Stereo imaging with spaceborne radars

NASA Technical Reports Server (NTRS)

Leberl, F.; Kobrick, M.

1983-01-01

Stereo viewing is a valuable tool in photointerpretation and is used for the quantitative reconstruction of the three dimensional shape of a topographical surface. Stereo viewing refers to a visual perception of space by presenting an overlapping image pair to an observer so that a three dimensional model is formed in the brain. Some of the observer's function is performed by machine correlation of the overlapping images - so called automated stereo correlation. The direct perception of space with two eyes is often called natural binocular vision; techniques of generating three dimensional models of the surface from two sets of monocular image measurements is the topic of stereology.

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.

Three-dimensional characterization of pigment dispersion in dried paint films using focused ion beam-scanning electron microscopy.

PubMed

Lin, Jui-Ching; Heeschen, William; Reffner, John; Hook, John

2012-04-01

The combination of integrated focused ion beam-scanning electron microscope (FIB-SEM) serial sectioning and imaging techniques with image analysis provided quantitative characterization of three-dimensional (3D) pigment dispersion in dried paint films. The focused ion beam in a FIB-SEM dual beam system enables great control in slicing paints, and the sectioning process can be synchronized with SEM imaging providing high quality serial cross-section images for 3D reconstruction. Application of Euclidean distance map and ultimate eroded points image analysis methods can provide quantitative characterization of 3D particle distribution. It is concluded that 3D measurement of binder distribution in paints is effective to characterize the order of pigment dispersion in dried paint films.

An overview of contemporary nuclear cardiology.

PubMed

Lewin, Howard C; Sciammarella, Maria G; Watters, Thomas A; Alexander, Herbert G

2004-01-01

Myocardial perfusion single photon emission computed tomography (SPECT) is a widely utilized noninvasive imaging modality for the diagnosis, prognosis, and risk stratification of coronary artery disease. It is clearly superior to the traditional planar technique in terms of imaging contrast and consequent diagnostic and prognostic yield. The strength of SPECT images is largely derived from the three-dimensional, volumetric nature of its image. Thus, this modality permits three-dimensional assessment and quantitation of the perfused myocardium and functional assessment through electrocardiographic gating of the perfusion images.

Label-free imaging of the dynamics of cell-to-cell string-like structure bridging in the free-space by low-coherent quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2013-03-01

We succeeded in utilizing our low-coherent quantitative phase microscopy (LC-QPM) to achieve label-free and three-dimensional imaging of string-like structures bridging the free-space between live cells. In past studies, three dimensional morphology of the string-like structures between cells had been investigated by electron microscopies and fluorescence microscopies and these structures were called "membrane nanotubes" or "tunneling nanotubes." However, use of electron microscopy inevitably kills these cells and fluorescence microscopy is itself a potentially invasive method. To achieve noninvasive imaging of live cells, we applied our LC-QPM which is a reflection-type, phase resolved and full-field interference microscope employing a low-coherent light source. LC-QPM is able to visualize the three-dimensional morphology of live cells without labeling by means of low-coherence interferometry. The lateral (diffraction limit) and longitudinal (coherence-length) spatial resolution of LC-QPM were respectively 0.49 and 0.93 micrometers and the repeatability of the phase measurement was 0.02 radians (1.0 nm). We successfully obtained three-dimensional morphology of live cultured epithelial cells (cell type: HeLa, derived from cervix cancer) and were able to clearly observe the individual string-like structures interconnecting the cells. When we performed volumetric imaging, a 80 micrometer by 60 micrometer by 6.5 micrometer volume was scanned every 5.67 seconds and 70 frames of a three-dimensional movie were recorded for a duration of 397 seconds. Moreover, the optical phase images gave us detailed information about the three-dimensional morphology of the string-like structure at sub-wavelength resolution. We believe that our LC-QPM will be a useful tool for the study of three-dimensional morphology of live cells.

Cardiovascular Imaging and Image Processing: Theory and Practice - 1975

NASA Technical Reports Server (NTRS)

Harrison, Donald C. (Editor); Sandler, Harold (Editor); Miller, Harry A. (Editor); Hood, Manley J. (Editor); Purser, Paul E. (Editor); Schmidt, Gene (Editor)

1975-01-01

Ultrasonography was examined in regard to the developmental highlights and present applicatons of cardiac ultrasound. Doppler ultrasonic techniques and the technology of miniature acoustic element arrays were reported. X-ray angiography was discussed with special considerations on quantitative three dimensional dynamic imaging of structure and function of the cardiopulmonary and circulatory systems in all regions of the body. Nuclear cardiography and scintigraphy, three--dimensional imaging of the myocardium with isotopes, and the commercialization of the echocardioscope were studied.

Three-dimensional label-free imaging and quantification of lipid droplets in live hepatocytes

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Lee, Seoeun; Yoon, Jonghee; Heo, Jihan; Choi, Chulhee; Park, Yongkeun

2016-11-01

Lipid droplets (LDs) are subcellular organelles with important roles in lipid storage and metabolism and involved in various diseases including cancer, obesity, and diabetes. Conventional methods, however, have limited ability to provide quantitative information on individual LDs and have limited capability for three-dimensional (3-D) imaging of LDs in live cells especially for fast acquisition of 3-D dynamics. Here, we present an optical method based on 3-D quantitative phase imaging to measure the 3-D structural distribution and biochemical parameters (concentration and dry mass) of individual LDs in live cells without using exogenous labelling agents. The biochemical change of LDs under oleic acid treatment was quantitatively investigated, and 4-D tracking of the fast dynamics of LDs revealed the intracellular transport of LDs in live cells.

Quantitative three-dimensional photoacoustic tomography of the finger joints: an in vivo study

NASA Astrophysics Data System (ADS)

Sun, Yao; Sobel, Eric; Jiang, Huabei

2009-11-01

We present for the first time in vivo full three-dimensional (3-D) photoacoustic tomography (PAT) of the distal interphalangeal joint in a human subject. Both absorbed energy density and absorption coefficient images of the joint are quantitatively obtained using our finite-element-based photoacoustic image reconstruction algorithm coupled with the photon diffusion equation. The results show that major anatomical features in the joint along with the side arteries can be imaged with a 1-MHz transducer in a spherical scanning geometry. In addition, the cartilages associated with the joint can be quantitatively differentiated from the phalanx. This in vivo study suggests that the 3-D PAT method described has the potential to be used for early diagnosis of joint diseases such as osteoarthritis and rheumatoid arthritis.

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

PubMed

Knowles, David W; Biggin, Mark D

2013-01-01

Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy-based approaches to establish permanent, quantitative datasets-atlases-that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. Copyright © 2013 Wiley Periodicals, Inc.

Quantitative volumetric Raman imaging of three dimensional cell cultures

NASA Astrophysics Data System (ADS)

Kallepitis, Charalambos; Bergholt, Mads S.; Mazo, Manuel M.; Leonardo, Vincent; Skaalure, Stacey C.; Maynard, Stephanie A.; Stevens, Molly M.

2017-03-01

The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.

