution mismatch.

Ultrahigh-resolution imaging of the human brain with phase-cycled balanced steady-state free precession at 7 T.

PubMed

Zeineh, Michael M; Parekh, Mansi B; Zaharchuk, Greg; Su, Jason H; Rosenberg, Jarrett; Fischbein, Nancy J; Rutt, Brian K

2014-05-01

The objectives of this study were to acquire ultra-high resolution images of the brain using balanced steady-state free precession (bSSFP) at 7 T and to identify the potential utility of this sequence. Eight volunteers participated in this study after providing informed consent. Each volunteer was scanned with 8 phase cycles of bSSFP at 0.4-mm isotropic resolution using 0.5 number of excitations and 2-dimensional parallel acceleration of 1.75 × 1.75. Each phase cycle required 5 minutes of scanning, with pauses between the phase cycles allowing short periods of rest. The individual phase cycles were aligned and then averaged. The same volunteers underwent scanning using 3-dimensional (3D) multiecho gradient recalled echo at 0.8-mm isotropic resolution, 3D Cube T2 at 0.7-mm isotropic resolution, and thin-section coronal oblique T2-weighted fast spin echo at 0.22 × 0.22 × 2.0-mm resolution for comparison. Two neuroradiologists assessed image quality and potential research and clinical utility. The volunteers generally tolerated the scan sessions well, and composite high-resolution bSSFP images were produced for each volunteer. Rater analysis demonstrated that bSSFP had a superior 3D visualization of the microarchitecture of the hippocampus, very good contrast to delineate the borders of the subthalamic nucleus, and relatively good B1 homogeneity throughout. In addition to an excellent visualization of the cerebellum, subtle details of the brain and skull base anatomy were also easier to identify on the bSSFP images, including the line of Gennari, membrane of Liliequist, and cranial nerves. Balanced steady-state free precession had a strong iron contrast similar to or better than the comparison sequences. However, cortical gray-white contrast was significantly better with Cube T2 and T2-weighted fast spin echo. Balanced steady-state free precession can facilitate ultrahigh-resolution imaging of the brain. Although total imaging times are long, the individually short phase cycles can be acquired separately, improving examination tolerability. These images may be beneficial for studies of the hippocampus, iron-containing structures such as the subthalamic nucleus and line of Gennari, and the basal cisterns and their contents.

2D and 3D MALDI-imaging: conceptual strategies for visualization and data mining.

PubMed

Thiele, Herbert; Heldmann, Stefan; Trede, Dennis; Strehlow, Jan; Wirtz, Stefan; Dreher, Wolfgang; Berger, Judith; Oetjen, Janina; Kobarg, Jan Hendrik; Fischer, Bernd; Maass, Peter

2014-01-01

3D imaging has a significant impact on many challenges in life sciences, because biology is a 3-dimensional phenomenon. Current 3D imaging-technologies (various types MRI, PET, SPECT) are labeled, i.e. they trace the localization of a specific compound in the body. In contrast, 3D MALDI mass spectrometry-imaging (MALDI-MSI) is a label-free method imaging the spatial distribution of molecular compounds. It complements 3D imaging labeled methods, immunohistochemistry, and genetics-based methods. However, 3D MALDI-MSI cannot tap its full potential due to the lack of statistical methods for analysis and interpretation of large and complex 3D datasets. To overcome this, we established a complete and robust 3D MALDI-MSI pipeline combined with efficient computational data analysis methods for 3D edge preserving image denoising, 3D spatial segmentation as well as finding colocalized m/z values, which will be reviewed here in detail. Furthermore, we explain, why the integration and correlation of the MALDI imaging data with other imaging modalities allows to enhance the interpretation of the molecular data and provides visualization of molecular patterns that may otherwise not be apparent. Therefore, a 3D data acquisition workflow is described generating a set of 3 different dimensional images representing the same anatomies. First, an in-vitro MRI measurement is performed which results in a three-dimensional image modality representing the 3D structure of the measured object. After sectioning the 3D object into N consecutive slices, all N slices are scanned using an optical digital scanner, enabling for performing the MS measurements. Scanning the individual sections results into low-resolution images, which define the base coordinate system for the whole pipeline. The scanned images conclude the information from the spatial (MRI) and the mass spectrometric (MALDI-MSI) dimension and are used for the spatial three-dimensional reconstruction of the object performed by image registration techniques. Different strategies for automatic serial image registration applied to MS datasets are outlined in detail. The third image modality is histology driven, i.e. a digital scan of the histological stained slices in high-resolution. After fusion of reconstructed scan images and MRI the slice-related coordinates of the mass spectra can be propagated into 3D-space. After image registration of scan images and histological stained images, the anatomical information from histology is fused with the mass spectra from MALDI-MSI. As a result of the described pipeline we have a set of 3 dimensional images representing the same anatomies, i.e. the reconstructed slice scans, the spectral images as well as corresponding clustering results, and the acquired MRI. Great emphasis is put on the fact that the co-registered MRI providing anatomical details improves the interpretation of 3D MALDI images. The ability to relate mass spectrometry derived molecular information with in vivo and in vitro imaging has potentially important implications. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013. Published by Elsevier B.V.

SU-E-T-296: Dosimetric Analysis of Small Animal Image-Guided Irradiator Using High Resolution Optical CT Imaging of 3D Dosimeters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Na, Y; Qian, X; Wuu, C

Purpose: To verify the dosimetric characteristics of a small animal image-guided irradiator using a high-resolution of optical CT imaging of 3D dosimeters. Methods: PRESAEGE 3D dosimeters were used to determine dosimetric characteristics of a small animal image-guided irradiator and compared with EBT2 films. Cylindrical PRESAGE dosimeters with 7cm height and 6cm diameter were placed along the central axis of the beam. The films were positioned between 6×6cm{sup 2} cubed plastic water phantoms perpendicular to the beam direction with multiple depths. PRESAGE dosimeters and EBT2 films were then irradiated with the irradiator beams at 220kVp and 13mA. Each of irradiated PRESAGEmore » dosimeters named PA1, PA2, PB1, and PB2, was independently scanned using a high-resolution single laser beam optical CT scanner. The transverse images were reconstructed with a 0.1mm high-resolution pixel. A commercial Epson Expression 10000XL flatbed scanner was used for readout of irradiated EBT2 films at a 0.4mm pixel resolution. PDD curves and beam profiles were measured for the irradiated PRESAGE dosimeters and EBT2 films. Results: The PDD agreements between the irradiated PRESAGE dosimeter PA1, PA2, PB1, PB2 and the EB2 films were 1.7, 2.3, 1.9, and 1.9% for the multiple depths at 1, 5, 10, 15, 20, 30, 40 and 50mm, respectively. The FWHM measurements for each PRESAEGE dosimeter and film agreed with 0.5, 1.1, 0.4, and 1.7%, respectively, at 30mm depth. Both PDD and FWHM measurements for the PRESAGE dosimeters and the films agreed overall within 2%. The 20%–80% penumbral widths of each PRESAGE dosimeter and the film at a given depth were respectively found to be 0.97, 0.91, 0.79, 0.88, and 0.37mm. Conclusion: Dosimetric characteristics of a small animal image-guided irradiator have been demonstrated with the measurements of PRESAGE dosimeter and EB2 film. With the high resolution and accuracy obtained from this 3D dosimetry system, precise targeting small animal irradiation can be achieved.« less

Free-breathing 3D diffusion MRI for high-resolution hepatic metastasis characterization in small animals.

PubMed

Ribot, Emeline J; Trotier, Aurélien J; Castets, Charles R; Dallaudière, Benjamin; Thiaudière, Eric; Franconi, Jean-Michel; Miraux, Sylvain

2016-02-01

The goal of this study was to develop a 3D diffusion weighted sequence for free breathing liver imaging in small animals at high magnetic field. Hepatic metastases were detected and the apparent diffusion coefficients (ADC) were measured. A 3D SE-EPI sequence was developed by (i) inserting a water-selective excitation radiofrequency pulse to suppress adipose tissue signal and (ii) bipolar diffusion gradients to decrease the sensitivity to respiration motion. Mice with hepatic metastases were imaged at 7T by applying b values from 200 to 1100 s/mm(2). 3D images with high spatial resolution (182 × 156 × 125 µm) were obtained in only 8 min 32 s. The modified DW-SE-EPI sequence allowed to obtain 3D abdominal images of healthy mice with fat SNR 2.5 times lower than without any fat suppression method and sharpness 2.8 times higher than on respiration-triggered images. Due to the high spatial resolution, the core and the periphery of disseminated hepatic metastases were differentiated at high b-values only, demonstrating the presence of edema and proliferating cells (with ADC of 2.65 × 10(-3) and 1.55 × 10(-3) mm(2)/s, respectively). Furthermore, these metastases were accurately distinguished from proliferating ones within the same animal at high b-values (mean ADC of 0.38 × 10(-3) mm(2)/s). Metastases of less than 1.7 mm(3) diameter were detected. The new 3D SE-EPI sequence enabled to obtain diffusion information within liver metastases. In addition of intra-metastasis heterogeneity, differences in diffusion were measured between metastases within an animal. This sequence could be used to obtain diffusion information at high magnetic field.

How does c-view image quality compare with conventional 2D FFDM?

PubMed

Nelson, Jeffrey S; Wells, Jered R; Baker, Jay A; Samei, Ehsan

2016-05-01

The FDA approved the use of digital breast tomosynthesis (DBT) in 2011 as an adjunct to 2D full field digital mammography (FFDM) with the constraint that all DBT acquisitions must be paired with a 2D image to assure adequate interpretative information is provided. Recently manufacturers have developed methods to provide a synthesized 2D image generated from the DBT data with the hope of sparing patients the radiation exposure from the FFDM acquisition. While this much needed alternative effectively reduces the total radiation burden, differences in image quality must also be considered. The goal of this study was to compare the intrinsic image quality of synthesized 2D c-view and 2D FFDM images in terms of resolution, contrast, and noise. Two phantoms were utilized in this study: the American College of Radiology mammography accreditation phantom (ACR phantom) and a novel 3D printed anthropomorphic breast phantom. Both phantoms were imaged using a Hologic Selenia Dimensions 3D system. Analysis of the ACR phantom includes both visual inspection and objective automated analysis using in-house software. Analysis of the 3D anthropomorphic phantom includes visual assessment of resolution and Fourier analysis of the noise. Using ACR-defined scoring criteria for the ACR phantom, the FFDM images scored statistically higher than c-view according to both the average observer and automated scores. In addition, between 50% and 70% of c-view images failed to meet the nominal minimum ACR accreditation requirements-primarily due to fiber breaks. Software analysis demonstrated that c-view provided enhanced visualization of medium and large microcalcification objects; however, the benefits diminished for smaller high contrast objects and all low contrast objects. Visual analysis of the anthropomorphic phantom showed a measureable loss of resolution in the c-view image (11 lp/mm FFDM, 5 lp/mm c-view) and loss in detection of small microcalcification objects. Spectral analysis of the anthropomorphic phantom showed higher total noise magnitude in the FFDM image compared with c-view. Whereas the FFDM image contained approximately white noise texture, the c-view image exhibited marked noise reduction at midfrequency and high frequency with far less noise suppression at low frequencies resulting in a mottled noise appearance. Their analysis demonstrates many instances where the c-view image quality differs from FFDM. Compared to FFDM, c-view offers a better depiction of objects of certain size and contrast, but provides poorer overall resolution and noise properties. Based on these findings, the utilization of c-view images in the clinical setting requires careful consideration, especially if considering the discontinuation of FFDM imaging. Not explicitly explored in this study is how the combination of DBT + c-view performs relative to DBT + FFDM or FFDM alone.

Multi-resolution Gabor wavelet feature extraction for needle detection in 3D ultrasound

NASA Astrophysics Data System (ADS)

Pourtaherian, Arash; Zinger, Svitlana; Mihajlovic, Nenad; de With, Peter H. N.; Huang, Jinfeng; Ng, Gary C.; Korsten, Hendrikus H. M.

2015-12-01

Ultrasound imaging is employed for needle guidance in various minimally invasive procedures such as biopsy guidance, regional anesthesia and brachytherapy. Unfortunately, a needle guidance using 2D ultrasound is very challenging, due to a poor needle visibility and a limited field of view. Nowadays, 3D ultrasound systems are available and more widely used. Consequently, with an appropriate 3D image-based needle detection technique, needle guidance and interventions may significantly be improved and simplified. In this paper, we present a multi-resolution Gabor transformation for an automated and reliable extraction of the needle-like structures in a 3D ultrasound volume. We study and identify the best combination of the Gabor wavelet frequencies. High precision in detecting the needle voxels leads to a robust and accurate localization of the needle for the intervention support. Evaluation in several ex-vivo cases shows that the multi-resolution analysis significantly improves the precision of the needle voxel detection from 0.23 to 0.32 at a high recall rate of 0.75 (gain 40%), where a better robustness and confidence were confirmed in the practical experiments.

Multiplexed phase-space imaging for 3D fluorescence microscopy.

PubMed

Liu, Hsiou-Yuan; Zhong, Jingshan; Waller, Laura

2017-06-26

Optical phase-space functions describe spatial and angular information simultaneously; examples of optical phase-space functions include light fields in ray optics and Wigner functions in wave optics. Measurement of phase-space enables digital refocusing, aberration removal and 3D reconstruction. High-resolution capture of 4D phase-space datasets is, however, challenging. Previous scanning approaches are slow, light inefficient and do not achieve diffraction-limited resolution. Here, we propose a multiplexed method that solves these problems. We use a spatial light modulator (SLM) in the pupil plane of a microscope in order to sequentially pattern multiplexed coded apertures while capturing images in real space. Then, we reconstruct the 3D fluorescence distribution of our sample by solving an inverse problem via regularized least squares with a proximal accelerated gradient descent solver. We experimentally reconstruct a 101 Megavoxel 3D volume (1010×510×500µm with NA 0.4), demonstrating improved acquisition time, light throughput and resolution compared to scanning aperture methods. Our flexible patterning scheme further allows sparsity in the sample to be exploited for reduced data capture.

Accelerated high-resolution photoacoustic tomography via compressed sensing

NASA Astrophysics Data System (ADS)

Arridge, Simon; Beard, Paul; Betcke, Marta; Cox, Ben; Huynh, Nam; Lucka, Felix; Ogunlade, Olumide; Zhang, Edward

2016-12-01

Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant. We demonstrate that combining model-based, variational image reconstruction methods using spatial sparsity constraints with the development of novel PAT acquisition systems capable of sub-sampling the acoustic wave field can dramatically increase the acquisition speed while maintaining a good spatial resolution: first, we describe and model two general spatial sub-sampling schemes. Then, we discuss how to implement them using the FP interferometer and demonstrate the potential of these novel compressed sensing PAT devices through simulated data from a realistic numerical phantom and through measured data from a dynamic experimental phantom as well as from in vivo experiments. Our results show that images with good spatial resolution and contrast can be obtained from highly sub-sampled PAT data if variational image reconstruction techniques that describe the tissues structures with suitable sparsity-constraints are used. In particular, we examine the use of total variation (TV) regularization enhanced by Bregman iterations. These novel reconstruction strategies offer new opportunities to dramatically increase the acquisition speed of photoacoustic scanners that employ point-by-point sequential scanning as well as reducing the channel count of parallelized schemes that use detector arrays.

High-resolution Imaging of Deuterium-Tritium Capsule Implosions on the National Ignition Facility

NASA Astrophysics Data System (ADS)

Bachmann, Benjamin; Rygg, Ryan; Collins, Gilbert; Patel, Pravesh

2017-10-01

Highly-resolved 3-D simulations of inertial confinement fusion (ICF) implosions predict a hot spot plasma that exhibits complex micron-scale structure originating from a variety of 3-D perturbations. Experimental diagnosis of these conditions requires high spatial resolution imaging techniques. X-ray penumbral imaging can improve the spatial resolution over pinhole imaging while simultaneously increasing the detected photon yield at x-ray energies where the ablator opacity becomes negligible. Here we report on the first time-integrated x-ray penumbral imaging experiments of ICF capsule implosions at the National Ignition Facility that achieved spatial resolution as high as 4 micrometer. 6 to 30 keV hot spot images from layered DT implosions will be presented from a variety of experimental ICF campaigns, revealing previously unseen detail. It will be discussed how these and future results can be used to improve our physics understanding of inertially confined fusion plasmas by enabling spatially resolved measurements of hot spot properties, such as radiation energy, temperature or derived quantities. This work performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

Multiplexed 3D FRET imaging in deep tissue of live embryos

PubMed Central

Zhao, Ming; Wan, Xiaoyang; Li, Yu; Zhou, Weibin; Peng, Leilei

2015-01-01

Current deep tissue microscopy techniques are mostly restricted to intensity mapping of fluorophores, which significantly limit their applications in investigating biochemical processes in vivo. We present a deep tissue multiplexed functional imaging method that probes multiple Förster resonant energy transfer (FRET) sensors in live embryos with high spatial resolution. The method simultaneously images fluorescence lifetimes in 3D with multiple excitation lasers. Through quantitative analysis of triple-channel intensity and lifetime images, we demonstrated that Ca2+ and cAMP levels of live embryos expressing dual FRET sensors can be monitored simultaneously at microscopic resolution. The method is compatible with a broad range of FRET sensors currently available for probing various cellular biochemical functions. It opens the door to imaging complex cellular circuitries in whole live organisms. PMID:26387920

Handheld, rapidly switchable, anterior/posterior segment swept source optical coherence tomography probe

PubMed Central

Nankivil, Derek; Waterman, Gar; LaRocca, Francesco; Keller, Brenton; Kuo, Anthony N.; Izatt, Joseph A.

2015-01-01

We describe the first handheld, swept source optical coherence tomography (SSOCT) system capable of imaging both the anterior and posterior segments of the eye in rapid succession. A single 2D microelectromechanical systems (MEMS) scanner was utilized for both imaging modes, and the optical paths for each imaging mode were optimized for their respective application using a combination of commercial and custom optics. The system has a working distance of 26.1 mm and a measured axial resolution of 8 μm (in air). In posterior segment mode, the design has a lateral resolution of 9 μm, 7.4 mm imaging depth range (in air), 4.9 mm 6dB fall-off range (in air), and peak sensitivity of 103 dB over a 22° field of view (FOV). In anterior segment mode, the design has a lateral resolution of 24 μm, imaging depth range of 7.4 mm (in air), 6dB fall-off range of 4.5 mm (in air), depth-of-focus of 3.6 mm, and a peak sensitivity of 99 dB over a 17.5 mm FOV. In addition, the probe includes a wide-field iris imaging system to simplify alignment. A fold mirror assembly actuated by a bi-stable rotary solenoid was used to switch between anterior and posterior segment imaging modes, and a miniature motorized translation stage was used to adjust the objective lens position to correct for patient refraction between −12.6 and + 9.9 D. The entire probe weighs less than 630 g with a form factor of 20.3 x 9.5 x 8.8 cm. Healthy volunteers were imaged to illustrate imaging performance. PMID:26601014

A 3D imaging system integrating photoacoustic and fluorescence orthogonal projections for anatomical, functional and molecular assessment of rodent models

NASA Astrophysics Data System (ADS)

Brecht, Hans P.; Ivanov, Vassili; Dumani, Diego S.; Emelianov, Stanislav Y.; Anastasio, Mark A.; Ermilov, Sergey A.

2018-03-01

We have developed a preclinical 3D imaging instrument integrating photoacoustic tomography and fluorescence (PAFT) addressing known deficiencies in sensitivity and spatial resolution of the individual imaging components. PAFT is designed for simultaneous acquisition of photoacoustic and fluorescence orthogonal projections at each rotational position of a biological object, enabling direct registration of the two imaging modalities. Orthogonal photoacoustic projections are utilized to reconstruct large (21 cm3 ) volumes showing vascularized anatomical structures and regions of induced optical contrast with spatial resolution exceeding 100 µm. The major advantage of orthogonal fluorescence projections is significant reduction of background noise associated with transmitted or backscattered photons. The fluorescence imaging component of PAFT is used to boost detection sensitivity by providing low-resolution spatial constraint for the fluorescent biomarkers. PAFT performance characteristics were assessed by imaging optical and fluorescent contrast agents in tissue mimicking phantoms and in vivo. The proposed PAFT technology will enable functional and molecular volumetric imaging using fluorescent biomarkers, nanoparticles, and other photosensitive constructs mapped with high fidelity over robust anatomical structures, such as skin, central and peripheral vasculature, and internal organs.

Three-dimensional Hessian matrix-based quantitative vascular imaging of rat iris with optical-resolution photoacoustic microscopy in vivo

NASA Astrophysics Data System (ADS)

Zhao, Huangxuan; Wang, Guangsong; Lin, Riqiang; Gong, Xiaojing; Song, Liang; Li, Tan; Wang, Wenjia; Zhang, Kunya; Qian, Xiuqing; Zhang, Haixia; Li, Lin; Liu, Zhicheng; Liu, Chengbo

2018-04-01

For the diagnosis and evaluation of ophthalmic diseases, imaging and quantitative characterization of vasculature in the iris are very important. The recently developed photoacoustic imaging, which is ultrasensitive in imaging endogenous hemoglobin molecules, provides a highly efficient label-free method for imaging blood vasculature in the iris. However, the development of advanced vascular quantification algorithms is still needed to enable accurate characterization of the underlying vasculature. We have developed a vascular information quantification algorithm by adopting a three-dimensional (3-D) Hessian matrix and applied for processing iris vasculature images obtained with a custom-built optical-resolution photoacoustic imaging system (OR-PAM). For the first time, we demonstrate in vivo 3-D vascular structures of a rat iris with a the label-free imaging method and also accurately extract quantitative vascular information, such as vessel diameter, vascular density, and vascular tortuosity. Our results indicate that the developed algorithm is capable of quantifying the vasculature in the 3-D photoacoustic images of the iris in-vivo, thus enhancing the diagnostic capability of the OR-PAM system for vascular-related ophthalmic diseases in vivo.

Compact plane illumination plugin device to enable light sheet fluorescence imaging of multi-cellular organisms on an inverted wide-field microscope

PubMed Central

Guan, Zeyi; Lee, Juhyun; Jiang, Hao; Dong, Siyan; Jen, Nelson; Hsiai, Tzung; Ho, Chih-Ming; Fei, Peng

2015-01-01

We developed a compact plane illumination plugin (PIP) device which enabled plane illumination and light sheet fluorescence imaging on a conventional inverted microscope. The PIP device allowed the integration of microscope with tunable laser sheet profile, fast image acquisition, and 3-D scanning. The device is both compact, measuring approximately 15 by 5 by 5 cm, and cost-effective, since we employed consumer electronics and an inexpensive device molding method. We demonstrated that PIP provided significant contrast and resolution enhancement to conventional microscopy through imaging different multi-cellular fluorescent structures, including 3-D branched cells in vitro and live zebrafish embryos. Imaging with the integration of PIP greatly reduced out-of-focus contamination and generated sharper contrast in acquired 2-D plane images when compared with the stand-alone inverted microscope. As a result, the dynamic fluid domain of the beating zebrafish heart was clearly segmented and the functional monitoring of the heart was achieved. Furthermore, the enhanced axial resolution established by thin plane illumination of PIP enabled the 3-D reconstruction of the branched cellular structures, which leads to the improvement on the functionality of the wide field microscopy. PMID:26819828

Compact plane illumination plugin device to enable light sheet fluorescence imaging of multi-cellular organisms on an inverted wide-field microscope.

PubMed

Guan, Zeyi; Lee, Juhyun; Jiang, Hao; Dong, Siyan; Jen, Nelson; Hsiai, Tzung; Ho, Chih-Ming; Fei, Peng

2016-01-01

We developed a compact plane illumination plugin (PIP) device which enabled plane illumination and light sheet fluorescence imaging on a conventional inverted microscope. The PIP device allowed the integration of microscope with tunable laser sheet profile, fast image acquisition, and 3-D scanning. The device is both compact, measuring approximately 15 by 5 by 5 cm, and cost-effective, since we employed consumer electronics and an inexpensive device molding method. We demonstrated that PIP provided significant contrast and resolution enhancement to conventional microscopy through imaging different multi-cellular fluorescent structures, including 3-D branched cells in vitro and live zebrafish embryos. Imaging with the integration of PIP greatly reduced out-of-focus contamination and generated sharper contrast in acquired 2-D plane images when compared with the stand-alone inverted microscope. As a result, the dynamic fluid domain of the beating zebrafish heart was clearly segmented and the functional monitoring of the heart was achieved. Furthermore, the enhanced axial resolution established by thin plane illumination of PIP enabled the 3-D reconstruction of the branched cellular structures, which leads to the improvement on the functionality of the wide field microscopy.

Limiting factors in atomic resolution cryo electron microscopy: No simple tricks

PubMed Central

Zhang, Xing; Zhou, Z. Hong

2013-01-01

To bring cryo electron microscopy (cryoEM) of large biological complexes to atomic resolution, several factors – in both cryoEM image acquisition and 3D reconstruction – that may be neglected at low resolution become significantly limiting. Here we present thorough analyses of four limiting factors: (a) electron-beam tilt, (b) inaccurate determination of defocus values, (c) focus gradient through particles, and (d) particularly for large particles, dynamic (multiple) scattering of electrons. We also propose strategies to cope with these factors: (a) the divergence and direction tilt components of electron-beam tilt could be reduced by maintaining parallel illumination and by using a coma-free alignment procedure, respectively. Moreover, the effect of all beam tilt components, including spiral tilt, could be eliminated by use of a spherical aberration corrector. (b) More accurate measurement of defocus value could be obtained by imaging areas adjacent to the target area at high electron dose and by measuring the image shift induced by tilting the electron beam. (c) Each known Fourier coefficient in the Fourier transform of a cryoEM image is the sum of two Fourier coefficients of the 3D structure, one on each of two curved ‘characteristic surfaces’ in 3D Fourier space. We describe a simple model-based iterative method that could recover these two Fourier coefficients on the two characteristic surfaces. (d) The effect of dynamic scattering could be corrected by deconvolution of a transfer function. These analyses and our proposed strategies offer useful guidance for future experimental designs targeting atomic resolution cryoEM reconstruction. PMID:21627992

View planetary differentiation process through high-resolution 3D imaging

NASA Astrophysics Data System (ADS)

Fei, Y.

2011-12-01

Core-mantle separation is one of the most important processes in planetary evolution, defining the structure and chemical distribution in the planets. Iron-dominated core materials could migrate through silicate mantle to the core by efficient liquid-liquid separation and/or by percolation of liquid metal through solid silicate matrix. We can experimentally simulate these processes to examine the efficiency and time of core formation and its geochemical signatures. The quantitative measure of the efficiency of percolation is usually the dihedral angle, related to the interfacial energies of the liquid and solid phases. To determine the true dihedral angle at high pressure and temperatures, it is necessary to measure the relative frequency distributions of apparent dihedral angles between the quenched liquid metal and silicate grains for each experiment. Here I present a new imaging technique to visualize the distribution of liquid metal in silicate matrix in 3D by combination of focus ion beam (FIB) milling and high-resolution SEM image. The 3D volume rendering provides precise determination of the dihedral angle and quantitative measure of volume fraction and connectivity. I have conducted a series of experiments using mixtures of San Carlos olivine and Fe-S (10wt%S) metal with different metal-silicate ratios, up to 25 GPa and at temperatures above 1800C. High-quality 3D volume renderings were reconstructed from FIB serial sectioning and imaging with 10-nm slice thickness and 14-nm image resolution for each quenched sample. The unprecedented spatial resolution at nano scale allows detailed examination of textural features and precise determination of the dihedral angle as a function of pressure, temperature and composition. The 3D reconstruction also allows direct assessment of connectivity in multi-phase matrix, providing a new way to investigate the efficiency of metal percolation in a real silicate mantle.

High-resolution 3D coronary vessel wall imaging with near 100% respiratory efficiency using epicardial fat tracking: reproducibility and comparison with standard methods.

PubMed

Scott, Andrew D; Keegan, Jennifer; Firmin, David N

2011-01-01

To quantitatively assess the performance and reproducibility of 3D spiral coronary artery wall imaging with beat-to-beat respiratory-motion-correction (B2B-RMC) compared to navigator gated 2D spiral and turbo-spin-echo (TSE) acquisitions. High-resolution (0.7 × 0.7 mm) cross-sectional right coronary wall acquisitions were performed in 10 subjects using four techniques (B2B-RMC 3D spiral with alternate (2RR) and single (1RR) R-wave gating, navigator-gated 2D spiral (2RR) and navigator-gated 2D TSE (2RR)) on two occasions. Wall thickness measurements were compared with repeated measures analysis of variance (ANOVA). Reproducibility was assessed with the intraclass correlation coefficient (ICC). In all, 91% (73/80) of acquisitions were successful (failures: four TSE, two 3D spiral (1RR) and one 3D spiral (2RR)). Respiratory efficiency of the B2B-RMC was less variable and substantially higher than for navigator gating (99.6 ± 1.2% vs. 39.0 ± 7.5%, P < 0.0001). Coronary wall thicknesses (± standard deviation [SD]) were not significantly different: 1.10 ± 0.14 mm (3D spiral (2RR)), 1.20 ± 0.16 mm (3D spiral (1RR)), 1.14 ± 0.15 mm (2D spiral), and 1.21 ± 0.17 mm (TSE). Wall thickness reproducibility ranged from good (ICC = 0.65, 3D spiral (1RR)) to excellent (ICC = 0.87, 3D spiral (2RR)). High-resolution 3D spiral imaging with B2B-RMC permits coronary vessel wall assessment over multiple thin contiguous slices in a clinically feasible duration. Excellent reproducibility of the technique potentially enables studies of disease progression/regression. Copyright © 2010 Wiley-Liss, Inc.

Multimodal Hierarchical Imaging of Serial Sections for Finding Specific Cellular Targets within Large Volumes

PubMed Central

Wacker, Irene U.; Veith, Lisa; Spomer, Waldemar; Hofmann, Andreas; Thaler, Marlene; Hillmer, Stefan; Gengenbach, Ulrich; Schröder, Rasmus R.

2018-01-01

Targeting specific cells at ultrastructural resolution within a mixed cell population or a tissue can be achieved by hierarchical imaging using a combination of light and electron microscopy. Samples embedded in resin are sectioned into arrays consisting of ribbons of hundreds of ultrathin sections and deposited on pieces of silicon wafer or conductively coated coverslips. Arrays are imaged at low resolution using a digital consumer like smartphone camera or light microscope (LM) for a rapid large area overview, or a wide field fluorescence microscope (fluorescence light microscopy (FLM)) after labeling with fluorophores. After post-staining with heavy metals, arrays are imaged in a scanning electron microscope (SEM). Selection of targets is possible from 3D reconstructions generated by FLM or from 3D reconstructions made from the SEM image stacks at intermediate resolution if no fluorescent markers are available. For ultrastructural analysis, selected targets are finally recorded in the SEM at high-resolution (a few nanometer image pixels). A ribbon-handling tool that can be retrofitted to any ultramicrotome is demonstrated. It helps with array production and substrate removal from the sectioning knife boat. A software platform that allows automated imaging of arrays in the SEM is discussed. Compared to other methods generating large volume EM data, such as serial block-face SEM (SBF-SEM) or focused ion beam SEM (FIB-SEM), this approach has two major advantages: (1) The resin-embedded sample is conserved, albeit in a sliced-up version. It can be stained in different ways and imaged with different resolutions. (2) As the sections can be post-stained, it is not necessary to use samples strongly block-stained with heavy metals to introduce contrast for SEM imaging or render the tissue blocks conductive. This makes the method applicable to a wide variety of materials and biological questions. Particularly prefixed materials e.g., from biopsy banks and pathology labs, can directly be embedded and reconstructed in 3D. PMID:29630046

Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis.

PubMed

Yang, Yu-Jiao; Wang, Shuai; Zhang, Biao; Shen, Hong-Bin

2018-06-25

As a relatively new technology to solve the three-dimensional (3D) structure of a protein or protein complex, single-particle reconstruction (SPR) of cryogenic electron microscopy (cryo-EM) images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role in promoting methodology development of SPR and structural biology. Because there is no benchmark map in the generation of a new structure, how to realize the resolution estimation of a new map is still an open problem. Existing approaches try to generate a hypothetical benchmark map by reconstructing two 3D models from two halves of the original 2D images for cross-reference, which may result in a premature estimation with a half-data model. In this paper, we report a new self-reference-based resolution estimation protocol, called SRes, that requires only a single reconstructed 3D map. The core idea of SRes is to perform a multiscale spectral analysis (MSSA) on the map through multiple size-variable masks segmenting the map. The MSSA-derived multiscale spectral signal-to-noise ratios (mSSNRs) reveal that their corresponding estimated resolutions will show a cliff jump phenomenon, indicating a significant change in the SSNR properties. The critical point on the cliff borderline is demonstrated to be the right estimator for the resolution of the map.

Label free cell tracking in 3D tissue engineering constructs with high resolution imaging

NASA Astrophysics Data System (ADS)

Smith, W. A.; Lam, K.-P.; Dempsey, K. P.; Mazzocchi-Jones, D.; Richardson, J. B.; Yang, Y.

2014-02-01

Within the field of tissue engineering there is an emphasis on studying 3-D live tissue structures. Consequently, to investigate and identify cellular activities and phenotypes in a 3-D environment for all in vitro experiments, including shape, migration/proliferation and axon projection, it is necessary to adopt an optical imaging system that enables monitoring 3-D cellular activities and morphology through the thickness of the construct for an extended culture period without cell labeling. This paper describes a new 3-D tracking algorithm developed for Cell-IQ®, an automated cell imaging platform, which has been equipped with an environmental chamber optimized to enable capturing time-lapse sequences of live cell images over a long-term period without cell labeling. As an integral part of the algorithm, a novel auto-focusing procedure was developed for phase contrast microscopy equipped with 20x and 40x objectives, to provide a more accurate estimation of cell growth/trajectories by allowing 3-D voxels to be computed at high spatiotemporal resolution and cell density. A pilot study was carried out in a phantom system consisting of horizontally aligned nanofiber layers (with precise spacing between them), to mimic features well exemplified in cellular activities of neuronal growth in a 3-D environment. This was followed by detailed investigations concerning axonal projections and dendritic circuitry formation in a 3-D tissue engineering construct. Preliminary work on primary animal neuronal cells in response to chemoattractant and topographic cue within the scaffolds has produced encouraging results.

Spatial resolution limits for the isotropic-3D PET detector X’tal cube

NASA Astrophysics Data System (ADS)

Yoshida, Eiji; Tashima, Hideaki; Hirano, Yoshiyuki; Inadama, Naoko; Nishikido, Fumihiko; Murayama, Hideo; Yamaya, Taiga

2013-11-01

Positron emission tomography (PET) has become a popular imaging method in metabolism, neuroscience, and molecular imaging. For dedicated human brain and small animal PET scanners, high spatial resolution is needed to visualize small objects. To improve the spatial resolution, we are developing the X’tal cube, which is our new PET detector to achieve isotropic 3D positioning detectability. We have shown that the X’tal cube can achieve 1 mm3 uniform crystal identification performance with the Anger-type calculation even at the block edges. We plan to develop the X’tal cube with even smaller 3D grids for sub-millimeter crystal identification. In this work, we investigate spatial resolution of a PET scanner based on the X’tal cube using Monte Carlo simulations for predicting resolution performance in smaller 3D grids. For spatial resolution evaluation, a point source emitting 511 keV photons was simulated by GATE for all physical processes involved in emission and interaction of positrons. We simulated two types of animal PET scanners. The first PET scanner had a detector ring 14.6 cm in diameter composed of 18 detectors. The second PET scanner had a detector ring 7.8 cm in diameter composed of 12 detectors. After the GATE simulations, we converted the interacting 3D position information to digitalized positions for realistic segmented crystals. We simulated several X’tal cubes with cubic crystals from (0.5 mm)3 to (2 mm)3 in size. Also, for evaluating the effect of DOI resolution, we simulated several X’tal cubes with crystal thickness from (0.5 mm)3 to (9 mm)3. We showed that sub-millimeter spatial resolution was possible using cubic crystals smaller than (1.0 mm)3 even with the assumed physical processes. Also, the weighted average spatial resolutions of both PET scanners with (0.5 mm)3 cubic crystals were 0.53 mm (14.6 cm ring diameter) and 0.48 mm (7.8 cm ring diameter). For the 7.8 cm ring diameter, spatial resolution with 0.5×0.5×1.0 mm3 crystals was improved 39% relative to the (1 mm)3 cubic crystals. On the other hand, spatial resolution with (0.5 mm)3 cubic crystals was improved 47% relative to the (1 mm)3 cubic crystals. The X’tal cube promises better spatial resolution for the 3D crystal block with isotropic resolution.