A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

PubMed

Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

2013-01-21

A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

Three-dimensional morphological imaging of human induced pluripotent stem cells by using low-coherence quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Kakuno, Yumi; Goto, Kentaro; Fukami, Tadashi; Sugiyama, Norikazu; Iwai, Hidenao; Mizuguchi, Yoshinori; Yamashita, Yutaka

2014-03-01

There is an increasing need for non-invasive imaging techniques in the field of stem cell research. Label-free techniques are the best choice for assessment of stem cells because the cells remain intact after imaging and can be used for further studies such as differentiation induction. To develop a high-resolution label-free imaging system, we have been working on a low-coherence quantitative phase microscope (LC-QPM). LC-QPM is a Linnik-type interference microscope equipped with nanometer-resolution optical-path-length control and capable of obtaining three-dimensional volumetric images. The lateral and vertical resolutions of our system are respectively 0.5 and 0.93 μm and this performance allows capturing sub-cellular morphological features of live cells without labeling. Utilizing LC-QPM, we reported on three-dimensional imaging of membrane fluctuations, dynamics of filopodia, and motions of intracellular organelles. In this presentation, we report three-dimensional morphological imaging of human induced pluripotent stem cells (hiPS cells). Two groups of monolayer hiPS cell cultures were prepared so that one group was cultured in a suitable culture medium that kept the cells undifferentiated, and the other group was cultured in a medium supplemented with retinoic acid, which forces the stem cells to differentiate. The volumetric images of the 2 groups show distinctive differences, especially in surface roughness. We believe that our LC-QPM system will prove useful in assessing many other stem cell conditions.

Dependence of quantitative accuracy of CT perfusion imaging on system parameters

NASA Astrophysics Data System (ADS)

Li, Ke; Chen, Guang-Hong

2017-03-01

Deconvolution is a popular method to calculate parametric perfusion parameters from four dimensional CT perfusion (CTP) source images. During the deconvolution process, the four dimensional space is squeezed into three-dimensional space by removing the temporal dimension, and a prior knowledge is often used to suppress noise associated with the process. These additional complexities confound the understanding about deconvolution-based CTP imaging system and how its quantitative accuracy depends on parameters and sub-operations involved in the image formation process. Meanwhile, there has been a strong clinical need in answering this question, as physicians often rely heavily on the quantitative values of perfusion parameters to make diagnostic decisions, particularly during an emergent clinical situation (e.g. diagnosis of acute ischemic stroke). The purpose of this work was to develop a theoretical framework that quantitatively relates the quantification accuracy of parametric perfusion parameters with CTP acquisition and post-processing parameters. This goal was achieved with the help of a cascaded systems analysis for deconvolution-based CTP imaging systems. Based on the cascaded systems analysis, the quantitative relationship between regularization strength, source image noise, arterial input function, and the quantification accuracy of perfusion parameters was established. The theory could potentially be used to guide developments of CTP imaging technology for better quantification accuracy and lower radiation dose.

Computer system for definition of the quantitative geometry of musculature from CT images.

PubMed

Daniel, Matej; Iglic, Ales; Kralj-Iglic, Veronika; Konvicková, Svatava

2005-02-01

The computer system for quantitative determination of musculoskeletal geometry from computer tomography (CT) images has been developed. The computer system processes series of CT images to obtain three-dimensional (3D) model of bony structures where the effective muscle fibres can be interactively defined. Presented computer system has flexible modular structure and is suitable also for educational purposes.

A method for three-dimensional quantitative observation of the microstructure of biological samples

NASA Astrophysics Data System (ADS)

Wang, Pengfei; Chen, Dieyan; Ma, Wanyun; Wu, Hongxin; Ji, Liang; Sun, Jialin; Lv, Danyu; Zhang, Lu; Li, Ying; Tian, Ning; Zheng, Jinggao; Zhao, Fengying

2009-07-01

Contemporary biology has developed into the era of cell biology and molecular biology, and people try to study the mechanism of all kinds of biological phenomena at the microcosmic level now. Accurate description of the microstructure of biological samples is exigent need from many biomedical experiments. This paper introduces a method for 3-dimensional quantitative observation on the microstructure of vital biological samples based on two photon laser scanning microscopy (TPLSM). TPLSM is a novel kind of fluorescence microscopy, which has excellence in its low optical damage, high resolution, deep penetration depth and suitability for 3-dimensional (3D) imaging. Fluorescent stained samples were observed by TPLSM, and afterward the original shapes of them were obtained through 3D image reconstruction. The spatial distribution of all objects in samples as well as their volumes could be derived by image segmentation and mathematic calculation. Thus the 3-dimensionally and quantitatively depicted microstructure of the samples was finally derived. We applied this method to quantitative analysis of the spatial distribution of chromosomes in meiotic mouse oocytes at metaphase, and wonderful results came out last.

Comparison of three-dimensional analysis and stereological techniques for quantifying lithium-ion battery electrode microstructures.

PubMed

Taiwo, Oluwadamilola O; Finegan, Donal P; Eastwood, David S; Fife, Julie L; Brown, Leon D; Darr, Jawwad A; Lee, Peter D; Brett, Daniel J L; Shearing, Paul R

2016-09-01

Lithium-ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium-ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3-D imaging techniques, quantitative assessment of 3-D microstructures from 2-D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two-dimensional (2-D) data sets. In this study, stereological prediction and three-dimensional (3-D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium-ion battery electrodes were imaged using synchrotron-based X-ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2-D image sections generated from tomographic imaging, whereas direct 3-D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2-D image sections is bound to be associated with ambiguity and that volume-based 3-D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially-dependent parameters, such as tortuosity and pore-phase connectivity. © 2016 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.

Wave field restoration using three-dimensional Fourier filtering method.

PubMed

Kawasaki, T; Takai, Y; Ikuta, T; Shimizu, R

2001-11-01

A wave field restoration method in transmission electron microscopy (TEM) was mathematically derived based on a three-dimensional (3D) image formation theory. Wave field restoration using this method together with spherical aberration correction was experimentally confirmed in through-focus images of amorphous tungsten thin film, and the resolution of the reconstructed phase image was successfully improved from the Scherzer resolution limit to the information limit. In an application of this method to a crystalline sample, the surface structure of Au(110) was observed in a profile-imaging mode. The processed phase image showed quantitatively the atomic relaxation of the topmost layer.

High-resolution ab initio three-dimensional x-ray diffraction microscopy

DOE PAGES

Chapman, Henry N.; Barty, Anton; Marchesini, Stefano; ...

2006-01-01

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatialmore » resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.« less

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.

Quantitative geomorphologic studies from spaceborne platforms

NASA Technical Reports Server (NTRS)

Williams, R. S., Jr.

1985-01-01

Although LANDSAT images of our planet represent a quantum improvement in the availability of a global image-data set for independent or comparative regional geomorphic studies of landforms, such images have several limitations which restrict their suitability for quantitative geomorphic investigations. The three most serious deficiencies are: (1) photogrammetric inaccuracies, (2) two-dimensional nature of the data, and (3) spatial resolution. These deficiencies are discussed, as well as the use of stereoscopic images and laser altimeter data.

Three-dimensional real-time imaging of bi-phasic flow through porous media

NASA Astrophysics Data System (ADS)

Sharma, Prerna; Aswathi, P.; Sane, Anit; Ghosh, Shankar; Bhattacharya, S.

2011-11-01

We present a scanning laser-sheet video imaging technique to image bi-phasic flow in three-dimensional porous media in real time with pore-scale spatial resolution, i.e., 35 μm and 500 μm for directions parallel and perpendicular to the flow, respectively. The technique is illustrated for the case of viscous fingering. Using suitable image processing protocols, both the morphology and the movement of the two-fluid interface, were quantitatively estimated. Furthermore, a macroscopic parameter such as the displacement efficiency obtained from a microscopic (pore-scale) analysis demonstrates the versatility and usefulness of the method.

High-resolution three-dimensional partially coherent diffraction imaging.

PubMed

Clark, J N; Huang, X; Harder, R; Robinson, I K

2012-01-01

The wave properties of light, particularly its coherence, are responsible for interference effects, which can be exploited in powerful imaging applications. Coherent diffractive imaging relies heavily on coherence and has recently experienced rapid growth. Coherent diffractive imaging recovers an object from its diffraction pattern by computational phasing with the potential of wavelength-limited resolution. Diminished coherence results in reconstructions that suffer from artefacts or fail completely. Here we demonstrate ab initio phasing of partially coherent diffraction patterns in three dimensions, while simultaneously determining the coherence properties of the illuminating wavefield. Both the dramatic improvements in image interpretability and the three-dimensional evaluation of the coherence will have broad implications for quantitative imaging of nanostructures and wavefield characterization with X-rays and electrons.

Three-dimensional reconstruction of TMJ MR images: a technical note and case report.

PubMed

Kitai, Noriyuki; Eriksson, Lars; Kreiborg, Sven; Wagner, Aase; Takada, Kenji

2004-01-01

MR images of the temporomandibular joint at occlusion and at various stages of mouth opening were registered and reconstructed three-dimensionally before and after a modified condylotomy in a patient with painful disk displacement. Following the condylotomy, the condyle/disk relationship had become normalized in all three planes of space at closed mouth and during mouth opening. The post-operative distances of the condylar and diskal paths had increased when compared with the preoperative distances. The three-dimensional visualizing method may, besides providing diagnostic advantages, be a valuable tool for qualitative and quantitative documentation of the efficiency of different treatment methods for normalization of the disk/condyle relationship in patients with TMJ disk displacement.

Three-dimensional confocal microscopy of the living cornea and ocular lens

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1991-07-01

The three-dimensional reconstruction of the optic zone of the cornea and the ocular crystalline lens has been accomplished using confocal microscopy and volume rendering computer techniques. A laser scanning confocal microscope was used in the reflected light mode to obtain the two-dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with a 488 nm wavelength. The microscope objective was a Leitz X25, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133 three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their 'beaded' cell borders, basal lamina, nerve plexus, nerve fibers, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in- situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers. The three-dimensional data sets of the cornea and the ocular lens were reconstructed in the computer using volume rendering techniques. Stereo pairs were also created of the two- dimensional ocular images for visualization. The stack of two-dimensional images was reconstructed into a three-dimensional object using volume rendering techniques. This demonstration of the three-dimensional visualization of the intact, enucleated eye provides an important step toward quantitative three-dimensional morphometry of the eye. The important aspects of three-dimensional reconstruction are discussed.

Quantitative Large-Scale Three-Dimensional Imaging of Human Kidney Biopsies: A Bridge to Precision Medicine in Kidney Disease.

PubMed

Winfree, Seth; Dagher, Pierre C; Dunn, Kenneth W; Eadon, Michael T; Ferkowicz, Michael; Barwinska, Daria; Kelly, Katherine J; Sutton, Timothy A; El-Achkar, Tarek M

2018-06-05

Kidney biopsy remains the gold standard for uncovering the pathogenesis of acute and chronic kidney diseases. However, the ability to perform high resolution, quantitative, molecular and cellular interrogation of this precious tissue is still at a developing stage compared to other fields such as oncology. Here, we discuss recent advances in performing large-scale, three-dimensional (3D), multi-fluorescence imaging of kidney biopsies and quantitative analysis referred to as 3D tissue cytometry. This approach allows the accurate measurement of specific cell types and their spatial distribution in a thick section spanning the entire length of the biopsy. By uncovering specific disease signatures, including rare occurrences, and linking them to the biology in situ, this approach will enhance our understanding of disease pathogenesis. Furthermore, by providing accurate quantitation of cellular events, 3D cytometry may improve the accuracy of prognosticating the clinical course and response to therapy. Therefore, large-scale 3D imaging and cytometry of kidney biopsy is poised to become a bridge towards personalized medicine for patients with kidney disease. © 2018 S. Karger AG, Basel.

Three-dimensional analysis of alveolar bone resorption by image processing of 3-D dental CT images

NASA Astrophysics Data System (ADS)

Nagao, Jiro; Kitasaka, Takayuki; Mori, Kensaku; Suenaga, Yasuhito; Yamada, Shohzoh; Naitoh, Munetaka

2006-03-01

We have developed a novel system that provides total support for assessment of alveolar bone resorption, caused by periodontitis, based on three-dimensional (3-D) dental CT images. In spite of the difficulty in perceiving the complex 3-D shape of resorption, dentists assessing resorption location and severity have been relying on two-dimensional radiography and probing, which merely provides one-dimensional information (depth) about resorption shape. However, there has been little work on assisting assessment of the disease by 3-D image processing and visualization techniques. This work provides quantitative evaluation results and figures for our system that measures the three-dimensional shape and spread of resorption. It has the following functions: (1) measures the depth of resorption by virtually simulating probing in the 3-D CT images, taking advantage of image processing of not suffering obstruction by teeth on the inter-proximal sides and much smaller measurement intervals than the conventional examination; (2) visualizes the disposition of the depth by movies and graphs; (3) produces a quantitative index and intuitive visual representation of the spread of resorption in the inter-radicular region in terms of area; and (4) calculates the volume of resorption as another severity index in the inter-radicular region and the region outside it. Experimental results in two cases of 3-D dental CT images and a comparison of the results with the clinical examination results and experts' measurements of the corresponding patients confirmed that the proposed system gives satisfying results, including 0.1 to 0.6mm of resorption measurement (probing) error and fairly intuitive presentation of measurement and calculation results.

Radiologic-Pathologic Analysis of Contrast-enhanced and Diffusion-weighted MR Imaging in Patients with HCC after TACE: Diagnostic Accuracy of 3D Quantitative Image Analysis

PubMed Central

Chapiro, Julius; Wood, Laura D.; Lin, MingDe; Duran, Rafael; Cornish, Toby; Lesage, David; Charu, Vivek; Schernthaner, Rüdiger; Wang, Zhijun; Tacher, Vania; Savic, Lynn Jeanette; Kamel, Ihab R.

2014-01-01

Purpose To evaluate the diagnostic performance of three-dimensional (3Dthree-dimensional) quantitative enhancement-based and diffusion-weighted volumetric magnetic resonance (MR) imaging assessment of hepatocellular carcinoma (HCChepatocellular carcinoma) lesions in determining the extent of pathologic tumor necrosis after transarterial chemoembolization (TACEtransarterial chemoembolization). Materials and Methods This institutional review board–approved retrospective study included 17 patients with HCChepatocellular carcinoma who underwent TACEtransarterial chemoembolization before surgery. Semiautomatic 3Dthree-dimensional volumetric segmentation of target lesions was performed at the last MR examination before orthotopic liver transplantation or surgical resection. The amount of necrotic tumor tissue on contrast material–enhanced arterial phase MR images and the amount of diffusion-restricted tumor tissue on apparent diffusion coefficient (ADCapparent diffusion coefficient) maps were expressed as a percentage of the total tumor volume. Visual assessment of the extent of tumor necrosis and tumor response according to European Association for the Study of the Liver (EASLEuropean Association for the Study of the Liver) criteria was performed. Pathologic tumor necrosis was quantified by using slide-by-slide segmentation. Correlation analysis was performed to evaluate the predictive values of the radiologic techniques. Results At histopathologic examination, the mean percentage of tumor necrosis was 70% (range, 10%–100%). Both 3Dthree-dimensional quantitative techniques demonstrated a strong correlation with tumor necrosis at pathologic examination (R2 = 0.9657 and R2 = 0.9662 for quantitative EASLEuropean Association for the Study of the Liver and quantitative ADCapparent diffusion coefficient, respectively) and a strong intermethod agreement (R2 = 0.9585). Both methods showed a significantly lower discrepancy with pathologically measured necrosis (residual standard error [RSEresidual standard error] = 6.38 and 6.33 for quantitative EASLEuropean Association for the Study of the Liver and quantitative ADCapparent diffusion coefficient, respectively), when compared with non-3Dthree-dimensional techniques (RSEresidual standard error = 12.18 for visual assessment). Conclusion This radiologic-pathologic correlation study demonstrates the diagnostic accuracy of 3Dthree-dimensional quantitative MR imaging techniques in identifying pathologically measured tumor necrosis in HCChepatocellular carcinoma lesions treated with TACEtransarterial chemoembolization. © RSNA, 2014 Online supplemental material is available for this article. PMID:25028783

In vivo, label-free, three-dimensional quantitative imaging of liver surface using multi-photon microscopy

NASA Astrophysics Data System (ADS)

Zhuo, Shuangmu; Yan, Jie; Kang, Yuzhan; Xu, Shuoyu; Peng, Qiwen; So, Peter T. C.; Yu, Hanry

2014-07-01

Various structural features on the liver surface reflect functional changes in the liver. The visualization of these surface features with molecular specificity is of particular relevance to understanding the physiology and diseases of the liver. Using multi-photon microscopy (MPM), we have developed a label-free, three-dimensional quantitative and sensitive method to visualize various structural features of liver surface in living rat. MPM could quantitatively image the microstructural features of liver surface with respect to the sinuosity of collagen fiber, the elastic fiber structure, the ratio between elastin and collagen, collagen content, and the metabolic state of the hepatocytes that are correlative with the pathophysiologically induced changes in the regions of interest. This study highlights the potential of this technique as a useful tool for pathophysiological studies and possible diagnosis of the liver diseases with further development.