Automatic transfer function generation for volume rendering of high-resolution x-ray 3D digital mammography images

NASA Astrophysics Data System (ADS)

Alyassin, Abdal M.

2002-05-01

3D Digital mammography (3DDM) is a new technology that provides high resolution X-ray breast tomographic data. Like any other tomographic medical imaging modalities, viewing a stack of tomographic images may require time especially if the images are of large matrix size. In addition, it may cause difficulty to conceptually construct 3D breast structures. Therefore, there is a need to readily visualize the data in 3D. However, one of the issues that hinder the usage of volume rendering (VR) is finding an automatic way to generate transfer functions that efficiently map the important diagnostic information in the data. We have developed a method that randomly samples the volume. Based on the mean and the standard deviation of these samples, the technique determines the lower limit and upper limit of a piecewise linear ramp transfer function. We have volume rendered several 3DDM data using this technique and compared visually the outcome with the result from a conventional automatic technique. The transfer function generated through the proposed technique provided superior VR images over the conventional technique. Furthermore, the improvement in the reproducibility of the transfer function correlated with the number of samples taken from the volume at the expense of the processing time.

Photogrammetric 3d Building Reconstruction from Thermal Images

NASA Astrophysics Data System (ADS)

Maset, E.; Fusiello, A.; Crosilla, F.; Toldo, R.; Zorzetto, D.

2017-08-01

This paper addresses the problem of 3D building reconstruction from thermal infrared (TIR) images. We show that a commercial Computer Vision software can be used to automatically orient sequences of TIR images taken from an Unmanned Aerial Vehicle (UAV) and to generate 3D point clouds, without requiring any GNSS/INS data about position and attitude of the images nor camera calibration parameters. Moreover, we propose a procedure based on Iterative Closest Point (ICP) algorithm to create a model that combines high resolution and geometric accuracy of RGB images with the thermal information deriving from TIR images. The process can be carried out entirely by the aforesaid software in a simple and efficient way.

Future directions in 3-dimensional imaging and neurosurgery: stereoscopy and autostereoscopy.

PubMed

Christopher, Lauren A; William, Albert; Cohen-Gadol, Aaron A

2013-01-01

Recent advances in 3-dimensional (3-D) stereoscopic imaging have enabled 3-D display technologies in the operating room. We find 2 beneficial applications for the inclusion of 3-D imaging in clinical practice. The first is the real-time 3-D display in the surgical theater, which is useful for the neurosurgeon and observers. In surgery, a 3-D display can include a cutting-edge mixed-mode graphic overlay for image-guided surgery. The second application is to improve the training of residents and observers in neurosurgical techniques. This article documents the requirements of both applications for a 3-D system in the operating room and for clinical neurosurgical training, followed by a discussion of the strengths and weaknesses of the current and emerging 3-D display technologies. An important comparison between a new autostereoscopic display without glasses and current stereo display with glasses improves our understanding of the best applications for 3-D in neurosurgery. Today's multiview autostereoscopic display has 3 major benefits: It does not require glasses for viewing; it allows multiple views; and it improves the workflow for image-guided surgery registration and overlay tasks because of its depth-rendering format and tools. Two current limitations of the autostereoscopic display are that resolution is reduced and depth can be perceived as too shallow in some cases. Higher-resolution displays will be available soon, and the algorithms for depth inference from stereo can be improved. The stereoscopic and autostereoscopic systems from microscope cameras to displays were compared by the use of recorded and live content from surgery. To the best of our knowledge, this is the first report of application of autostereoscopy in neurosurgery.

From Panoramic Photos to a Low-Cost Photogrammetric Workflow for Cultural Heritage 3d Documentation

NASA Astrophysics Data System (ADS)

D'Annibale, E.; Tassetti, A. N.; Malinverni, E. S.

2013-07-01

The research aims to optimize a workflow of architecture documentation: starting from panoramic photos, tackling available instruments and technologies to propose an integrated, quick and low-cost solution of Virtual Architecture. The broader research background shows how to use spherical panoramic images for the architectural metric survey. The input data (oriented panoramic photos), the level of reliability and Image-based Modeling methods constitute an integrated and flexible 3D reconstruction approach: from the professional survey of cultural heritage to its communication in virtual museum. The proposed work results from the integration and implementation of different techniques (Multi-Image Spherical Photogrammetry, Structure from Motion, Imagebased Modeling) with the aim to achieve high metric accuracy and photorealistic performance. Different documentation chances are possible within the proposed workflow: from the virtual navigation of spherical panoramas to complex solutions of simulation and virtual reconstruction. VR tools make for the integration of different technologies and the development of new solutions for virtual navigation. Image-based Modeling techniques allow 3D model reconstruction with photo realistic and high-resolution texture. High resolution of panoramic photo and algorithms of panorama orientation and photogrammetric restitution vouch high accuracy and high-resolution texture. Automated techniques and their following integration are subject of this research. Data, advisably processed and integrated, provide different levels of analysis and virtual reconstruction joining the photogrammetric accuracy to the photorealistic performance of the shaped surfaces. Lastly, a new solution of virtual navigation is tested. Inside the same environment, it proposes the chance to interact with high resolution oriented spherical panorama and 3D reconstructed model at once.

A 3D scanning laser endoscope architecture utilizing a circular piezoelectric membrane

NASA Astrophysics Data System (ADS)

Khayatzadeh, Ramin; Çivitci, Fehmi; Ferhanoğlu, Onur

2017-12-01

A piezo-scanning fiber endoscopic device architecture is proposed for 3D imaging or ablation. The endoscopic device consists of a piezoelectric membrane that is placed perpendicular to the optical axis, a fiber optic cable that extends out from and actuated by the piezoelectric membrane, and one or multiple lenses for beam delivery and collection. Unlike its counterparts that utilize piezoelectric cylinders for fiber actuation, the proposed architecture offers quasi-static actuation in the axial direction along with resonant actuation in the lateral directions forming a 3D scanning pattern, allowing adjustment of the focus plane. The actuation of the four-quadrant piezoelectric membrane involves driving of two orthogonal electrodes with AC signals for lateral scanning, while simultaneously driving all electrodes for axial scanning and focus adjustment. We have characterized piezoelectric membranes (5 -15mm diameter) with varying sizes to monitor axial displacement behavior with respect to applied DC voltage. We also demonstrate simultaneous lateral and axial actuation on a resolution target, and observe the change of lateral resolution on a selected plane through performing 1D cross-sectional images, as an indicator of focal shift through axial actuation. Based on experimental results, we identify the optical and geometrical parameters for optimal 3D imaging of tissue samples. Our findings reveal that a simple piezoelectric membrane, having comparable dimensions and drive voltage requirement with off-the-shelf MEMS scanner chips, offers tissue epithelial imaging with sub-cellular resolution.

3D printing for orthopedic applications: from high resolution cone beam CT images to life size physical models

NASA Astrophysics Data System (ADS)

Jackson, Amiee; Ray, Lawrence A.; Dangi, Shusil; Ben-Zikri, Yehuda K.; Linte, Cristian A.

2017-03-01

With increasing resolution in image acquisition, the project explores capabilities of printing toward faithfully reflecting detail and features depicted in medical images. To improve safety and efficiency of orthopedic surgery and spatial conceptualization in training and education, this project focused on generating virtual models of orthopedic anatomy from clinical quality computed tomography (CT) image datasets and manufacturing life-size physical models of the anatomy using 3D printing tools. Beginning with raw micro CT data, several image segmentation techniques including thresholding, edge recognition, and region-growing algorithms available in packages such as ITK-SNAP, MITK, or Mimics, were utilized to separate bone from surrounding soft tissue. After converting the resulting data to a standard 3D printing format, stereolithography (STL), the STL file was edited using Meshlab, Netfabb, and Meshmixer. The editing process was necessary to ensure a fully connected surface (no loose elements), positive volume with manifold geometry (geometry possible in the 3D physical world), and a single, closed shell. The resulting surface was then imported into a "slicing" software to scale and orient for printing on a Flashforge Creator Pro. In printing, relationships between orientation, print bed volume, model quality, material use and cost, and print time were considered. We generated anatomical models of the hand, elbow, knee, ankle, and foot from both low-dose high-resolution cone-beam CT images acquired using the soon to be released scanner developed by Carestream, as well as scaled models of the skeletal anatomy of the arm and leg, together with life-size models of the hand and foot.

Using Synchrotron Radiation Microtomography to Investigate Multi-scale Three-dimensional Microelectronic Packages.

PubMed

Carlton, Holly D; Elmer, John W; Li, Yan; Pacheco, Mario; Goyal, Deepak; Parkinson, Dilworth Y; MacDowell, Alastair A

2016-04-13

Synchrotron radiation micro-tomography (SRµT) is a non-destructive three-dimensional (3D) imaging technique that offers high flux for fast data acquisition times with high spatial resolution. In the electronics industry there is serious interest in performing failure analysis on 3D microelectronic packages, many which contain multiple levels of high-density interconnections. Often in tomography there is a trade-off between image resolution and the volume of a sample that can be imaged. This inverse relationship limits the usefulness of conventional computed tomography (CT) systems since a microelectronic package is often large in cross sectional area 100-3,600 mm(2), but has important features on the micron scale. The micro-tomography beamline at the Advanced Light Source (ALS), in Berkeley, CA USA, has a setup which is adaptable and can be tailored to a sample's properties, i.e., density, thickness, etc., with a maximum allowable cross-section of 36 x 36 mm. This setup also has the option of being either monochromatic in the energy range ~7-43 keV or operating with maximum flux in white light mode using a polychromatic beam. Presented here are details of the experimental steps taken to image an entire 16 x 16 mm system within a package, in order to obtain 3D images of the system with a spatial resolution of 8.7 µm all within a scan time of less than 3 min. Also shown are results from packages scanned in different orientations and a sectioned package for higher resolution imaging. In contrast a conventional CT system would take hours to record data with potentially poorer resolution. Indeed, the ratio of field-of-view to throughput time is much higher when using the synchrotron radiation tomography setup. The description below of the experimental setup can be implemented and adapted for use with many other multi-materials.

3-D photoacoustic and pulse echo imaging of prostate tumor progression in the mouse window chamber

NASA Astrophysics Data System (ADS)

Bauer, Daniel R.; Olafsson, Ragnar; Montilla, Leonardo G.; Witte, Russell S.

2011-02-01

Understanding the tumor microenvironment is critical to characterizing how cancers operate and predicting their response to treatment. We describe a novel, high-resolution coregistered photoacoustic (PA) and pulse echo (PE) ultrasound system used to image the tumor microenvironment. Compared to traditional optical systems, the platform provides complementary contrast and important depth information. Three mice are implanted with a dorsal skin flap window chamber and injected with PC-3 prostate tumor cells transfected with green fluorescent protein. The ensuing tumor invasion is mapped during three weeks or more using simultaneous PA and PE imaging at 25 MHz, combined with optical and fluorescent techniques. Pulse echo imaging provides details of tumor structure and the surrounding environment with 100-μm3 resolution. Tumor size increases dramatically with an average volumetric growth rate of 5.35 mm3/day, correlating well with 2-D fluorescent imaging (R = 0.97, p < 0.01). Photoacoustic imaging is able to track the underlying vascular network and identify hemorrhaging, while PA spectroscopy helps classify blood vessels according to their optical absorption spectrum, suggesting variation in blood oxygen saturation. Photoacoustic and PE imaging are safe, translational modalities that provide enhanced depth resolution and complementary contrast to track the tumor microenvironment, evaluate new cancer therapies, and develop molecular contrast agents in vivo.

Evaluation of Heterogeneous Metabolic Profile in an Orthotopic Human Glioblastoma Xenograft Model Using Compressed Sensing Hyperpolarized 3D 13C Magnetic Resonance Spectroscopic Imaging

PubMed Central

Park, Ilwoo; Hu, Simon; Bok, Robert; Ozawa, Tomoko; Ito, Motokazu; Mukherjee, Joydeep; Phillips, Joanna J.; James, C. David; Pieper, Russell O.; Ronen, Sabrina M.; Vigneron, Daniel B.; Nelson, Sarah J.

2013-01-01

High resolution compressed sensing hyperpolarized 13C magnetic resonance spectroscopic imaging was applied in orthotopic human glioblastoma xenografts for quantitative assessment of spatial variations in 13C metabolic profiles and comparison with histopathology. A new compressed sensing sampling design with a factor of 3.72 acceleration was implemented to enable a factor of 4 increase in spatial resolution. Compressed sensing 3D 13C magnetic resonance spectroscopic imaging data were acquired from a phantom and 10 tumor-bearing rats following injection of hyperpolarized [1-13C]-pyruvate using a 3T scanner. The 13C metabolic profiles were compared with hematoxylin and eosin staining and carbonic anhydrase 9 staining. The high-resolution compressed sensing 13C magnetic resonance spectroscopic imaging data enabled the differentiation of distinct 13C metabolite patterns within abnormal tissues with high specificity in similar scan times compared to the fully sampled method. The results from pathology confirmed the different characteristics of 13C metabolic profiles between viable, non-necrotic, nonhypoxic tumor, and necrotic, hypoxic tissue. PMID:22851374

Evaluation of heterogeneous metabolic profile in an orthotopic human glioblastoma xenograft model using compressed sensing hyperpolarized 3D 13C magnetic resonance spectroscopic imaging.

PubMed

Park, Ilwoo; Hu, Simon; Bok, Robert; Ozawa, Tomoko; Ito, Motokazu; Mukherjee, Joydeep; Phillips, Joanna J; James, C David; Pieper, Russell O; Ronen, Sabrina M; Vigneron, Daniel B; Nelson, Sarah J

2013-07-01

High resolution compressed sensing hyperpolarized (13)C magnetic resonance spectroscopic imaging was applied in orthotopic human glioblastoma xenografts for quantitative assessment of spatial variations in (13)C metabolic profiles and comparison with histopathology. A new compressed sensing sampling design with a factor of 3.72 acceleration was implemented to enable a factor of 4 increase in spatial resolution. Compressed sensing 3D (13)C magnetic resonance spectroscopic imaging data were acquired from a phantom and 10 tumor-bearing rats following injection of hyperpolarized [1-(13)C]-pyruvate using a 3T scanner. The (13)C metabolic profiles were compared with hematoxylin and eosin staining and carbonic anhydrase 9 staining. The high-resolution compressed sensing (13)C magnetic resonance spectroscopic imaging data enabled the differentiation of distinct (13)C metabolite patterns within abnormal tissues with high specificity in similar scan times compared to the fully sampled method. The results from pathology confirmed the different characteristics of (13)C metabolic profiles between viable, non-necrotic, nonhypoxic tumor, and necrotic, hypoxic tissue. Copyright © 2012 Wiley Periodicals, Inc.

Requirement of spatiotemporal resolution for imaging intracellular temperature distribution

NASA Astrophysics Data System (ADS)

Hiroi, Noriko; Tanimoto, Ryuichi; , Kaito, Ii; Ozeki, Mitsunori; Mashimo, Kota; Funahashi, Akira

2017-04-01

Intracellular temperature distribution is an emerging target in biology nowadays. Because thermal diffusion is rapid dynamics in comparison with molecular diffusion, we need a spatiotemporally high-resolution imaging technology to catch this phenomenon. We demonstrate that time-lapse imaging which consists of single-shot 3D volume images acquired at high-speed camera rate is desired for the imaging of intracellular thermal diffusion based on the simulation results of thermal diffusion from a nucleus to cytosol.

Integrating histology and MRI in the first digital brain of common squirrel monkey, Saimiri sciureus

NASA Astrophysics Data System (ADS)

Sun, Peizhen; Parvathaneni, Prasanna; Schilling, Kurt G.; Gao, Yurui; Janve, Vaibhav; Anderson, Adam; Landman, Bennett A.

2015-03-01

This effort is a continuation of development of a digital brain atlas of the common squirrel monkey, Saimiri sciureus, a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. Here, we present the integration of histology with multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. The central concept of this work is to use block face photography to establish an intermediate common space in coordinate system which preserves the high resolution in-plane resolution of histology while enabling 3-D correspondence with MRI. In vivo MRI acquisitions include high resolution T2 structural imaging (300 μm isotropic) and low resolution diffusion tensor imaging (600 um isotropic). Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging (both 300 μm isotropic). Cortical regions were manually annotated on the co-registered volumes based on published histological sections in-plane. We describe mapping of histology and MRI based data of the common squirrel monkey and construction of a viewing tool that enable online viewing of these datasets. The previously descried atlas MRI is used for its deformation to provide accurate conformation to the MRI, thus adding information at the histological level to the MRI volume. This paper presents the mapping of single 2D image slice in block face as a proof of concept and this can be extended to map the atlas space in 3D coordinate system as part of the future work and can be loaded to an XNAT system for further use.

A hybrid approach for fusing 4D-MRI temporal information with 3D-CT for the study of lung and lung tumor motion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Y. X.; Van Reeth, E.; Poh, C. L., E-mail: clpoh@ntu.edu.sg

2015-08-15

Purpose: Accurate visualization of lung motion is important in many clinical applications, such as radiotherapy of lung cancer. Advancement in imaging modalities [e.g., computed tomography (CT) and MRI] has allowed dynamic imaging of lung and lung tumor motion. However, each imaging modality has its advantages and disadvantages. The study presented in this paper aims at generating synthetic 4D-CT dataset for lung cancer patients by combining both continuous three-dimensional (3D) motion captured by 4D-MRI and the high spatial resolution captured by CT using the authors’ proposed approach. Methods: A novel hybrid approach based on deformable image registration (DIR) and finite elementmore » method simulation was developed to fuse a static 3D-CT volume (acquired under breath-hold) and the 3D motion information extracted from 4D-MRI dataset, creating a synthetic 4D-CT dataset. Results: The study focuses on imaging of lung and lung tumor. Comparing the synthetic 4D-CT dataset with the acquired 4D-CT dataset of six lung cancer patients based on 420 landmarks, accurate results (average error <2 mm) were achieved using the authors’ proposed approach. Their hybrid approach achieved a 40% error reduction (based on landmarks assessment) over using only DIR techniques. Conclusions: The synthetic 4D-CT dataset generated has high spatial resolution, has excellent lung details, and is able to show movement of lung and lung tumor over multiple breathing cycles.« less

A Novel 2D Image Compression Algorithm Based on Two Levels DWT and DCT Transforms with Enhanced Minimize-Matrix-Size Algorithm for High Resolution Structured Light 3D Surface Reconstruction

NASA Astrophysics Data System (ADS)

Siddeq, M. M.; Rodrigues, M. A.

2015-09-01

Image compression techniques are widely used on 2D image 2D video 3D images and 3D video. There are many types of compression techniques and among the most popular are JPEG and JPEG2000. In this research, we introduce a new compression method based on applying a two level discrete cosine transform (DCT) and a two level discrete wavelet transform (DWT) in connection with novel compression steps for high-resolution images. The proposed image compression algorithm consists of four steps. (1) Transform an image by a two level DWT followed by a DCT to produce two matrices: DC- and AC-Matrix, or low and high frequency matrix, respectively, (2) apply a second level DCT on the DC-Matrix to generate two arrays, namely nonzero-array and zero-array, (3) apply the Minimize-Matrix-Size algorithm to the AC-Matrix and to the other high-frequencies generated by the second level DWT, (4) apply arithmetic coding to the output of previous steps. A novel decompression algorithm, Fast-Match-Search algorithm (FMS), is used to reconstruct all high-frequency matrices. The FMS-algorithm computes all compressed data probabilities by using a table of data, and then using a binary search algorithm for finding decompressed data inside the table. Thereafter, all decoded DC-values with the decoded AC-coefficients are combined in one matrix followed by inverse two levels DCT with two levels DWT. The technique is tested by compression and reconstruction of 3D surface patches. Additionally, this technique is compared with JPEG and JPEG2000 algorithm through 2D and 3D root-mean-square-error following reconstruction. The results demonstrate that the proposed compression method has better visual properties than JPEG and JPEG2000 and is able to more accurately reconstruct surface patches in 3D.

Adaptive-optics SLO imaging combined with widefield OCT and SLO enables precise 3D localization of fluorescent cells in the mouse retina.

PubMed

Zawadzki, Robert J; Zhang, Pengfei; Zam, Azhar; Miller, Eric B; Goswami, Mayank; Wang, Xinlei; Jonnal, Ravi S; Lee, Sang-Hyuck; Kim, Dae Yu; Flannery, John G; Werner, John S; Burns, Marie E; Pugh, Edward N

2015-06-01

Adaptive optics scanning laser ophthalmoscopy (AO-SLO) has recently been used to achieve exquisite subcellular resolution imaging of the mouse retina. Wavefront sensing-based AO typically restricts the field of view to a few degrees of visual angle. As a consequence the relationship between AO-SLO data and larger scale retinal structures and cellular patterns can be difficult to assess. The retinal vasculature affords a large-scale 3D map on which cells and structures can be located during in vivo imaging. Phase-variance OCT (pv-OCT) can efficiently image the vasculature with near-infrared light in a label-free manner, allowing 3D vascular reconstruction with high precision. We combined widefield pv-OCT and SLO imaging with AO-SLO reflection and fluorescence imaging to localize two types of fluorescent cells within the retinal layers: GFP-expressing microglia, the resident macrophages of the retina, and GFP-expressing cone photoreceptor cells. We describe in detail a reflective afocal AO-SLO retinal imaging system designed for high resolution retinal imaging in mice. The optical performance of this instrument is compared to other state-of-the-art AO-based mouse retinal imaging systems. The spatial and temporal resolution of the new AO instrumentation was characterized with angiography of retinal capillaries, including blood-flow velocity analysis. Depth-resolved AO-SLO fluorescent images of microglia and cone photoreceptors are visualized in parallel with 469 nm and 663 nm reflectance images of the microvasculature and other structures. Additional applications of the new instrumentation are discussed.

Micro axial tomography: A miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy

NASA Astrophysics Data System (ADS)

Staier, Florian; Eipel, Heinz; Matula, Petr; Evsikov, Alexei V.; Kozubek, Michal; Cremer, Christoph; Hausmann, Michael

2011-09-01

With the development of novel fluorescence techniques, high resolution light microscopy has become a challenging technique for investigations of the three-dimensional (3D) micro-cosmos in cells and sub-cellular components. So far, all fluorescence microscopes applied for 3D imaging in biosciences show a spatially anisotropic point spread function resulting in an anisotropic optical resolution or point localization precision. To overcome this shortcoming, micro axial tomography was suggested which allows object tilting on the microscopic stage and leads to an improvement in localization precision and spatial resolution. Here, we present a miniaturized device which can be implemented in a motor driven microscope stage. The footprint of this device corresponds to a standard microscope slide. A special glass fiber can manually be adjusted in the object space of the microscope lens. A stepwise fiber rotation can be controlled by a miniaturized stepping motor incorporated into the device. By means of a special mounting device, test particles were fixed onto glass fibers, optically localized with high precision, and automatically rotated to obtain views from different perspective angles under which distances of corresponding pairs of objects were determined. From these angle dependent distance values, the real 3D distance was calculated with a precision in the ten nanometer range (corresponding here to an optical resolution of 10-30 nm) using standard microscopic equipment. As a proof of concept, the spindle apparatus of a mature mouse oocyte was imaged during metaphase II meiotic arrest under different perspectives. Only very few images registered under different rotation angles are sufficient for full 3D reconstruction. The results indicate the principal advantage of the micro axial tomography approach for many microscopic setups therein and also those of improved resolutions as obtained by high precision localization determination.

Electrical impedance tomography in 3D using two electrode planes: characterization and evaluation.

PubMed

Wagenaar, Justin; Adler, Andy

2016-06-01

Electrical impedance tomography (EIT) uses body surface electrical stimulation and measurements to create conductivity images; it shows promise as a non-invasive technology to monitor the distribution of lung ventilation. Most applications of EIT have placed electrodes in a 2D ring around the thorax, and thus produced 2D cross-sectional images. These images are unable to distinguish out-of-plane contributions, or to image volumetric effects. Volumetric EIT can be calculated using multiple electrode planes and a 3D reconstruction algorithm. However, while 3D reconstruction algorithms are available, little has been done to understand the performance of 3D EIT in terms of the measurement configurations available. The goal of this paper is to characterize the phantom and in vivo performance of 3D EIT with two electrode planes. First, phantom measurements are used to measure the reconstruction characteristics of seven stimulation and measurement configurations. Measurements were then performed on eight healthy volunteers as a function of body posture, postures, and with various electrode configurations. Phantom results indicate that 3D EIT using two rings of electrodes provides reasonable resolution in the electrode plane but low vertical resolution. For volunteers, functional EIT images are created from inhalation curve features to analyze the effect of posture (standing, sitting, supine and decline) on regional lung behaviour. An ability to detect vertical changes in lung volume distribution was shown for two electrode configurations. Based on tank and volunteer results, we recommend the use of the 'square' stimulation and measurement pattern for two electrode plane EIT.

Development of an EMC3-EIRENE Synthetic Imaging Diagnostic

NASA Astrophysics Data System (ADS)

Meyer, William; Allen, Steve; Samuell, Cameron; Lore, Jeremy

2017-10-01

2D and 3D flow measurements are critical for validating numerical codes such as EMC3-EIRENE. Toroidal symmetry assumptions preclude tomographic reconstruction of 3D flows from single camera views. In addition, the resolution of the grids utilized in numerical code models can easily surpass the resolution of physical camera diagnostic geometries. For these reasons we have developed a Synthetic Imaging Diagnostic capability for forward projection comparisons of EMC3-EIRENE model solutions with the line integrated images from the Doppler Coherence Imaging diagnostic on DIII-D. The forward projection matrix is 2.8 Mpixel by 6.4 Mcells for the non-axisymmetric case we present. For flow comparisons, both simple line integral, and field aligned component matrices must be calculated. The calculation of these matrices is a massive embarrassingly parallel problem and performed with a custom dispatcher that allows processing platforms to join mid-problem as they become available, or drop out if resources are needed for higher priority tasks. The matrices are handled using standard sparse matrix techniques. Prepared by LLNL under Contract DE-AC52-07NA27344. This material is based upon work supported by the U.S. DOE, Office of Science, Office of Fusion Energy Sciences. LLNL-ABS-734800.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Stressed-out Enceladus 3-D

NASA Image and Video Library

2005-03-24

This high-resolution stereo anaglyph captured by NASA Cassini spacecraft of Saturn moon Enceladus shows a region of craters softened by time and torn apart by tectonic stresses. 3D glasses are necessary to view this image.

Evaluation of a 3D local multiresolution algorithm for the correction of partial volume effects in positron emission tomography.

PubMed

Le Pogam, Adrien; Hatt, Mathieu; Descourt, Patrice; Boussion, Nicolas; Tsoumpas, Charalampos; Turkheimer, Federico E; Prunier-Aesch, Caroline; Baulieu, Jean-Louis; Guilloteau, Denis; Visvikis, Dimitris

2011-09-01

Partial volume effects (PVEs) are consequences of the limited spatial resolution in emission tomography leading to underestimation of uptake in tissues of size similar to the point spread function (PSF) of the scanner as well as activity spillover between adjacent structures. Among PVE correction methodologies, a voxel-wise mutual multiresolution analysis (MMA) was recently introduced. MMA is based on the extraction and transformation of high resolution details from an anatomical image (MR/CT) and their subsequent incorporation into a low-resolution PET image using wavelet decompositions. Although this method allows creating PVE corrected images, it is based on a 2D global correlation model, which may introduce artifacts in regions where no significant correlation exists between anatomical and functional details. A new model was designed to overcome these two issues (2D only and global correlation) using a 3D wavelet decomposition process combined with a local analysis. The algorithm was evaluated on synthetic, simulated and patient images, and its performance was compared to the original approach as well as the geometric transfer matrix (GTM) method. Quantitative performance was similar to the 2D global model and GTM in correlated cases. In cases where mismatches between anatomical and functional information were present, the new model outperformed the 2D global approach, avoiding artifacts and significantly improving quality of the corrected images and their quantitative accuracy. A new 3D local model was proposed for a voxel-wise PVE correction based on the original mutual multiresolution analysis approach. Its evaluation demonstrated an improved and more robust qualitative and quantitative accuracy compared to the original MMA methodology, particularly in the absence of full correlation between anatomical and functional information.

Simulation of High-Resolution Magnetic Resonance Images on the IBM Blue Gene/L Supercomputer Using SIMRI

DOE PAGES

Baum, K. G.; Menezes, G.; Helguera, M.

2011-01-01

Medical imaging system simulators are tools that provide a means to evaluate system architecture and create artificial image sets that are appropriate for specific applications. We have modified SIMRI, a Bloch equation-based magnetic resonance image simulator, in order to successfully generate high-resolution 3D MR images of the Montreal brain phantom using Blue Gene/L systems. Results show that redistribution of the workload allows an anatomically accurate 256 3 voxel spin-echo simulation in less than 5 hours when executed on an 8192-node partition of a Blue Gene/L system.

Simulation of High-Resolution Magnetic Resonance Images on the IBM Blue Gene/L Supercomputer Using SIMRI.

PubMed

Baum, K G; Menezes, G; Helguera, M

2011-01-01

Medical imaging system simulators are tools that provide a means to evaluate system architecture and create artificial image sets that are appropriate for specific applications. We have modified SIMRI, a Bloch equation-based magnetic resonance image simulator, in order to successfully generate high-resolution 3D MR images of the Montreal brain phantom using Blue Gene/L systems. Results show that redistribution of the workload allows an anatomically accurate 256(3) voxel spin-echo simulation in less than 5 hours when executed on an 8192-node partition of a Blue Gene/L system.

Comparison of reconstruction methods and quantitative accuracy in Siemens Inveon PET scanner

NASA Astrophysics Data System (ADS)

Ram Yu, A.; Kim, Jin Su; Kang, Joo Hyun; Moo Lim, Sang

2015-04-01

PET reconstruction is key to the quantification of PET data. To our knowledge, no comparative study of reconstruction methods has been performed to date. In this study, we compared reconstruction methods with various filters in terms of their spatial resolution, non-uniformities (NU), recovery coefficients (RCs), and spillover ratios (SORs). In addition, the linearity of reconstructed radioactivity between linearity of measured and true concentrations were also assessed. A Siemens Inveon PET scanner was used in this study. Spatial resolution was measured with NEMA standard by using a 1 mm3 sized 18F point source. Image quality was assessed in terms of NU, RC and SOR. To measure the effect of reconstruction algorithms and filters, data was reconstructed using FBP, 3D reprojection algorithm (3DRP), ordered subset expectation maximization 2D (OSEM 2D), and maximum a posteriori (MAP) with various filters or smoothing factors (β). To assess the linearity of reconstructed radioactivity, image quality phantom filled with 18F was used using FBP, OSEM and MAP (β =1.5 & 5 × 10-5). The highest achievable volumetric resolution was 2.31 mm3 and the highest RCs were obtained when OSEM 2D was used. SOR was 4.87% for air and 3.97% for water, obtained OSEM 2D reconstruction was used. The measured radioactivity of reconstruction image was proportional to the injected one for radioactivity below 16 MBq/ml when FBP or OSEM 2D reconstruction methods were used. By contrast, when the MAP reconstruction method was used, activity of reconstruction image increased proportionally, regardless of the amount of injected radioactivity. When OSEM 2D or FBP were used, the measured radioactivity concentration was reduced by 53% compared with true injected radioactivity for radioactivity <16 MBq/ml. The OSEM 2D reconstruction method provides the highest achievable volumetric resolution and highest RC among all the tested methods and yields a linear relation between the measured and true concentrations for radioactivity Our data collectively showed that OSEM 2D reconstruction method provides quantitatively accurate reconstructed PET data results.

D Reconstruction from Uav-Based Hyperspectral Images

NASA Astrophysics Data System (ADS)

Liu, L.; Xu, L.; Peng, J.

2018-04-01

Reconstructing the 3D profile from a set of UAV-based images can obtain hyperspectral information, as well as the 3D coordinate of any point on the profile. Our images are captured from the Cubert UHD185 (UHD) hyperspectral camera, which is a new type of high-speed onboard imaging spectrometer. And it can get both hyperspectral image and panchromatic image simultaneously. The panchromatic image have a higher spatial resolution than hyperspectral image, but each hyperspectral image provides considerable information on the spatial spectral distribution of the object. Thus there is an opportunity to derive a high quality 3D point cloud from panchromatic image and considerable spectral information from hyperspectral image. The purpose of this paper is to introduce our processing chain that derives a database which can provide hyperspectral information and 3D position of each point. First, We adopt a free and open-source software, Visual SFM which is based on structure from motion (SFM) algorithm, to recover 3D point cloud from panchromatic image. And then get spectral information of each point from hyperspectral image by a self-developed program written in MATLAB. The production can be used to support further research and applications.

Elemental and topographical imaging of microscopic variations in deposition on NSTX-U and DIII-D samples

NASA Astrophysics Data System (ADS)

Skinner, C. H.; Kaita, R.; Koel, B. E.; Chrobak, C. P.; Wampler, W. R.

2017-10-01

Tokamak plasma facing components (PFCs) have surface roughness that can cause microscopic spatial variations in erosion and deposition and hence influence material migration. Previous RBS measurements showed indirect evidence for this but the spatial (0.5mm) resolution was insufficient for direct imaging. We will present elemental images at sub-micron resolution of deposition on NSTX-U and DiMES samples that show strong microscopic variations and correlate this with 3D topographical maps of surface irregularities. The elemental imaging is performed with a Scanning Auger Microprobe (SAM) that measures element-specific Auger electrons excited by an SEM electron beam. 3D topographical maps of the samples are performed with a Leica DCM 3D confocal light microscope and compared to the elemental deposition pattern. The initial results appear consistent with erosion at the downstream edges of the surface pores exposed to the incident ion flux, whereas the deeper regions are shadowed and serve as deposition traps. Support was provided through DOE Contract Numbers DE-AC02-09CH11466, DE-FC02-04ER54698 and DE-NA0003525.

Performance evaluation of a two detector camera for real-time video.

PubMed

Lochocki, Benjamin; Gambín-Regadera, Adrián; Artal, Pablo

2016-12-20

Single pixel imaging can be the preferred method over traditional 2D-array imaging in spectral ranges where conventional cameras are not available. However, when it comes to real-time video imaging, single pixel imaging cannot compete with the framerates of conventional cameras, especially when high-resolution images are desired. Here we evaluate the performance of an imaging approach using two detectors simultaneously. First, we present theoretical results on how low SNR affects final image quality followed by experimentally determined results. Obtained video framerates were doubled compared to state of the art systems, resulting in a framerate from 22 Hz for a 32×32 resolution to 0.75 Hz for a 128×128 resolution image. Additionally, the two detector imaging technique enables the acquisition of images with a resolution of 256×256 in less than 3 s.

Three-dimensional scanning transmission electron microscopy of biological specimens.

PubMed

de Jonge, Niels; Sougrat, Rachid; Northan, Brian M; Pennycook, Stephen J

2010-02-01

A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset.

Three-Dimensional Scanning Transmission Electron Microscopy of Biological Specimens

PubMed Central

de Jonge, Niels; Sougrat, Rachid; Northan, Brian M.; Pennycook, Stephen J.

2010-01-01

A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2–3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset. PMID:20082729

Evaluation of microvascular anastomosis using real-time ultrahigh resolution Fourier domain Doppler optical coherence tomography

PubMed Central

Huang, Yong; Tong, Dedi; Zhu, Shan; Wu, Lehao; Mao, Qi; Ibrahim, Zuhaib; Lee, WP Andrew; Brandacher, Gerald; Kang, Jin U.