In vivo, label-free, three-dimensional quantitative imaging of liver surface using multi-photon microscopy

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

Zhuo, Shuangmu, E-mail: shuangmuzhuo@gmail.com, E-mail: hanry-yu@nuhs.edu.sg; Institute of Laser and Optoelectronics Technology, Fujian Normal University, Fuzhou 350007; Yan, Jie

2014-07-14

Various structural features on the liver surface reflect functional changes in the liver. The visualization of these surface features with molecular specificity is of particular relevance to understanding the physiology and diseases of the liver. Using multi-photon microscopy (MPM), we have developed a label-free, three-dimensional quantitative and sensitive method to visualize various structural features of liver surface in living rat. MPM could quantitatively image the microstructural features of liver surface with respect to the sinuosity of collagen fiber, the elastic fiber structure, the ratio between elastin and collagen, collagen content, and the metabolic state of the hepatocytes that are correlativemore » with the pathophysiologically induced changes in the regions of interest. This study highlights the potential of this technique as a useful tool for pathophysiological studies and possible diagnosis of the liver diseases with further development.« less

75 FR 77882 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-14

... of federally-funded research and development. Foreign patent applications are filed on selected... applications. Software System for Quantitative Assessment of Vasculature in Three Dimensional Images... vascular networks from medical and basic research images. Deregulation of angiogenesis plays a major role...

Non-destructive phase contrast hard x-ray imaging to reveal the three-dimensional microstructure of soft and hard tissues

NASA Astrophysics Data System (ADS)

Khimchenko, Anna; Schulz, Georg; Deyhle, Hans; Hieber, Simone E.; Hasan, Samiul; Bikis, Christos; Schulz, Joachim; Costeur, Loïc.; Müller, Bert

2016-04-01

X-ray imaging in the absorption contrast mode is an established method of visualising calcified tissues such as bone and teeth. Physically soft tissues such as brain or muscle are often imaged using magnetic resonance imaging (MRI). However, the spatial resolution of MRI is insufficient for identifying individual biological cells within three-dimensional tissue. X-ray grating interferometry (XGI) has advantages for the investigation of soft tissues or the simultaneous three-dimensional visualisation of soft and hard tissues. Since laboratory microtomography (μCT) systems have better accessibility than tomography set-ups at synchrotron radiation facilities, a great deal of effort has been invested in optimising XGI set-ups for conventional μCT systems. In this conference proceeding, we present how a two-grating interferometer is incorporated into a commercially available nanotom m (GE Sensing and Inspection Technologies GmbH) μCT system to extend its capabilities toward phase contrast. We intend to demonstrate superior contrast in spiders (Hogna radiata (Fam. Lycosidae) and Xysticus erraticus (Fam. Thomisidae)), as well as the simultaneous visualisation of hard and soft tissues. XGI is an imaging modality that provides quantitative data, and visualisation is an important part of biomimetics; consequently, hard X-ray imaging provides a sound basis for bioinspiration, bioreplication and biomimetics and allows for the quantitative comparison of biofabricated products with their natural counterparts.

Three-dimensional in vitro cancer spheroid models for Photodynamic Therapy: Strengths and Opportunities

NASA Astrophysics Data System (ADS)

Evans, Conor

2015-03-01

Three dimensional, in vitro spheroid cultures offer considerable utility for the development and testing of anticancer photodynamic therapy regimens. More complex than monolayer cultures, three-dimensional spheroid systems replicate many of the important cell-cell and cell-matrix interactions that modulate treatment response in vivo. Simple enough to be grown by the thousands and small enough to be optically interrogated, spheroid cultures lend themselves to high-content and high-throughput imaging approaches. These advantages have enabled studies investigating photosensitizer uptake, spatiotemporal patterns of therapeutic response, alterations in oxygen diffusion and consumption during therapy, and the exploration of mechanisms that underlie therapeutic synergy. The use of quantitative imaging methods, in particular, has accelerated the pace of three-dimensional in vitro photodynamic therapy studies, enabling the rapid compilation of multiple treatment response parameters in a single experiment. Improvements in model cultures, the creation of new molecular probes of cell state and function, and innovations in imaging toolkits will be important for the advancement of spheroid culture systems for future photodynamic therapy studies.

Electrical Capacitance Volume Tomography: Design and Applications

PubMed Central

Wang, Fei; Marashdeh, Qussai; Fan, Liang-Shih; Warsito, Warsito

2010-01-01

This article reports recent advances and progress in the field of electrical capacitance volume tomography (ECVT). ECVT, developed from the two-dimensional electrical capacitance tomography (ECT), is a promising non-intrusive imaging technology that can provide real-time three-dimensional images of the sensing domain. Images are reconstructed from capacitance measurements acquired by electrodes placed on the outside boundary of the testing vessel. In this article, a review of progress on capacitance sensor design and applications to multi-phase flows is presented. The sensor shape, electrode configuration, and the number of electrodes that comprise three key elements of three-dimensional capacitance sensors are illustrated. The article also highlights applications of ECVT sensors on vessels of various sizes from 1 to 60 inches with complex geometries. Case studies are used to show the capability and validity of ECVT. The studies provide qualitative and quantitative real-time three-dimensional information of the measuring domain under study. Advantages of ECVT render it a favorable tool to be utilized for industrial applications and fundamental multi-phase flow research. PMID:22294905

Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs.

PubMed

Sonnaert, Maarten; Kerckhofs, Greet; Papantoniou, Ioannis; Van Vlierberghe, Sandra; Boterberg, Veerle; Dubruel, Peter; Luyten, Frank P; Schrooten, Jan; Geris, Liesbet

2015-01-01

To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial 'design of experiments' approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology.

X-ray Phase Contrast Allows Three Dimensional, Quantitative Imaging of Hydrogel Implants

DOE PAGES

Appel, Alyssa A.; Larson, Jeffrey C.; Jiang, Bin; ...

2015-10-20

Three dimensional imaging techniques are needed for the evaluation and assessment of biomaterials used for tissue engineering and drug delivery applications. Hydrogels are a particularly popular class of materials for medical applications but are difficult to image in tissue using most available imaging modalities. Imaging techniques based on X-ray Phase Contrast (XPC) have shown promise for tissue engineering applications due to their ability to provide image contrast based on multiple X-ray properties. In this manuscript we describe results using XPC to image a model hydrogel and soft tissue structure. Porous fibrin loaded poly(ethylene glycol) hydrogels were synthesized and implanted inmore » a rodent subcutaneous model. Samples were explanted and imaged with an analyzer-based XPC technique and processed and stained for histology for comparison. Both hydrogel and soft tissues structures could be identified in XPC images. Structure in skeletal muscle adjacent could be visualized and invading fibrovascular tissue could be quantified. In quantitative results, there were no differences between XPC and the gold-standard histological measurements. These results provide evidence of the significant potential of techniques based on XPC for 3D imaging of hydrogel structure and local tissue response.« less

Label-free three-dimensional imaging of cell nucleus using third-harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Lin, Jian; Zheng, Wei; Wang, Zi; Huang, Zhiwei

2014-09-01

We report the implementation of the combined third-harmonic generation (THG) and two-photon excited fluorescence (TPEF) microscopy for label-free three-dimensional (3-D) imaging of cell nucleus morphological changes in liver tissue. THG imaging shows regular spherical shapes of normal hepatocytes nuclei with inner chromatin structures while revealing the condensation of chromatins and nuclear fragmentations in hepatocytes of diseased liver tissue. Colocalized THG and TPEF imaging provides complementary information of cell nuclei and cytoplasm in tissue. This work suggests that 3-D THG microscopy has the potential for quantitative analysis of nuclear morphology in cells at a submicron-resolution without the need for DNA staining.

Label-free three-dimensional imaging of cell nucleus using third-harmonic generation microscopy

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

Lin, Jian; Zheng, Wei; Wang, Zi

2014-09-08

We report the implementation of the combined third-harmonic generation (THG) and two-photon excited fluorescence (TPEF) microscopy for label-free three-dimensional (3-D) imaging of cell nucleus morphological changes in liver tissue. THG imaging shows regular spherical shapes of normal hepatocytes nuclei with inner chromatin structures while revealing the condensation of chromatins and nuclear fragmentations in hepatocytes of diseased liver tissue. Colocalized THG and TPEF imaging provides complementary information of cell nuclei and cytoplasm in tissue. This work suggests that 3-D THG microscopy has the potential for quantitative analysis of nuclear morphology in cells at a submicron-resolution without the need for DNA staining.

Quantitative and qualitative measure of intralaboratory two-dimensional protein gel reproducibility and the effects of sample preparation, sample load, and image analysis.

PubMed

Choe, Leila H; Lee, Kelvin H

2003-10-01

We investigate one approach to assess the quantitative variability in two-dimensional gel electrophoresis (2-DE) separations based on gel-to-gel variability, sample preparation variability, sample load differences, and the effect of automation on image analysis. We observe that 95% of spots present in three out of four replicate gels exhibit less than a 0.52 coefficient of variation (CV) in fluorescent stain intensity (% volume) for a single sample run on multiple gels. When four parallel sample preparations are performed, this value increases to 0.57. We do not observe any significant change in quantitative value for an increase or decrease in sample load of 30% when using appropriate image analysis variables. Increasing use of automation, while necessary in modern 2-DE experiments, does change the observed level of quantitative and qualitative variability among replicate gels. The number of spots that change qualitatively for a single sample run in parallel varies from a CV = 0.03 for fully manual analysis to CV = 0.20 for a fully automated analysis. We present a systematic method by which a single laboratory can measure gel-to-gel variability using only three gel runs.

Three-dimensional hydrogen microscopy using a high-energy proton probe

NASA Astrophysics Data System (ADS)

Dollinger, G.; Reichart, P.; Datzmann, G.; Hauptner, A.; Körner, H.-J.

2003-01-01

It is a challenge to measure two-dimensional or three-dimensional (3D) hydrogen profiles on a micrometer scale. Quantitative hydrogen analyses of micrometer resolution are demonstrated utilizing proton-proton scattering at a high-energy proton microprobe. It has more than an-order-of-magnitude better position resolution and in addition higher sensitivity than any other technique for 3D hydrogen analyses. This type of hydrogen imaging opens plenty room to characterize microstructured materials, and semiconductor devices or objects in microbiology. The first hydrogen image obtained with a 10 MeV proton microprobe shows the hydrogen distribution of the microcapillary system being present in the wing of a mayfly and demonstrates the potential of the method.

Quantitative evaluation of the fetal cerebellar vermis using the median view on three-dimensional ultrasound.

PubMed

Zhao, Dan; Liu, Wei; Cai, Ailu; Li, Jingyu; Chen, Lizhu; Wang, Bing

2013-02-01

The purpose of this study was to investigate the effectiveness for quantitative evaluation of cerebellar vermis using three-dimensional (3D) ultrasound and to establish a nomogram for Chinese fetal vermis measurements during gestation. Sonographic examinations were performed in normal fetuses and in cases suspected of the diagnosis of vermian rotation. 3D median planes were obtained with both OMNIVIEW and tomographic ultrasound imaging. Measurements of the cerebellar vermis were highly correlated between two-dimensional and 3D median planes. The diameter of the cerebellar vermis follows growth approximately predicted by the quadratic regression equation. The normal vermis was almost parallel to the brain stem, with the average angle degree to be <2° in normal fetuses. The average angle degree of the 9 cases of vermian rotation was >5°. Three-dimensional median planes are obtained more easily than two-dimensional ones, and allow accurate measurements of the cerebellar vermis. The 3D approach may enable rapid assessment of fetal cerebral anatomy in standard examination. Measurements of cerebellar vermis may provide a quantitative index for prenatal diagnosis of posterior fossa malformations. © 2012 John Wiley & Sons, Ltd.

Three-dimensional modeling and quantitative analysis of gap junction distributions in cardiac tissue.

PubMed

Lackey, Daniel P; Carruth, Eric D; Lasher, Richard A; Boenisch, Jan; Sachse, Frank B; Hitchcock, Robert W

2011-11-01

Gap junctions play a fundamental role in intercellular communication in cardiac tissue. Various types of heart disease including hypertrophy and ischemia are associated with alterations of the spatial arrangement of gap junctions. Previous studies applied two-dimensional optical and electron-microscopy to visualize gap junction arrangements. In normal cardiomyocytes, gap junctions were primarily found at cell ends, but can be found also in more central regions. In this study, we extended these approaches toward three-dimensional reconstruction of gap junction distributions based on high-resolution scanning confocal microscopy and image processing. We developed methods for quantitative characterization of gap junction distributions based on analysis of intensity profiles along the principal axes of myocytes. The analyses characterized gap junction polarization at cell ends and higher-order statistical image moments of intensity profiles. The methodology was tested in rat ventricular myocardium. Our analysis yielded novel quantitative data on gap junction distributions. In particular, the analysis demonstrated that the distributions exhibit significant variability with respect to polarization, skewness, and kurtosis. We suggest that this methodology provides a quantitative alternative to current approaches based on visual inspection, with applications in particular in characterization of engineered and diseased myocardium. Furthermore, we propose that these data provide improved input for computational modeling of cardiac conduction.

Preparation of wholemount mouse intestine for high-resolution three-dimensional imaging using two-photon microscopy.

PubMed

Appleton, P L; Quyn, A J; Swift, S; Näthke, I

2009-05-01

Visualizing overall tissue architecture in three dimensions is fundamental for validating and integrating biochemical, cell biological and visual data from less complex systems such as cultured cells. Here, we describe a method to generate high-resolution three-dimensional image data of intact mouse gut tissue. Regions of highest interest lie between 50 and 200 mum within this tissue. The quality and usefulness of three-dimensional image data of tissue with such depth is limited owing to problems associated with scattered light, photobleaching and spherical aberration. Furthermore, the highest-quality oil-immersion lenses are designed to work at a maximum distance of

Determination of left ventricular volume, ejection fraction, and myocardial mass by real-time three-dimensional echocardiography

NASA Technical Reports Server (NTRS)

Qin, J. X.; Shiota, T.; Thomas, J. D.