2014-01-01

Background Evolution and improvements in microsurgical techniques and tools have paved the way for super-microsurgical anastomoses with vessel diameters often approaching below 0.8 mm in the clinical realm and even smaller (0.2–0.3 mm) in murine models. Several imaging and monitoring devices have been introduced for post-operative monitoring but intra-operative guidance, assessment and predictability have remained limited to binocular optical microscope and surgeon’s experience. We present a high-resolution real time 3D imaging modality for intra-operative evaluation of luminal narrowing, thrombus formation and flow alterations. Methods An imaging modality that provides immediate, in-depth high resolution 3D structure view and flow information of the anastomosed site called phase resolved Doppler optical coherence tomography (PRDOCT) was developed. 22 mouse femoral artery anastomoses and 17 mouse venous anastomoses were performed and evaluated with PRDOCT. Flow status, vessel inner lumen 3D structure, and early thrombus detection were analyzed based on PRDOCT imaging results. Initial PRDOCT based predictions were correlated with actual long term surgical outcomes. Eventually four cases of mouse orthotopic limb transplantation were carried out and PRDOCT predicted long term patency were confirmed by actual results. Results PRDOCT was able to provide high-resolution 3D visualization of the vessel flow status and vessel inner lumen. The assessments based on PRDOCT visualization shows a 92% sensitivity and 90% specificity for arterial anastomoses and 90% sensitivity and 86% specificity for venous anastomoses. Conclusions PRDOCT is an effective evaluation tool for microvascular anastomosis. It can predict the long term vessel patency with high sensitivity and specificity. PMID:25811583

3D range-gated super-resolution imaging based on stereo matching for moving platforms and targets

NASA Astrophysics Data System (ADS)

Sun, Liang; Wang, Xinwei; Zhou, Yan

2017-11-01

3D range-gated superresolution imaging is a novel 3D reconstruction technique for target detection and recognition with good real-time performance. However, for moving targets or platforms such as airborne, shipborne, remote operated vehicle and autonomous vehicle, 3D reconstruction has a large error or failure. In order to overcome this drawback, we propose a method of stereo matching for 3D range-gated superresolution reconstruction algorithm. In experiment, the target is a doll of Mario with a height of 38cm at the location of 34m, and we obtain two successive frame images of the Mario. To confirm our method is effective, we transform the original images with translation, rotation, scale and perspective, respectively. The experimental result shows that our method has a good result of 3D reconstruction for moving targets or platforms.

Low-count PET image restoration using sparse representation

NASA Astrophysics Data System (ADS)

Li, Tao; Jiang, Changhui; Gao, Juan; Yang, Yongfeng; Liang, Dong; Liu, Xin; Zheng, Hairong; Hu, Zhanli

2018-04-01

In the field of positron emission tomography (PET), reconstructed images are often blurry and contain noise. These problems are primarily caused by the low resolution of projection data. Solving this problem by improving hardware is an expensive solution, and therefore, we attempted to develop a solution based on optimizing several related algorithms in both the reconstruction and image post-processing domains. As sparse technology is widely used, sparse prediction is increasingly applied to solve this problem. In this paper, we propose a new sparse method to process low-resolution PET images. Two dictionaries (D1 for low-resolution PET images and D2 for high-resolution PET images) are learned from a group real PET image data sets. Among these two dictionaries, D1 is used to obtain a sparse representation for each patch of the input PET image. Then, a high-resolution PET image is generated from this sparse representation using D2. Experimental results indicate that the proposed method exhibits a stable and superior ability to enhance image resolution and recover image details. Quantitatively, this method achieves better performance than traditional methods. This proposed strategy is a new and efficient approach for improving the quality of PET images.

Multimodal-3D imaging based on μMRI and μCT techniques bridges the gap with histology in visualization of the bone regeneration process.

PubMed

Sinibaldi, R; Conti, A; Sinjari, B; Spadone, S; Pecci, R; Palombo, M; Komlev, V S; Ortore, M G; Tromba, G; Capuani, S; Guidotti, R; De Luca, F; Caputi, S; Traini, T; Della Penna, S

2018-03-01

Bone repair/regeneration is usually investigated through X-ray computed microtomography (μCT) supported by histology of extracted samples, to analyse biomaterial structure and new bone formation processes. Magnetic resonance imaging (μMRI) shows a richer tissue contrast than μCT, despite at lower resolution, and could be combined with μCT in the perspective of conducting non-destructive 3D investigations of bone. A pipeline designed to combine μMRI and μCT images of bone samples is here described and applied on samples of extracted human jawbone core following bone graft. We optimized the coregistration procedure between μCT and μMRI images to avoid bias due to the different resolutions and contrasts. Furthermore, we used an Adaptive Multivariate Clustering, grouping homologous voxels in the coregistered images, to visualize different tissue types within a fused 3D metastructure. The tissue grouping matched the 2D histology applied only on 1 slice, thus extending the histology labelling in 3D. Specifically, in all samples, we could separate and map 2 types of regenerated bone, calcified tissue, soft tissues, and/or fat and marrow space. Remarkably, μMRI and μCT alone were not able to separate the 2 types of regenerated bone. Finally, we computed volumes of each tissue in the 3D metastructures, which might be exploited by quantitative simulation. The 3D metastructure obtained through our pipeline represents a first step to bridge the gap between the quality of information obtained from 2D optical microscopy and the 3D mapping of the bone tissue heterogeneity and could allow researchers and clinicians to non-destructively characterize and follow-up bone regeneration. Copyright © 2017 John Wiley & Sons, Ltd.

Making 3D movies of Northern Lights

NASA Astrophysics Data System (ADS)

Hivon, Eric; Mouette, Jean; Legault, Thierry

2017-10-01

We describe the steps necessary to create three-dimensional (3D) movies of Northern Lights or Aurorae Borealis out of real-time images taken with two distant high-resolution fish-eye cameras. Astrometric reconstruction of the visible stars is used to model the optical mapping of each camera and correct for it in order to properly align the two sets of images. Examples of the resulting movies can be seen at http://www.iap.fr/aurora3d

Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project

PubMed Central

Uğurbil, Kamil; Xu, Junqian; Auerbach, Edward J.; Moeller, Steen; Vu, An; Duarte-Carvajalino, Julio M.; Lenglet, Christophe; Wu, Xiaoping; Schmitter, Sebastian; Van de Moortele, Pierre Francois; Strupp, John; Sapiro, Guillermo; De Martino, Federico; Wang, Dingxin; Harel, Noam; Garwood, Michael; Chen, Liyong; Feinberg, David A.; Smith, Stephen M.; Miller, Karla L.; Sotiropoulos, Stamatios N; Jbabdi, Saad; Andersson, Jesper L; Behrens, Timothy EJ; Glasser, Matthew F.; Van Essen, David; Yacoub, Essa

2013-01-01

The human connectome project (HCP) relies primarily on three complementary magnetic resonance (MR) methods. These are: 1) resting state functional MR imaging (rfMRI) which uses correlations in the temporal fluctuations in an fMRI time series to deduce ‘functional connectivity’; 2) diffusion imaging (dMRI), which provides the input for tractography algorithms used for the reconstruction of the complex axonal fiber architecture; and 3) task based fMRI (tfMRI), which is employed to identify functional parcellation in the human brain in order to assist analyses of data obtained with the first two methods. We describe technical improvements and optimization of these methods as well as instrumental choices that impact speed of acquisition of fMRI and dMRI images at 3 Tesla, leading to whole brain coverage with 2 mm isotropic resolution in 0.7 second for fMRI, and 1.25 mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7 Tesla magnetic field are also presented, targeting higher resolution, specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields and power deposition. Results demonstrate that overall, these approaches represent a significant advance in MR imaging of the human brain to investigate brain function and structure. PMID:23702417

Adaptive optics and the eye (super resolution OCT).

PubMed

Miller, D T; Kocaoglu, O P; Wang, Q; Lee, S

2011-03-01

The combination of adaptive optics (AO) and optical coherence tomography (OCT) was first reported 8 years ago and has undergone tremendous technological advances since then. The technical benefits of adding AO to OCT (increased lateral resolution, smaller speckle, and enhanced sensitivity) increase the imaging capability of OCT in ways that make it well suited for three-dimensional (3D) cellular imaging in the retina. Today, AO-OCT systems provide ultrahigh 3D resolution (3 × 3 × 3 μm³) and ultrahigh speed (up to an order of magnitude faster than commercial OCT). AO-OCT systems have been used to capture volume images of retinal structures, previously only visible with histology, and are being used for studying clinical conditions. Here, we present representative examples of cellular structures that can be visualized with AO-OCT. We overview three studies from our laboratory that used ultrahigh-resolution AO-OCT to measure the cross-sectional profiles of individual bundles in the retinal nerve fiber layer; the diameters of foveal capillaries that define the terminal rim of the foveal avascular zone; and the spacing and length of individual cone photoreceptor outer segments as close as 0.5° from the fovea center.

Three-dimensional imaging of nanoscale materials by using coherent x-rays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miao, Jianwei

X-ray crystallography is currently the primary methodology used to determine the 3D structure of materials and macromolecules. However, many nanostructures, disordered materials, biomaterials, hybrid materials and biological specimens are noncrystalline and, hence, their structures are not accessible by X-ray crystallography. Probing these structures therefore requires the employment of different approaches. A very promising technique currently under rapid development is X-ray diffraction microscopy (or lensless imaging), in which the coherent X-ray diffraction pattern of a noncrystalline specimen is measured and then directly phased to obtain a high-resolution image. Through the DOE support over the past three years, we have applied X-raymore » diffraction microscopy to quantitative imaging of GaN quantum dot particles, and revealed the internal GaN-Ga2O3 core shell structure in three dimensions. By exploiting the abrupt change in the scattering cross-section near electronic resonances, we carried out the first experimental demonstration of resonant X-ray diffraction microscopy for element specific imaging. We performed nondestructive and quantitative imaging of buried Bi structures inside a Si crystal by directly phasing coherent X-ray diffraction patterns acquired below and above the Bi M5 edge. We have also applied X-ray diffraction microscopy to nondestructive imaging of mineral crystals inside biological composite materials - intramuscular fish bone - at the nanometer scale resolution. We identified mineral crystals in collagen fibrils at different stages of mineralization and proposed a dynamic mechanism to account for the nucleation and growth of mineral crystals in the collagen matrix. In addition, we have also discovered a novel 3D imaging modality, denoted ankylography, which allows for complete 3D structure determination without the necessity of sample titling or scanning. We showed that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is determined by the 2D spherical pattern. We confirmed the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution from a 2D spherical diffraction pattern alone. As X-ray free electron lasers are under rapid development worldwide, ankylography may open up a new horizon to obtain the 3D structure of a non-crystalline specimen from a single pulse and allow time-resolved 3D structure determination of disordered materials.« less

Three-dimensional Visualization of Ultrasound Backscatter Statistics by Window-modulated Compounding Nakagami Imaging.

PubMed

Zhou, Zhuhuang; Wu, Shuicai; Lin, Man-Yen; Fang, Jui; Liu, Hao-Li; Tsui, Po-Hsiang

2018-05-01

In this study, the window-modulated compounding (WMC) technique was integrated into three-dimensional (3D) ultrasound Nakagami imaging for improving the spatial visualization of backscatter statistics. A 3D WMC Nakagami image was produced by summing and averaging a number of 3D Nakagami images (number of frames denoted as N) formed using sliding cubes with varying side lengths ranging from 1 to N times the transducer pulse. To evaluate the performance of the proposed 3D WMC Nakagami imaging method, agar phantoms with scatterer concentrations ranging from 2 to 64 scatterers/mm 3 were made, and six stages of fatty liver (zero, one, two, four, six, and eight weeks) were induced in rats by methionine-choline-deficient diets (three rats for each stage, total n = 18). A mechanical scanning system with a 5-MHz focused single-element transducer was used for ultrasound radiofrequency data acquisition. The experimental results showed that 3D WMC Nakagami imaging was able to characterize different scatterer concentrations. Backscatter statistics were visualized with various numbers of frames; N = 5 reduced the estimation error of 3D WMC Nakagami imaging in visualizing the backscatter statistics. Compared with conventional 3D Nakagami imaging, 3D WMC Nakagami imaging improved the image smoothness without significant image resolution degradation, and it can thus be used for describing different stages of fatty liver in rats.

Restoring the spatial resolution of refocus images on 4D light field

NASA Astrophysics Data System (ADS)

Lim, JaeGuyn; Park, ByungKwan; Kang, JooYoung; Lee, SeongDeok

2010-01-01

This paper presents the method for generating a refocus image with restored spatial resolution on a plenoptic camera, which functions controlling the depth of field after capturing one image unlike a traditional camera. It is generally known that the camera captures 4D light field (angular and spatial information of light) within a limited 2D sensor and results in reducing 2D spatial resolution due to inevitable 2D angular data. That's the reason why a refocus image is composed of a low spatial resolution compared with 2D sensor. However, it has recently been known that angular data contain sub-pixel spatial information such that the spatial resolution of 4D light field can be increased. We exploit the fact for improving the spatial resolution of a refocus image. We have experimentally scrutinized that the spatial information is different according to the depth of objects from a camera. So, from the selection of refocused regions (corresponding depth), we use corresponding pre-estimated sub-pixel spatial information for reconstructing spatial resolution of the regions. Meanwhile other regions maintain out-of-focus. Our experimental results show the effect of this proposed method compared to existing method.

Region-of-interest cone beam computed tomography (ROI CBCT) with a high resolution CMOS detector.

PubMed

Jain, A; Takemoto, H; Silver, M D; Nagesh, S V S; Ionita, C N; Bednarek, D R; Rudin, S

Cone beam computed tomography (CBCT) systems with rotational gantries that have standard flat panel detectors (FPD) are widely used for the 3D rendering of vascular structures using Feldkamp cone beam reconstruction algorithms. One of the inherent limitations of these systems is limited resolution (<3 lp/mm). There are systems available with higher resolution but their small FOV limits them to small animal imaging only. In this work, we report on region-of-interest (ROI) CBCT with a high resolution CMOS detector (75 μm pixels, 600 μm HR-CsI) mounted with motorized detector changer on a commercial FPD-based C-arm angiography gantry (194 μm pixels, 600 μm HL-CsI). A cylindrical CT phantom and neuro stents were imaged with both detectors. For each detector a total of 209 images were acquired in a rotational protocol. The technique parameters chosen for the FPD by the imaging system were used for the CMOS detector. The anti-scatter grid was removed and the incident scatter was kept the same for both detectors with identical collimator settings. The FPD images were reconstructed for the 10 cm x10 cm FOV and the CMOS images were reconstructed for a 3.84 cm × 3.84 cm FOV. Although the reconstructed images from the CMOS detector demonstrated comparable contrast to the FPD images, the reconstructed 3D images of the neuro stent clearly showed that the CMOS detector improved delineation of smaller objects such as the stent struts (~70 μm) compared to the FPD. Further development and the potential for substantial clinical impact are suggested.

Demonstration of a large-size horizontal light-field display based on the LED panel and the micro-pinhole unit array

NASA Astrophysics Data System (ADS)

Yang, Le; Sang, Xinzhu; Yu, Xunbo; Liu, Boyang; Liu, Li; Yang, Shenwu; Yan, Binbin; Du, Jingyan; Gao, Chao

2018-05-01

A 54-inch horizontal-parallax only light-field display based on the light-emitting diode (LED) panel and the micro-pinhole unit array (MPUA) is demonstrated. Normally, the perceived 3D effect of the three-dimensional (3D) display with smooth motion parallax and abundant light-field information can be enhanced with increasing the density of viewpoints. However, the density of viewpoints is inversely proportional to the spatial display resolution for the conventional integral imaging. Here, a special MPUA is designed and fabricated, and the displayed 3D scene constructed by the proposed horizontal light-field display is presented. Compared with the conventional integral imaging, both the density of horizontal viewpoints and the spatial display resolution are significantly improved. In the experiment, A 54-inch horizontal light-field display with 42.8° viewing angle based on the LED panel with the resolution of 1280 × 720 and the MPUA is realized, which can provide natural 3D visual effect to observers with high quality.

Video stereo-laparoscopy system

NASA Astrophysics Data System (ADS)

Xiang, Yang; Hu, Jiasheng; Jiang, Huilin

2006-01-01

Minimally invasive surgery (MIS) has contributed significantly to patient care by reducing the morbidity associated with more invasive procedures. MIS procedures have become standard treatment for gallbladder disease and some abdominal malignancies. The imaging system has played a major role in the evolving field of minimally invasive surgery (MIS). The image need to have good resolution, large magnification, especially, the image need to have depth cue at the same time the image have no flicker and suit brightness. The video stereo-laparoscopy system can meet the demand of the doctors. This paper introduces the 3d video laparoscopy has those characteristic, field frequency: 100Hz, the depth space: 150mm, resolution: 10pl/mm. The work principle of the system is introduced in detail, and the optical system and time-division stereo-display system are described briefly in this paper. The system has focusing image lens, it can image on the CCD chip, the optical signal can change the video signal, and through A/D switch of the image processing system become the digital signal, then display the polarized image on the screen of the monitor through the liquid crystal shutters. The doctors with the polarized glasses can watch the 3D image without flicker of the tissue or organ. The 3D video laparoscope system has apply in the MIS field and praised by doctors. Contrast to the traditional 2D video laparoscopy system, it has some merit such as reducing the time of surgery, reducing the problem of surgery and the trained time.

Compact LED-based full-field optical coherence microscopy for high-resolution high-speed in vivo imaging

NASA Astrophysics Data System (ADS)

Ogien, Jonas; Dubois, Arnaud

2017-02-01

This work reports on a compact full-field optical coherence microscopy (FF-OCM) setup specifically designed to meet the needs for in vivo imaging, illuminated by a high-brightness broadband light emitting diode (LED). Broadband LEDs have spectra potentially large enough to provide imaging spatial resolutions similar to those reached using conventional halogen lamps, but their radiance can be much higher, which leads to high speed acquisition and makes in vivo imaging possible. We introduce a FF-OCM setup using a 2.3 W broadband LED, with an interferometer designed to be as compact as possible in order to provide the basis for a portable system that will make it possible to fully benefit from the capacity for in vivo imaging by providing the ability to image any region of interest in real-time. The interferometer part of the compact FF-OCM setup weighs 210 g for a size of 11x11x5 cm3. Using this setup, a sub-micron axial resolution was reached, with a detection sensitivity of 68 dB at an imaging rate of 250 Hz. Due to the high imaging rate, the sensitivity could be improved by accumulation while maintaining an acquisition time short enough for in vivo imaging. It was possible to reach a sensitivity of 75 dB at a 50 Hz imaging rate. High resolution in vivo human skin images were obtained with this setup and compared with images of excised human skin, showing high similarity.

Small animal optoacoustic tomography system for molecular imaging of contrast agents

NASA Astrophysics Data System (ADS)

Su, Richard; Liopo, Anton; Ermilov, Sergey A.; Oraevsky, Alexander A.

2016-03-01

We developed a new and improved Laser Optoacoustic Imaging System, LOIS-3D for preclinical research applications in small animal models. The advancements include (i) a new stabilized imaging module with a more homogeneous illumination of the mouse yielding a better spatial resolution (<0.2 mm) and (ii) a new low noise amplifier incorporated into the ultrasonic probe and providing the noise equivalent pressure around 2 Pa resulting in increased signal-to-noise ratio and the optical absorption sensitivity of about 0.15 cm-1. We also improved scan time and the image reconstruction times. This prototype has been commercialized for a number of biomedical research applications, such as imaging vascularization and measuring hemoglobin / oxyhemoglobin distribution in the organs as well as imaging exogenous or endogenous optoacoustic contrast agents. As examples, we present in vivo experiments using phantoms and mice with and without tumor injected with contrast agents with indocyanine green (ICG). LOIS-3D was capable of detecting ~1-2 pmole of the ICG, in tissues with relatively low blood content. With its high sensitivity and excellent spatial resolution LOIS-3D is an advanced alternative to fluorescence and bioluminescence based modalities for molecular imaging in live mice.

Experimental study on the 3D image reconstruction in a truncated Archimedean-like spiral geometry with a long-rectangular detector and its image characteristics

NASA Astrophysics Data System (ADS)

Hong, Daeki; Cho, Heemoon; Cho, Hyosung; Choi, Sungil; Je, Uikyu; Park, Yeonok; Park, Chulkyu; Lim, Hyunwoo; Park, Soyoung; Woo, Taeho

2015-11-01

In this work, we performed a feasibility study on the three-dimensional (3D) image reconstruction in a truncated Archimedean-like spiral geometry with a long-rectangular detector for application to high-accurate, cost-effective dental x-ray imaging. Here an x-ray tube and a detector rotate together around the rotational axis several times and, concurrently, the detector moves horizontally in the detector coordinate at a constant speed to cover the whole imaging volume during the projection data acquisition. We established a table-top setup which mainly consists of an x-ray tube (60 kVp, 5 mA), a narrow CMOS-type detector (198-μm pixel resolution, 184 (W)×1176 (H) pixel dimension), and a rotational stage for sample mounting and performed a systematic experiment to demonstrate the viability of the proposed approach to volumetric dental imaging. For the image reconstruction, we employed a compressed-sensing (CS)-based algorithm, rather than a common filtered-backprojection (FBP) one, for more accurate reconstruction. We successfully reconstructed 3D images of considerably high quality and investigated the image characteristics in terms of the image value profile, the contrast-to-noise ratio (CNR), and the spatial resolution.

Gas scintillation glass GEM detector for high-resolution X-ray imaging and CT

NASA Astrophysics Data System (ADS)

Fujiwara, T.; Mitsuya, Y.; Fushie, T.; Murata, K.; Kawamura, A.; Koishikawa, A.; Toyokawa, H.; Takahashi, H.

2017-04-01

A high-spatial-resolution X-ray-imaging gaseous detector has been developed with a single high-gas-gain glass gas electron multiplier (G-GEM), scintillation gas, and optical camera. High-resolution X-ray imaging of soft elements is performed with a spatial resolution of 281 μm rms and an effective area of 100×100 mm. In addition, high-resolution X-ray 3D computed tomography (CT) is successfully demonstrated with the gaseous detector. It shows high sensitivity to low-energy X-rays, which results in high-contrast radiographs of objects containing elements with low atomic numbers. In addition, the high yield of scintillation light enables fast X-ray imaging, which is an advantage for constructing CT images with low-energy X-rays.

T2* mapping and delayed gadolinium-enhanced magnetic resonance imaging in cartilage (dGEMRIC) of humeral articular cartilage--a histologically controlled study.

PubMed

Bittersohl, Bernd; Kircher, Jörn; Miese, Falk R; Dekkers, Christin; Habermeyer, Peter; Fröbel, Julia; Antoch, Gerald; Krauspe, Rüdiger; Zilkens, Christoph

2015-10-01

Cartilage biochemical imaging modalities that include the magnetic resonance imaging (MRI) techniques of T2* mapping (sensitive to water content and collagen fiber network) and delayed gadolinium-enhanced MRI of cartilage (dGEMRIC, sensitive to the glycosaminoglycan content) can be effective instruments for early diagnosis and reliable follow-up of cartilage damage. The purpose of this study was to provide T2* mapping and dGEMRIC values in various histologic grades of cartilage degeneration in humeral articular cartilage. A histologically controlled in vitro study was conducted that included human humeral head cartilage specimens with various histologic grades of cartilage degeneration. High-resolution, 3-dimensional (3D) T2* mapping and dGEMRIC were performed that enabled the correlation of MRI and histology data. Cartilage degeneration was graded according to the Mankin score, which evaluates surface morphology, cellularity, toluidine blue staining, and tidemark integrity. SPSS software was used for statistical analyses. Both MRI mapping values decreased significantly (P < .001) with increasing cartilage degeneration. Spearman rank analysis revealed a significant correlation (correlation coefficients ranging from -0.315 to 0.784; P < .001) between the various histologic parameters and the T2* and T1Gd mapping values. This study demonstrates the feasibility of 3D T2* and dGEMRIC to identify various histologic grades of cartilage damage of humeral articular cartilage. With regard to the advantages of these mapping techniques with high image resolution and the ability to accomplish a 3D biochemically sensitive imaging, we consider that these imaging techniques can make a positive contribution to the currently evolving science and practice of cartilage biochemical imaging. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography

PubMed Central

Chen, Lingling; Alexandrov, Yuriy; Kumar, Sunil; Andrews, Natalie; Dallman, Margaret J.; French, Paul M. W.; McGinty, James

2015-01-01

We describe an angular multiplexed imaging technique for 3-D in vivo cell tracking of sparse cell distributions and optical projection tomography (OPT) with superior time-lapse resolution and a significantly reduced light dose compared to volumetric time-lapse techniques. We demonstrate that using dual axis OPT, where two images are acquired simultaneously at different projection angles, can enable localization and tracking of features in 3-D with a time resolution equal to the camera frame rate. This is achieved with a 200x reduction in light dose compared to an equivalent volumetric time-lapse single camera OPT acquisition with 200 projection angles. We demonstrate the application of this technique to mapping the 3-D neutrophil migration pattern observed over ~25.5 minutes in a live 2 day post-fertilisation transgenic LysC:GFP zebrafish embryo following a tail wound. PMID:25909009

Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography.

PubMed

Chen, Lingling; Alexandrov, Yuriy; Kumar, Sunil; Andrews, Natalie; Dallman, Margaret J; French, Paul M W; McGinty, James

2015-04-01

We describe an angular multiplexed imaging technique for 3-D in vivo cell tracking of sparse cell distributions and optical projection tomography (OPT) with superior time-lapse resolution and a significantly reduced light dose compared to volumetric time-lapse techniques. We demonstrate that using dual axis OPT, where two images are acquired simultaneously at different projection angles, can enable localization and tracking of features in 3-D with a time resolution equal to the camera frame rate. This is achieved with a 200x reduction in light dose compared to an equivalent volumetric time-lapse single camera OPT acquisition with 200 projection angles. We demonstrate the application of this technique to mapping the 3-D neutrophil migration pattern observed over ~25.5 minutes in a live 2 day post-fertilisation transgenic LysC:GFP zebrafish embryo following a tail wound.

Multi-slice ptychography with large numerical aperture multilayer Laue lenses

DOE PAGES

Ozturk, Hande; Yan, Hanfei; He, Yan; ...

2018-05-09

Here, the highly convergent x-ray beam focused by multilayer Laue lenses with large numerical apertures is used as a three-dimensional (3D) probe to image layered structures with an axial separation larger than the depth of focus. Instead of collecting weakly scattered high-spatial-frequency signals, the depth-resolving power is provided purely by the intense central cone diverged from the focused beam. Using the multi-slice ptychography method combined with the on-the-fly scan scheme, two layers of nanoparticles separated by 10 μm are successfully reconstructed with 8.1 nm lateral resolution and with a dwell time as low as 0.05 s per scan point. Thismore » approach obtains high-resolution images with extended depth of field, which paves the way for multi-slice ptychography as a high throughput technique for high-resolution 3D imaging of thick samples.« less

Multi-slice ptychography with large numerical aperture multilayer Laue lenses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozturk, Hande; Yan, Hanfei; He, Yan

Here, the highly convergent x-ray beam focused by multilayer Laue lenses with large numerical apertures is used as a three-dimensional (3D) probe to image layered structures with an axial separation larger than the depth of focus. Instead of collecting weakly scattered high-spatial-frequency signals, the depth-resolving power is provided purely by the intense central cone diverged from the focused beam. Using the multi-slice ptychography method combined with the on-the-fly scan scheme, two layers of nanoparticles separated by 10 μm are successfully reconstructed with 8.1 nm lateral resolution and with a dwell time as low as 0.05 s per scan point. Thismore » approach obtains high-resolution images with extended depth of field, which paves the way for multi-slice ptychography as a high throughput technique for high-resolution 3D imaging of thick samples.« less

Volumetric 3D Display System with Static Screen

NASA Technical Reports Server (NTRS)

Geng, Jason

2011-01-01

Current display technology has relied on flat, 2D screens that cannot truly convey the third dimension of visual information: depth. In contrast to conventional visualization that is primarily based on 2D flat screens, the volumetric 3D display possesses a true 3D display volume, and places physically each 3D voxel in displayed 3D images at the true 3D (x,y,z) spatial position. Each voxel, analogous to a pixel in a 2D image, emits light from that position to form a real 3D image in the eyes of the viewers. Such true volumetric 3D display technology provides both physiological (accommodation, convergence, binocular disparity, and motion parallax) and psychological (image size, linear perspective, shading, brightness, etc.) depth cues to human visual systems to help in the perception of 3D objects. In a volumetric 3D display, viewers can watch the displayed 3D images from a completely 360 view without using any special eyewear. The volumetric 3D display techniques may lead to a quantum leap in information display technology and can dramatically change the ways humans interact with computers, which can lead to significant improvements in the efficiency of learning and knowledge management processes. Within a block of glass, a large amount of tiny dots of voxels are created by using a recently available machining technique called laser subsurface engraving (LSE). The LSE is able to produce tiny physical crack points (as small as 0.05 mm in diameter) at any (x,y,z) location within the cube of transparent material. The crack dots, when illuminated by a light source, scatter the light around and form visible voxels within the 3D volume. The locations of these tiny voxels are strategically determined such that each can be illuminated by a light ray from a high-resolution digital mirror device (DMD) light engine. The distribution of these voxels occupies the full display volume within the static 3D glass screen. This design eliminates any moving screen seen in previous approaches, so there is no image jitter, and has an inherent parallel mechanism for 3D voxel addressing. High spatial resolution is possible with a full color display being easy to implement. The system is low-cost and low-maintenance.

Usefulness of high-resolution 3D multifusion medical imaging for preoperative planning in patients with posterior fossa hemangioblastoma: technical note.

PubMed

Yoshino, Masanori; Nakatomi, Hirofumi; Kin, Taichi; Saito, Toki; Shono, Naoyuki; Nomura, Seiji; Nakagawa, Daichi; Takayanagi, Shunsaku; Imai, Hideaki; Oyama, Hiroshi; Saito, Nobuhito

2017-07-01

Successful resection of hemangioblastoma depends on preoperative assessment of the precise locations of feeding arteries and draining veins. Simultaneous 3D visualization of feeding arteries, draining veins, and surrounding structures is needed. The present study evaluated the usefulness of high-resolution 3D multifusion medical imaging (hr-3DMMI) for preoperative planning of hemangioblastoma. The hr-3DMMI combined MRI, MR angiography, thin-slice CT, and 3D rotated angiography. Surface rendering was mainly used for the creation of hr-3DMMI using multiple thresholds to create 3D models, and processing took approximately 3-5 hours. This hr-3DMMI technique was used in 5 patients for preoperative planning and the imaging findings were compared with the operative findings. Hr-3DMMI could simulate the whole 3D tumor as a unique sphere and show the precise penetration points of both feeding arteries and draining veins with the same spatial relationships as the original tumor. All feeding arteries and draining veins were found intraoperatively at the same position as estimated preoperatively, and were occluded as planned preoperatively. This hr-3DMMI technique could demonstrate the precise locations of feeding arteries and draining veins preoperatively and estimate the appropriate route for resection of the tumor. Hr-3DMMI is expected to be a very useful support tool for surgery of hemangioblastoma.

Photon-Counting H33D Detector for Biological Fluorescence Imaging

PubMed Central

Michalet, X.; Siegmund, O.H.W.; Vallerga, J.V.; Jelinsky, P.; Millaud, J.E.; Weiss, S.

2010-01-01

We have developed a photon-counting High-temporal and High-spatial resolution, High-throughput 3-Dimensional detector (H33D) for biological imaging of fluorescent samples. The design is based on a 25 mm diameter S20 photocathode followed by a 3-microchannel plate stack, and a cross delay line anode. We describe the bench performance of the H33D detector, as well as preliminary imaging results obtained with fluorescent beads, quantum dots and live cells and discuss applications of future generation detectors for single-molecule imaging and high-throughput study of biomolecular interactions. PMID:20151021

72-directional display having VGA resolution for high-appearance image generation

NASA Astrophysics Data System (ADS)

Takaki, Yasuhiro; Dairiki, Takeshi

2006-02-01

The high-density directional display, which was originally developed in order to realize a natural 3D display, is not only a 3D display but also a high-appearance display. The appearances of objects, such as glare and transparency, are the results of the reflection and the refraction of rays. The faithful reproduction of such appearances of objects is impossible using conventional 2D displays because rays diffuse on the display screen. The high-density directional display precisely controls the horizontal ray directions so that it can reproduce the appearances of objects. The fidelity of the reproduction of object appearances depends on the ray angle sampling pitch. The angle sampling pitch is determined by considering the human eye imaging system. In the present study the high-appearance display which has the resolution of 640×400 and emits rays in 72 different horizontal directions with the angle pitch of 0.38° was constructed. Two 72-directional displays were combined, each of which consisted of a high-resolution LCD panel (3,840×2,400) and a slanted lenticular sheet. Two images produced by two displays were superimposed by a half mirror. A slit array was placed at the focal plane of the lenticular sheet for each display to reduce the horizontal image crosstalk in the combined image. The impression analysis shows that the high-appearance display provides higher appearances and presence than the conventional 2D displays do.

Capturing method for integral three-dimensional imaging using multiviewpoint robotic cameras

NASA Astrophysics Data System (ADS)

Ikeya, Kensuke; Arai, Jun; Mishina, Tomoyuki; Yamaguchi, Masahiro

2018-03-01

Integral three-dimensional (3-D) technology for next-generation 3-D television must be able to capture dynamic moving subjects with pan, tilt, and zoom camerawork as good as in current TV program production. We propose a capturing method for integral 3-D imaging using multiviewpoint robotic cameras. The cameras are controlled through a cooperative synchronous system composed of a master camera controlled by a camera operator and other reference cameras that are utilized for 3-D reconstruction. When the operator captures a subject using the master camera, the region reproduced by the integral 3-D display is regulated in real space according to the subject's position and view angle of the master camera. Using the cooperative control function, the reference cameras can capture images at the narrowest view angle that does not lose any part of the object region, thereby maximizing the resolution of the image. 3-D models are reconstructed by estimating the depth from complementary multiviewpoint images captured by robotic cameras arranged in a two-dimensional array. The model is converted into elemental images to generate the integral 3-D images. In experiments, we reconstructed integral 3-D images of karate players and confirmed that the proposed method satisfied the above requirements.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, C. Shan; Hayworth, Kenneth J.; Lu, Zhiyuan

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) can automatically generate 3D images with superior z-axis resolution, yielding data that needs minimal image registration and related post-processing. Obstacles blocking wider adoption of FIB-SEM include slow imaging speed and lack of long-term system stability, which caps the maximum possible acquisition volume. Here, we present techniques that accelerate image acquisition while greatly improving FIB-SEM reliability, allowing the system to operate for months and generating continuously imaged volumes > 10 6 ?m 3 . These volumes are large enough for connectomics, where the excellent z resolution can help in tracing of small neuronal processesmore » and accelerate the tedious and time-consuming human proofreading effort. Even higher resolution can be achieved on smaller volumes. We present example data sets from mammalian neural tissue, Drosophila brain, and Chlamydomonas reinhardtii to illustrate the power of this novel high-resolution technique to address questions in both connectomics and cell biology.« less

Evaluation of high resolution ultrasound as a tool for assessing the 3D volume of blood clots during in vitro thrombolysis.

PubMed

Auboire, Laurent; Escoffre, Jean-Michel; Fouan, Damien; Jacquet, Jean-René; Ossant, Frédéric; Grégoire, Jean-Marc; Bouakaz, Ayache

2017-07-24

Thrombosis is a major cause of several diseases, i.e. myocardial infarction, cerebral stroke and pulmonary embolism. Thrombolytic therapies are required to induce fast and efficient recanalization of occluded vessels. To evaluate the in vitro efficacy of these thrombolytic strategies, measuring clot dissolution is essential. This study aimed to evaluate and validate high resolution ultrasound as a tool to assess the exact volume of clots in 3D and in real time during in vitro thrombolytic drug testing. This new method was validated by measuring the effects of concentration range of recombinant tissue type plasminogen activator on a blood clot during complete occlusion or 70% stenosis of a vessel. This study shows that high resolution ultrasound imaging allows for a real-time assessment of the 3D volume of a blood clot with negligible inter- and intra-operator variabilities. The conclusions drawn from this study demonstrate the promising potential of high resolution ultrasound imaging for the in vitro assessment of new thrombolytic drugs.

How does C-VIEW image quality compare with conventional 2D FFDM?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Jeffrey S., E-mail: nelson.jeffrey@duke.edu; Wells, Jered R.; Baker, Jay A.

Purpose: The FDA approved the use of digital breast tomosynthesis (DBT) in 2011 as an adjunct to 2D full field digital mammography (FFDM) with the constraint that all DBT acquisitions must be paired with a 2D image to assure adequate interpretative information is provided. Recently manufacturers have developed methods to provide a synthesized 2D image generated from the DBT data with the hope of sparing patients the radiation exposure from the FFDM acquisition. While this much needed alternative effectively reduces the total radiation burden, differences in image quality must also be considered. The goal of this study was to comparemore » the intrinsic image quality of synthesized 2D C-VIEW and 2D FFDM images in terms of resolution, contrast, and noise. Methods: Two phantoms were utilized in this study: the American College of Radiology mammography accreditation phantom (ACR phantom) and a novel 3D printed anthropomorphic breast phantom. Both phantoms were imaged using a Hologic Selenia Dimensions 3D system. Analysis of the ACR phantom includes both visual inspection and objective automated analysis using in-house software. Analysis of the 3D anthropomorphic phantom includes visual assessment of resolution and Fourier analysis of the noise. Results: Using ACR-defined scoring criteria for the ACR phantom, the FFDM images scored statistically higher than C-VIEW according to both the average observer and automated scores. In addition, between 50% and 70% of C-VIEW images failed to meet the nominal minimum ACR accreditation requirements—primarily due to fiber breaks. Software analysis demonstrated that C-VIEW provided enhanced visualization of medium and large microcalcification objects; however, the benefits diminished for smaller high contrast objects and all low contrast objects. Visual analysis of the anthropomorphic phantom showed a measureable loss of resolution in the C-VIEW image (11 lp/mm FFDM, 5 lp/mm C-VIEW) and loss in detection of small microcalcification objects. Spectral analysis of the anthropomorphic phantom showed higher total noise magnitude in the FFDM image compared with C-VIEW. Whereas the FFDM image contained approximately white noise texture, the C-VIEW image exhibited marked noise reduction at midfrequency and high frequency with far less noise suppression at low frequencies resulting in a mottled noise appearance. Conclusions: Their analysis demonstrates many instances where the C-VIEW image quality differs from FFDM. Compared to FFDM, C-VIEW offers a better depiction of objects of certain size and contrast, but provides poorer overall resolution and noise properties. Based on these findings, the utilization of C-VIEW images in the clinical setting requires careful consideration, especially if considering the discontinuation of FFDM imaging. Not explicitly explored in this study is how the combination of DBT + C-VIEW performs relative to DBT + FFDM or FFDM alone.« less

Cartography of asteroids and comet nuclei from low resolution data

NASA Technical Reports Server (NTRS)

Stooke, Philip J.

1992-01-01

High resolution images of non-spherical objects, such as Viking images of Phobos and the anticipated Galileo images of Gaspra, lend themselves to conventional planetary cartographic procedures: control network analysis, stereophotogrammetry, image mosaicking in 2D or 3D, and airbrush mapping. There remains the problem of a suitable map projection for bodies which are extremely elongated or irregular in shape. Many bodies will soon be seen at lower resolution (5-30 pixels across the disk) in images from speckle interferometry, the Hubble Space Telescope, ground-based radar, distinct spacecraft encounters, and closer images degraded by smear. Different data with similar effective resolutions are available from stellar occultations, radar or lightcurve convex hulls, lightcurve modeling of albedo variations, and cometary jet modeling. With such low resolution, conventional methods of shape determination will be less useful or will fail altogether, leaving limb and terminator topography as the principal sources of topographic information. A method for shape determination based on limb and terminator topography was developed. It has been applied to the nucleus of Comet Halley and the jovian satellite Amalthea. The Amalthea results are described to give an example of the cartographic possibilities and problems of anticipated data sets.

A New Sparse Representation Framework for Reconstruction of an Isotropic High Spatial Resolution MR Volume From Orthogonal Anisotropic Resolution Scans.

PubMed

Jia, Yuanyuan; Gholipour, Ali; He, Zhongshi; Warfield, Simon K

2017-05-01

In magnetic resonance (MR), hardware limitations, scan time constraints, and patient movement often result in the acquisition of anisotropic 3-D MR images with limited spatial resolution in the out-of-plane views. Our goal is to construct an isotropic high-resolution (HR) 3-D MR image through upsampling and fusion of orthogonal anisotropic input scans. We propose a multiframe super-resolution (SR) reconstruction technique based on sparse representation of MR images. Our proposed algorithm exploits the correspondence between the HR slices and the low-resolution (LR) sections of the orthogonal input scans as well as the self-similarity of each input scan to train pairs of overcomplete dictionaries that are used in a sparse-land local model to upsample the input scans. The upsampled images are then combined using wavelet fusion and error backprojection to reconstruct an image. Features are learned from the data and no extra training set is needed. Qualitative and quantitative analyses were conducted to evaluate the proposed algorithm using simulated and clinical MR scans. Experimental results show that the proposed algorithm achieves promising results in terms of peak signal-to-noise ratio, structural similarity image index, intensity profiles, and visualization of small structures obscured in the LR imaging process due to partial volume effects. Our novel SR algorithm outperforms the nonlocal means (NLM) method using self-similarity, NLM method using self-similarity and image prior, self-training dictionary learning-based SR method, averaging of upsampled scans, and the wavelet fusion method. Our SR algorithm can reduce through-plane partial volume artifact by combining multiple orthogonal MR scans, and thus can potentially improve medical image analysis, research, and clinical diagnosis.

Custom Super-Resolution Microscope for the Structural Analysis of Nanostructures

DTIC Science & Technology

2018-05-29

research community. As part of our validation of the new design approach, we performed two - color imaging of pairs of adjacent oligo probes hybridized...nanostructures and biological targets. Our microscope features a large field of view and custom optics that facilitate 3D imaging and enhanced contrast in...our imaging throughput by creating two microscopy platforms for high-throughput, super-resolution materials characterization, with the AO set-up being

High temporal resolution dynamic contrast-enhanced MRI using compressed sensing-combined sequence in quantitative renal perfusion measurement.

PubMed

Chen, Bin; Zhao, Kai; Li, Bo; Cai, Wenchao; Wang, Xiaoying; Zhang, Jue; Fang, Jing

2015-10-01

To demonstrate the feasibility of the improved temporal resolution by using compressed sensing (CS) combined imaging sequence in dynamic contrast-enhanced MRI (DCE-MRI) of kidney, and investigate its quantitative effects on renal perfusion measurements. Ten rabbits were included in the accelerated scans with a CS-combined 3D pulse sequence. To evaluate the image quality, the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were compared between the proposed CS strategy and the conventional full sampling method. Moreover, renal perfusion was estimated by using the separable compartmental model in both CS simulation and realistic CS acquisitions. The CS method showed DCE-MRI images with improved temporal resolution and acceptable image contrast, while presenting significantly higher SNR than the fully sampled images (p<.01) at 2-, 3- and 4-X acceleration. In quantitative measurements, renal perfusion results were in good agreement with the fully sampled one (concordance correlation coefficient=0.95, 0.91, 0.88) at 2-, 3- and 4-X acceleration in CS simulation. Moreover, in realistic acquisitions, the estimated perfusion by the separable compartmental model exhibited no significant differences (p>.05) between each CS-accelerated acquisition and the full sampling method. The CS-combined 3D sequence could improve the temporal resolution for DCE-MRI in kidney while yielding diagnostically acceptable image quality, and it could provide effective measurements of renal perfusion. Copyright © 2015 Elsevier Inc. All rights reserved.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

Ge, Bing-Hui; Li, Fang-Hua; Li, Xue-Ming; Wang, Yu-Mei; Chi, Zhen-Hua; Jin, Chang-Qing

2008-09-01

The crystal structure of the minor phase, named superstructure II, existing in multiferroic compound BiMnO3 has been studied by electron diffraction and high-resolution transmission electron microscopy. Domains of major and minor phases coexisting in BiMnO3 were observed in high-resolution electron microscope images. The unit cell of minor phase was determined to be triclinic with the size 4×4×4 times as large as the distorted perovskite subcell. The [111] and [10bar 1] projected structure maps of the minor phase have been derived from the corresponding images by means of the image processing. A possible rough three-dimensional (3D) structure model was proposed based on the 3D structural information extracted from the two projected structure maps. Since there is no inversion centre in the proposed model, the minor phase may contribute to the ferroelectric property of BiMnO3.

Nanoscale Pore Imaging and Pore Scale Fluid Flow Modeling in Chalk

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomutsa, Liviu; Silin, Dmitriy

2004-08-19

For many rocks of high economic interest such as chalk, diatomite, tight gas sands or coal, nanometer scale resolution is needed to resolve the 3D-pore structure, which controls the flow and trapping of fluids in the rocks. Such resolutions cannot be achieved with existing tomographic technologies. A new 3D imaging method, based on serial sectioning and using the Focused Ion Beam (FIB) technology has been developed. FIB allows for the milling of layers as thin as 10 nanometers by using accelerated Ga+ ions to sputter atoms from the sample surface. After each milling step, as a new surface is exposed,more » a 2D image of this surface is generated. Next, the 2D images are stacked to reconstruct the 3D pore or grain structure. Resolutions as high as 10 nm are achievable using such a technique. A new robust method of pore-scale fluid flow modeling has been developed and applied to sandstone and chalk samples. The method uses direct morphological analysis of the pore space to characterize the petrophysical properties of diverse formations. Not only petrophysical properties (porosity, permeability, relative permeability and capillary pressures) can be computed but also flow processes, such as those encountered in various IOR approaches, can be simulated. Petrophysical properties computed with the new method using the new FIB data will be presented. Present study is a part of the development of an Electronic Core Laboratory at LBNL/UCB.« less

Submicron-resolution photoacoustic microscopy of endogenous light-absorbing biomolecules

NASA Astrophysics Data System (ADS)

Zhang, Chi

Photoacoustic imaging in biomedicine has the unique advantage of probing endogenous light absorbers at various length scales with a 100% relative sensitivity. Among the several modalities of photoacoustic imaging, optical-resolution photoacoustic microscopy (OR-PAM) can achieve high spatial resolution, on the order of optical wavelength, at <1 mm depth in biological tissue (the optical ballistic regime). OR-PAM has been applied successfully to structural and functional imaging of blood vasculature and red blood cells in vivo. Any molecules which absorb sufficient light at certain wavelengths can potentially be imaged by PAM. Compared with pure optical imaging, which typically targets fluorescent markers, label-free PAM avoids the major concerns that the fluorescent labeling probes may disturb the function of biomolecules and may have an insufficient density. This dissertation aims to advance label-free OR-PAM to the subcellular scale. The first part of this dissertation describes the technological advancement of PAM yielding high spatial resolution in 3D. The lateral resolution was improved by using optical objectives with high numerical apertures for optical focusing. The axial resolution was improved by using broadband ultrasonic transducers for ultrasound detection. We achieved 220 nm lateral resolution in transmission mode, 0.43 microm lateral resolution in reflection mode, 7.6 microm axial resolution in normal tissue, and 5.8 microm axial resolution with silicone oil immersion/injection. The achieved lateral resolution and axial resolution were the finest reported at the time. With high-resolution in 3D, PAM was demonstrated to resolve cellular and subcellular structures in vivo, such as red blood cells and melanosomes in melanoma cells. Compared with previous PAM systems, our high-resolution PAM could resolve capillaries in mouse ears more clearly. As an example application, we demonstrated intracellular temperature imaging, assisted by fluorescence signal detection, with sub-degree temperature resolution and sub-micron lateral resolution. The second part of this dissertation describes the exploration of endogenous light-absorbing biomolecules for PAM. We demonstrated cytochromes and myoglobin as new absorption contrasts for PAM and identified the corresponding optimal wavelengths for imaging. Fixed fibroblasts on slides and mouse ear sections were imaged by PAM at 422 nm and 250 nm wavelengths to reveal cytoplasms and nuclei, respectively, as confirmed by standard hematoxylin and eosin (H&E) histology. By imaging a blood-perfused mouse heart at 532 nm down to 150 microm in depth, we derived the myocardial sheet thickness and the cleavage height from an undehydrated heart for the first time. The findings promote PAM at new wavelengths and open up new possibilities for characterizing biological tissue. Of particular interest, dual-wavelength PAM around 250 nm and 420 nm wavelengths is analogous to H&E histology. The last part of this dissertation describes the development of sectioning photoacoustic microscopy (SPAM), based on the advancement in spatial resolution and new contrasts for PAM, with applications in brain histology. Label-free SPAM, assisted by a microtome, acquires serial distortion-free images of a specimen on the surface. By exciting cell nuclei at 266 nm wavelength with high resolution, SPAM could pinpoint cell nuclei sensitively and specifically in the mouse brain section, as confirmed by H&E histology. SPAM was demonstrated to generate high-resolution 3D images, highlighting cell nuclei, of formalin-fixed paraffin-embedded mouse brains without tissue staining or clearing. SPAM can potentially serve as a high-throughput and minimal-artifact substitute for histology, probe many other biomolecules and cells, and become a universal tool for animal or human whole-organ microscopy, with diverse applications in life sciences.

Three-dimensional reconstruction of Roman coins from photometric image sets

NASA Astrophysics Data System (ADS)

MacDonald, Lindsay; Moitinho de Almeida, Vera; Hess, Mona

2017-01-01

A method is presented for increasing the spatial resolution of the three-dimensional (3-D) digital representation of coins by combining fine photometric detail derived from a set of photographic images with accurate geometric data from a 3-D laser scanner. 3-D reconstructions were made of the obverse and reverse sides of two ancient Roman denarii by processing sets of images captured under directional lighting in an illumination dome. Surface normal vectors were calculated by a "bounded regression" technique, excluding both shadow and specular components of reflection from the metallic surface. Because of the known difficulty in achieving geometric accuracy when integrating photometric normals to produce a digital elevation model, the low spatial frequencies were replaced by those derived from the point cloud produced by a 3-D laser scanner. The two datasets were scaled and registered by matching the outlines and correlating the surface gradients. The final result was a realistic rendering of the coins at a spatial resolution of 75 pixels/mm (13-μm spacing), in which the fine detail modulated the underlying geometric form of the surface relief. The method opens the way to obtain high quality 3-D representations of coins in collections to enable interactive online viewing.

Is phase measurement necessary for incoherent holographic 3D imaging?

NASA Astrophysics Data System (ADS)

Rosen, Joseph; Vijayakumar, A.; Rai, Mani Ratnam; Mukherjee, Saswata

2018-02-01

Incoherent digital holography can be used for several applications, among which are high resolution fluorescence microscopy and imaging through a scattering medium. Historically, an incoherent digital hologram has been usually recorded by self-interference systems in which both interfering beams are originated from the same observed object. The self-interference system enables to read the phase distribution of the wavefronts propagating from an object and consequently to decode the 3D location of the object points. In this presentation, we survey several cases in which 3D holographic imaging can be done without the phase information and without two-wave interference.

Trans-Dimensional Bayesian Imaging of 3-D Crustal and Upper Mantle Structure in Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.

2016-12-01

Imaging 3-D structures using stepwise inversions of ambient noise and receiver function data is now a routine work. Here, we carry out the inversion in the trans-dimensional and hierarchical extension of the Bayesian framework to obtain rigorous estimates of uncertainty and high-resolution images of crustal and upper mantle structures beneath Northeast (NE) Asia. The methods inherently account for data sensitivities by means of using adaptive parameterizations and treating data noise as free parameters. Therefore, parsimonious results from the methods are balanced out between model complexity and data fitting. This allows fully exploiting data information, preventing from over- or under-estimation of the data fit, and increases model resolution. In addition, the reliability of results is more rigorously checked through the use of Bayesian uncertainties. It is shown by various synthetic recovery tests that complex and spatially variable features are well resolved in our resulting images of NE Asia. Rayleigh wave phase and group velocity tomograms (8-70 s), a 3-D shear-wave velocity model from depth inversions of the estimated dispersion maps, and regional 3-D models (NE China, the Korean Peninsula, and the Japanese islands) from joint inversions with receiver function data of dense networks are presented. High-resolution models are characterized by a number of tectonically meaningful features. We focus our interpretation on complex patterns of sub-lithospheric low velocity structures that extend from back-arc regions to continental margins. We interpret the anomalies in conjunction with distal and distributed intraplate volcanoes in NE Asia. Further discussion on other imaged features will be presented.

High-resolution MRI of cranial nerves in posterior fossa at 3.0 T.

PubMed

Guo, Zi-Yi; Chen, Jing; Liang, Qi-Zhou; Liao, Hai-Yan; Cheng, Qiong-Yue; Fu, Shui-Xi; Chen, Cai-Xiang; Yu, Dan

2013-02-01

To evaluate the influence of high-resolution imaging obtainable with the higher field strength of 3.0 T on the visualization of the brain nerves in the posterior fossa. In total, 20 nerves were investigated on MRI of 12 volunteers each and selected for comparison, respectively, with the FSE sequences with 5 mm and 2 mm section thicknesses and gradient recalled echo (GRE) sequences acquired with a 3.0-T scanner. The MR images were evaluated by three independent readers who rated image quality according to depiction of anatomic detail and contrast with use of a rating scale. In general, decrease of the slice thickness showed a significant increase in the detection of nerves as well as in the image quality characteristics. Comparing FSE and GRE imaging, the course of brain nerves and brainstem vessels was visualized best with use of the three-dimensional (3D) pulse sequence. The comparison revealed the clear advantage of a thin section. The increased resolution enabled immediate identification of all brainstem nerves. GRE sequence most distinctly and confidently depicted pertinent structures and enables 3D reconstruction to illustrate complex relations of the brainstem. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

Multiscale study on stochastic reconstructions of shale samples

NASA Astrophysics Data System (ADS)

Lili, J.; Lin, M.; Jiang, W. B.

2016-12-01

Shales are known to have multiscale pore systems, composed of macroscale fractures, micropores, and nanoscale pores within gas or oil-producing organic material. Also, shales are fissile and laminated, and the heterogeneity in horizontal is quite different from that in vertical. Stochastic reconstructions are extremely useful in situations where three-dimensional information is costly and time consuming. Thus the purpose of our paper is to reconstruct stochastically equiprobable 3D models containing information from several scales. In this paper, macroscale and microscale images of shale structure in the Lower Silurian Longmaxi are obtained by X-ray microtomography and nanoscale images are obtained by scanning electron microscopy. Each image is representative for all given scales and phases. Especially, the macroscale is four times coarser than the microscale, which in turn is four times lower in resolution than the nanoscale image. Secondly, the cross correlation-based simulation method (CCSIM) and the three-step sampling method are combined together to generate stochastic reconstructions for each scale. It is important to point out that the boundary points of pore and matrix are selected based on multiple-point connectivity function in the sampling process, and thus the characteristics of the reconstructed image can be controlled indirectly. Thirdly, all images with the same resolution are developed through downscaling and upscaling by interpolation, and then we merge multiscale categorical spatial data into a single 3D image with predefined resolution (the microscale image). 30 realizations using the given images and the proposed method are generated. The result reveals that the proposed method is capable of preserving the multiscale pore structure, both vertically and horizontally, which is necessary for accurate permeability prediction. The variogram curves and pore-size distribution for both original 3D sample and the generated 3D realizations are compared. The result indicates that the agreement between the original 3D sample and the generated stochastic realizations is excellent. This work is supported by "973" Program (2014CB239004), the Key Instrument Developing Project of the CAS (ZDYZ2012-1-08-02) and the National Natural Science Foundation of China (Grant No. 41574129).

Geometric validation of self-gating k-space-sorted 4D-MRI vs 4D-CT using a respiratory motion phantom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yue, Yong, E-mail: yong.yue@cshs.org; Yang, Wensha; McKenzie, Elizabeth

Purpose: MRI is increasingly being used for radiotherapy planning, simulation, and in-treatment-room motion monitoring. To provide more detailed temporal and spatial MR data for these tasks, we have recently developed a novel self-gated (SG) MRI technique with advantage of k-space phase sorting, high isotropic spatial resolution, and high temporal resolution. The current work describes the validation of this 4D-MRI technique using a MRI- and CT-compatible respiratory motion phantom and comparison to 4D-CT. Methods: The 4D-MRI sequence is based on a spoiled gradient echo-based 3D projection reconstruction sequence with self-gating for 4D-MRI at 3 T. Respiratory phase is resolved by usingmore » SG k-space lines as the motion surrogate. 4D-MRI images are reconstructed into ten temporal bins with spatial resolution 1.56 × 1.56 × 1.56 mm{sup 3}. A MRI-CT compatible phantom was designed to validate the performance of the 4D-MRI sequence and 4D-CT imaging. A spherical target (diameter 23 mm, volume 6.37 ml) filled with high-concentration gadolinium (Gd) gel is embedded into a plastic box (35 × 40 × 63 mm{sup 3}) and stabilized with low-concentration Gd gel. The phantom, driven by an air pump, is able to produce human-type breathing patterns between 4 and 30 respiratory cycles/min. 4D-CT of the phantom has been acquired in cine mode, and reconstructed into ten phases with slice thickness 1.25 mm. The 4D images sets were imported into a treatment planning software for target contouring. The geometrical accuracy of the 4D MRI and CT images has been quantified using target volume, flattening, and eccentricity. The target motion was measured by tracking the centroids of the spheres in each individual phase. Motion ground-truth was obtained from input signals and real-time video recordings. Results: The dynamic phantom has been operated in four respiratory rate (RR) settings, 6, 10, 15, and 20/min, and was scanned with 4D-MRI and 4D-CT. 4D-CT images have target-stretching, partial-missing, and other motion artifacts in various phases, whereas the 4D-MRI images are visually free of those artifacts. Volume percentage difference for the 6.37 ml target ranged from 5.3% ± 4.3% to 10.3% ± 5.9% for 4D-CT, and 1.47 ± 0.52 to 2.12 ± 1.60 for 4D-MRI. With an increase of respiratory rate, the target volumetric and geometric deviations increase for 4D-CT images while remaining stable for the 4D-MRI images. Target motion amplitude errors at different RRs were measured with a range of 0.66–1.25 mm for 4D-CT and 0.2–0.42 mm for 4D-MRI. The results of Mann–Whitney tests indicated that 4D-MRI significantly outperforms 4D-CT in phase-based target volumetric (p = 0.027) and geometric (p < 0.001) measures. Both modalities achieve equivalent accuracy in measuring motion amplitude (p = 0.828). Conclusions: The k-space self-gated 4D-MRI technique provides a robust method for accurately imaging phase-based target motion and geometry. Compared to 4D-CT, the current 4D-MRI technique demonstrates superior spatiotemporal resolution, and robust resistance to motion artifacts caused by fast target motion and irregular breathing patterns. The technique can be used extensively in abdominal targeting, motion gating, and toward implementing MRI-based adaptive radiotherapy.« less

Fast high resolution reconstruction in multi-slice and multi-view cMRI

NASA Astrophysics Data System (ADS)

Velasco Toledo, Nelson; Romero Castro, Eduardo

2015-01-01

Cardiac magnetic resonance imaging (cMRI) is an useful tool in diagnosis, prognosis and research since it functionally tracks the heart structure. Although useful, this imaging technique is limited in spatial resolution because heart is a constant moving organ, also there are other non controled conditions such as patient movements and volumetric changes during apnea periods when data is acquired, those conditions limit the time to capture high quality information. This paper presents a very fast and simple strategy to reconstruct high resolution 3D images from a set of low resolution series of 2D images. The strategy is based on an information reallocation algorithm which uses the DICOM header to relocate voxel intensities in a regular grid. An interpolation method is applied to fill empty places with estimated data, the interpolation resamples the low resolution information to estimate the missing information. As a final step a gaussian filter that denoises the final result. A reconstructed image evaluation is performed using as a reference a super-resolution reconstructed image. The evaluation reveals that the method maintains the general heart structure with a small loss in detailed information (edge sharpening and blurring), some artifacts related with input information quality are detected. The proposed method requires low time and computational resources.

Simultaneous multi-slice combined with PROPELLER.

PubMed

Norbeck, Ola; Avventi, Enrico; Engström, Mathias; Rydén, Henric; Skare, Stefan

2018-08-01

Simultaneous multi-slice (SMS) imaging is an advantageous method for accelerating MRI scans, allowing reduced scan time, increased slice coverage, or high temporal resolution with limited image quality penalties. In this work we combine the advantages of SMS acceleration with the motion correction and artifact reduction capabilities of the PROPELLER technique. A PROPELLER sequence was developed with support for CAIPIRINHA and phase optimized multiband radio frequency pulses. To minimize the time spent on acquiring calibration data, both in-plane-generalized autocalibrating partial parallel acquisition (GRAPPA) and slice-GRAPPA weights for all PROPELLER blade angles were calibrated on a single fully sampled PROPELLER blade volume. Therefore, the proposed acquisition included a single fully sampled blade volume, with the remaining blades accelerated in both the phase and slice encoding directions without additional auto calibrating signal lines. Comparison to 3D RARE was performed as well as demonstration of 3D motion correction performance on the SMS PROPELLER data. We show that PROPELLER acquisitions can be efficiently accelerated with SMS using a short embedded calibration. The potential in combining these two techniques was demonstrated with a high quality 1.0 × 1.0 × 1.0 mm 3 resolution T 2 -weighted volume, free from banding artifacts, and capable of 3D retrospective motion correction, with higher effective resolution compared to 3D RARE. With the combination of SMS acceleration and PROPELLER imaging, thin-sliced reformattable T 2 -weighted image volumes with 3D retrospective motion correction capabilities can be rapidly acquired with low sensitivity to flow and head motion. Magn Reson Med 80:496-506, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Water Selective Imaging and bSSFP Banding Artifact Correction in Humans and Small Animals at 3T and 7T, Respectively

PubMed Central

Ribot, Emeline J.; Wecker, Didier; Trotier, Aurélien J.; Dallaudière, Benjamin; Lefrançois, William; Thiaudière, Eric; Franconi, Jean-Michel; Miraux, Sylvain

2015-01-01

Introduction The purpose of this paper is to develop an easy method to generate both fat signal and banding artifact free 3D balanced Steady State Free Precession (bSSFP) images at high magnetic field. Methods In order to suppress fat signal and bSSFP banding artifacts, two or four images were acquired with the excitation frequency of the water-selective binomial radiofrequency pulse set On Resonance or shifted by a maximum of 3/4TR. Mice and human volunteers were imaged at 7T and 3T, respectively to perform whole-body and musculoskeletal imaging. “Sum-Of-Square” reconstruction was performed and combined or not with parallel imaging. Results The frequency selectivity of 1-2-3-2-1 or 1-3-3-1 binomial pulses was preserved after (3/4TR) frequency shifting. Consequently, whole body small animal 3D imaging was performed at 7T and enabled visualization of small structures within adipose tissue like lymph nodes. In parallel, this method allowed 3D musculoskeletal imaging in humans with high spatial resolution at 3T. The combination with parallel imaging allowed the acquisition of knee images with ~500μm resolution images in less than 2min. In addition, ankles, full head coverage and legs of volunteers were imaged, demonstrating the possible application of the method also for large FOV. Conclusion In conclusion, this robust method can be applied in small animals and humans at high magnetic fields. The high SNR and tissue contrast obtained in short acquisition times allows to prescribe bSSFP sequence for several preclinical and clinical applications. PMID:26426849

Implementation of parallel transmit beamforming using orthogonal frequency division multiplexing--achievable resolution and interbeam interference.

PubMed

Demi, Libertario; Viti, Jacopo; Kusters, Lieneke; Guidi, Francesco; Tortoli, Piero; Mischi, Massimo

2013-11-01

The speed of sound in the human body limits the achievable data acquisition rate of pulsed ultrasound scanners. To overcome this limitation, parallel beamforming techniques are used in ultrasound 2-D and 3-D imaging systems. Different parallel beamforming approaches have been proposed. They may be grouped into two major categories: parallel beamforming in reception and parallel beamforming in transmission. The first category is not optimal for harmonic imaging; the second category may be more easily applied to harmonic imaging. However, inter-beam interference represents an issue. To overcome these shortcomings and exploit the benefit of combining harmonic imaging and high data acquisition rate, a new approach has been recently presented which relies on orthogonal frequency division multiplexing (OFDM) to perform parallel beamforming in transmission. In this paper, parallel transmit beamforming using OFDM is implemented for the first time on an ultrasound scanner. An advanced open platform for ultrasound research is used to investigate the axial resolution and interbeam interference achievable with parallel transmit beamforming using OFDM. Both fundamental and second-harmonic imaging modalities have been considered. Results show that, for fundamental imaging, axial resolution in the order of 2 mm can be achieved in combination with interbeam interference in the order of -30 dB. For second-harmonic imaging, axial resolution in the order of 1 mm can be achieved in combination with interbeam interference in the order of -35 dB.

Correction of a Depth-Dependent Lateral Distortion in 3D Super-Resolution Imaging

PubMed Central

Manley, Suliana

2015-01-01

Three-dimensional (3D) localization-based super-resolution microscopy (SR) requires correction of aberrations to accurately represent 3D structure. Here we show how a depth-dependent lateral shift in the apparent position of a fluorescent point source, which we term `wobble`, results in warped 3D SR images and provide a software tool to correct this distortion. This system-specific, lateral shift is typically > 80 nm across an axial range of ~ 1 μm. A theoretical analysis based on phase retrieval data from our microscope suggests that the wobble is caused by non-rotationally symmetric phase and amplitude aberrations in the microscope’s pupil function. We then apply our correction to the bacterial cytoskeletal protein FtsZ in live bacteria and demonstrate that the corrected data more accurately represent the true shape of this vertically-oriented ring-like structure. We also include this correction method in a registration procedure for dual-color, 3D SR data and show that it improves target registration error (TRE) at the axial limits over an imaging depth of 1 μm, yielding TRE values of < 20 nm. This work highlights the importance of correcting aberrations in 3D SR to achieve high fidelity between the measurements and the sample. PMID:26600467

Super-resolution reconstruction for 4D computed tomography of the lung via the projections onto convex sets approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yu, E-mail: yuzhang@smu.edu.cn, E-mail: qianjinfeng08@gmail.com; Wu, Xiuxiu; Yang, Wei

2014-11-01

Purpose: The use of 4D computed tomography (4D-CT) of the lung is important in lung cancer radiotherapy for tumor localization and treatment planning. Sometimes, dense sampling is not acquired along the superior–inferior direction. This disadvantage results in an interslice thickness that is much greater than in-plane voxel resolutions. Isotropic resolution is necessary for multiplanar display, but the commonly used interpolation operation blurs images. This paper presents a super-resolution (SR) reconstruction method to enhance 4D-CT resolution. Methods: The authors assume that the low-resolution images of different phases at the same position can be regarded as input “frames” to reconstruct high-resolution images.more » The SR technique is used to recover high-resolution images. Specifically, the Demons deformable registration algorithm is used to estimate the motion field between different “frames.” Then, the projection onto convex sets approach is implemented to reconstruct high-resolution lung images. Results: The performance of the SR algorithm is evaluated using both simulated and real datasets. Their method can generate clearer lung images and enhance image structure compared with cubic spline interpolation and back projection (BP) method. Quantitative analysis shows that the proposed algorithm decreases the root mean square error by 40.8% relative to cubic spline interpolation and 10.2% versus BP. Conclusions: A new algorithm has been developed to improve the resolution of 4D-CT. The algorithm outperforms the cubic spline interpolation and BP approaches by producing images with markedly improved structural clarity and greatly reduced artifacts.« less

3D X-ray ultra-microscopy of bone tissue.

PubMed

Langer, M; Peyrin, F

2016-02-01

We review the current X-ray techniques with 3D imaging capability at the nano-scale: transmission X-ray microscopy, ptychography and in-line phase nano-tomography. We further review the different ultra-structural features that have so far been resolved: the lacuno-canalicular network, collagen orientation, nano-scale mineralization and their use as basis for mechanical simulations. X-ray computed tomography at the micro-metric scale is increasingly considered as the reference technique in imaging of bone micro-structure. The trend has been to push towards increasingly higher resolution. Due to the difficulty of realizing optics in the hard X-ray regime, the magnification has mainly been due to the use of visible light optics and indirect detection of the X-rays, which limits the attainable resolution with respect to the wavelength of the visible light used in detection. Recent developments in X-ray optics and instrumentation have allowed to implement several types of methods that achieve imaging that is limited in resolution by the X-ray wavelength, thus enabling computed tomography at the nano-scale. We review here the X-ray techniques with 3D imaging capability at the nano-scale: transmission X-ray microscopy, ptychography and in-line phase nano-tomography. Further, we review the different ultra-structural features that have so far been resolved and the applications that have been reported: imaging of the lacuno-canalicular network, direct analysis of collagen orientation, analysis of mineralization on the nano-scale and use of 3D images at the nano-scale to drive mechanical simulations. Finally, we discuss the issue of going beyond qualitative description to quantification of ultra-structural features.

High-frame-rate imaging of biological samples with optoacoustic micro-tomography

NASA Astrophysics Data System (ADS)

Deán-Ben, X. Luís.; López-Schier, Hernán.; Razansky, Daniel

2018-02-01

Optical microscopy remains a major workhorse in biological discovery despite the fact that light scattering limits its applicability to depths of ˜ 1 mm in scattering tissues. Optoacoustic imaging has been shown to overcome this barrier by resolving optical absorption with microscopic resolution in significantly deeper regions. Yet, the time domain is paramount for the observation of biological dynamics in living systems that exhibit fast motion. Commonly, acquisition of microscopy data involves raster scanning across the imaged volume, which significantly limits temporal resolution in 3D. To overcome these limitations, we have devised a fast optoacoustic micro-tomography (OMT) approach based on simultaneous acquisition of 3D image data with a high-density hemispherical ultrasound array having effective detection bandwidth around 25 MHz. We performed experiments by imaging tissue-mimicking phantoms and zebrafish larvae, demonstrating that OMT can provide nearly cellular resolution and imaging speed of 100 volumetric frames per second. As opposed to other optical microscopy techniques, OMT is a hybrid method that resolves optical absorption contrast acoustically using unfocused light excitation. Thus, no penetration barriers are imposed by light scattering in deep tissues, suggesting it as a powerful approach for multi-scale functional and molecular imaging applications.

New Algorithm to Enable Construction and Display of 3D Structures from Scanning Probe Microscopy Images Acquired Layer-by-Layer.

PubMed

Deng, William Nanqiao; Wang, Shuo; Ventrici de Souza, Joao; Kuhl, Tonya L; Liu, Gang-Yu

2018-06-25

Scanning probe microscopy (SPM), such as atomic force microscopy (AFM), is widely known for high-resolution imaging of surface structures and nanolithography in two dimensions (2D), providing important physical insights into surface science and material science. This work reports a new algorithm to enable construction and display of layer-by-layer 3D structures from SPM images. The algorithm enables alignment of SPM images acquired during layer-by-layer deposition and removal of redundant features and faithfully constructs the deposited 3D structures. The display uses a "see-through" strategy to enable the structure of each layer to be visible. The results demonstrate high spatial accuracy as well as algorithm versatility; users can set parameters for reconstruction and display as per image quality and research needs. To the best of our knowledge, this method represents the first report to enable SPM technology for 3D imaging construction and display. The detailed algorithm is provided to facilitate usage of the same approach in any SPM software. These new capabilities support wide applications of SPM that require 3D image reconstruction and display, such as 3D nanoprinting and 3D additive and subtractive manufacturing and imaging.

Carotid arterial wall MRI at 3T using 3D variable-flip-angle turbo spin-echo (TSE) with flow-sensitive dephasing (FSD).