2000-01-01

Reconstructed three-dimensional (3-D) echocardiography is an accurate and reproducible method of assessing left ventricular (LV) functions. However, it has limitations for clinical study due to the requirement of complex computer and echocardiographic analysis systems, electrocardiographic/respiratory gating, and prolonged imaging times. Real-time 3-D echocardiography has a major advantage of conveniently visualizing the entire cardiac anatomy in three dimensions and of potentially accurately quantifying LV volumes, ejection fractions, and myocardial mass in patients even in the presence of an LV aneurysm. Although the image quality of the current real-time 3-D echocardiographic methods is not optimal, its widespread clinical application is possible because of the convenient and fast image acquisition. We review real-time 3-D echocardiographic image acquisition and quantitative analysis for the evaluation of LV function and LV mass.

Determination of left ventricular volume, ejection fraction, and myocardial mass by real-time three-dimensional echocardiography.

PubMed

Qin, J X; Shiota, T; Thomas, J D

2000-11-01

Reconstructed three-dimensional (3-D) echocardiography is an accurate and reproducible method of assessing left ventricular (LV) functions. However, it has limitations for clinical study due to the requirement of complex computer and echocardiographic analysis systems, electrocardiographic/respiratory gating, and prolonged imaging times. Real-time 3-D echocardiography has a major advantage of conveniently visualizing the entire cardiac anatomy in three dimensions and of potentially accurately quantifying LV volumes, ejection fractions, and myocardial mass in patients even in the presence of an LV aneurysm. Although the image quality of the current real-time 3-D echocardiographic methods is not optimal, its widespread clinical application is possible because of the convenient and fast image acquisition. We review real-time 3-D echocardiographic image acquisition and quantitative analysis for the evaluation of LV function and LV mass.

Scattering calculation and image reconstruction using elevation-focused beams

PubMed Central

Duncan, David P.; Astheimer, Jeffrey P.; Waag, Robert C.

2009-01-01

Pressure scattered by cylindrical and spherical objects with elevation-focused illumination and reception has been analytically calculated, and corresponding cross sections have been reconstructed with a two-dimensional algorithm. Elevation focusing was used to elucidate constraints on quantitative imaging of three-dimensional objects with two-dimensional algorithms. Focused illumination and reception are represented by angular spectra of plane waves that were efficiently computed using a Fourier interpolation method to maintain the same angles for all temporal frequencies. Reconstructions were formed using an eigenfunction method with multiple frequencies, phase compensation, and iteration. The results show that the scattered pressure reduces to a two-dimensional expression, and two-dimensional algorithms are applicable when the region of a three-dimensional object within an elevation-focused beam is approximately constant in elevation. The results also show that energy scattered out of the reception aperture by objects contained within the focused beam can result in the reconstructed values of attenuation slope being greater than true values at the boundary of the object. Reconstructed sound speed images, however, appear to be relatively unaffected by the loss in scattered energy. The broad conclusion that can be drawn from these results is that two-dimensional reconstructions require compensation to account for uncaptured three-dimensional scattering. PMID:19425653

Scattering calculation and image reconstruction using elevation-focused beams.

PubMed

Duncan, David P; Astheimer, Jeffrey P; Waag, Robert C

2009-05-01

Pressure scattered by cylindrical and spherical objects with elevation-focused illumination and reception has been analytically calculated, and corresponding cross sections have been reconstructed with a two-dimensional algorithm. Elevation focusing was used to elucidate constraints on quantitative imaging of three-dimensional objects with two-dimensional algorithms. Focused illumination and reception are represented by angular spectra of plane waves that were efficiently computed using a Fourier interpolation method to maintain the same angles for all temporal frequencies. Reconstructions were formed using an eigenfunction method with multiple frequencies, phase compensation, and iteration. The results show that the scattered pressure reduces to a two-dimensional expression, and two-dimensional algorithms are applicable when the region of a three-dimensional object within an elevation-focused beam is approximately constant in elevation. The results also show that energy scattered out of the reception aperture by objects contained within the focused beam can result in the reconstructed values of attenuation slope being greater than true values at the boundary of the object. Reconstructed sound speed images, however, appear to be relatively unaffected by the loss in scattered energy. The broad conclusion that can be drawn from these results is that two-dimensional reconstructions require compensation to account for uncaptured three-dimensional scattering.

Objective breast tissue image classification using Quantitative Transmission ultrasound tomography

NASA Astrophysics Data System (ADS)

Malik, Bilal; Klock, John; Wiskin, James; Lenox, Mark

2016-12-01

Quantitative Transmission Ultrasound (QT) is a powerful and emerging imaging paradigm which has the potential to perform true three-dimensional image reconstruction of biological tissue. Breast imaging is an important application of QT and allows non-invasive, non-ionizing imaging of whole breasts in vivo. Here, we report the first demonstration of breast tissue image classification in QT imaging. We systematically assess the ability of the QT images’ features to differentiate between normal breast tissue types. The three QT features were used in Support Vector Machines (SVM) classifiers, and classification of breast tissue as either skin, fat, glands, ducts or connective tissue was demonstrated with an overall accuracy of greater than 90%. Finally, the classifier was validated on whole breast image volumes to provide a color-coded breast tissue volume. This study serves as a first step towards a computer-aided detection/diagnosis platform for QT.

Morphological imaging and quantification of axial xylem tissue in Fraxinus excelsior L. through X-ray micro-computed tomography.

PubMed

Koddenberg, Tim; Militz, Holger

2018-05-05

The popularity of X-ray based imaging methods has continued to increase in research domains. In wood research, X-ray micro-computed tomography (XμCT) is useful for structural studies examining the three-dimensional and complex xylem tissue of trees qualitatively and quantitatively. In this study, XμCT made it possible to visualize and quantify the spatial xylem organization of the angiosperm species Fraxinus excelsior L. on the microscopic level. Through image analysis, it was possible to determine morphological characteristics of the cellular axial tissue (vessel elements, fibers, and axial parenchyma cells) three-dimensionally. X-ray imaging at high resolutions provides very distinct visual insight into the xylem structure. Numerical analyses performed through semi-automatic procedures made it possible to quickly quantify cell characteristics (length, diameter, and volume of cells). Use of various spatial resolutions (0.87-5 μm) revealed boundaries users should be aware of. Nevertheless, our findings, both qualitative and quantitative, demonstrate XμCT to be a valuable tool for studying the spatial cell morphology of F. excelsior. Copyright © 2018. Published by Elsevier Ltd.

Three-Dimensional Model of the Scatterer Distribution in Cirrhotic Liver

NASA Astrophysics Data System (ADS)

Yamaguchi, Tadashi; Nakamura, Keigo; Hachiya, Hiroyuki

2003-05-01

Ultrasonic B-mode images are affected by changes in scatterer distribution. It is hard to estimate the relationship between the ultrasonic image and the tissue structure quantitatively because we cannot observe the continuous stages of liver cirrhosis tissue clinically, particularly the beginning stage. In this paper, we propose a three-dimensional modeling method of scatterer distribution for normal and cirrhotic livers to confirm the influence of the change in the form of scatterer distribution on echo information. The algorithm of the method includes parameters which determine the expansion of nodules and fibers. Using the B-mode images which are obtained from these scatterer distributions, we analyze the relationship between the changes in the form of biological tissue and the changes in the B-mode images during progressive liver cirrhosis.

Three-dimensional optical tomographic imaging of supersonic jets through inversion of phase data obtained through the transport-of-intensity equation.

PubMed

Hemanth, Thayyullathil; Rajesh, Langoju; Padmaram, Renganathan; Vasu, R Mohan; Rajan, Kanjirodan; Patnaik, Lalit M

2004-07-20

We report experimental results of quantitative imaging in supersonic circular jets by using a monochromatic light probe. An expanding cone of light interrogates a three-dimensional volume of a supersonic steady-state flow from a circular jet. The distortion caused to the spherical wave by the presence of the jet is determined through our measuring normal intensity transport. A cone-beam tomographic algorithm is used to invert wave-front distortion to changes in refractive index introduced by the flow. The refractive index is converted into density whose cross sections reveal shock and other characteristics of the flow.