PubMed

Fan, Zhaoyang; Zhang, Zhuoli; Chung, Yiu-Cho; Weale, Peter; Zuehlsdorff, Sven; Carr, James; Li, Debiao

2010-03-01

To evaluate the effectiveness of flow-sensitive dephasing (FSD) magnetization preparation in improving blood signal suppression of three-dimensional (3D) turbo spin-echo (TSE) sequence (SPACE) for isotropic high-spatial-resolution carotid arterial wall imaging at 3T. The FSD-prepared SPACE sequence (FSD-SPACE) was implemented by adding two identical FSD gradient pulses right before and after the first refocusing 180 degrees -pulse of the SPACE sequence in all three orthogonal directions. Nine healthy volunteers were imaged at 3T with SPACE, FSD-SPACE, and multislice T2-weighted 2D TSE coupled with saturation band (SB-TSE). Apparent carotid wall-lumen contrast-to-noise ratio (aCNR(w-l)) and apparent lumen area (aLA) at the locations with residual-blood (rb) signal shown on SPACE images were compared between SPACE and FSD-SPACE. Carotid aCNR(w-l) and lumen (LA) and wall area (WA) measured from FSD-SPACE were compared to those measured from SB-TSE. Plaque-mimicking flow artifacts identified in seven carotids on SPACE images were eliminated on FSD-SPACE images. The FSD preparation resulted in slightly reduced aCNR(w-l) (P = 0.025), but significantly improved aCNR between the wall and rb regions (P < 0.001) and larger aLA (P < 0.001). Compared to SB-TSE, FSD-SPACE offered comparable aCNR(w-l) with much higher spatial resolution, shorter imaging time, and larger artery coverage. The LA and WA measurements from the two techniques were in good agreement based on intraclasss correlation coefficient (0.988 and 0.949, respectively; P < 0.001) and Bland-Altman analyses. FSD-SPACE is a time-efficient 3D imaging technique for carotid arterial wall with superior spatial resolution and blood signal suppression.

3D high-resolution radar imaging of small body interiors

NASA Astrophysics Data System (ADS)

Sava, Paul; Asphaug, Erik

2017-10-01

Answering fundamental questions about the origin and evolution of small planetary bodies hinges on our ability to image their interior structure in detail and at high resolution (Asphaug, 2009). We often infer internal structure from surface observations, e.g. that comet 67P/Churyumov-Gerasimenko is a primordial agglomeration of cometesimals (Massironi et al., 2015). However, the interior structure is not easily accessible without systematic imaging using, e.g., radar transmission and reflection data, as suggested by the CONSERT experiment on Rosetta. Interior imaging depends on observations from multiple viewpoints, as in medical tomography.We discuss radar imaging using methodology adapted from terrestrial exploration seismology (Sava et al., 2015). We primarily focus on full wavefield methods that facilitate high quality imaging of small body interiors characterized by complex structure and large contrasts of physical properties. We consider the case of a monostatic system (co-located transmitters and receivers) operated at two frequency bands, centered around 5 and 15 MHz, from a spacecraft in slow polar orbit around a spinning comet nucleus. Assuming that the spin period is significantly (e.g. 5x) faster than the orbital period, this configuration allows repeated views from multiple directions (Safaeinili et al., 2002)Using realistic numerical experiments, we argue that (1) the comet/asteroid imaging problem is intrinsically 3D and conventional SAR methodology does not satisfy imaging, sampling and resolution requirements; (2) imaging at different frequency bands can provide information about internal surfaces (through migration) and internal volumes (through tomography); (3) interior imaging can be accomplished progressively as data are being acquired through successive orbits around the studied object; (4) imaging resolution can go beyond the apparent radar frequency band by deconvolution of the point-spread-function characterizing the imaging system; and (5) exploiting the known (and complex) exterior shape of the studied body facilitates high-resolution imaging and tomography comparable with what could be accomplished by bi/multi-static systems.

4-mm-diameter three-dimensional imaging endoscope with steerable camera for minimally invasive surgery (3-D-MARVEL).

PubMed

Bae, Sam Y; Korniski, Ronald J; Shearn, Michael; Manohara, Harish M; Shahinian, Hrayr

2017-01-01

High-resolution three-dimensional (3-D) imaging (stereo imaging) by endoscopes in minimally invasive surgery, especially in space-constrained applications such as brain surgery, is one of the most desired capabilities. Such capability exists at larger than 4-mm overall diameters. We report the development of a stereo imaging endoscope of 4-mm maximum diameter, called Multiangle, Rear-Viewing Endoscopic Tool (MARVEL) that uses a single-lens system with complementary multibandpass filter (CMBF) technology to achieve 3-D imaging. In addition, the system is endowed with the capability to pan from side-to-side over an angle of [Formula: see text], which is another unique aspect of MARVEL for such a class of endoscopes. The design and construction of a single-lens, CMBF aperture camera with integrated illumination to generate 3-D images, and the actuation mechanism built into it is summarized.

Depth resolved hyperspectral imaging spectrometer based on structured light illumination and Fourier transform interferometry

PubMed Central

Choi, Heejin; Wadduwage, Dushan; Matsudaira, Paul T.; So, Peter T.C.

2014-01-01

A depth resolved hyperspectral imaging spectrometer can provide depth resolved imaging both in the spatial and the spectral domain. Images acquired through a standard imaging Fourier transform spectrometer do not have the depth-resolution. By post processing the spectral cubes (x, y, λ) obtained through a Sagnac interferometer under uniform illumination and structured illumination, spectrally resolved images with depth resolution can be recovered using structured light illumination algorithms such as the HiLo method. The proposed scheme is validated with in vitro specimens including fluorescent solution and fluorescent beads with known spectra. The system is further demonstrated in quantifying spectra from 3D resolved features in biological specimens. The system has demonstrated depth resolution of 1.8 μm and spectral resolution of 7 nm respectively. PMID:25360367

Demosaiced pixel super-resolution for multiplexed holographic color imaging

PubMed Central

Wu, Yichen; Zhang, Yibo; Luo, Wei; Ozcan, Aydogan

2016-01-01

To synthesize a holographic color image, one can sequentially take three holograms at different wavelengths, e.g., at red (R), green (G) and blue (B) parts of the spectrum, and digitally merge them. To speed up the imaging process by a factor of three, a Bayer color sensor-chip can also be used to demultiplex three wavelengths that simultaneously illuminate the sample and digitally retrieve individual set of holograms using the known transmission spectra of the Bayer color filters. However, because the pixels of different channels (R, G, B) on a Bayer color sensor are not at the same physical location, conventional demosaicing techniques generate color artifacts in holographic imaging using simultaneous multi-wavelength illumination. Here we demonstrate that pixel super-resolution can be merged into the color de-multiplexing process to significantly suppress the artifacts in wavelength-multiplexed holographic color imaging. This new approach, termed Demosaiced Pixel Super-Resolution (D-PSR), generates color images that are similar in performance to sequential illumination at three wavelengths, and therefore improves the speed of holographic color imaging by 3-fold. D-PSR method is broadly applicable to holographic microscopy applications, where high-resolution imaging and multi-wavelength illumination are desired. PMID:27353242

Speckle-field digital holographic microscopy.

PubMed

Park, YongKeun; Choi, Wonshik; Yaqoob, Zahid; Dasari, Ramachandra; Badizadegan, Kamran; Feld, Michael S

2009-07-20

The use of coherent light in conventional holographic phase microscopy (HPM) poses three major drawbacks: poor spatial resolution, weak depth sectioning, and fixed pattern noise due to unwanted diffraction. Here, we report a technique which can overcome these drawbacks, but maintains the advantage of phase microscopy - high contrast live cell imaging and 3D imaging. A speckle beam of a complex spatial pattern is used for illumination to reduce fixed pattern noise and to improve optical sectioning capability. By recording of the electric field of speckle, we demonstrate high contrast 3D live cell imaging without the need for axial scanning - neither objective lens nor sample stage. This technique has great potential in studying biological samples with improved sensitivity, resolution and optical sectioning capability.

Informatics in radiology: Intuitive user interface for 3D image manipulation using augmented reality and a smartphone as a remote control.

PubMed

Nakata, Norio; Suzuki, Naoki; Hattori, Asaki; Hirai, Naoya; Miyamoto, Yukio; Fukuda, Kunihiko

2012-01-01

Although widely used as a pointing device on personal computers (PCs), the mouse was originally designed for control of two-dimensional (2D) cursor movement and is not suited to complex three-dimensional (3D) image manipulation. Augmented reality (AR) is a field of computer science that involves combining the physical world and an interactive 3D virtual world; it represents a new 3D user interface (UI) paradigm. A system for 3D and four-dimensional (4D) image manipulation has been developed that uses optical tracking AR integrated with a smartphone remote control. The smartphone is placed in a hard case (jacket) with a 2D printed fiducial marker for AR on the back. It is connected to a conventional PC with an embedded Web camera by means of WiFi. The touch screen UI of the smartphone is then used as a remote control for 3D and 4D image manipulation. Using this system, the radiologist can easily manipulate 3D and 4D images from computed tomography and magnetic resonance imaging in an AR environment with high-quality image resolution. Pilot assessment of this system suggests that radiologists will be able to manipulate 3D and 4D images in the reading room in the near future. Supplemental material available at http://radiographics.rsna.org/lookup/suppl/doi:10.1148/rg.324115086/-/DC1.

Ophthalmic magnetic resonance imaging at 7 T using a 6-channel transceiver radiofrequency coil array in healthy subjects and patients with intraocular masses.

PubMed

Graessl, Andreas; Muhle, Maximilian; Schwerter, Michael; Rieger, Jan; Oezerdem, Celal; Santoro, Davide; Lysiak, Darius; Winter, Lukas; Hezel, Fabian; Waiczies, Sonia; Guthoff, Rudolf F; Falke, Karen; Hosten, Norbert; Hadlich, Stefan; Krueger, Paul-Christian; Langner, Soenke; Stachs, Oliver; Niendorf, Thoralf

2014-05-01

This study was designed to examine the feasibility of ophthalmic magnetic resonance imaging (MRI) at 7 T using a local 6-channel transmit/receive radiofrequency (RF) coil array in healthy volunteers and patients with intraocular masses. A novel 6-element transceiver RF coil array that makes uses of loop elements and that is customized for eye imaging at 7 T is proposed. Considerations influencing the RF coil design and the characteristics of the proposed RF coil array are presented. Numerical electromagnetic field simulations were conducted to enhance the RF coil characteristics. Specific absorption rate simulations and a thorough assessment of RF power deposition were performed to meet the safety requirements. Phantom experiments were carried out to validate the electromagnetic field simulations and to assess the real performance of the proposed transceiver array. Certified approval for clinical studies was provided by a local notified body before the in vivo studies. The suitability of the RF coil to image the human eye, optical nerve, and orbit was examined in an in vivo feasibility study including (a) 3-dimensional (3D) gradient echo (GRE) imaging, (b) inversion recovery 3D GRE imaging, and (c) 2D T2-weighted fast spin-echo imaging. For this purpose, healthy adult volunteers (n = 17; mean age, 34 ± 11 years) and patients with intraocular masses (uveal melanoma, n = 5; mean age, 57 ± 6 years) were investigated. All subjects tolerated all examinations well with no relevant adverse events. The 6-channel coil array supports high-resolution 3D GRE imaging with a spatial resolution as good as 0.2 × 0.2 × 1.0 mm, which facilitates the depiction of anatomical details of the eye. Rather, uniform signal intensity across the eye was found. A mean signal-to-noise ratio of approximately 35 was found for the lens, whereas the vitreous humor showed a signal-to-noise ratio of approximately 30. The lens-vitreous humor contrast-to-noise ratio was 8, which allows good differentiation between the lens and the vitreous compartment. Inversion recovery prepared 3D GRE imaging using a spatial resolution of 0.4 × 0.4 × 1.0 mm was found to be feasible. T2-weighted 2D fast spin-echo imaging with the proposed RF coil afforded a spatial resolution of 0.25 × 0.25 × 0.7 mm. This work provides valuable information on the feasibility of ophthalmic MRI at 7 T using a dedicated 6-channel transceiver coil array that supports the acquisition of high-contrast, high-spatial resolution images in healthy volunteers and patients with intraocular masses. The results underscore the challenges of ocular imaging at 7 T and demonstrate that these issues can be offset by using tailored RF coil hardware. The benefits of such improvements would be in positive alignment with explorations that are designed to examine the potential of MRI for the assessment of spatial arrangements of the eye segments and their masses with the ultimate goal to provide imaging means for guiding treatment decisions in ophthalmological diseases.

Extracting the inclination angle of nerve fibers within the human brain with 3D-PLI independent of system properties

NASA Astrophysics Data System (ADS)

Reckfort, Julia; Wiese, Hendrik; Dohmen, Melanie; Grässel, David; Pietrzyk, Uwe; Zilles, Karl; Amunts, Katrin; Axer, Markus

2013-09-01

The neuroimaging technique 3D-polarized light imaging (3D-PLI) has opened up new avenues to study the complex nerve fiber architecture of the human brain at sub-millimeter spatial resolution. This polarimetry technique is applicable to histological sections of postmortem brains utilizing the birefringence of nerve fibers caused by the regular arrangement of lipids and proteins in the myelin sheaths surrounding axons. 3D-PLI provides a three-dimensional description of the anatomical wiring scheme defined by the in-section direction angle and the out-of-section inclination angle. To date, 3D-PLI is the only available method that allows bridging the microscopic and the macroscopic description of the fiber architecture of the human brain. Here we introduce a new approach to retrieve the inclination angle of the fibers independently of the properties of the used polarimeters. This is relevant because the image resolution and the signal transmission inuence the measured birefringent signal (retardation) significantly. The image resolution was determined using the USAF- 1951 testchart applying the Rayleigh criterion. The signal transmission was measured by elliptical polarizers applying the Michelson contrast and histological slices of the optic tract of a postmortem brain. Based on these results, a modified retardation-inclination transfer function was proposed to extract the fiber inclination. The comparison of the actual and the inclination angles calculated with the theoretically proposed and the modified transfer function revealed a significant improvement in the extraction of the fiber inclinations.

Lack of robustness of textural measures obtained from 3D brain tumor MRIs impose a need for standardization.

PubMed

Molina, David; Pérez-Beteta, Julián; Martínez-González, Alicia; Martino, Juan; Velasquez, Carlos; Arana, Estanislao; Pérez-García, Víctor M

2017-01-01

Textural measures have been widely explored as imaging biomarkers in cancer. However, their robustness under dynamic range and spatial resolution changes in brain 3D magnetic resonance images (MRI) has not been assessed. The aim of this work was to study potential variations of textural measures due to changes in MRI protocols. Twenty patients harboring glioblastoma with pretreatment 3D T1-weighted MRIs were included in the study. Four different spatial resolution combinations and three dynamic ranges were studied for each patient. Sixteen three-dimensional textural heterogeneity measures were computed for each patient and configuration including co-occurrence matrices (CM) features and run-length matrices (RLM) features. The coefficient of variation was used to assess the robustness of the measures in two series of experiments corresponding to (i) changing the dynamic range and (ii) changing the matrix size. No textural measures were robust under dynamic range changes. Entropy was the only textural feature robust under spatial resolution changes (coefficient of variation under 10% in all cases). Textural measures of three-dimensional brain tumor images are not robust neither under dynamic range nor under matrix size changes. Standards should be harmonized to use textural features as imaging biomarkers in radiomic-based studies. The implications of this work go beyond the specific tumor type studied here and pose the need for standardization in textural feature calculation of oncological images.

Synthetic light-needle photoacoustic microscopy for extended depth of field (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yang, Jiamiao; Gong, Lei; Xu, Xiao; Hai, Pengfei; Suzuki, Yuta; Wang, Lihong V.

2017-03-01

Photoacoustic microscopy (PAM) has been extensively applied in biomedical study because of its ability to visualize tissue morphology and physiology in vivo in three dimensions (3D). However, conventional PAM suffers from a rapidly decreasing resolution away from the focal plane because of the limited depth of focus of an objective lens, which deteriorates the volumetric imaging quality inevitably. Here, we propose a novel method to synthesize an ultra-long light needle to extend a microscope's depth of focus beyond its physical limitations with wavefront engineering method. Furthermore, it enables an improved lateral resolution that exceeds the diffraction limit of the objective lens. The virtual light needle can be flexibly synthesized anywhere throughout the imaging volume without mechanical scanning. Benefiting from these advantages, we developed a synthetic light needle photoacoustic microscopy (SLN-PAM) to achieve an extended depth of field (DOF), sub-diffraction and motionless volumetric imaging. The DOF of our SLN-PAM system is up to 1800 µm, more than 30-fold improvement over that gained by conventional PAM. Our system also achieves the lateral resolution of 1.8 µm (characterized at 532 nm and 0.1 NA objective), about 50% higher than the Rayleigh diffraction limit. Its superior imaging performance was demonstrated by 3D imaging of both non-biological and biological samples. This extended DOF, sub-diffraction and motionless 3D PAM will open up new opportunities for potential biomedical applications.

Neuroanatomical phenotyping of the mouse brain with three-dimensional autofluorescence imaging

PubMed Central

Wong, Michael D.; Dazai, Jun; Altaf, Maliha; Mark Henkelman, R.; Lerch, Jason P.; Nieman, Brian J.

2012-01-01

The structural organization of the brain is important for normal brain function and is critical to understand in order to evaluate changes that occur during disease processes. Three-dimensional (3D) imaging of the mouse brain is necessary to appreciate the spatial context of structures within the brain. In addition, the small scale of many brain structures necessitates resolution at the ∼10 μm scale. 3D optical imaging techniques, such as optical projection tomography (OPT), have the ability to image intact large specimens (1 cm3) with ∼5 μm resolution. In this work we assessed the potential of autofluorescence optical imaging methods, and specifically OPT, for phenotyping the mouse brain. We found that both specimen size and fixation methods affected the quality of the OPT image. Based on these findings we developed a specimen preparation method to improve the images. Using this method we assessed the potential of optical imaging for phenotyping. Phenotypic differences between wild-type male and female mice were quantified using computer-automated methods. We found that optical imaging of the endogenous autofluorescence in the mouse brain allows for 3D characterization of neuroanatomy and detailed analysis of brain phenotypes. This will be a powerful tool for understanding mouse models of disease and development and is a technology that fits easily within the workflow of biology and neuroscience labs. PMID:22718750

Three-Dimensional Imaging of Lipids and Metabolites in Tissues by Nanospray Desorption Electrospray Ionization Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lanekoff, Ingela T.; Burnum-Johnson, Kristin E.; Thomas, Mathew

Abstract Three-dimensional (3D) imaging of tissue sections is a new frontier in mass spectrometry imaging (MSI). Here we report on fast 3D imaging of lipids and metabolites associated with mouse uterine decidual cells and embryo at the implantation site on day 6 of pregnancy. 2D imaging of 16-20 serial tissue sections deposited on the same glass slide was performed using nanospray desorption electrospray ionization (nano-DESI) – an ambient ionization technique that enables sensitive localized analysis of analytes on surfaces without special sample pre-treatment. In this proof-of-principle study, nano-DESI was coupled to a high-resolution Q-Exactive instrument operated at high repetition ratemore » of >5 Hz with moderate mass resolution of 35,000 (m/Δm at m/z 200), which enabled acquisition of the entire 3D image with a spatial resolution of ~150 μm in less than 4.5 hours. The results demonstrate localization of acetylcholine in the primary decidual zone (PDZ) of the implantation site throughout the depth of the tissue examined, indicating an important role of this signaling molecule in decidualization. Choline and phosphocholine – metabolites associated with cell growth – are enhanced in the PDZ and abundant in other cellular regions of the implantation site. Very different 3D distributions were obtained for fatty acids (FA), oleic acid and linoleic acid (FA 18:1 and FA 18:2), differing only by one double bond. Localization of FA 18:2 in the PDZ indicates its important role in decidualization while FA 18:1 is distributed more evenly throughout the tissue. In contrast, several lysophosphatidylcholines (LPC) observed in this study show donut-like distributions with localization around the PDZ. Complementary distributions with minimal overlap were observed for LPC 18:0 and FA 18:2 while the 3D image of the potential precursor phosphatidylcholine (PC 36:2) showed a significant overlap with both LPC 18:0 and FA 18:2.« less

Resolution enhancement in a double-helix phase engineered scanning microscope (RESCH microscope) (Presentation Recording)

NASA Astrophysics Data System (ADS)

Jesacher, Alexander; Ritsch-Marte, Monika; Piestun, Rafael

2015-08-01

Recently we introduced RESCH microscopy [1] - a scanning microscope that allows slightly refocusing the sample after the acquisition has been performed, solely by performing appropriate data post-processing. The microscope features a double-helix phase-engineered emission point spread function in combination with camera-based detection. Based on the principle of transverse resolution enhancement in Image Scanning Microscopy [2,3], we demonstrate similar resolution improvement in RESCH. Furthermore, we outline a pathway for how the collected 3D sample information can be used to construct sharper optical sections. [1] A. Jesacher, M. Ritsch-Marte and R. Piestun, accepted for Optica. [2] C.J.R. Sheppard, "Super-resolution in Confocal imaging," Optik, 80, 53-54 (1988). [3] C.B. Müller and J. Enderlein "Image Scanning Microscopy," Phys. Rev. Lett. 104, 198101 (2010).

Multimodality optical imaging of embryonic heart microstructure

PubMed Central

Yelin, Ronit; Yelin, Dvir; Oh, Wang-Yuhl; Yun, Seok H.; Boudoux, Caroline; Vakoc, Benjamin J.; Bouma, Brett E.; Tearney, Guillermo J.

2009-01-01

Study of developmental heart defects requires the visualization of the microstructure and function of the embryonic myocardium, ideally with minimal alterations to the specimen. We demonstrate multiple endogenous contrast optical techniques for imaging the Xenopus laevis tadpole heart. Each technique provides distinct and complementary imaging capabilities, including: 1. 3-D coherence microscopy with subcellular (1 to 2 µm) resolution in fixed embryos, 2. real-time reflectance confocal microscopy with large penetration depth in vivo, and 3. ultra-high speed (up to 900 frames per second) that enables real-time 4-D high resolution imaging in vivo. These imaging modalities can provide a comprehensive picture of the morphologic and dynamic phenotype of the embryonic heart. The potential of endogenous-contrast optical microscopy is demonstrated for investigation of the teratogenic effects of ethanol. Microstructural abnormalities associated with high levels of ethanol exposure are observed, including compromised heart looping and loss of ventricular trabecular mass. PMID:18163837

Multimodality optical imaging of embryonic heart microstructure.

PubMed

Yelin, Ronit; Yelin, Dvir; Oh, Wang-Yuhl; Yun, Seok H; Boudoux, Caroline; Vakoc, Benjamin J; Bouma, Brett E; Tearney, Guillermo J

2007-01-01

Study of developmental heart defects requires the visualization of the microstructure and function of the embryonic myocardium, ideally with minimal alterations to the specimen. We demonstrate multiple endogenous contrast optical techniques for imaging the Xenopus laevis tadpole heart. Each technique provides distinct and complementary imaging capabilities, including: 1. 3-D coherence microscopy with subcellular (1 to 2 microm) resolution in fixed embryos, 2. real-time reflectance confocal microscopy with large penetration depth in vivo, and 3. ultra-high speed (up to 900 frames per second) that enables real-time 4-D high resolution imaging in vivo. These imaging modalities can provide a comprehensive picture of the morphologic and dynamic phenotype of the embryonic heart. The potential of endogenous-contrast optical microscopy is demonstrated for investigation of the teratogenic effects of ethanol. Microstructural abnormalities associated with high levels of ethanol exposure are observed, including compromised heart looping and loss of ventricular trabecular mass.

High-Resolution Isotropic Three-Dimensional MR Imaging of the Extraforaminal Segments of the Cranial Nerves.

PubMed

Wen, Jessica; Desai, Naman S; Jeffery, Dean; Aygun, Nafi; Blitz, Ari

2018-02-01

High-resolution isotropic 3-dimensional (D) MR imaging with and without contrast is now routinely used for imaging evaluation of cranial nerve anatomy and pathologic conditions. The anatomic details of the extraforaminal segments are well-visualized on these techniques. A wide range of pathologic entities may cause enhancement or displacement of the nerve, which is now visible to an extent not available on standard 2D imaging. This article highlights the anatomy of extraforaminal segments of the cranial nerves and uses select cases to illustrate the utility and power of these sequences, with a focus on constructive interference in steady-state. Copyright © 2017 Elsevier Inc. All rights reserved.

Image formation analysis and high resolution image reconstruction for plenoptic imaging systems.

PubMed

Shroff, Sapna A; Berkner, Kathrin

2013-04-01

Plenoptic imaging systems are often used for applications like refocusing, multimodal imaging, and multiview imaging. However, their resolution is limited to the number of lenslets. In this paper we investigate paraxial, incoherent, plenoptic image formation, and develop a method to recover some of the resolution for the case of a two-dimensional (2D) in-focus object. This enables the recovery of a conventional-resolution, 2D image from the data captured in a plenoptic system. We show simulation results for a plenoptic system with a known response and Gaussian sensor noise.

Determination of scattering structures from spatial coherence measurements.

PubMed

Zarubin, A M

1996-03-01

A new method of structure determination and microscopic imaging with short-wavelength radiations (charged particles, X-rays, neutrons), based on measurements of the modulus and the phase of the degree of spatial coherence of the scattered radiation, is developed. The underlying principle of the method--transfer of structural information about the scattering potential via spatial coherence of the secondary (scattering) source of radiation formed by this potential--is expressed by the generalization of the van Cittert-Zernike theorem to wave and particle scattering [A.M. Zarubin, Opt. Commun. 100 (1993) 491; Opt. Commun. 102 (1993) 543]. Shearing interferometric techniques are proposed for implementing the above measurements; the limits of spatial resolution attainable by reconstruction of the absolute square of a 3D scattering potential and its 2D projections from the measurements are analyzed. It is shown theoretically that 3D imaging with atomic resolution can be realized in a "synthetic aperture" electron or ion microscope and that a 3D resolution of about 6 nm can be obtained with a "synthetic aperture" X-ray microscope. A proof-of-principle optical experiment is presented.

3D digital subtraction angiography of intracranial aneurysms: comparison of flat panel detector with conventional image intensifier TV system using a vascular phantom.

PubMed

Kakeda, S; Korogi, Y; Ohnari, N; Hatakeyama, Y; Moriya, J; Oda, N; Nishino, K; Miyamoto, W

2007-05-01

Compared with the image intensifier (I.I.)-TV system, the flat panel detector (FPD) system of direct conversion type has several theoretic advantages, such as higher spatial resolution, wide dynamic range, and no image distortion. The purpose of this study was to compare the image quality of 3D digital subtraction angiography (DSA) in the FPD and conventional I.I.-TV systems using a vascular phantom. An anthropomorphic vascular phantom was designed to simulate the various intracranial aneurysms with aneurysmal bleb. The tubes of this vascular phantom were filled with 2 concentrations of contrast material (300 and 150 mg I/mL), and we obtained 3D DSA using the FPD and I.I.-TV systems. First, 2 blinded radiologists compared the volume-rendering images for 3D DSA on the FPD and I.I.-TV systems, looking for pseudostenosis artifacts. Then, 2 other radiologists independently evaluated both systems for the depiction of the simulated aneurysm and aneurysmal bleb using a 5-point scale. For the degree of the pseudostenosis artifacts at the M1 segment of the middle cerebral artery at 300 mg I/mL, 3D DSA with FPD system showed mild stenoses, whereas severe stenoses were observed at 3D DSA with I.I.-TV system. At both concentrations, the FPD system was significantly superior to I.I.-TV system regarding the depiction of aneurysm and aneurysmal bleb. Compared with the I.I.-TV system, the FPD system could create high-resolution 3D DSA combined with a reduction of the pseudostenosis artifacts.

High spatial resolution free-breathing 3D late gadolinium enhancement cardiac magnetic resonance imaging in ischaemic and non-ischaemic cardiomyopathy: quantitative assessment of scar mass and image quality.

PubMed

Bizino, Maurice B; Tao, Qian; Amersfoort, Jacob; Siebelink, Hans-Marc J; van den Bogaard, Pieter J; van der Geest, Rob J; Lamb, Hildo J

2018-04-06

To compare breath-hold (BH) with navigated free-breathing (FB) 3D late gadolinium enhancement cardiac MRI (LGE-CMR) MATERIALS AND METHODS: Fifty-one patients were retrospectively included (34 ischaemic cardiomyopathy, 14 non-ischaemic cardiomyopathy, three discarded). BH and FB 3D phase sensitive inversion recovery sequences were performed at 3T. FB datasets were reformatted into normal resolution (FB-NR, 1.46x1.46x10mm) and high resolution (FB-HR, isotropic 0.91-mm voxels). Scar mass, scar edge sharpness (SES), SNR and CNR were compared using paired-samples t-test, Pearson correlation and Bland-Altman analysis. Scar mass was similar in BH and FB-NR (mean ± SD: 15.5±18.0 g vs. 15.5±16.9 g, p=0.997), with good correlation (r=0.953), and no bias (mean difference ± SD: 0.00±5.47 g). FB-NR significantly overestimated scar mass compared with FB-HR (15.5±16.9 g vs 14.4±15.6 g; p=0.007). FB-NR and FB-HR correlated well (r=0.988), but Bland-Altman demonstrated systematic bias (1.15±2.84 g). SES was similar in BH and FB-NR (p=0.947), but significantly higher in FB-HR than FB-NR (p<0.01). SNR and CNR were lower in BH than FB-NR (p<0.01), and lower in FB-HR than FB-NR (p<0.01). Navigated free-breathing 3D LGE-CMR allows reliable scar mass quantification comparable to breath-hold. During free-breathing, spatial resolution can be increased resulting in improved sharpness and reduced scar mass. • Navigated free-breathing 3D late gadolinium enhancement is reliable for myocardial scar quantification. • High-resolution 3D late gadolinium enhancement increases scar sharpness • Ischaemic and non-ischaemic cardiomyopathy patients can be imaged using free-breathing LGE CMR.

Quantifying metal-induced susceptibility artifacts of the instrumented spine at 1.5T using fast-spin echo and 3D-multispectral MRI.

PubMed

Kaushik, S Sivaram; Karr, Robin; Runquist, Matthew; Marszalkowski, Cathy; Sharma, Abhishiek; Rand, Scott D; Maiman, Dennis; Koch, Kevin M

2017-01-01

To evaluate magnetic resonance imaging (MRI) artifacts near metallic spinal instrumentation using both conventional metal artifact reduction sequences (MARS) and 3D multispectral imaging sequences (3D-MSI). Both MARS and 3D-MSI images were acquired in 10 subjects with titanium spinal hardware on a 1.5T GE 450W scanner. Clinical computed tomography (CT) images were used to measure the volume of the implant using seed-based region growing. Using 30-40 landmarks, the MARS and 3D-MSI images were coregistered to the CT images. Three independent users manually segmented the artifact volume from both MR sequences. For five L-spine subjects, one user independently segmented the nerve root in both MARS and 3D-MSI images. For all 10 subjects, the measured artifact volume for the 3D-MSI images closely matched that of the CT implant volume (absolute error: 4.3 ± 2.0 cm 3 ). The MARS artifact volume was ∼8-fold higher than that of the 3D-MSI images (30.7 ± 20.2, P = 0.002). The average nerve root volume for the MARS images was 24 ± 7.3% lower than the 3D-MSI images (P = 0.06). Compared to 3D-MSI images, the higher-resolution MARS images may help study features farther away from the implant surface. However, the MARS images retained substantial artifacts in the slice-dimension that result in a larger artifact volume. These artifacts have the potential to obscure physiologically relevant features, and can be mitigated with 3D-MSI sequences. Hence, MR study protocols may benefit with the inclusion both MARS and 3D-MSI sequences to accurately study pathology near the spine. 2 J. Magn. Reson. Imaging 2017;45:51-58. © 2016 International Society for Magnetic Resonance in Medicine.

Localization-based super-resolution imaging meets high-content screening.

PubMed

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

Ultra-high-speed variable focus optics for novel applications in advanced imaging

NASA Astrophysics Data System (ADS)

Kang, S.; Dotsenko, E.; Amrhein, D.; Theriault, C.; Arnold, C. B.

2018-02-01

With the advancement of ultra-fast manufacturing technologies, high speed imaging with high 3D resolution has become increasingly important. Here we show the use of an ultra-high-speed variable focus optical element, the TAG Lens, to enable new ways to acquire 3D information from an object. The TAG Lens uses sound to adjust the index of refraction profile in a liquid and thereby can achieve focal scanning rates greater than 100 kHz. When combined with a high-speed pulsed LED and a high-speed camera, we can exploit this phenomenon to achieve high-resolution imaging through large depths. By combining the image acquisition with digital image processing, we can extract relevant parameters such as tilt and angle information from objects in the image. Due to the high speeds at which images can be collected and processed, we believe this technique can be used as an efficient method of industrial inspection and metrology for high throughput applications.

Virtual reality 3D headset based on DMD light modulators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernacki, Bruce E.; Evans, Allan; Tang, Edward

We present the design of an immersion-type 3D headset suitable for virtual reality applications based upon digital micro-mirror devices (DMD). Our approach leverages silicon micro mirrors offering 720p resolution displays in a small form-factor. Supporting chip sets allow rapid integration of these devices into wearable displays with high resolution and low power consumption. Applications include night driving, piloting of UAVs, fusion of multiple sensors for pilots, training, vision diagnostics and consumer gaming. Our design is described in which light from the DMD is imaged to infinity and the user’s own eye lens forms a real image on the user’s retina.

Validity of computational hemodynamics in human arteries based on 3D time-of-flight MR angiography and 2D electrocardiogram gated phase contrast images

NASA Astrophysics Data System (ADS)

Yu, Huidan (Whitney); Chen, Xi; Chen, Rou; Wang, Zhiqiang; Lin, Chen; Kralik, Stephen; Zhao, Ye

2015-11-01

In this work, we demonstrate the validity of 4-D patient-specific computational hemodynamics (PSCH) based on 3-D time-of-flight (TOF) MR angiography (MRA) and 2-D electrocardiogram (ECG) gated phase contrast (PC) images. The mesoscale lattice Boltzmann method (LBM) is employed to segment morphological arterial geometry from TOF MRA, to extract velocity profiles from ECG PC images, and to simulate fluid dynamics on a unified GPU accelerated computational platform. Two healthy volunteers are recruited to participate in the study. For each volunteer, a 3-D high resolution TOF MRA image and 10 2-D ECG gated PC images are acquired to provide the morphological geometry and the time-varying flow velocity profiles for necessary inputs of the PSCH. Validation results will be presented through comparisons of LBM vs. 4D Flow Software for flow rates and LBM simulation vs. MRA measurement for blood flow velocity maps. Indiana University Health (IUH) Values Fund.

Large depth high-precision FMCW tomography using a distributed feedback laser array

NASA Astrophysics Data System (ADS)

DiLazaro, Thomas; Nehmetallah, George

2018-02-01

Swept-source optical coherence tomography (SS-OCT) has been widely employed in the medical industry for the high resolution imaging of subsurface biological structures. SS-OCT typically exhibits axial resolutions on the order of tens of microns at speeds of hundreds of kilohertz. Using the same coherent heterodyne detection technique, frequency modulated continuous wave (FMCW) ladar has been used for highly precise ranging for distances up to kilometers. Distributed feedback lasers (DFBs) have been used as a simple and inexpensive source for FMCW ranging. Here, we use a bandwidth-combined DFB array for sub-surface volume imaging at a 27 μm axial resolution over meters of distance. 2D and 3D tomographic images of several semi-transparent and diffuse objects at distances up to 10 m will be presented.

Zebrafish skeleton development: High resolution micro-CT and FIB-SEM block surface serial imaging for phenotype identification

PubMed Central

Silvent, Jeremie; Akiva, Anat; Brumfeld, Vlad; Reznikov, Natalie; Rechav, Katya; Yaniv, Karina; Addadi, Lia; Weiner, Steve

2017-01-01

Although bone is one of the most studied living materials, many questions about the manner in which bones form remain unresolved, including fine details of the skeletal structure during development. In this study, we monitored skeleton development of zebrafish larvae, using calcein fluorescence, high-resolution micro-CT 3D images and FIB-SEM in the block surface serial imaging mode. We compared calcein staining of the skeletons of the wild type and nacre mutants, which are transparent zebrafish, with micro-CT for the first 30 days post fertilization embryos, and identified significant differences. We quantified the bone volumes and mineral contents of bones, including otoliths, during development, and showed that such developmental differences, including otolith development, could be helpful in identifying phenotypes. In addition, high-resolution imaging revealed the presence of mineralized aggregates in the notochord, before the formation of the first bone in the axial skeleton. These structures might play a role in the storage of the mineral. Our results highlight the potential of these high-resolution 3D approaches to characterize the zebrafish skeleton, which in turn could prove invaluable information for better understanding the development and the characterization of skeletal phenotypes. PMID:29220379

3-D ultrasound volume reconstruction using the direct frame interpolation method.

PubMed

Scheipers, Ulrich; Koptenko, Sergei; Remlinger, Rachel; Falco, Tony; Lachaine, Martin

2010-11-01

A new method for 3-D ultrasound volume reconstruction using tracked freehand 3-D ultrasound is proposed. The method is based on solving the forward volume reconstruction problem using direct interpolation of high-resolution ultrasound B-mode image frames. A series of ultrasound B-mode image frames (an image series) is acquired using the freehand scanning technique and position sensing via optical tracking equipment. The proposed algorithm creates additional intermediate image frames by directly interpolating between two or more adjacent image frames of the original image series. The target volume is filled using the original frames in combination with the additionally constructed frames. Compared with conventional volume reconstruction methods, no additional filling of empty voxels or holes within the volume is required, because the whole extent of the volume is defined by the arrangement of the original and the additionally constructed B-mode image frames. The proposed direct frame interpolation (DFI) method was tested on two different data sets acquired while scanning the head and neck region of different patients. The first data set consisted of eight B-mode 2-D frame sets acquired under optimal laboratory conditions. The second data set consisted of 73 image series acquired during a clinical study. Sample volumes were reconstructed for all 81 image series using the proposed DFI method with four different interpolation orders, as well as with the pixel nearest-neighbor method using three different interpolation neighborhoods. In addition, volumes based on a reduced number of image frames were reconstructed for comparison of the different methods' accuracy and robustness in reconstructing image data that lies between the original image frames. The DFI method is based on a forward approach making use of a priori information about the position and shape of the B-mode image frames (e.g., masking information) to optimize the reconstruction procedure and to reduce computation times and memory requirements. The method is straightforward, independent of additional input or parameters, and uses the high-resolution B-mode image frames instead of usually lower-resolution voxel information for interpolation. The DFI method can be considered as a valuable alternative to conventional 3-D ultrasound reconstruction methods based on pixel or voxel nearest-neighbor approaches, offering better quality and competitive reconstruction time.

Applied 3D printing for microscopy in health science research

NASA Astrophysics Data System (ADS)

Brideau, Craig; Zareinia, Kourosh; Stys, Peter

2015-03-01

The rapid prototyping capability offered by 3D printing is considered advantageous for commercial applications. However, the ability to quickly produce precision custom devices is highly beneficial in the research laboratory setting as well. Biological laboratories require the manipulation and analysis of delicate living samples, thus the ability to create custom holders, support equipment, and adapters allow the extension of existing laboratory machines. Applications include camera adapters and stage sample holders for microscopes, surgical guides for tissue preparation, and small precision tools customized to unique specifications. Where high precision is needed, especially the reproduction of fine features, a printer with a high resolution is needed. However, the introduction of cheaper, lower resolution commercial printers have been shown to be more than adequate for less demanding projects. For direct manipulation of delicate samples, biocompatible raw materials are often required, complicating the printing process. This paper will examine some examples of 3D-printed objects for laboratory use, and provide an overview of the requirements for 3D printing for this application. Materials, printing resolution, production, and ease of use will all be reviewed with an eye to producing better printers and techniques for laboratory applications. Specific case studies will highlight applications for 3D-printed devices in live animal imaging for both microscopy and Magnetic Resonance Imaging.

Turbulence imaging and applications using beam emission spectroscopy on DIII-D (invited)

NASA Astrophysics Data System (ADS)

McKee, G. R.; Fenzi, C.; Fonck, R. J.; Jakubowski, M.

2003-03-01

Two-dimensional measurements of density fluctuations are obtained in the radial and poloidal plane of the DIII-D tokamak with the Beam Emission Spectroscopy (BES) diagnostic system. The goals are to visualize the spatial structure and time evolution of turbulent eddies, as well as to obtain the 2D statistical properties of turbulence. The measurements are obtained with an array of localized BES spatial channels configured to image a midplane region of the plasma. 32 channels have been deployed, each with a spatial resolution of about 1 cm in the radial and poloidal directions, thus providing measurements of turbulence in the wave number range 0

3D ultrafast ultrasound imaging in vivo.

PubMed

Provost, Jean; Papadacci, Clement; Arango, Juan Esteban; Imbault, Marion; Fink, Mathias; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

2014-10-07

Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32  ×  32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra--and inter-observer variability.

The future of structural fieldwork - UAV assisted aerial photogrammetry

NASA Astrophysics Data System (ADS)

Vollgger, Stefan; Cruden, Alexander

2015-04-01

Unmanned aerial vehicles (UAVs), commonly referred to as drones, are opening new and low cost possibilities to acquire high-resolution aerial images and digital surface models (DSM) for applications in structural geology. UAVs can be programmed to fly autonomously along a user defined grid to systematically capture high-resolution photographs, even in difficult to access areas. The photographs are subsequently processed using software that employ SIFT (scale invariant feature transform) and SFM (structure from motion) algorithms. These photogrammetric routines allow the extraction of spatial information (3D point clouds, digital elevation models, 3D meshes, orthophotos) from 2D images. Depending on flight altitude and camera setup, sub-centimeter spatial resolutions can be achieved. By "digitally mapping" georeferenced 3D models and images, orientation data can be extracted directly and used to analyse the structural framework of the mapped object or area. We present UAV assisted aerial mapping results from a coastal platform near Cape Liptrap (Victoria, Australia), where deformed metasediments of the Palaeozoic Lachlan Fold Belt are exposed. We also show how orientation and spatial information of brittle and ductile structures extracted from the photogrammetric model can be linked to the progressive development of folds and faults in the region. Even though there are both technical and legislative limitations, which might prohibit the use of UAVs without prior commercial licensing and training, the benefits that arise from the resulting high-resolution, photorealistic models can substantially contribute to the collection of new data and insights for applications in structural geology.

Demosaiced pixel super-resolution in digital holography for multiplexed computational color imaging on-a-chip (Conference Presentation)

NASA Astrophysics Data System (ADS)

Wu, Yichen; Zhang, Yibo; Luo, Wei; Ozcan, Aydogan

2017-03-01

Digital holographic on-chip microscopy achieves large space-bandwidth-products (e.g., >1 billion) by making use of pixel super-resolution techniques. To synthesize a digital holographic color image, one can take three sets of holograms representing the red (R), green (G) and blue (B) parts of the spectrum and digitally combine them to synthesize a color image. The data acquisition efficiency of this sequential illumination process can be improved by 3-fold using wavelength-multiplexed R, G and B illumination that simultaneously illuminates the sample, and using a Bayer color image sensor with known or calibrated transmission spectra to digitally demultiplex these three wavelength channels. This demultiplexing step is conventionally used with interpolation-based Bayer demosaicing methods. However, because the pixels of different color channels on a Bayer image sensor chip are not at the same physical location, conventional interpolation-based demosaicing process generates strong color artifacts, especially at rapidly oscillating hologram fringes, which become even more pronounced through digital wave propagation and phase retrieval processes. Here, we demonstrate that by merging the pixel super-resolution framework into the demultiplexing process, such color artifacts can be greatly suppressed. This novel technique, termed demosaiced pixel super-resolution (D-PSR) for digital holographic imaging, achieves very similar color imaging performance compared to conventional sequential R,G,B illumination, with 3-fold improvement in image acquisition time and data-efficiency. We successfully demonstrated the color imaging performance of this approach by imaging stained Pap smears. The D-PSR technique is broadly applicable to high-throughput, high-resolution digital holographic color microscopy techniques that can be used in resource-limited-settings and point-of-care offices.

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D)

PubMed Central

Li, Weizhe; Germain, Ronald N.

2017-01-01

Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact Ce3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, Ce3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques. PMID:28808033

On-line 3D motion estimation using low resolution MRI

NASA Astrophysics Data System (ADS)

Glitzner, M.; de Senneville, B. Denis; Lagendijk, J. J. W.; Raaymakers, B. W.; Crijns, S. P. M.

2015-08-01

Image processing such as deformable image registration finds its way into radiotherapy as a means to track non-rigid anatomy. With the advent of magnetic resonance imaging (MRI) guided radiotherapy, intrafraction anatomy snapshots become technically feasible. MRI provides the needed tissue signal for high-fidelity image registration. However, acquisitions, especially in 3D, take a considerable amount of time. Pushing towards real-time adaptive radiotherapy, MRI needs to be accelerated without degrading the quality of information. In this paper, we investigate the impact of image resolution on the quality of motion estimations. Potentially, spatially undersampled images yield comparable motion estimations. At the same time, their acquisition times would reduce greatly due to the sparser sampling. In order to substantiate this hypothesis, exemplary 4D datasets of the abdomen were downsampled gradually. Subsequently, spatiotemporal deformations are extracted consistently using the same motion estimation for each downsampled dataset. Errors between the original and the respectively downsampled version of the dataset are then evaluated. Compared to ground-truth, results show high similarity of deformations estimated from downsampled image data. Using a dataset with {{≤ft(2.5 \\text{mm}\\right)}3} voxel size, deformation fields could be recovered well up to a downsampling factor of 2, i.e. {{≤ft(5 \\text{mm}\\right)}3} . In a therapy guidance scenario MRI, imaging speed could accordingly increase approximately fourfold, with acceptable loss of estimated motion quality.

3D registration of intravascular optical coherence tomography and cryo-image volumes for microscopic-resolution validation

NASA Astrophysics Data System (ADS)

Prabhu, David; Mehanna, Emile; Gargesha, Madhusudhana; Wen, Di; Brandt, Eric; van Ditzhuijzen, Nienke S.; Chamie, Daniel; Yamamoto, Hirosada; Fujino, Yusuke; Farmazilian, Ali; Patel, Jaymin; Costa, Marco; Bezerra, Hiram G.; Wilson, David L.

2016-03-01

High resolution, 100 frames/sec intravascular optical coherence tomography (IVOCT) can distinguish plaque types, but further validation is needed, especially for automated plaque characterization. We developed experimental and 3D registration methods, to provide validation of IVOCT pullback volumes using microscopic, brightfield and fluorescent cryoimage volumes, with optional, exactly registered cryo-histology. The innovation was a method to match an IVOCT pullback images, acquired in the catheter reference frame, to a true 3D cryo-image volume. Briefly, an 11-parameter, polynomial virtual catheter was initialized within the cryo-image volume, and perpendicular images were extracted, mimicking IVOCT image acquisition. Virtual catheter parameters were optimized to maximize cryo and IVOCT lumen overlap. Local minima were possible, but when we started within reasonable ranges, every one of 24 digital phantom cases converged to a good solution with a registration error of only +1.34+/-2.65μm (signed distance). Registration was applied to 10 ex-vivo cadaver coronary arteries (LADs), resulting in 10 registered cryo and IVOCT volumes yielding a total of 421 registered 2D-image pairs. Image overlays demonstrated high continuity between vascular and plaque features. Bland- Altman analysis comparing cryo and IVOCT lumen area, showed mean and standard deviation of differences as 0.01+/-0.43 mm2. DICE coefficients were 0.91+/-0.04. Finally, visual assessment on 20 representative cases with easily identifiable features suggested registration accuracy within one frame of IVOCT (+/-200μm), eliminating significant misinterpretations introduced by 1mm errors in the literature. The method will provide 3D data for training of IVOCT plaque algorithms and can be used for validation of other intravascular imaging modalities.

Cone-beam micro computed tomography dedicated to the breast.

PubMed

Sarno, Antonio; Mettivier, Giovanni; Di Lillo, Francesca; Cesarelli, Mario; Bifulco, Paolo; Russo, Paolo

2016-12-01

We developed a scanner for micro computed tomography dedicated to the breast (BµCT) with a high resolution flat-panel detector and a microfocus X-ray tube. We evaluated the system spatial resolution via the 3D modulation transfer function (MTF). In addition to conventional absorption-based X-ray imaging, such a prototype showed capabilities for propagation-based phase-contrast and related edge enhancement effects in 3D imaging. The system limiting spatial resolution is 6.2mm -1 (MTF at 10%) in the vertical direction and 3.8mm -1 in the radial direction, values which compare favorably with the spatial resolution reached by mini focus breast CT scanners of other groups. The BµCT scanner was able to detect both microcalcification clusters and masses in an anthropomorphic breast phantom at a dose comparable to that of two-view mammography. The use of a breast holder is proposed in order to have 1-2min long scan times without breast motion artifacts. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Fast susceptibility-weighted imaging with three-dimensional short-axis propeller (SAP)-echo-planar imaging.

PubMed

Holdsworth, Samantha J; Yeom, Kristen W; Moseley, Michael E; Skare, S

2015-05-01

Susceptibility-weighted imaging (SWI) in neuroimaging can be challenging due to long scan times of three-dimensional (3D) gradient recalled echo (GRE), while faster techniques such as 3D interleaved echo-planar imaging (iEPI) are prone to motion artifacts. Here we outline and implement a 3D short-axis propeller echo-planar imaging (SAP-EPI) trajectory as a faster, motion-correctable approach for SWI. Experiments were conducted on a 3T MRI system. The 3D SAP-EPI, 3D iEPI, and 3D GRE SWI scans were acquired on two volunteers. Controlled motion experiments were conducted to test the motion-correction capability of 3D SAP-EPI. The 3D SAP-EPI SWI data were acquired on two pediatric patients as a potential alternative to 2D GRE used clinically. The 3D GRE images had a better target resolution (0.47 × 0.94 × 2 mm, scan time = 5 min), iEPI and SAP-EPI images (resolution = 0.94 × 0.94 × 2 mm) were acquired in a faster scan time (1:52 min) with twice the brain coverage. SAP-EPI showed motion-correction capability and some immunity to undersampling from rejected data. While 3D SAP-EPI suffers from some geometric distortion, its short scan time and motion-correction capability suggest that SAP-EPI may be a useful alternative to GRE and iEPI for use in SWI, particularly in uncooperative patients. © 2014 Wiley Periodicals, Inc.

A deep learning approach for pose estimation from volumetric OCT data.

PubMed

Gessert, Nils; Schlüter, Matthias; Schlaefer, Alexander

2018-05-01

Tracking the pose of instruments is a central problem in image-guided surgery. For microscopic scenarios, optical coherence tomography (OCT) is increasingly used as an imaging modality. OCT is suitable for accurate pose estimation due to its micrometer range resolution and volumetric field of view. However, OCT image processing is challenging due to speckle noise and reflection artifacts in addition to the images' 3D nature. We address pose estimation from OCT volume data with a new deep learning-based tracking framework. For this purpose, we design a new 3D convolutional neural network (CNN) architecture to directly predict the 6D pose of a small marker geometry from OCT volumes. We use a hexapod robot to automatically acquire labeled data points which we use to train 3D CNN architectures for multi-output regression. We use this setup to provide an in-depth analysis on deep learning-based pose estimation from volumes. Specifically, we demonstrate that exploiting volume information for pose estimation yields higher accuracy than relying on 2D representations with depth information. Supporting this observation, we provide quantitative and qualitative results that 3D CNNs effectively exploit the depth structure of marker objects. Regarding the deep learning aspect, we present efficient design principles for 3D CNNs, making use of insights from the 2D deep learning community. In particular, we present Inception3D as a new architecture which performs best for our application. We show that our deep learning approach reaches errors at our ground-truth label's resolution. We achieve a mean average error of 14.89 ± 9.3 µm and 0.096 ± 0.072° for position and orientation learning, respectively. Copyright © 2018 Elsevier B.V. All rights reserved.

Volumetric Forest Change Detection Through Vhr Satellite Imagery

NASA Astrophysics Data System (ADS)

Akca, Devrim; Stylianidis, Efstratios; Smagas, Konstantinos; Hofer, Martin; Poli, Daniela; Gruen, Armin; Sanchez Martin, Victor; Altan, Orhan; Walli, Andreas; Jimeno, Elisa; Garcia, Alejandro

2016-06-01

Quick and economical ways of detecting of planimetric and volumetric changes of forest areas are in high demand. A research platform, called FORSAT (A satellite processing platform for high resolution forest assessment), was developed for the extraction of 3D geometric information from VHR (very-high resolution) imagery from satellite optical sensors and automatic change detection. This 3D forest information solution was developed during a Eurostars project. FORSAT includes two main units. The first one is dedicated to the geometric and radiometric processing of satellite optical imagery and 2D/3D information extraction. This includes: image radiometric pre-processing, image and ground point measurement, improvement of geometric sensor orientation, quasiepipolar image generation for stereo measurements, digital surface model (DSM) extraction by using a precise and robust image matching approach specially designed for VHR satellite imagery, generation of orthoimages, and 3D measurements in single images using mono-plotting and in stereo images as well as triplets. FORSAT supports most of the VHR optically imagery commonly used for civil applications: IKONOS, OrbView - 3, SPOT - 5 HRS, SPOT - 5 HRG, QuickBird, GeoEye-1, WorldView-1/2, Pléiades 1A/1B, SPOT 6/7, and sensors of similar type to be expected in the future. The second unit of FORSAT is dedicated to 3D surface comparison for change detection. It allows users to import digital elevation models (DEMs), align them using an advanced 3D surface matching approach and calculate the 3D differences and volume changes between epochs. To this end our 3D surface matching method LS3D is being used. FORSAT is a single source and flexible forest information solution with a very competitive price/quality ratio, allowing expert and non-expert remote sensing users to monitor forests in three and four dimensions from VHR optical imagery for many forest information needs. The capacity and benefits of FORSAT have been tested in six case studies located in Austria, Cyprus, Spain, Switzerland and Turkey, using optical data from different sensors and with the purpose to monitor forest with different geometric characteristics. The validation run on Cyprus dataset is reported and commented.

Triangulation Based 3D Laser Imaging for Fracture Orientation Analysis

NASA Astrophysics Data System (ADS)

Mah, J.; Claire, S.; Steve, M.

2009-05-01

Laser imaging has recently been identified as a potential tool for rock mass characterization. This contribution focuses on the application of triangulation based, short-range laser imaging to determine fracture orientation and surface texture. This technology measures the distance to the target by triangulating the projected and reflected laser beams, and also records the reflection intensity. In this study, we acquired 3D laser images of rock faces using the Laser Camera System (LCS), a portable instrument developed by Neptec Design Group (Ottawa, Canada). The LCS uses an infrared laser beam and is immune to the lighting conditions. The maximum image resolution is 1024 x 1024 volumetric image elements. Depth resolution is 0.5 mm at 5 m. An above ground field trial was conducted at a blocky road cut with well defined joint sets (Kingston, Ontario). An underground field trial was conducted at the Inco 175 Ore body (Sudbury, Ontario) where images were acquired in the dark and the joint set features were more subtle. At each site, from a distance of 3 m away from the rock face, a grid of six images (approximately 1.6 m by 1.6 m) was acquired at maximum resolution with 20% overlap between adjacent images. This corresponds to a density of 40 image elements per square centimeter. Polyworks, a high density 3D visualization software tool, was used to align and merge the images into a single digital triangular mesh. The conventional method of determining fracture orientations is by manual measurement using a compass. In order to be accepted as a substitute for this method, the LCS should be capable of performing at least to the capabilities of manual measurements. To compare fracture orientation estimates derived from the 3D laser images to manual measurements, 160 inclinometer readings were taken at the above ground site. Three prominent joint sets (strike/dip: 236/09, 321/89, 325/01) were identified by plotting the joint poles on a stereonet. Underground, two main joint sets (strike/dip: 060/00, 114/86) were identified from 49 manual inclinometer measurements A stereonet of joint poles from the 3D laser data was generated using the commercial software Split-FX. Joint sets were identified successfully and their orientations correlated well with the hand measurements. However, Split-Fx overlays a simply 2D grid of equal-sized triangles onto the 3D surface and requires significant user input. In a more automated approach, we have developed a MATLAB script which directly imports the Polyworks 3D triangular mesh. A typical mesh is composed of over 1 million triangles of variable sizes: smooth regions are represented by large triangles, whereas rough surfaces are captured by several smaller triangles. Using the triangle vertices, the script computes the strike and dip of each triangle. This approach opens possibilities for statistical analysis of a large population of fracture orientation estimates, including surface texture. The methodology will be used to evaluate both synthetic and field data.

DMD-based LED-illumination super-resolution and optical sectioning microscopy.

PubMed

Dan, Dan; Lei, Ming; Yao, Baoli; Wang, Wen; Winterhalder, Martin; Zumbusch, Andreas; Qi, Yujiao; Xia, Liang; Yan, Shaohui; Yang, Yanlong; Gao, Peng; Ye, Tong; Zhao, Wei

2013-01-01

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.

DMD-based LED-illumination Super-resolution and optical sectioning microscopy

PubMed Central

Dan, Dan; Lei, Ming; Yao, Baoli; Wang, Wen; Winterhalder, Martin; Zumbusch, Andreas; Qi, Yujiao; Xia, Liang; Yan, Shaohui; Yang, Yanlong; Gao, Peng; Ye, Tong; Zhao, Wei

2013-01-01

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×107 pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens. PMID:23346373

Fast integrated intravascular photoacoustic/ultrasound catheter

NASA Astrophysics Data System (ADS)

Choi, Changhoon; Cho, Seunghee; Kim, Taehoon; Park, Sungjo; Park, Hyoeun; Kim, Jinmoo; Lee, Seunghoon; Kang, Yeonsu; Jang, Kiyuk; Kim, Chulhong

2016-03-01

In cardiology, a vulnerable plaque is considered to be a key subject because it is strongly related to atherosclerosis and acute myocardial infarction. Because conventional intravascular imaging devices exhibit several limitations with regard to vulnerable plaque detection, the need for an effective lipid imaging modality has been continuously suggested. Photoacoustic (PA) imaging is a medical imaging technique with a high level of ultrasound (US) resolution and strong optical contrast. In this study, we successfully developed an integrated intravascular photoacoustic/ultrasound (IV-PAUS) imaging system with a catheter diameter of 1.2 mm for lipid-rich atherosclerosis imaging. An Nd:YAG pulsed laser with an excitation wavelength of 1064 nm was utilized. IV-PAUS offers 5-mm depth penetration and axial and lateral PA imaging resolutions of 94 μm and 203 μm, respectively, as determined by imaging a 6-μm carbon fiber. We initially obtained 3-dimensional (3D) co-registered PA/US images of metal stents. Subsequently, we successfully obtained 3D coregistered PA/US ex vivo images using an iliac artery from a rabbit atherosclerosis model. Accordingly, lipid-rich plaques were sufficiently differentiated from normal tissue in the ex vivo experiment. We validated these findings histologically to confirm the lipid content.

High resolution 3D imaging of synchrotron generated microbeams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gagliardi, Frank M., E-mail: frank.gagliardi@wbrc.org.au; Cornelius, Iwan; Blencowe, Anton

2015-12-15

Purpose: Microbeam radiation therapy (MRT) techniques are under investigation at synchrotrons worldwide. Favourable outcomes from animal and cell culture studies have proven the efficacy of MRT. The aim of MRT researchers currently is to progress to human clinical trials in the near future. The purpose of this study was to demonstrate the high resolution and 3D imaging of synchrotron generated microbeams in PRESAGE® dosimeters using laser fluorescence confocal microscopy. Methods: Water equivalent PRESAGE® dosimeters were fabricated and irradiated with microbeams on the Imaging and Medical Beamline at the Australian Synchrotron. Microbeam arrays comprised of microbeams 25–50 μm wide with 200more » or 400 μm peak-to-peak spacing were delivered as single, cross-fire, multidirectional, and interspersed arrays. Imaging of the dosimeters was performed using a NIKON A1 laser fluorescence confocal microscope. Results: The spatial fractionation of the MRT beams was clearly visible in 2D and up to 9 mm in depth. Individual microbeams were easily resolved with the full width at half maximum of microbeams measured on images with resolutions of as low as 0.09 μm/pixel. Profiles obtained demonstrated the change of the peak-to-valley dose ratio for interspersed MRT microbeam arrays and subtle variations in the sample positioning by the sample stage goniometer were measured. Conclusions: Laser fluorescence confocal microscopy of MRT irradiated PRESAGE® dosimeters has been validated in this study as a high resolution imaging tool for the independent spatial and geometrical verification of MRT beam delivery.« less

Three-Dimensional Optical Coherence Tomography

NASA Technical Reports Server (NTRS)

Gutin, Mikhail; Wang, Xu-Ming; Gutin, Olga

2009-01-01

Three-dimensional (3D) optical coherence tomography (OCT) is an advanced method of noninvasive infrared imaging of tissues in depth. Heretofore, commercial OCT systems for 3D imaging have been designed principally for external ophthalmological examination. As explained below, such systems have been based on a one-dimensional OCT principle, and in the operation of such a system, 3D imaging is accomplished partly by means of a combination of electronic scanning along the optical (Z) axis and mechanical scanning along the two axes (X and Y) orthogonal to the optical axis. In 3D OCT, 3D imaging involves a form of electronic scanning (without mechanical scanning) along all three axes. Consequently, the need for mechanical adjustment is minimal and the mechanism used to position the OCT probe can be correspondingly more compact. A 3D OCT system also includes a probe of improved design and utilizes advanced signal- processing techniques. Improvements in performance over prior OCT systems include finer resolution, greater speed, and greater depth of field.

Measurable realistic image-based 3D mapping

NASA Astrophysics Data System (ADS)

Liu, W.; Wang, J.; Wang, J. J.; Ding, W.; Almagbile, A.

2011-12-01

Maps with 3D visual models are becoming a remarkable feature of 3D map services. High-resolution image data is obtained for the construction of 3D visualized models.The3D map not only provides the capabilities of 3D measurements and knowledge mining, but also provides the virtual experienceof places of interest, such as demonstrated in the Google Earth. Applications of 3D maps are expanding into the areas of architecture, property management, and urban environment monitoring. However, the reconstruction of high quality 3D models is time consuming, and requires robust hardware and powerful software to handle the enormous amount of data. This is especially for automatic implementation of 3D models and the representation of complicated surfacesthat still need improvements with in the visualisation techniques. The shortcoming of 3D model-based maps is the limitation of detailed coverage since a user can only view and measure objects that are already modelled in the virtual environment. This paper proposes and demonstrates a 3D map concept that is realistic and image-based, that enables geometric measurements and geo-location services. Additionally, image-based 3D maps provide more detailed information of the real world than 3D model-based maps. The image-based 3D maps use geo-referenced stereo images or panoramic images. The geometric relationships between objects in the images can be resolved from the geometric model of stereo images. The panoramic function makes 3D maps more interactive with users but also creates an interesting immersive circumstance. Actually, unmeasurable image-based 3D maps already exist, such as Google street view, but only provide virtual experiences in terms of photos. The topographic and terrain attributes, such as shapes and heights though are omitted. This paper also discusses the potential for using a low cost land Mobile Mapping System (MMS) to implement realistic image 3D mapping, and evaluates the positioning accuracy that a measureable realistic image-based (MRI) system can produce. The major contribution here is the implementation of measurable images on 3D maps to obtain various measurements from real scenes.

Superresolution upgrade for confocal spinning disk systems using image scanning microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Isbaner, Sebastian; Hähnel, Dirk; Gregor, Ingo; Enderlein, Jörg

2017-02-01

Confocal Spinning Disk Systems are widely used for 3D cell imaging because they offer the advantage of optical sectioning at high framerates and are easy to use. However, as in confocal microscopy, the imaging resolution is diffraction limited, which can be theoretically improved by a factor of 2 using the principle of Image Scanning Microscopy (ISM) [1]. ISM with a Confocal Spinning Disk setup (CSDISM) has been shown to improve contrast as well as lateral resolution (FWHM) from 201 +/- 20 nm to 130 +/- 10 nm at 488 nm excitation. A minimum total acquisition time of one second per ISM image makes this method highly suitable for 3D live cell imaging [2]. Here, we present a multicolor implementation of CSDISM for the popular Micro-Manager Open Source Microscopy platform. Since changes in the optical path are not necessary, this will allow any researcher to easily upgrade their standard Confocal Spinning Disk system at remarkable low cost ( 5000 USD) with an ISM superresolution option. [1]. Müller, C.B. and Enderlein, J. Image Scanning Microscopy. Physical Review Letters 104, (2010). [2]. Schulz, O. et al. Resolution doubling in fluorescence microscopy with confocal spinning-disk image scanning microscopy. Proceedings of the National Academy of Sciences of the United States of America 110, 21000-5 (2013).

The linac coherent light source single particle imaging road map

PubMed Central

Aquila, A.; Barty, A.; Bostedt, C.; Boutet, S.; Carini, G.; dePonte, D.; Drell, P.; Doniach, S.; Downing, K. H.; Earnest, T.; Elmlund, H.; Elser, V.; Gühr, M.; Hajdu, J.; Hastings, J.; Hau-Riege, S. P.; Huang, Z.; Lattman, E. E.; Maia, F. R. N. C.; Marchesini, S.; Ourmazd, A.; Pellegrini, C.; Santra, R.; Schlichting, I.; Schroer, C.; Spence, J. C. H.; Vartanyants, I. A.; Wakatsuki, S.; Weis, W. I.; Williams, G. J.

2015-01-01

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources. PMID:26798801

The linac coherent light source single particle imaging road map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aquila, A.; Barty, A.; Bostedt, C.

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electronmore » laser sources.« less

Acceleration of image-based resolution modelling reconstruction using an expectation maximization nested algorithm.

PubMed

Angelis, G I; Reader, A J; Markiewicz, P J; Kotasidis, F A; Lionheart, W R; Matthews, J C

2013-08-07

Recent studies have demonstrated the benefits of a resolution model within iterative reconstruction algorithms in an attempt to account for effects that degrade the spatial resolution of the reconstructed images. However, these algorithms suffer from slower convergence rates, compared to algorithms where no resolution model is used, due to the additional need to solve an image deconvolution problem. In this paper, a recently proposed algorithm, which decouples the tomographic and image deconvolution problems within an image-based expectation maximization (EM) framework, was evaluated. This separation is convenient, because more computational effort can be placed on the image deconvolution problem and therefore accelerate convergence. Since the computational cost of solving the image deconvolution problem is relatively small, multiple image-based EM iterations do not significantly increase the overall reconstruction time. The proposed algorithm was evaluated using 2D simulations, as well as measured 3D data acquired on the high-resolution research tomograph. Results showed that bias reduction can be accelerated by interleaving multiple iterations of the image-based EM algorithm solving the resolution model problem, with a single EM iteration solving the tomographic problem. Significant improvements were observed particularly for voxels that were located on the boundaries between regions of high contrast within the object being imaged and for small regions of interest, where resolution recovery is usually more challenging. Minor differences were observed using the proposed nested algorithm, compared to the single iteration normally performed, when an optimal number of iterations are performed for each algorithm. However, using the proposed nested approach convergence is significantly accelerated enabling reconstruction using far fewer tomographic iterations (up to 70% fewer iterations for small regions). Nevertheless, the optimal number of nested image-based EM iterations is hard to be defined and it should be selected according to the given application.

Human brain diffusion tensor imaging at submillimeter isotropic resolution on a 3 Tesla clinical MRI scanner

PubMed Central

Chang, Hing-Chiu; Sundman, Mark; Petit, Laurent; Guhaniyogi, Shayan; Chu, Mei-Lan; Petty, Christopher; Song, Allen W.; Chen, Nan-kuei

2015-01-01

The advantages of high-resolution diffusion tensor imaging (DTI) have been demonstrated in a recent post-mortem human brain study (Miller et al., NeuroImage 2011;57(1):167–181), showing that white matter fiber tracts can be much more accurately detected in data at submillimeter isotropic resolution. To our knowledge, in vivo human brain DTI at submillimeter isotropic resolution has not been routinely achieved yet because of the difficulty in simultaneously achieving high resolution and high signal-to-noise ratio (SNR) in DTI scans. Here we report a 3D multi-slab interleaved EPI acquisition integrated with multiplexed sensitivity encoded (MUSE) reconstruction, to achieve high-quality, high-SNR and submillimeter isotropic resolution (0.85 × 0.85 × 0.85 mm3) in vivo human brain DTI on a 3 Tesla clinical MRI scanner. In agreement with the previously reported post-mortem human brain DTI study, our in vivo data show that the structural connectivity networks of human brains can be mapped more accurately and completely with high-resolution DTI as compared with conventional DTI (e.g., 2 × 2 × 2 mm3). PMID:26072250

3D printed phantoms of retinal photoreceptor cells for evaluating adaptive optics imaging modalities

NASA Astrophysics Data System (ADS)

Kedia, Nikita; Liu, Zhuolin; Sochol, Ryan; Hammer, Daniel X.; Agrawal, Anant

2018-02-01

Adaptive optics-enabled optical coherence tomography (AO-OCT) and scanning laser ophthalmoscopy (AO-SLO) devices can resolve retinal cones and rods in three dimensions. To evaluate the improved resolution of AO-OCT and AO-SLO, a phantom that mimics retinal anatomy at the cellular level is required. We used a two-photon polymerization approach to fabricate three-dimensional (3D) photoreceptor phantoms modeled on the central foveal cones. By using a femtosecond laser to selectively photocure precise locations within a liquid-based photoresist via two-photon absorption, we produced high-resolution phantoms with μm-level dimensions similar to true anatomy. In this work, we present two phantoms to evaluate the resolution limits of an AO imaging system: one that models only the outer segments of the photoreceptor cells at varying retinal eccentricities and another that contains anatomically relevant features of the full-length photoreceptor. With these phantoms we are able to quantitatively estimate transverse resolution of an AO system and produce images that are comparable to those found in the human retina.

Fast High Resolution Volume Carving for 3D Plant Shoot Reconstruction

PubMed Central

Scharr, Hanno; Briese, Christoph; Embgenbroich, Patrick; Fischbach, Andreas; Fiorani, Fabio; Müller-Linow, Mark

2017-01-01

Volume carving is a well established method for visual hull reconstruction and has been successfully applied in plant phenotyping, especially for 3d reconstruction of small plants and seeds. When imaging larger plants at still relatively high spatial resolution (≤1 mm), well known implementations become slow or have prohibitively large memory needs. Here we present and evaluate a computationally efficient algorithm for volume carving, allowing e.g., 3D reconstruction of plant shoots. It combines a well-known multi-grid representation called “Octree” with an efficient image region integration scheme called “Integral image.” Speedup with respect to less efficient octree implementations is about 2 orders of magnitude, due to the introduced refinement strategy “Mark and refine.” Speedup is about a factor 1.6 compared to a highly optimized GPU implementation using equidistant voxel grids, even without using any parallelization. We demonstrate the application of this method for trait derivation of banana and maize plants. PMID:29033961

Experiments on terahertz 3D scanning microscopic imaging

NASA Astrophysics Data System (ADS)

Zhou, Yi; Li, Qi

2016-10-01

Compared with the visible light and infrared, terahertz (THz) radiation can penetrate nonpolar and nonmetallic materials. There are many studies on the THz coaxial transmission confocal microscopy currently. But few researches on the THz dual-axis reflective confocal microscopy were reported. In this paper, we utilized a dual-axis reflective confocal scanning microscope working at 2.52 THz. In contrast with the THz coaxial transmission confocal microscope, the microscope adopted in this paper can attain higher axial resolution at the expense of reduced lateral resolution, revealing more satisfying 3D imaging capability. Objects such as Chinese characters "Zhong-Hua" written in paper with a pencil and a combined sheet metal which has three layers were scanned. The experimental results indicate that the system can extract two Chinese characters "Zhong," "Hua" or three layers of the combined sheet metal. It can be predicted that the microscope can be applied to biology, medicine and other fields in the future due to its favorable 3D imaging capability.

IDEAL 3D spoiled gradient echo of the articular cartilage of the knee on 3.0 T MRI: a comparison with conventional 3.0 T fast spin-echo T2 fat saturation image.