LED-based interference-reflection microscopy combined with optical tweezers for quantitative three-dimensional microtubule imaging.

PubMed

Simmert, Steve; Abdosamadi, Mohammad Kazem; Hermsdorf, Gero; Schäffer, Erik

2018-05-28

Optical tweezers combined with various microscopy techniques are a versatile tool for single-molecule force spectroscopy. However, some combinations may compromise measurements. Here, we combined optical tweezers with total-internal-reflection-fluorescence (TIRF) and interference-reflection microscopy (IRM). Using a light-emitting diode (LED) for IRM illumination, we show that single microtubules can be imaged with high contrast. Furthermore, we converted the IRM interference pattern of an upward bent microtubule to its three-dimensional (3D) profile calibrated against the optical tweezers and evanescent TIRF field. In general, LED-based IRM is a powerful method for high-contrast 3D microscopy.

3-D Ultrafast Doppler Imaging Applied to the Noninvasive and Quantitative Imaging of Blood Vessels in Vivo

PubMed Central

Provost, J.; Papadacci, C.; Demene, C.; Gennisson, J-L.; Tanter, M.; Pernot, M.

2016-01-01

Ultrafast Doppler Imaging was introduced as a technique to quantify blood flow in an entire 2-D field of view, expanding the field of application of ultrasound imaging to the highly sensitive anatomical and functional mapping of blood vessels. We have recently developed 3-D Ultrafast Ultrasound Imaging, a technique that can produce thousands of ultrasound volumes per second, based on three-dimensional plane and diverging wave emissions, and demonstrated its clinical feasibility in human subjects in vivo. In this study, we show that non-invasive 3-D Ultrafast Power Doppler, Pulsed Doppler, and Color Doppler Imaging can be used to perform quantitative imaging of blood vessels in humans when using coherent compounding of three-dimensional tilted plane waves. A customized, programmable, 1024-channel ultrasound system was designed to perform 3-D Ultrafast Imaging. Using a 32X32, 3-MHz matrix phased array (Vermon, France), volumes were beamformed by coherently compounding successive tilted plane wave emissions. Doppler processing was then applied in a voxel-wise fashion. 3-D Ultrafast Power Doppler Imaging was first validated by imaging Tygon tubes of varying diameter and its in vivo feasibility was demonstrated by imaging small vessels in the human thyroid. Simultaneous 3-D Color and Pulsed Doppler Imaging using compounded emissions were also applied in the carotid artery and the jugular vein in one healthy volunteer. PMID:26276956

Systems Imaging of the Immune Synapse.

PubMed

Ambler, Rachel; Ruan, Xiangtao; Murphy, Robert F; Wülfing, Christoph

2017-01-01

Three-dimensional live cell imaging of the interaction of T cells with antigen-presenting cells (APCs) visualizes the subcellular distributions of signaling intermediates during T cell activation at thousands of resolved positions within a cell. These information-rich maps of local protein concentrations are a valuable resource in understanding T cell signaling. Here, we describe a protocol for the efficient acquisition of such imaging data and their computational processing to create four-dimensional maps of local concentrations. This protocol allows quantitative analysis of T cell signaling as it occurs inside live cells with resolution in time and space across thousands of cells.

Imaging Cerebral Microhemorrhages in Military Service Members with Chronic Traumatic Brain Injury

PubMed Central

Liu, Wei; Soderlund, Karl; Senseney, Justin S.; Joy, David; Yeh, Ping-Hong; Ollinger, John; Sham, Elyssa B.; Liu, Tian; Wang, Yi; Oakes, Terrence R.; Riedy, Gerard

2017-01-01

Purpose To detect cerebral microhemorrhages in military service members with chronic traumatic brain injury by using susceptibility-weighted magnetic resonance (MR) imaging. The longitudinal evolution of microhemorrhages was monitored in a subset of patients by using quantitative susceptibility mapping. Materials and Methods The study was approved by the Walter Reed National Military Medical Center institutional review board and is compliant with HIPAA guidelines. All participants underwent two-dimensional conventional gradient-recalled-echo MR imaging and three-dimensional flow-compensated multi-echo gradient-recalled-echo MR imaging (processed to generate susceptibility-weighted images and quantitative susceptibility maps), and a subset of patients underwent follow-up imaging. Microhemorrhages were identified by two radiologists independently. Comparisons of microhemorrhage number, size, and magnetic susceptibility derived from quantitative susceptibility maps between baseline and follow-up imaging examinations were performed by using the paired t test. Results Among the 603 patients, cerebral microhemorrhages were identified in 43 patients, with six excluded for further analysis owing to artifacts. Seventy-seven percent (451 of 585) of the microhemorrhages on susceptibility-weighted images had a more conspicuous appearance than on gradient-recalled-echo images. Thirteen of the 37 patients underwent follow-up imaging examinations. In these patients, a smaller number of microhemorrhages were identified at follow-up imaging compared with baseline on quantitative susceptibility maps (mean ± standard deviation, 9.8 microhemorrhages ± 12.8 vs 13.7 microhemorrhages ± 16.6; P = .019). Quantitative susceptibility mapping–derived quantitative measures of microhemorrhages also decreased over time: −0.85 mm3 per day ± 1.59 for total volume (P = .039) and −0.10 parts per billion per day ± 0.14 for mean magnetic susceptibility (P = .016). Conclusion The number of microhemorrhages and quantitative susceptibility mapping–derived quantitative measures of microhemorrhages all decreased over time, suggesting that hemosiderin products undergo continued, subtle evolution in the chronic stage. PMID:26371749

Imaging Cerebral Microhemorrhages in Military Service Members with Chronic Traumatic Brain Injury.

PubMed

Liu, Wei; Soderlund, Karl; Senseney, Justin S; Joy, David; Yeh, Ping-Hong; Ollinger, John; Sham, Elyssa B; Liu, Tian; Wang, Yi; Oakes, Terrence R; Riedy, Gerard

2016-02-01

To detect cerebral microhemorrhages in military service members with chronic traumatic brain injury by using susceptibility-weighted magnetic resonance (MR) imaging. The longitudinal evolution of microhemorrhages was monitored in a subset of patients by using quantitative susceptibility mapping. The study was approved by the Walter Reed National Military Medical Center institutional review board and is compliant with HIPAA guidelines. All participants underwent two-dimensional conventional gradient-recalled-echo MR imaging and three-dimensional flow-compensated multiecho gradient-recalled-echo MR imaging (processed to generate susceptibility-weighted images and quantitative susceptibility maps), and a subset of patients underwent follow-up imaging. Microhemorrhages were identified by two radiologists independently. Comparisons of microhemorrhage number, size, and magnetic susceptibility derived from quantitative susceptibility maps between baseline and follow-up imaging examinations were performed by using the paired t test. Among the 603 patients, cerebral microhemorrhages were identified in 43 patients, with six excluded for further analysis owing to artifacts. Seventy-seven percent (451 of 585) of the microhemorrhages on susceptibility-weighted images had a more conspicuous appearance than on gradient-recalled-echo images. Thirteen of the 37 patients underwent follow-up imaging examinations. In these patients, a smaller number of microhemorrhages were identified at follow-up imaging compared with baseline on quantitative susceptibility maps (mean ± standard deviation, 9.8 microhemorrhages ± 12.8 vs 13.7 microhemorrhages ± 16.6; P = .019). Quantitative susceptibility mapping-derived quantitative measures of microhemorrhages also decreased over time: -0.85 mm(3) per day ± 1.59 for total volume (P = .039) and -0.10 parts per billion per day ± 0.14 for mean magnetic susceptibility (P = .016). The number of microhemorrhages and quantitative susceptibility mapping-derived quantitative measures of microhemorrhages all decreased over time, suggesting that hemosiderin products undergo continued, subtle evolution in the chronic stage. © RSNA, 2015.