PubMed

Han, Chul Hee; Park, Hee Jin; Lee, So Yeon; Chung, Eun Chul; Choi, Seon Hyeong; Yun, Ji Sup; Rho, Myung Ho

2015-12-01

Many two-dimensional (2D) morphologic cartilage imaging sequences have disadvantages such as long acquisition time, inadequate spatial resolution, suboptimal tissue contrast, and image degradation secondary to artifacts. IDEAL imaging can overcome these disadvantages. To compare sound-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and quality of two different methods of imaging that include IDEAL 3D SPGR and 3.0-T FSE T2 fat saturation (FS) imaging and to evaluate the utility of IDEAL 3D SPGR for knee joint imaging. SNR and CNR of the patellar and femoral cartilages were measured and calculated. Two radiologists performed subjective scoring of all images for three measures: general image quality, FS, and cartilage evaluation. SNR and CNR values were compared by paired Student's t-tests. Mean SNRs of patellar and femoral cartilages were 90% and 66% higher, respectively, for IDEAL 3D SPGR. CNRs of patellar cartilages and joint fluids were 2.4 times higher for FSE T2 FS, and CNR between the femoral cartilage and joint fluid was 2.2 times higher for FSE T2 FS. General image quality and FS were superior using FSE T2 FS compared to those of IDEAL 3D SPGR imaging according to both readers, while cartilage evaluation was superior using IDEAL 3D SPGR. Additionally, cartilage injuries were more prominent in IDEAL 3D SPGR than in FSE T2FS according to both readers. IDEAL 3D SPGR images show excellent visualization of patellar and femoral cartilages in 3.0 T and can compensate for the weaknesses of FSE T2 FS in the evaluation of cartilage injuries. © The Foundation Acta Radiologica 2014.

Digital Fresnel reflection holography for high-resolution 3D near-wall flow measurement.

PubMed

Kumar, S Santosh; Hong, Jiarong

2018-05-14

We propose a novel backscatter holographic imaging system, as a compact and effective tool for 3D near-wall flow diagnostics at high resolutions, utilizing light reflected at the solid-liquid interface as a reference beam. The technique is fully calibrated, and is demonstrated in a densely seeded channel to achieve a spatial resolution of near-wall flows equivalent to or exceeding prior digital inline holographic measurements using local tracer seeding technique. Additionally, we examined the effects of seeding concentration and laser coherence on the measurement resolution and sample volume resolved, demonstrating the potential to manipulate sample domain by tuning the laser coherence profile.

Comparing the Effect of Different Voxel Resolutions for Assessment of Vertical Root Fracture of Permanent Teeth

PubMed Central

Uzun, Ismail; Gunduz, Kaan; Celenk, Peruze; Avsever, Hakan; Orhan, Kaan; Canitezer, Gozde; Ozmen, Bilal; Cicek, Ersan; Egrioglu, Erol

2015-01-01

Background: The teeth with undiagnosed vertical root fractures (VRFs) are likely to receive endodontic treatment or retreatment, leading to frustration and inappropriate endodontic therapies. Moreover, many cases of VRFs cannot be diagnosed definitively until the extraction of tooth. Objectives: This study aimed to assess the use of different voxel resolutions of two different cone beam computerized tomography (CBCT) units in the detection VRFs in vitro. Materials and Methods: The study material comprised 74 extracted human mandibular single rooted premolar teeth without root fractures that had not undergone any root-canal treatment. Images were obtained by two different CBCT units. Four image sets were obtained as follows: 1) 3D Accuitomo 170, 4 × 4 cm field of view (FOV) (0.080 mm3); 2) 3D Accuitomo 170. 6 × 6 cm FOV (0.125 mm3); 3) NewTom 3G, 6˝ (0.16 mm3) and 4) NewTom 3G, 9˝ FOV (0.25 mm3). Kappa coefficients were calculated to assess both intra- and inter-observer agreements for each image set. Results: No significant differences were found among observers or voxel sizes, with high average Z (Az) results being reported for all groups. Both intra- and inter-observer agreement values were relatively better for 3D Accuitomo 170 images than the images from NewTom 3G. The highest Az and kappa values were obtained with 3D Accuitomo 170, 4 × 4 cm FOV (0.080 mm3) images. Conclusion: No significant differences were found among observers or voxel sizes, with high Az results reported for all groups. PMID:26557279

EISCAT Aperture Synthesis Imaging (EASI _3D) for the EISCAT_3D Project

NASA Astrophysics Data System (ADS)

La Hoz, Cesar; Belyey, Vasyl

2012-07-01

Aperture Synthesis Imaging Radar (ASIR) is one of the technologies adopted by the EISCAT_3D project to endow it with imaging capabilities in 3-dimensions that includes sub-beam resolution. Complemented by pulse compression, it will provide 3-dimensional images of certain types of incoherent scatter radar targets resolved to about 100 metres at 100 km range, depending on the signal-to-noise ratio. This ability will open new research opportunities to map small structures associated with non-homogeneous, unstable processes such as aurora, summer and winter polar radar echoes (PMSE and PMWE), Natural Enhanced Ion Acoustic Lines (NEIALs), structures excited by HF ionospheric heating, meteors, space debris, and others. The underlying physico-mathematical principles of the technique are the same as the technique employed in radioastronomy to image stellar objects; both require sophisticated inversion techniques to obtain reliable images.

Note: An improved 3D imaging system for electron-electron coincidence measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Yun Fei; Lee, Suk Kyoung; Adhikari, Pradip

We demonstrate an improved imaging system that can achieve highly efficient 3D detection of two electrons in coincidence. The imaging system is based on a fast frame complementary metal-oxide semiconductor camera and a high-speed waveform digitizer. We have shown previously that this detection system is capable of 3D detection of ions and electrons with good temporal and spatial resolution. Here, we show that with a new timing analysis algorithm, this system can achieve an unprecedented dead-time (<0.7 ns) and dead-space (<1 mm) when detecting two electrons. A true zero dead-time detection is also demonstrated.

Note: An improved 3D imaging system for electron-electron coincidence measurements

NASA Astrophysics Data System (ADS)

Lin, Yun Fei; Lee, Suk Kyoung; Adhikari, Pradip; Herath, Thushani; Lingenfelter, Steven; Winney, Alexander H.; Li, Wen

2015-09-01

We demonstrate an improved imaging system that can achieve highly efficient 3D detection of two electrons in coincidence. The imaging system is based on a fast frame complementary metal-oxide semiconductor camera and a high-speed waveform digitizer. We have shown previously that this detection system is capable of 3D detection of ions and electrons with good temporal and spatial resolution. Here, we show that with a new timing analysis algorithm, this system can achieve an unprecedented dead-time (<0.7 ns) and dead-space (<1 mm) when detecting two electrons. A true zero dead-time detection is also demonstrated.

Three-dimensional Optical Coherence Tomography for Optical Biopsy of Lymph Nodes and Assessment of Metastatic Disease

PubMed Central

John, Renu; Adie, Steven G.; Chaney, Eric J.; Marjanovic, Marina; Tangella, Krishnarao V.; Boppart, Stephen A.

2013-01-01

Background Numerous techniques have been developed for localizing lymph nodes before surgical resection and for their histological assessment. Nondestructive high-resolution transcapsule optical imaging of lymph nodes offers the potential for in situ assessment of metastatic involvement, potentially during surgical procedures. Methods Three-dimensional optical coherence tomography (3-D OCT) was used for imaging and assessing resected popliteal lymph nodes from a preclinical rat metastatic tumor model over a 9-day time-course study after tumor induction. The spectral-domain OCT system utilized a center wavelength of 800 nm, provided axial and transverse resolutions of 3 and 12 µm, respectively, and performed imaging at 10,000 axial scans per second. Results OCT is capable of providing high-resolution labelfree images of intact lymph node microstructure based on intrinsic optical scattering properties with penetration depths of ~1–2 mm. The results demonstrate that OCT is capable of differentiating normal, reactive, and metastatic lymph nodes based on microstructural changes. The optical scattering and structural changes revealed by OCT from day 3 to day 9 after the injection of tumor cells into the lymphatic system correlate with inflammatory and immunological changes observed in the capsule, precortical regions, follicles, and germination centers found during histopathology. Conclusions We report for the first time a longitudinal study of 3-D transcapsule OCT imaging of intact lymph nodes demonstrating microstructural changes during metastatic infiltration. These results demonstrate the potential of OCT as a technique for intraoperative, real-time in situ 3-D optical biopsy of lymph nodes for the intraoperative staging of cancer. PMID:22688663

High-frequency 3D echodentographic imaging modality for early assessment of periodontal diseases: in vitro study

NASA Astrophysics Data System (ADS)

Mahmoud, Ahmed M.; Ngan, Peter; Crout, Richard; Mukdadi, Osama M.

2009-02-01

The use of ultrasound in dentistry is still an open growing area of research. Currently, there is a lack of imaging modalities to accurately predict minute structures and defects in the jawbone. In particular, the inability of 2D radiographic images to detect bony periodontal defects resulted from infection of the periodontium. This study investigates the feasibility of high frequency ultrasound to reconstruct high resolution 3D surface images of human jawbone. Methods: A dentate and non-dentate mandibles were used in this study. The system employs high frequency single-element ultrasound focused transducers (15-30 MHz) for scanning. Continuous acquisition using a 1 GHz data acquisition card is synchronized with a high precision two-dimensional stage positioning system of +/-1 μm resolution for acquiring accurate and quantitative measurements of the mandible in vitro. Radio frequency (RF) signals are acquired laterally 44-45.5 μm apart for each frame. Different frames are reconstructed 500 μm apart for the 3D reconstruction. Signal processing algorithms are applied on the received ultrasound signals for filtering, focusing, and envelope detection before frame reconstruction. Furthermore, an edge detection technique is adopted to detect the bone surface in each frame. Finally, all edges are combined together in order to render a 3D surface image of the jawbone. Major anatomical landmarks on the resultant images were confirmed with the anatomical structures on the mandibles to show the efficacy of the system. Comparison were also made with conventional 2D radiographs to show the superiority of the ultrasound imaging system in diagnosing small defects in the lateral, axial and elevation planes of space. Results: The landmarks on all ultrasound images matched with those on the mandible, indicating the efficacy of the system in detecting small structures in human jaw bones. Comparison with conventional 2D radiographic images of the same mandible showed superiority of the 3D ultrasound images in detecting defects in the elevation plane of space. These results suggest that the high frequency ultrasound system shows great potential in providing a non-invasive method to characterize the jawbone and detect periodontal diseases at earlier stages.

MPI as high temporal resolution imaging technique for in vivo bolus tracking of Ferucarbotran in mouse model

NASA Astrophysics Data System (ADS)

Jung, C.; Salamon, J.; Hofmann, M.; Kaul, M. G.; Adam, G.; Ittrich, H.; Knopp, T.

2016-03-01

Purpose: The goal of this study was to achieve a real time 3D visualisation of the murine cardiovascular system by intravenously injected superparamagnetic nanoparticles using Magnetic particle imaging (MPI). Material and Methods: MPI scans of FVB mice were performed using a 3D imaging sequence (1T/m gradient strength, 10mT drive-field strength). A dynamic scan with a temporal resolution of 21.5ms per 3D volume acquisition was performed. 50μl ferucarbotran (Resovist®, Bayer Healthcare AG) were injected into the tail vein after baseline MPI measurements. As MPI delivers no anatomic information, MRI scans at a 7T ClinScan (Bruker) were performed using a T2-weighted 2D TSE sequence. The reconstruction of the MPI data was performed on the MPI console (ParaVision 6.0/MPI, Bruker). Image fusion was done using additional image processing software (Imalytics, Philips). The dynamic information was extracted using custom software developed in the Julia programming environment. Results: The combined MRI-MPI measurements were carried out successfully. MPI data clearly demonstrated the passage of the SPIO tracer through the inferior vena cava, the heart and finally the liver. By co-registration with MRI the anatomical regions were identified. Due to the volume frame rate of about 46 volumes per second a signal modulation with the frequency of the heart beat was detectable and a heart beat of 520 beats per minute (bpm) has been assumed. Moreover, the blood flow velocity of approximately 5cm/s in the vena cava has been estimated. Conclusions: The high temporal resolution of MPI allows real-time imaging and bolus tracking of intravenous injected nanoparticles and offers a real time tool to assess blood flow velocity.

An update on intraoperative three-dimensional transesophageal echocardiography

PubMed Central

2017-01-01

Transesophageal echocardiography (TEE) was first used routinely in the operating rooms in the 1980s to facilitate surgical decision-making. Since then, TEE has evolved from the standard two-dimensional (2D) exam to include focused real-time three-dimensional (RT-3D) imaging both inside and outside the operating rooms. Improved spatial and temporal resolution due to technological advances has expedited surgical interventions in diseased valves. 3D imaging has also emerged as a crucial adjunct in percutaneous interventions for structural heart disease. With continued advancement in software, RT-3D TEE will continue to impact perioperative decisions. PMID:28540070

Enhancing the image resolution in a single-pixel sub-THz imaging system based on compressed sensing

NASA Astrophysics Data System (ADS)

Alkus, Umit; Ermeydan, Esra Sengun; Sahin, Asaf Behzat; Cankaya, Ilyas; Altan, Hakan

2018-04-01

Compressed sensing (CS) techniques allow for faster imaging when combined with scan architectures, which typically suffer from speed. This technique when implemented with a subterahertz (sub-THz) single detector scan imaging system provides images whose resolution is only limited by the pixel size of the pattern used to scan the image plane. To overcome this limitation, the image of the target can be oversampled; however, this results in slower imaging rates especially if this is done in two-dimensional across the image plane. We show that by implementing a one-dimensional (1-D) scan of the image plane, a modified approach to CS theory applied with an appropriate reconstruction algorithm allows for successful reconstruction of the reflected oversampled image of a target placed in standoff configuration from the source. The experiments are done in reflection mode configuration where the operating frequency is 93 GHz and the corresponding wavelength is λ = 3.2 mm. To reconstruct the image with fewer samples, CS theory is applied using masks where the pixel size is 5 mm × 5 mm, and each mask covers an image area of 5 cm × 5 cm, meaning that the basic image is resolved as 10 × 10 pixels. To enhance the resolution, the information between two consecutive pixels is used, and oversampling along 1-D coupled with a modification of the masks in CS theory allowed for oversampled images to be reconstructed rapidly in 20 × 20 and 40 × 40 pixel formats. These are then compared using two different reconstruction algorithms, TVAL3 and ℓ1-MAGIC. The performance of these methods is compared for both simulated signals and real signals. It is found that the modified CS theory approach coupled with the TVAL3 reconstruction process, even when scanning along only 1-D, allows for rapid precise reconstruction of the oversampled target.

Whole-heart coronary MRA with 3D affine motion correction using 3D image-based navigation.

PubMed

Henningsson, Markus; Prieto, Claudia; Chiribiri, Amedeo; Vaillant, Ghislain; Razavi, Reza; Botnar, René M

2014-01-01

Robust motion correction is necessary to minimize respiratory motion artefacts in coronary MR angiography (CMRA). The state-of-the-art method uses a 1D feet-head translational motion correction approach, and data acquisition is limited to a small window in the respiratory cycle, which prolongs the scan by a factor of 2-3. The purpose of this work was to implement 3D affine motion correction for Cartesian whole-heart CMRA using a 3D navigator (3D-NAV) to allow for data acquisition throughout the whole respiratory cycle. 3D affine transformations for different respiratory states (bins) were estimated by using 3D-NAV image acquisitions which were acquired during the startup profiles of a steady-state free precession sequence. The calculated 3D affine transformations were applied to the corresponding high-resolution Cartesian image acquisition which had been similarly binned, to correct for respiratory motion between bins. Quantitative and qualitative comparisons showed no statistical difference between images acquired with the proposed method and the reference method using a diaphragmatic navigator with a narrow gating window. We demonstrate that 3D-NAV and 3D affine correction can be used to acquire Cartesian whole-heart 3D coronary artery images with 100% scan efficiency with similar image quality as with the state-of-the-art gated and corrected method with approximately 50% scan efficiency. Copyright © 2013 Wiley Periodicals, Inc.

Fourier Domain Optical Coherence Tomography With 3D and En Face Imaging of the Punctum and Vertical Canaliculus: A Step Toward Establishing a Normative Database.

PubMed

Kamal, Saurabh; Ali, Mohammad Javed; Ali, Mohammad Hasnat; Naik, Milind N

2016-01-01

To report the features of Fourier domain optical coherence tomography imaging of the normal punctum and vertical canaliculus. Prospective, interventional series of consecutive healthy and asymptomatic adults, who volunteered for optical coherence tomography imaging, were included in the study. Fourier domain optical coherence tomography images of the punctum and vertical canaliculus along with 3D and En face images were captured using the RTVue scanner with a corneal adaptor module and a wide-angled lens. Maximum punctal diameter, mid-canalicular diameter, and vertical canalicular height were calculated. Statistical analysis was performed using Pearson correlation test, and scatter plot matrices were analyzed. A total of 103 puncta of 52 healthy subjects were studied. Although all the images could depict the punctum and vertical canaliculus and all the desired measurements could be obtained, occasional tear debris within the canaliculus was found to be interfering with the imaging. The mean maximum punctal diameter, mid-canalicular diameter, and vertical canalicular height were recorded as 214.71 ± 73 μm, 125.04 ± 60.69 μm, and 890.41 ± 154.76 μm, respectively, with an insignificant correlation between them. The maximum recorded vertical canalicular height in all the cases was far less than the widely reported depth of 2 mm. High-resolution 3D and En face images provided a detailed topography of punctal surface and overview of vertical canaliculus. Fourier domain optical coherence tomography with 3D and En face imaging is a useful noninvasive modality to image the proximal lacrimal system with consistently reproducible high-resolution images. This is likely to help clinicians in the management of proximal lacrimal disorders.

Final Project Report: Imaging Fault Zones Using a Novel Elastic Reverse-Time Migration Imaging Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Lianjie; Chen, Ting; Tan, Sirui

Imaging fault zones and fractures is crucial for geothermal operators, providing important information for reservoir evaluation and management strategies. However, there are no existing techniques available for directly and clearly imaging fault zones, particularly for steeply dipping faults and fracture zones. In this project, we developed novel acoustic- and elastic-waveform inversion methods for high-resolution velocity model building. In addition, we developed acoustic and elastic reverse-time migration methods for high-resolution subsurface imaging of complex subsurface structures and steeply-dipping fault/fracture zones. We first evaluated and verified the improved capabilities of our newly developed seismic inversion and migration imaging methods using synthetic seismicmore » data. Our numerical tests verified that our new methods directly image subsurface fracture/fault zones using surface seismic reflection data. We then applied our novel seismic inversion and migration imaging methods to a field 3D surface seismic dataset acquired at the Soda Lake geothermal field using Vibroseis sources. Our migration images of the Soda Lake geothermal field obtained using our seismic inversion and migration imaging algorithms revealed several possible fault/fracture zones. AltaRock Energy, Inc. is working with Cyrq Energy, Inc. to refine the geologic interpretation at the Soda Lake geothermal field. Trenton Cladouhos, Senior Vice President R&D of AltaRock, was very interested in our imaging results of 3D surface seismic data from the Soda Lake geothermal field. He planed to perform detailed interpretation of our images in collaboration with James Faulds and Holly McLachlan of University of Nevada at Reno. Using our high-resolution seismic inversion and migration imaging results can help determine the optimal locations to drill wells for geothermal energy production and reduce the risk of geothermal exploration.« less

In vivo cellular imaging with microscopes enabled by MEMS scanners

NASA Astrophysics Data System (ADS)

Ra, Hyejun

High-resolution optical imaging plays an important role in medical diagnosis and biomedical research. Confocal microscopy is a widely used imaging method for obtaining cellular and sub-cellular images of biological tissue in reflectance and fluorescence modes. Its characteristic optical sectioning capability also enables three-dimensional (3-D) image reconstruction. However, its use has mostly been limited to excised tissues due to the requirement of high numerical aperture (NA) lenses for cellular resolution. Microscope miniaturization can enable in vivo imaging to make possible early cancer diagnosis and biological studies in the innate environment. In this dissertation, microscope miniaturization for in vivo cellular imaging is presented. The dual-axes confocal (DAC) architecture overcomes limitations of the conventional single-axis confocal (SAC) architecture to allow for miniaturization with high resolution. A microelectromechanical systems (MEMS) scanner is the central imaging component that is key in miniaturization of the DAC architecture. The design, fabrication, and characterization of the two-dimensional (2-D) MEMS scanner are presented. The gimbaled MEMS scanner is fabricated on a double silicon-on-insulator (SOI) wafer and is actuated by self-aligned vertical electrostatic combdrives. The imaging performance of the MEMS scanner in a DAC configuration is shown in a breadboard microscope setup, where reflectance and fluorescence imaging is demonstrated. Then, the MEMS scanner is integrated into a miniature DAC microscope. The whole imaging system is integrated into a portable unit for research in small animal models of human biology and disease. In vivo 3-D imaging is demonstrated on mouse skin models showing gene transfer and siRNA silencing. The siRNA silencing process is sequentially imaged in one mouse over time.

Time-resolved 3D pulmonary perfusion MRI: comparison of different k-space acquisition strategies at 1.5 and 3 T.

PubMed

Attenberger, Ulrike I; Ingrisch, Michael; Dietrich, Olaf; Herrmann, Karin; Nikolaou, Konstantin; Reiser, Maximilian F; Schönberg, Stefan O; Fink, Christian

2009-09-01

Time-resolved pulmonary perfusion MRI requires both high temporal and spatial resolution, which can be achieved by using several nonconventional k-space acquisition techniques. The aim of this study is to compare the image quality of time-resolved 3D pulmonary perfusion MRI with different k-space acquisition techniques in healthy volunteers at 1.5 and 3 T. Ten healthy volunteers underwent contrast-enhanced time-resolved 3D pulmonary MRI on 1.5 and 3 T using the following k-space acquisition techniques: (a) generalized autocalibrating partial parallel acquisition (GRAPPA) with an internal acquisition of reference lines (IRS), (b) GRAPPA with a single "external" acquisition of reference lines (ERS) before the measurement, and (c) a combination of GRAPPA with an internal acquisition of reference lines and view sharing (VS). The spatial resolution was kept constant at both field strengths to exclusively evaluate the influences of the temporal resolution achieved with the different k-space sampling techniques on image quality. The temporal resolutions were 2.11 seconds IRS, 1.31 seconds ERS, and 1.07 VS at 1.5 T and 2.04 seconds IRS, 1.30 seconds ERS, and 1.19 seconds VS at 3 T.Image quality was rated by 2 independent radiologists with regard to signal intensity, perfusion homogeneity, artifacts (eg, wrap around, noise), and visualization of pulmonary vessels using a 3 point scale (1 = nondiagnostic, 2 = moderate, 3 = good). Furthermore, the signal-to-noise ratio in the lungs was assessed. At 1.5 T the lowest image quality (sum score: 154) was observed for the ERS technique and the highest quality for the VS technique (sum score: 201). In contrast, at 3 T images acquired with VS were hampered by strong artifacts and image quality was rated significantly inferior (sum score: 137) compared with IRS (sum score: 180) and ERS (sum score: 174). Comparing 1.5 and 3 T, in particular the overall rating of the IRS technique (sum score: 180) was very similar at both field strengths. At 1.5 T the peak signal-to-noise ratio of the ERS was significantly lower in comparison to the IRS and the VS technique (14.6 vs. 26.7 and 39.6 respectively, P < 0.004). Using the IRS sampling algorithm comparable image quality and SNR can be achieved at 1.5 and 3 T. At 1.5 T VS offers the best possible solution for the conflicting requirements between a further increased temporal resolution and image quality. In consequence the gain of increased scanning efficiency from advanced k[r]-space sampling acquisition techniques can be exploited for a further improvement of image quality of pulmonary perfusion MRI.

Structured illumination 3D microscopy using adaptive lenses and multimode fibers

NASA Astrophysics Data System (ADS)

Czarske, Jürgen; Philipp, Katrin; Koukourakis, Nektarios

2017-06-01

Microscopic techniques with high spatial and temporal resolution are required for in vivo studying biological cells and tissues. Adaptive lenses exhibit strong potential for fast motion-free axial scanning. However, they also lead to a degradation of the achievable resolution because of aberrations. This hurdle can be overcome by digital optical technologies. We present a novel High-and-Low-frequency (HiLo) 3D-microscope using structured illumination and an adaptive lens. Uniform illumination is used to obtain optical sectioning for the high-frequency (Hi) components of the image, and nonuniform illumination is needed to obtain optical sectioning for the low-frequency (Lo) components of the image. Nonuniform illumination is provided by a multimode fiber. It ensures robustness against optical aberrations of the adaptive lens. The depth-of-field of our microscope can be adjusted a-posteriori by computational optics. It enables to create flexible scans, which compensate for irregular axial measurement positions. The adaptive HiLo 3D-microscope provides an axial scanning range of 1 mm with an axial resolution of about 4 microns and sub-micron lateral resolution over the full scanning range. In result, volumetric measurements with high temporal and spatial resolution are provided. Demonstration measurements of zebrafish embryos with reporter gene-driven fluorescence in the thyroid gland are presented.

Enhanced truncated-correlation photothermal coherence tomography with application to deep subsurface defect imaging and 3-dimensional reconstructions

NASA Astrophysics Data System (ADS)

Tavakolian, Pantea; Sivagurunathan, Koneswaran; Mandelis, Andreas

2017-07-01

Photothermal diffusion-wave imaging is a promising technique for non-destructive evaluation and medical applications. Several diffusion-wave techniques have been developed to produce depth-resolved planar images of solids and to overcome imaging depth and image blurring limitations imposed by the physics of parabolic diffusion waves. Truncated-Correlation Photothermal Coherence Tomography (TC-PCT) is the most successful class of these methodologies to-date providing 3-D subsurface visualization with maximum depth penetration and high axial and lateral resolution. To extend the depth range and axial and lateral resolution, an in-depth analysis of TC-PCT, a novel imaging system with improved instrumentation, and an optimized reconstruction algorithm over the original TC-PCT technique is developed. Thermal waves produced by a laser chirped pulsed heat source in a finite thickness solid and the image reconstruction algorithm are investigated from the theoretical point of view. 3-D visualization of subsurface defects utilizing the new TC-PCT system is reported. The results demonstrate that this method is able to detect subsurface defects at the depth range of ˜4 mm in a steel sample, which exhibits dynamic range improvement by a factor of 2.6 compared to the original TC-PCT. This depth does not represent the upper limit of the enhanced TC-PCT. Lateral resolution in the steel sample was measured to be ˜31 μm.

Wavelength scanning digital interference holography for high-resolution ophthalmic imaging

NASA Astrophysics Data System (ADS)

Potcoava, Mariana C.; Kim, M. K.; Kay, Christine N.

2009-02-01

An improved digital interference holography (DIH) technique suitable for fundus images is proposed. This technique incorporates a dispersion compensation algorithm to compensate for the unknown axial length of the eye. Using this instrument we acquired successfully tomographic fundus images in human eye with narrow axial resolution less than 5μm. The optic nerve head together with the surrounding retinal vasculature were constructed. We were able to quantify a depth of 84μm between the retinal fiber and the retinal pigmented epithelium layers. DIH provides high resolution 3D information which could potentially aid in guiding glaucoma diagnosis and treatment.

Ultrahigh speed 1050nm swept source / Fourier domain OCT retinal and anterior segment imaging at 100,000 to 400,000 axial scans per second

PubMed Central

Potsaid, Benjamin; Baumann, Bernhard; Huang, David; Barry, Scott; Cable, Alex E.; Schuman, Joel S.; Duker, Jay S.; Fujimoto, James G.

2011-01-01

We demonstrate ultrahigh speed swept source/Fourier domain ophthalmic OCT imaging using a short cavity swept laser at 100,000–400,000 axial scan rates. Several design configurations illustrate tradeoffs in imaging speed, sensitivity, axial resolution, and imaging depth. Variable rate A/D optical clocking is used to acquire linear-in-k OCT fringe data at 100kHz axial scan rate with 5.3um axial resolution in tissue. Fixed rate sampling at 1 GSPS achieves a 7.5mm imaging range in tissue with 6.0um axial resolution at 100kHz axial scan rate. A 200kHz axial scan rate with 5.3um axial resolution over 4mm imaging range is achieved by buffering the laser sweep. Dual spot OCT using two parallel interferometers achieves 400kHz axial scan rate, almost 2X faster than previous 1050nm ophthalmic results and 20X faster than current commercial instruments. Superior sensitivity roll-off performance is shown. Imaging is demonstrated in the human retina and anterior segment. Wide field 12×12mm data sets include the macula and optic nerve head. Small area, high density imaging shows individual cone photoreceptors. The 7.5mm imaging range configuration can show the cornea, iris, and anterior lens in a single image. These improvements in imaging speed and depth range provide important advantages for ophthalmic imaging. The ability to rapidly acquire 3D-OCT data over a wide field of view promises to simplify examination protocols. The ability to image fine structures can provide detailed information on focal pathologies. The large imaging range and improved image penetration at 1050nm wavelengths promises to improve performance for instrumentation which images both the retina and anterior eye. These advantages suggest that swept source OCT at 1050nm wavelengths will play an important role in future ophthalmic instrumentation. PMID:20940894

High resolution MR microscopy

NASA Astrophysics Data System (ADS)

Ciobanu, Luisa

Magnetic resonance imaging (MRI) microscopy [1] has the potential to bring the full capabilities of NMR to arbitrarily specified localized positions within small samples. The most interesting target of study is the living biological cell, with typical dimensions ˜100 mum, but with substructures that are much smaller, such as the cell nucleus (typically ˜10 mu m) and mitochondria (1--10 mum). One anticipates that the development of MR microscopy with resolution at the level of these substructures or better and with a wide, three dimensional field-of-view could open a new avenue of investigation into the biology of the living cell. Although the first MR image of a single biological cell was reported in 1987 [2], the cell imaged had quite large (˜1 mm diameter) spatial dimensions and the resolution obtained (on the order of 10 mu m) was not adequate for meaningful imaging of more typically sized cells. The quest for higher resolution has continued. In 1989 Zhou et al. [3] obtained fully three dimensional images with spatial resolution of (6.37 mum)3, or 260 femtoliters. While better "in-plane" resolutions (i.e., the resolution in 2 of the 3 spatial dimensions) have since been obtained, [4, 5] this volume resolution was not exceeded until quite recently by Lee et al., [6] who report 2D images having volume resolution of 75 mum 3 and in-plane resolution of 1 mum. In parallel with these advances in raw resolution several investigators [7, 8, 9] have focused on localized spectroscopy and/or chemical shift imaging. The key obstacles to overcome in MR microscopy are (1) the loss of signal to noise that occurs when observing small volumes and (2) molecular diffusion during the measurement or encoding. To date the problem of sensitivity has typically been addressed by employing small micro-coil receivers. [10] The problem of molecular diffusion can only be defeated with strong magnetic field gradients that can encode spatial information quickly. We report MR microscopy images on phantoms [11, 12] and biological samples (paramecia, algae, brain tissue, lipidic mesophases) obtained using using magnetic field gradients as large as 50 Tesla/meter (5000 G/cm) [13] and micro-coils [14]. Images have voxel resolution as high as (3.7 mum by 3.3 mum by 3.3 mum), or 41 mu m3 (41 femtoliters, containing 2.7 x 10 12 proton spins) [12], marginally the highest voxel resolution reported to date. They are also fully three dimensional, with wide fields of view.

First flight of the Gamma-Ray Imager/Polarimeter for Solar flares (GRIPS) instrument

NASA Astrophysics Data System (ADS)

Duncan, Nicole; Saint-Hilaire, P.; Shih, A. Y.; Hurford, G. J.; Bain, H. M.; Amman, M.; Mochizuki, B. A.; Hoberman, J.; Olson, J.; Maruca, B. A.; Godbole, N. M.; Smith, D. M.; Sample, J.; Kelley, N. A.; Zoglauer, A.; Caspi, A.; Kaufmann, P.; Boggs, S.; Lin, R. P.

2016-07-01

The Gamma-Ray Imager/Polarimeter for Solar flares (GRIPS) instrument is a balloon-borne telescope designed to study solar- are particle acceleration and transport. We describe GRIPS's first Antarctic long-duration flight in January 2016 and report preliminary calibration and science results. Electron and ion dynamics, particle abundances and the ambient plasma conditions in solar flares can be understood by examining hard X-ray (HXR) and gamma-ray emission (20 keV to 10 MeV). Enhanced imaging, spectroscopy and polarimetry of are emissions in this energy range are needed to study particle acceleration and transport questions. The GRIPS instrument is specifically designed to answer questions including: What causes the spatial separation between energetic electrons producing hard X-rays and energetic ions producing gamma-ray lines? How anisotropic are the relativistic electrons, and why can they dominate in the corona? How do the compositions of accelerated and ambient material vary with space and time, and why? GRIPS's key technological improvements over the current solar state of the art at HXR/gamma-ray energies, the Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI), include 3D position-sensitive germanium detectors (3D-GeDs) and a single-grid modulation collimator, the multi-pitch rotating modulator (MPRM). The 3D-GeDs have spectral FWHM resolution of a few hundred keV and spatial resolution <1 mm3. For photons that Compton scatter, usually > 150 keV, the energy deposition sites can be tracked, providing polarization measurements as well as enhanced background reduction through Compton imaging. Each of GRIPS's detectors has 298 electrode strips read out with ASIC/FPGA electronics. In GRIPS's energy range, indirect imaging methods provide higher resolution than focusing optics or Compton imaging techniques. The MPRM gridimaging system has a single-grid design which provides twice the throughput of a bi-grid imaging system like RHESSI. The grid is composed of 2.5 cm deep tungsten-copper slats, and quasi-continuous FWHM angular coverage from 12.5-162 arcsecs are achieved by varying the slit pitch between 1-13 mm. This angular resolution is capable of imaging the separate magnetic loop footpoint emissions in a variety of are sizes. In comparison, RHESSI's 35-arcsec resolution at similar energies makes the footpoints resolvable in only the largest ares.

Imaging the 3D flow around swimming Chlamydomonas reinhardtii using digital inline holographic microscopy

NASA Astrophysics Data System (ADS)

Welch, Kyle; Kumar, Santosh; Hong, Jiarong; Cheng, Xiang

2017-11-01

Understanding the 3D flow induced by microswimmers is paramount to revealing how they interact with each other and their environment. While many studies have measured 2D projections of flow fields around single microorganisms, reliable 3D measurement remains elusive due to the difficulty in imaging fast 3D fluid flows at submicron spatial and millisecond temporal scales. Here, we present a precision measurement of the 3D flow field induced by motile planktonic algae cells, Chlamydomonas reinhardtii. We manually capture and hold stationary a single alga using a micropipette, while still allowing it to beat its flagella in the breastroke pattern characteristic to C. reinhardtii. The 3D flow field around the alga is then tracked by employing fast holographic imaging on 1 um tracer particles, which leads to a spatial resolution of 100 nm along the optical axis and 40 nm in the imaging plane normal to the optical axis. We image the flow around a single alga continuously through thousands of flagellar beat cycles and aggregate that data into a complete 3D flow field. Our study demonstrates the power of holography in imaging fast complex microscopic flow structures and provides crucial information for understanding the detailed locomotion of swimming microorganisms.

3D Data Mapping and Real-Time Experiment Control and Visualization in Brain Slices.

PubMed

Navarro, Marco A; Hibbard, Jaime V K; Miller, Michael E; Nivin, Tyler W; Milescu, Lorin S

2015-10-20

Here, we propose two basic concepts that can streamline electrophysiology and imaging experiments in brain slices and enhance data collection and analysis. The first idea is to interface the experiment with a software environment that provides a 3D scene viewer in which the experimental rig, the brain slice, and the recorded data are represented to scale. Within the 3D scene viewer, the user can visualize a live image of the sample and 3D renderings of the recording electrodes with real-time position feedback. Furthermore, the user can control the instruments and visualize their status in real time. The second idea is to integrate multiple types of experimental data into a spatial and temporal map of the brain slice. These data may include low-magnification maps of the entire brain slice, for spatial context, or any other type of high-resolution structural and functional image, together with time-resolved electrical and optical signals. The entire data collection can be visualized within the 3D scene viewer. These concepts can be applied to any other type of experiment in which high-resolution data are recorded within a larger sample at different spatial and temporal coordinates. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Quantitative 3D investigation of Neuronal network in mouse spinal cord model

NASA Astrophysics Data System (ADS)

Bukreeva, I.; Campi, G.; Fratini, M.; Spanò, R.; Bucci, D.; Battaglia, G.; Giove, F.; Bravin, A.; Uccelli, A.; Venturi, C.; Mastrogiacomo, M.; Cedola, A.

2017-01-01

The investigation of the neuronal network in mouse spinal cord models represents the basis for the research on neurodegenerative diseases. In this framework, the quantitative analysis of the single elements in different districts is a crucial task. However, conventional 3D imaging techniques do not have enough spatial resolution and contrast to allow for a quantitative investigation of the neuronal network. Exploiting the high coherence and the high flux of synchrotron sources, X-ray Phase-Contrast multiscale-Tomography allows for the 3D investigation of the neuronal microanatomy without any aggressive sample preparation or sectioning. We investigated healthy-mouse neuronal architecture by imaging the 3D distribution of the neuronal-network with a spatial resolution of 640 nm. The high quality of the obtained images enables a quantitative study of the neuronal structure on a subject-by-subject basis. We developed and applied a spatial statistical analysis on the motor neurons to obtain quantitative information on their 3D arrangement in the healthy-mice spinal cord. Then, we compared the obtained results with a mouse model of multiple sclerosis. Our approach paves the way to the creation of a “database” for the characterization of the neuronal network main features for a comparative investigation of neurodegenerative diseases and therapies.

X-ray Tomography and Chemical Imaging within Butterfly Wing Scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen Jianhua; Lee Yaochang; Tang, M.-T.

2007-01-19

The rainbow like color of butterfly wings is associated with the internal and surface structures of the wing scales. While the photonic structure of the scales is believed to diffract specific lights at different angle, there is no adequate probe directly answering the 3-D structures with sufficient spatial resolution. The NSRRC nano-transmission x-ray microscope (nTXM) with tens nanometers spatial resolution is able to image biological specimens without artifacts usually introduced in sophisticated sample staining processes. With the intrinsic deep penetration of x-rays, the nTXM is capable of nondestructively investigating the internal structures of fragile and soft samples. In this study,more » we imaged the structure of butterfly wing scales in 3-D view with 60 nm spatial resolution. In addition, synchrotron-radiation-based Fourier transform Infrared (FT-IR) microspectroscopy was employed to analyze the chemical components with spatial information of the butterfly wing scales. Based on the infrared spectral images, we suggest that the major components of scale structure were rich in protein and polysaccharide.« less

Strategies for High-Resolution 3-D Millimeter Wave Imaging.

DTIC Science & Technology

1987-02-01

Co-Investigator K.S. Lee - Graduate Student (50%) P. Frangos - Graduate Student (50%) Y. Shen - Graduate Student (50%) K. Schultz - Graduate...period of this report: * P. Frangos (Ph.D.) - "One-Dinensionl Inverse Scattering: Exact Methods and Applications", * C.L. Werner (Ph.D.) - ŗ-D

Multiscale study for stochastic characterization of shale samples

NASA Astrophysics Data System (ADS)

Tahmasebi, Pejman; Javadpour, Farzam; Sahimi, Muhammad; Piri, Mohammad

2016-03-01

Characterization of shale reservoirs, which are typically of low permeability, is very difficult because of the presence of multiscale structures. While three-dimensional (3D) imaging can be an ultimate solution for revealing important complexities of such reservoirs, acquiring such images is costly and time consuming. On the other hand, high-quality 2D images, which are widely available, also reveal useful information about shales' pore connectivity and size. Most of the current modeling methods that are based on 2D images use limited and insufficient extracted information. One remedy to the shortcoming is direct use of qualitative images, a concept that we introduce in this paper. We demonstrate that higher-order statistics (as opposed to the traditional two-point statistics, such as variograms) are necessary for developing an accurate model of shales, and describe an efficient method for using 2D images that is capable of utilizing qualitative and physical information within an image and generating stochastic realizations of shales. We then further refine the model by describing and utilizing several techniques, including an iterative framework, for removing some possible artifacts and better pattern reproduction. Next, we introduce a new histogram-matching algorithm that accounts for concealed nanostructures in shale samples. We also present two new multiresolution and multiscale approaches for dealing with distinct pore structures that are common in shale reservoirs. In the multiresolution method, the original high-quality image is upscaled in a pyramid-like manner in order to achieve more accurate global and long-range structures. The multiscale approach integrates two images, each containing diverse pore networks - the nano- and microscale pores - using a high-resolution image representing small-scale pores and, at the same time, reconstructing large pores using a low-quality image. Eventually, the results are integrated to generate a 3D model. The methods are tested on two shale samples for which full 3D samples are available. The quantitative accuracy of the models is demonstrated by computing their morphological and flow properties and comparing them with those of the actual 3D images. The success of the method hinges upon the use of very different low- and high-resolution images.

Volume-rendering on a 3D hyperwall: A molecular visualization platform for research, education and outreach.

PubMed

MacDougall, Preston J; Henze, Christopher E; Volkov, Anatoliy

2016-11-01

We present a unique platform for molecular visualization and design that uses novel subatomic feature detection software in tandem with 3D hyperwall visualization technology. We demonstrate the fleshing-out of pharmacophores in drug molecules, as well as reactive sites in catalysts, focusing on subatomic features. Topological analysis with picometer resolution, in conjunction with interactive volume-rendering of the Laplacian of the electronic charge density, leads to new insight into docking and catalysis. Visual data-mining is done efficiently and in parallel using a 4×4 3D hyperwall (a tiled array of 3D monitors driven independently by slave GPUs but displaying high-resolution, synchronized and functionally-related images). The visual texture of images for a wide variety of molecular systems are intuitive to experienced chemists but also appealing to neophytes, making the platform simultaneously useful as a tool for advanced research as well as for pedagogical and STEM education outreach purposes. Copyright © 2016. Published by Elsevier Inc.

Video-rate volumetric neuronal imaging using 3D targeted illumination.

PubMed

Xiao, Sheng; Tseng, Hua-An; Gritton, Howard; Han, Xue; Mertz, Jerome

2018-05-21

Fast volumetric microscopy is required to monitor large-scale neural ensembles with high spatio-temporal resolution. Widefield fluorescence microscopy can image large 2D fields of view at high resolution and speed while remaining simple and costeffective. A focal sweep add-on can further extend the capacity of widefield microscopy by enabling extended-depth-of-field (EDOF) imaging, but suffers from an inability to reject out-of-focus fluorescence background. Here, by using a digital micromirror device to target only in-focus sample features, we perform EDOF imaging with greatly enhanced contrast and signal-to-noise ratio, while reducing the light dosage delivered to the sample. Image quality is further improved by the application of a robust deconvolution algorithm. We demonstrate the advantages of our technique for in vivo calcium imaging in the mouse brain.

High-resolution light-sheet microscopy: a simulation of an optical illumination system for oil immersion

NASA Astrophysics Data System (ADS)

Lu, Xiang; Heintzmann, Rainer; Leischner, Ulrich

2015-09-01

Light sheet microscopy is a microscopy technique characterized by an illumination from the side, perpendicular to the direction of observation. While this is often used and easy to implement for imaging samples with water-immersion, the application in combination with oil-immersion is less often used and requires a specific optimization. In this paper we present our design of a light-sheet illumination optical system with a ~1μm illumination thickness, a long working distance through the immersion oil, and including a focusing system allowing for moving the focus-spot of the lightsheet laterally through the field of view. This optical design allows for the acquisition of fluorescence images in 3D with isotropic resolution of below 1 micrometer of whole-mount samples with a size of ~1mm diameter. This technique enables high-resolution insights in the 3D structure of biological samples, e.g. for research of insect anatomy or for imaging of biopsies in medical diagnostics.

The Gamma-Ray Imager/Polarimeter for Solar Flares (GRIPS)

NASA Technical Reports Server (NTRS)

Shih, Albert Y.; Lin, Robert P.; Hurford, Gordon J.; Duncan, Nicole A.; Saint-Hilaire, Pascal; Bain, Hazel M.; Boggs, Steven E.; Zoglauer, Andreas C.; Smith, David M.; Tajima, Hiroyasu;

Using Satellite Images for Wireless Network Planing in Baku City

NASA Astrophysics Data System (ADS)

Gojamanov, M.; Ismayilov, J.

2013-04-01

It is a well known fact that the Information-Telecommunication and Space research technologies are the fields getting much more benefits from the achievements of the scientific and technical progress. In many cases, these areas supporting each other have improved the conditions for their further development. For instance, the intensive development in the field of the mobile communication has caused the rapid progress of the Space research technologies and vice versa.Today it is impossible to solve one of the most important tasks of the mobile communication as Radio Frecance planning without the 2D and 3D digital maps. The compiling of such maps is much more efficient by means of the space images. Because the quality of the space images has been improved and developed, especially at the both spectral and spatial resolution points. It has been possible to to use 8 Band images with the spatial resolution of 50 sm. At present, in relation to the function 3G of mobile communications one of the main issues facing mobile operator companies is a high-precision 3D digital maps. It should be noted that the number of mobile phone users in the Republic of Azerbaijan went forward other Community of Independent States Countries. Of course, using of aerial images for 3D mapping would be optimal. However, depending on a number of technical and administrative problems aerial photography cannot be used. Therefore, the experience of many countries shows that it will be more effective to use the space images with the higher resolution for these issues. Concerning the fact that the mobile communication within the city of Baku has included 3G function there were ordered stereo images wih the spatial resolution of 50 cm for the 150 sq.km territory occupying the central part of the city in order to compile 3D digital maps. The images collected from the WorldView-2 satellite are 4-Band Bundle(Pan+MS1) stereo images. Such kind of imagery enable to automatically classificate some required clutter classes.Meanwhile, there were created 12 GPS points in the territory and there have been held some appropriate observations in these points for the geodesic reference of the space images in the territory. Moreover, it would like to mention that there have been constructed 37 permanently acting GPS stations in the territory of Azerbaijan at present. It significantly facilitates the process of the geodesic reference of the space images in order to accomplish such kind of mentioned projects. The processing of the collected space images was accomplished by means of Erdas LPS 10 program. In the first stage there was created the main component of the 3D maps- Digital Elevevation Model. In this model the following clutter classes are presented: Open; Open areas in urban; Airport, Sea, Inland water; Forest; Parks in urban; Semi Open Area; Open Wet Area; Urban/Urban Mean; Dense urban, Villages, Industrial/Commercial, Residential/Suburban; Dense residential/Suburban; Block of BUILDINGS; Dense Urban High; Buildings, Urban Mixed, Mixed dense urban

Advanced Multivariate Inversion Techniques for High Resolution 3D Geophysical Modeling

DTIC Science & Technology

2011-09-01

of seismic ambient noise – has been used to image crustal Vs variation with a lateral resolution upward of 100 km either on regional or on sub...to East Africa, we solve for velocity structure in an area with less lateral heterogeneity but great tectonic complexity. To increase the...demonstrate correlation with crustal geology. Figure 1 shows the 3D S-wave velocity model obtained from the joint inversion. The low-velocity anomaly

Contrast-enhanced MR Angiography of the Abdomen with Highly Accelerated Acquisition Techniques

PubMed Central

Mostardi, Petrice M.; Glockner, James F.; Young, Phillip M.

2011-01-01

Purpose: To demonstrate that highly accelerated (net acceleration factor [Rnet] ≥ 10) acquisition techniques can be used to generate three-dimensional (3D) subsecond timing images, as well as diagnostic-quality high-spatial-resolution contrast material–enhanced (CE) renal magnetic resonance (MR) angiograms with a single split dose of contrast material. Materials and Methods: All studies were approved by the institutional review board and were HIPAA compliant; written consent was obtained from all participants. Twenty-two studies were performed in 10 female volunteers (average age, 47 years; range, 27–62 years) and six patients with renovascular disease (three women; average age, 48 years; range, 37–68 years; three men; average age, 60 years; range, 50–67 years; composite average age, 54 years; range, 38–68 years). The two-part protocol consisted of a low-dose (2 mL contrast material) 3D timing image with approximate 1-second frame time, followed by a high-spatial-resolution (1.0–1.6-mm isotropic voxels) breath-hold 3D renal MR angiogram (18 mL) over the full abdominal field of view. Both acquisitions used two-dimensional (2D) sensitivity encoding acceleration factor (R) of eight and 2D homodyne (HD) acceleration (RHD) of 1.4–1.8 for Rnet = R · RHD of 10 or higher. Statistical analysis included determination of mean values and standard deviations of image quality scores performed by two experienced reviewers with use of eight evaluation criteria. Results: The 2-mL 3D time-resolved image successfully portrayed progressive arterial filling in all 22 studies and provided an anatomic overview of the vasculature. Successful timing was also demonstrated in that the renal MR angiogram showed adequate or excellent portrayal of the main renal arteries in 21 of 22 studies. Conclusion: Two-dimensional acceleration techniques with Rnet of 10 or higher can be used in CE MR angiography to acquire (a) a 3D image series with 1-second frame time, allowing accurate bolus timing, and (b) a high-spatial-resolution renal angiogram. © RSNA, 2011 Supplemental material: http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.11110242/-/DC1 PMID:21900616

Integrating light-sheet imaging with virtual reality to recapitulate developmental cardiac mechanics.

PubMed

Ding, Yichen; Abiri, Arash; Abiri, Parinaz; Li, Shuoran; Chang, Chih-Chiang; Baek, Kyung In; Hsu, Jeffrey J; Sideris, Elias; Li, Yilei; Lee, Juhyun; Segura, Tatiana; Nguyen, Thao P; Bui, Alexander; Sevag Packard, René R; Fei, Peng; Hsiai, Tzung K

2017-11-16

Currently, there is a limited ability to interactively study developmental cardiac mechanics and physiology. We therefore combined light-sheet fluorescence microscopy (LSFM) with virtual reality (VR) to provide a hybrid platform for 3D architecture and time-dependent cardiac contractile function characterization. By taking advantage of the rapid acquisition, high axial resolution, low phototoxicity, and high fidelity in 3D and 4D (3D spatial + 1D time or spectra), this VR-LSFM hybrid methodology enables interactive visualization and quantification otherwise not available by conventional methods, such as routine optical microscopes. We hereby demonstrate multiscale applicability of VR-LSFM to (a) interrogate skin fibroblasts interacting with a hyaluronic acid-based hydrogel, (b) navigate through the endocardial trabecular network during zebrafish development, and (c) localize gene therapy-mediated potassium channel expression in adult murine hearts. We further combined our batch intensity normalized segmentation algorithm with deformable image registration to interface a VR environment with imaging computation for the analysis of cardiac contraction. Thus, the VR-LSFM hybrid platform demonstrates an efficient and robust framework for creating a user-directed microenvironment in which we uncovered developmental cardiac mechanics and physiology with high spatiotemporal resolution.

Integrating light-sheet imaging with virtual reality to recapitulate developmental cardiac mechanics

PubMed Central

Ding, Yichen; Abiri, Arash; Abiri, Parinaz; Li, Shuoran; Chang, Chih-Chiang; Hsu, Jeffrey J.; Sideris, Elias; Li, Yilei; Lee, Juhyun; Segura, Tatiana; Nguyen, Thao P.; Bui, Alexander; Sevag Packard, René R.; Hsiai, Tzung K.

2017-01-01

Currently, there is a limited ability to interactively study developmental cardiac mechanics and physiology. We therefore combined light-sheet fluorescence microscopy (LSFM) with virtual reality (VR) to provide a hybrid platform for 3D architecture and time-dependent cardiac contractile function characterization. By taking advantage of the rapid acquisition, high axial resolution, low phototoxicity, and high fidelity in 3D and 4D (3D spatial + 1D time or spectra), this VR-LSFM hybrid methodology enables interactive visualization and quantification otherwise not available by conventional methods, such as routine optical microscopes. We hereby demonstrate multiscale applicability of VR-LSFM to (a) interrogate skin fibroblasts interacting with a hyaluronic acid–based hydrogel, (b) navigate through the endocardial trabecular network during zebrafish development, and (c) localize gene therapy-mediated potassium channel expression in adult murine hearts. We further combined our batch intensity normalized segmentation algorithm with deformable image registration to interface a VR environment with imaging computation for the analysis of cardiac contraction. Thus, the VR-LSFM hybrid platform demonstrates an efficient and robust framework for creating a user-directed microenvironment in which we uncovered developmental cardiac mechanics and physiology with high spatiotemporal resolution. PMID:29202458

Isotropic resolution diffusion tensor imaging of lumbosacral and sciatic nerves using a phase‐corrected diffusion‐prepared 3D turbo spin echo

PubMed Central

Van, Anh T.; Weidlich, Dominik; Kooijman, Hendrick; Hock, Andreas; Rummeny, Ernst J.; Gersing, Alexandra; Kirschke, Jan S.; Karampinos, Dimitrios C.

2018-01-01

Purpose To perform in vivo isotropic‐resolution diffusion tensor imaging (DTI) of lumbosacral and sciatic nerves with a phase‐navigated diffusion‐prepared (DP) 3D turbo spin echo (TSE) acquisition and modified reconstruction incorporating intershot phase‐error correction and to investigate the improvement on image quality and diffusion quantification with the proposed phase correction. Methods Phase‐navigated DP 3D TSE included magnitude stabilizers to minimize motion and eddy‐current effects on the signal magnitude. Phase navigation of motion‐induced phase errors was introduced before readout in 3D TSE. DTI of lower back nerves was performed in vivo using 3D TSE and single‐shot echo planar imaging (ss‐EPI) in 13 subjects. Diffusion data were phase‐corrected per k z plane with respect to T2‐weighted data. The effects of motion‐induced phase errors on DTI quantification was assessed for 3D TSE and compared with ss‐EPI. Results Non–phase‐corrected 3D TSE resulted in artifacts in diffusion‐weighted images and overestimated DTI parameters in the sciatic nerve (mean diffusivity [MD] = 2.06 ± 0.45). Phase correction of 3D TSE DTI data resulted in reductions in all DTI parameters (MD = 1.73 ± 0.26) of statistical significance (P ≤ 0.001) and in closer agreement with ss‐EPI DTI parameters (MD = 1.62 ± 0.21). Conclusion DP 3D TSE with phase correction allows distortion‐free isotropic diffusion imaging of lower back nerves with robustness to motion‐induced artifacts and DTI quantification errors. Magn Reson Med 80:609–618, 2018. © 2018 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. PMID:29380414

Lack of robustness of textural measures obtained from 3D brain tumor MRIs impose a need for standardization

PubMed Central

Pérez-Beteta, Julián; Martínez-González, Alicia; Martino, Juan; Velasquez, Carlos; Arana, Estanislao; Pérez-García, Víctor M.

2017-01-01

Purpose Textural measures have been widely explored as imaging biomarkers in cancer. However, their robustness under dynamic range and spatial resolution changes in brain 3D magnetic resonance images (MRI) has not been assessed. The aim of this work was to study potential variations of textural measures due to changes in MRI protocols. Materials and methods Twenty patients harboring glioblastoma with pretreatment 3D T1-weighted MRIs were included in the study. Four different spatial resolution combinations and three dynamic ranges were studied for each patient. Sixteen three-dimensional textural heterogeneity measures were computed for each patient and configuration including co-occurrence matrices (CM) features and run-length matrices (RLM) features. The coefficient of variation was used to assess the robustness of the measures in two series of experiments corresponding to (i) changing the dynamic range and (ii) changing the matrix size. Results No textural measures were robust under dynamic range changes. Entropy was the only textural feature robust under spatial resolution changes (coefficient of variation under 10% in all cases). Conclusion Textural measures of three-dimensional brain tumor images are not robust neither under dynamic range nor under matrix size changes. Standards should be harmonized to use textural features as imaging biomarkers in radiomic-based studies. The implications of this work go beyond the specific tumor type studied here and pose the need for standardization in textural feature calculation of oncological images. PMID:28586353

4D electron tomography.

PubMed

Kwon, Oh-Hoon; Zewail, Ahmed H

2010-06-25

Electron tomography provides three-dimensional (3D) imaging of noncrystalline and crystalline equilibrium structures, as well as elemental volume composition, of materials and biological specimens, including those of viruses and cells. We report the development of 4D electron tomography by integrating the fourth dimension (time resolution) with the 3D spatial resolution obtained from a complete tilt series of 2D projections of an object. The different time frames of tomograms constitute a movie of the object in motion, thus enabling studies of nonequilibrium structures and transient processes. The method was demonstrated using carbon nanotubes of a bracelet-like ring structure for which 4D tomograms display different modes of motion, such as breathing and wiggling, with resonance frequencies up to 30 megahertz. Applications can now make use of the full space-time range with the nanometer-femtosecond resolution of ultrafast electron tomography.

4D Electron Tomography

NASA Astrophysics Data System (ADS)

Kwon, Oh-Hoon; Zewail, Ahmed H.

2010-06-01

Electron tomography provides three-dimensional (3D) imaging of noncrystalline and crystalline equilibrium structures, as well as elemental volume composition, of materials and biological specimens, including those of viruses and cells. We report the development of 4D electron tomography by integrating the fourth dimension (time resolution) with the 3D spatial resolution obtained from a complete tilt series of 2D projections of an object. The different time frames of tomograms constitute a movie of the object in motion, thus enabling studies of nonequilibrium structures and transient processes. The method was demonstrated using carbon nanotubes of a bracelet-like ring structure for which 4D tomograms display different modes of motion, such as breathing and wiggling, with resonance frequencies up to 30 megahertz. Applications can now make use of the full space-time range with the nanometer-femtosecond resolution of ultrafast electron tomography.

Fast 3D registration of multimodality tibial images with significant structural mismatch

NASA Astrophysics Data System (ADS)

Rajapakse, C. S.; Wald, M. J.; Magland, J.; Zhang, X. H.; Liu, X. S.; Guo, X. E.; Wehrli, F. W.

2009-02-01

Recently, micro-magnetic resonance imaging (μMRI) in conjunction with micro-finite element analysis has shown great potential in estimating mechanical properties - stiffness and elastic moduli - of bone in patients at risk of osteoporosis. Due to limited spatial resolution and signal-to-noise ratio achievable in vivo, the validity of estimated properties is often established by comparison to those derived from high-resolution micro-CT (μCT) images of cadaveric specimens. For accurate comparison of mechanical parameters derived from μMR and μCT images, analyzed 3D volumes have to be closely matched. The alignment of the micro structure (and the cortex) is often hampered by the fundamental differences of μMR and μCT images and variations in marrow content and cortical bone thickness. Here we present an intensity cross-correlation based registration algorithm coupled with segmentation for registering 3D tibial specimen images acquired by μMRI and μCT in the context of finite-element modeling to assess the bone's mechanical constants. The algorithm first generates three translational and three rotational parameters required to align segmented μMR and CT images from sub regions with high micro-structural similarities. These transformation parameters are then used to register the grayscale μMR and μCT images, which include both the cortex and trabecular bone. The intensity crosscorrelation maximization based registration algorithm described here is suitable for 3D rigid-body image registration applications where through-plane rotations are known to be relatively small. The close alignment of the resulting images is demonstrated quantitatively based on a voxel-overlap measure and qualitatively using visual inspection of the micro structure.

SU-E-J-229: Magnetic Resonance Imaging of Small Fiducial Markers for Proton Beam Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Y; James, J; Panda, A

2015-06-15

Purpose: For proton beam therapy, small fiducial markers are preferred for patient alignment due to less interference with the proton beam. Visualizing small fiducial markers can be challenging in MRI. This study intends to investigate MRI imaging protocols for better visualization of small fiducial markers. Methods: Two carbon and two coil-shaped gold markers were placed into a gel phantom. Both carbon markers had a diameter of 1mm and a length of 3mm. Both gold markers had a length of 5mm. One gold marker had a diameter of 0.5mm and the other had a diameter of 0.75mm. T1 VIBE, T2 SPACE,more » TrueFISP and susceptibility weighted (SW) images were acquired. To improve marker contrast, high spatial resolution was used to reduce partial volume effect. Slice thickness was 1.5mm for all four sequences and in-plane resolution was 0.6mm for TrueFISP, 0.7mm for T1 VIBE, and 0.8mm for T2 SPACE and SW. For comparison purpose, a 3D T1 VIBE image set at 3mm slice thickness and 1.2mm in-plane resolution was also acquired. Results: All markers were visible in all high-resolution image sets. In each image set, marker-induced signal void was the smallest (in diameter) for carbon markers, followed by the 0.5mm gold marker and the largest for the 0.75mm gold marker. The SW images had the largest marker-induced signal void. However, those might be confused by susceptibility-gradient-induced signal voids. T1 VIBE had good visualization of markers with nicely defined edges. T2 SPACE had reasonable visualization of markers but edges were slightly blurred. TrueFISP had good visualization of markers only if they were not masked by banding artifacts. As a comparison, all markers were hardly visible in the standard resolution T1 VIBE images. Conclusion: 3D high-resolution T1 VIBE and SW have great potential in providing good visualization of small fiducial markers for proton beam therapy.« less

Dynamic three-dimensional model of the coronary circulation

NASA Astrophysics Data System (ADS)

Lehmann, Glen; Gobbi, David G.; Dick, Alexander J.; Starreveld, Yves P.; Quantz, M.; Holdsworth, David W.; Drangova, Maria

2001-05-01

A realistic numerical three-dimensional (3D) model of the dynamics of human coronary arteries has been developed. High- resolution 3D images of the coronary arteries of an excised human heart were obtained using a C-arm based computed tomography (CT) system. Cine bi-plane coronary angiograms were then acquired from a patient with similar coronary anatomy. These angiograms were used to determine the vessel motion, which was applied to the static 3D coronary tree. Corresponding arterial bifurcations were identified in the 3D CT image and in the 2D angiograms. The 3D positions of the angiographic landmarks, which were known throughout the cardiac cycle, were used to warp the 3D image via a non-linear thin-plate spline algorithm. The result was a set or 30 dynamic volumetric images sampling a complete cardiac cycle. To the best of our knowledge, the model presented here is the first dynamic 3D model that provides a true representation of both the geometry and motion of a human coronary artery tree. In the future, similar models can be generated to represent different coronary anatomy and motion. Such models are expected to become an invaluable tool during the development of dynamic imaging techniques such as MRI, multi-slice CT and 3D angiography.

Ultrahigh speed endoscopic optical coherence tomography for gastroenterology.

PubMed

Tsai, Tsung-Han; Lee, Hsiang-Chieh; Ahsen, Osman O; Liang, Kaicheng; Giacomelli, Michael G; Potsaid, Benjamin M; Tao, Yuankai K; Jayaraman, Vijaysekhar; Figueiredo, Marisa; Huang, Qin; Cable, Alex E; Fujimoto, James; Mashimo, Hiroshi

2014-12-01

We describe an ultrahigh speed endoscopic swept source optical coherence tomography (OCT) system for clinical gastroenterology using a vertical-cavity surface-emitting laser (VCSEL) and micromotor imaging catheter. The system had a 600 kHz axial scan rate and 8 µm axial resolution in tissue. Imaging was performed with a 3.2 mm diameter imaging catheter at 400 frames per second with a 12 µm spot size. Three-dimensional OCT (3D-OCT) imaging was performed in patients with a cross section of pathologies undergoing upper and lower endoscopy. The use of distally actuated imaging catheters enabled OCT imaging with more flexibility, such as volumetric imaging in the small intestine and the assessment of hiatal hernia using retroflex imaging. The high rotational scanning stability of the micromotor enabled 3D volumetric imaging with micron scale volumetric accuracy for both en face OCT and cross-sectional imaging, as well as OCT angiography (OCTA) for 3D visualization of subsurface microvasculature. The ability to perform both structural and functional 3D OCT imaging in the GI tract with microscopic accuracy should enable a wide range of studies and enhance the sensitivity and specificity of OCT for detecting pathology.

Ultrahigh speed endoscopic optical coherence tomography for gastroenterology

PubMed Central

Tsai, Tsung-Han; Lee, Hsiang-Chieh; Ahsen, Osman O.; Liang, Kaicheng; Giacomelli, Michael G.; Potsaid, Benjamin M.; Tao, Yuankai K.; Jayaraman, Vijaysekhar; Figueiredo, Marisa; Huang, Qin; Cable, Alex E.; Fujimoto, James; Mashimo, Hiroshi

2014-01-01

We describe an ultrahigh speed endoscopic swept source optical coherence tomography (OCT) system for clinical gastroenterology using a vertical-cavity surface-emitting laser (VCSEL) and micromotor imaging catheter. The system had a 600 kHz axial scan rate and 8 µm axial resolution in tissue. Imaging was performed with a 3.2 mm diameter imaging catheter at 400 frames per second with a 12 µm spot size. Three-dimensional OCT (3D-OCT) imaging was performed in patients with a cross section of pathologies undergoing upper and lower endoscopy. The use of distally actuated imaging catheters enabled OCT imaging with more flexibility, such as volumetric imaging in the small intestine and the assessment of hiatal hernia using retroflex imaging. The high rotational scanning stability of the micromotor enabled 3D volumetric imaging with micron scale volumetric accuracy for both en face OCT and cross-sectional imaging, as well as OCT angiography (OCTA) for 3D visualization of subsurface microvasculature. The ability to perform both structural and functional 3D OCT imaging in the GI tract with microscopic accuracy should enable a wide range of studies and enhance the sensitivity and specificity of OCT for detecting pathology. PMID:25574446

Using Digital Earth to create online scientific reality tourist guides to tourist attractions in Taiwan, China

NASA Astrophysics Data System (ADS)

Ding, Yea-Chung

2010-11-01

In recent years national parks worldwide have introduced online virtual tourism, through which potential visitors can search for tourist information. Most virtual tourism websites are a simulation of an existing location, usually composed of panoramic images, a sequence of hyperlinked still or video images, and/or virtual models of the actual location. As opposed to actual tourism, a virtual tour is typically accessed on a personal computer or an interactive kiosk. Using modern Digital Earth techniques such as high resolution satellite images, precise GPS coordinates and powerful 3D WebGIS, however, it's possible to create more realistic scenic models to present natural terrain and man-made constructions in greater detail. This article explains how to create an online scientific reality tourist guide for the Jinguashi Gold Ecological Park at Jinguashi in northern Taiwan, China. This project uses high-resolution Formosat 2 satellite images and digital aerial images in conjunction with DTM to create a highly realistic simulation of terrain, with the addition of 3DMAX to add man-made constructions and vegetation. Using this 3D Geodatabase model in conjunction with INET 3D WebGIS software, we have found Digital Earth concept can greatly improve and expand the presentation of traditional online virtual tours on the websites.

Cyclops: single-pixel imaging lidar system based on compressive sensing

NASA Astrophysics Data System (ADS)

Magalhães, F.; Correia, M. V.; Farahi, F.; Pereira do Carmo, J.; Araújo, F. M.

2017-11-01

Mars and the Moon are envisaged as major destinations of future space exploration missions in the upcoming decades. Imaging LIDARs are seen as a key enabling technology in the support of autonomous guidance, navigation and control operations, as they can provide very accurate, wide range, high-resolution distance measurements as required for the exploration missions. Imaging LIDARs can be used at critical stages of these exploration missions, such as descent and selection of safe landing sites, rendezvous and docking manoeuvres, or robotic surface navigation and exploration. Despite these devices have been commercially available and used for long in diverse metrology and ranging applications, their size, mass and power consumption are still far from being suitable and attractive for space exploratory missions. Here, we describe a compact Single-Pixel Imaging LIDAR System that is based on a compressive sensing technique. The application of the compressive codes to a DMD array enables compression of the spatial information, while the collection of timing histograms correlated to the pulsed laser source ensures image reconstruction at the ranged distances. Single-pixel cameras have been compared with raster scanning and array based counterparts in terms of noise performance, and proved to be superior. Since a single photodetector is used, a better SNR and higher reliability is expected in contrast with systems using large format photodetector arrays. Furthermore, the event of failure of one or more micromirror elements in the DMD does not prevent full reconstruction of the images. This brings additional robustness to the proposed 3D imaging LIDAR. The prototype that was implemented has three modes of operation. Range Finder: outputs the average distance between the system and the area of the target under illumination; Attitude Meter: provides the slope of the target surface based on distance measurements in three areas of the target; 3D Imager: produces 3D ranged images of the target surface. The implemented prototype demonstrated a frame rate of 30 mHz for 16x16 pixels images, a transversal (xy) resolution of 2 cm at 10 m for images with 64x64 pixels and the range (z) resolution proved to be better than 1 cm. The experimental results obtained for the "3D imaging" mode of operation demonstrated that it was possible to reconstruct spherical smooth surfaces. The proposed solution demonstrates a great potential for: miniaturization; increase spatial resolution without using large format detector arrays; eliminate the need for scanning mechanisms; implementing simple and robust configurations.

Magnetic resonance imaging of third molars: developing a protocol suitable for forensic age estimation.

PubMed

De Tobel, Jannick; Hillewig, Elke; Bogaert, Stephanie; Deblaere, Karel; Verstraete, Koenraad

2017-03-01

Established dental age estimation methods in sub-adults study the development of third molar root apices on radiographs. In living individuals, however, avoiding ionising radiation is expedient. Studying dental development with magnetic resonance imaging complies with this requirement, adding the advantage of imaging in three dimensions. To elaborate the development of an MRI protocol to visualise all third molars for forensic age estimation, with particular attention to the development of the root apex. Ex vivo scans of porcine jaws and in vivo scans of 10 volunteers aged 17-25 years were performed to select adequate sequences. Studied parameters were T1 vs T2 weighting, ultrashort echo time (UTE), fat suppression, in plane resolution, slice thickness, 3D imaging, signal-to-noise ratio, and acquisition time. A bilateral four-channel flexible surface coil was used. Two observers evaluated the suitability of the images. T2-weighted images were preferred to T1-weighted images. To clearly distinguish root apices in (almost) fully developed third molars an in plane resolution of 0.33 × 0.33 mm 2 was deemed necessary. Taking acquisition time limits into account, only a T2 FSE sequence with slice thickness of 2 mm generated images with sufficient resolution and contrast. UTE, thinner slice T2 FSE and T2 3D FSE sequences could not generate the desired resolution within 6.5 minutes. Three Tesla MRI of the third molars is a feasible technique for forensic age estimation, in which a T2 FSE sequence can provide the desired in plane resolution within a clinically acceptable acquisition time.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

NASA Astrophysics Data System (ADS)

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing; He, You; Zhou, Guangzhao; Sun, Zhibin; Zhang, Jianhua; Huang, Qingjie; Xiao, Tiqiao; Jiang, Huaidong

2016-03-01

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique over conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ˜1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique overmore » conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ∼1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.« less

3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution.

PubMed

Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F

2016-02-01

The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution. Graphical Abstract ᅟ.

3D ToF-SIMS Analysis of Peptide Incorporation into MALDI Matrix Crystals with Sub-micrometer Resolution

NASA Astrophysics Data System (ADS)

Körsgen, Martin; Pelster, Andreas; Dreisewerd, Klaus; Arlinghaus, Heinrich F.

2016-02-01

The analytical sensitivity in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is largely affected by the specific analyte-matrix interaction, in particular by the possible incorporation of the analytes into crystalline MALDI matrices. Here we used time-of-flight secondary ion mass spectrometry (ToF-SIMS) to visualize the incorporation of three peptides with different hydrophobicities, bradykinin, Substance P, and vasopressin, into two classic MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (HCCA). For depth profiling, an Ar cluster ion beam was used to gradually sputter through the matrix crystals without causing significant degradation of matrix or biomolecules. A pulsed Bi3 ion cluster beam was used to image the lateral analyte distribution in the center of the sputter crater. Using this dual beam technique, the 3D distribution of the analytes and spatial segregation effects within the matrix crystals were imaged with sub-μm resolution. The technique could in the future enable matrix-enhanced (ME)-ToF-SIMS imaging of peptides in tissue slices at ultra-high resolution.