Dynamic three-dimensional phase-contrast technique in MRI: application to complex flow analysis around the artificial heart valve

NASA Astrophysics Data System (ADS)

Kim, Soo Jeong; Lee, Dong Hyuk; Song, Inchang; Kim, Nam Gook; Park, Jae-Hyeung; Kim, JongHyo; Han, Man Chung; Min, Byong Goo

1998-07-01

Phase-contrast (PC) method of magnetic resonance imaging (MRI) has bee used for quantitative measurements of flow velocity and volume flow rate. It is a noninvasive technique which provides an accurate two-dimensional velocity image. Moreover, Phase Contrast Cine magnetic resonance imaging combines the flow dependent contrast of PC-MRI with the ability of cardiac cine imaging to produce images throughout the cardiac cycle. However, the accuracy of the data acquired from the single through-plane velocity encoding can be reduced by the effect of flow direction, because in many practical cases flow directions are not uniform throughout the whole region of interest. In this study, we present dynamic three-dimensional velocity vector mapping method using PC-MRI which can visualize the complex flow pattern through 3D volume rendered images displayed dynamically. The direction of velocity mapping can be selected along any three orthogonal axes. By vector summation, the three maps can be combined to form a velocity vector map that determines the velocity regardless of the flow direction. At the same time, Cine method is used to observe the dynamic change of flow. We performed a phantom study to evaluate the accuracy of the suggested PC-MRI in continuous and pulsatile flow measurement. Pulsatile flow wave form is generated by the ventricular assistant device (VAD), HEMO-PULSA (Biomedlab, Seoul, Korea). We varied flow velocity, pulsatile flow wave form, and pulsing rate. The PC-MRI-derived velocities were compared with Doppler-derived results. The velocities of the two measurements showed a significant linear correlation. Dynamic three-dimensional velocity vector mapping was carried out for two cases. First, we applied to the flow analysis around the artificial heart valve in a flat phantom. We could observe the flow pattern around the valve through the 3-dimensional cine image. Next, it is applied to the complex flow inside the polymer sac that is used as ventricle in totally implantable artificial heart (TAH). As a result we could observe the flow pattern around the valves of the sac, though complex flow can not be detected correctly in the conventional phase contrast method. In addition, we could calculate the cardiac output from TAH sac by quantitative measurement of the volume of flow across the outlet valve.

Use of three-dimensional time-resolved phase-contrast magnetic resonance imaging with vastly undersampled isotropic projection reconstruction to assess renal blood flow in a renal cell carcinoma patient treated with sunitinib: a case report.

PubMed

Takayama, Tatsuya; Takehara, Yasuo; Sugiyama, Masataka; Sugiyama, Takayuki; Ishii, Yasuo; Johnson, Kevin E; Wieben, Oliver; Wakayama, Tetsuya; Sakahara, Harumi; Ozono, Seiichiro

2014-08-14

New imaging modalities to assess the efficacy of drugs that have molecular targets remain under development. Here, we describe for the first time the use of time-resolved three-dimensional phase-contrast magnetic resonance imaging to monitor changes in blood supply to a tumor during sunitinib treatment in a patient with localized renal cell carcinoma. A 43-year-old Japanese woman with a tumor-bearing but functional single kidney presented at our hospital in July 2012. Computed tomography and magnetic resonance imaging revealed a cT1aN0M0 renal cell carcinoma embedded in the upper central region of the left kidney. She was prescribed sunitinib as neoadjuvant therapy for 8 months, and then underwent partial nephrectomy. Tumor monitoring during this time was done using time-resolved three-dimensional phase-contrast magnetic resonance imaging, a recent technique which specifically measures blood flow in the various vessels of the kidney. This imaging allowed visualization of the redistribution of renal blood flow during treatment, and showed that flow to the tumor was decreased and flows to other areas increased. Of note, this change occurred in the absence of any change in tumor size. The ability of time-resolved three-dimensional phase-contrast magnetic resonance imaging to provide quantitative information on blood supply to tumors may be useful in monitoring the efficacy of sunitinib treatment.

Holographic intravital microscopy for 2-D and 3-D imaging intact circulating blood cells in microcapillaries of live mice

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Choe, Kibaek; Park, Inwon; Kim, Pilhan; Park, Yongkeun

2016-09-01

Intravital microscopy is an essential tool that reveals behaviours of live cells under conditions close to natural physiological states. So far, although various approaches for imaging cells in vivo have been proposed, most require the use of labelling and also provide only qualitative imaging information. Holographic imaging approach based on measuring the refractive index distributions of cells, however, circumvent these problems and offer quantitative and label-free imaging capability. Here, we demonstrate in vivo two- and three-dimensional holographic imaging of circulating blood cells in intact microcapillaries of live mice. The measured refractive index distributions of blood cells provide morphological and biochemical properties including three-dimensional cell shape, haemoglobin concentration, and haemoglobin contents at the individual cell level. With the present method, alterations in blood flow dynamics in live healthy and sepsis-model mice were also investigated.

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.

Cochlear implant-related three-dimensional characteristics determined by micro-computed tomography reconstruction.

PubMed

Ni, Yusu; Dai, Peidong; Dai, Chunfu; Li, Huawei

2017-01-01

To explore the structural characteristics of the cochlea in three-dimensional (3D) detail using 3D micro-computed tomography (mCT) image reconstruction of the osseous labyrinth, with the aim of improving the structural design of electrodes, the selection of stimulation sites, and the effectiveness of cochlear implantation. Three temporal bones were selected from among adult donors' temporal bone specimens. A micro-CT apparatus (GE eXplore) was used to scan three specimens with a voxel resolution of 45 μm. We obtained about 460 slices/specimen, which produced abundant data. The osseous labyrinth images of three specimens were reconstructed from mCT. The cochlea and its spiral characteristics were measured precisely using Able Software 3D-DOCTOR. The 3D images of the osseous labyrinth, including the cochlea, vestibule, and semicircular canals, were reconstructed. The 3D models of the cochlea showed the spatial relationships and surface structural characteristics. Quantitative data concerning the cochlea and its spiral structural characteristics were analyzed with regard to cochlear implantation. The 3D reconstruction of mCT images clearly displayed the detailed spiral structural characteristics of the osseous labyrinth. Quantitative data regarding the cochlea and its spiral structural characteristics could help to improve electrode structural design, signal processing, and the effectiveness of cochlear implantation. Clin. Anat. 30:39-43, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

NASA Astrophysics Data System (ADS)

Favicchio, Rosy; Psycharakis, Stylianos; Schönig, Kai; Bartsch, Dusan; Mamalaki, Clio; Papamatheakis, Joseph; Ripoll, Jorge; Zacharakis, Giannis

2016-02-01

Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture.

Computational hemodynamics of an implanted coronary stent based on three-dimensional cine angiography reconstruction.

PubMed

Chen, Mounter C Y; Lu, Po-Chien; Chen, James S Y; Hwang, Ned H C

2005-01-01

Coronary stents are supportive wire meshes that keep narrow coronary arteries patent, reducing the risk of restenosis. Despite the common use of coronary stents, approximately 20-35% of them fail due to restenosis. Flow phenomena adjacent to the stent may contribute to restenosis. Three-dimensional computational fluid dynamics (CFD) and reconstruction based on biplane cine angiography were used to assess coronary geometry and volumetric blood flows. A patient-specific left anterior descending (LAD) artery was reconstructed from single-plane x-ray imaging. With corresponding electrocardiographic signals, images from the same time phase were selected from the angiograms for dynamic three-dimensional reconstruction. The resultant three-dimensional LAD artery at end-diastole was adopted for detailed analysis. Both the geometries and flow fields, based on a computational model from CAE software (ANSYS and CATIA) and full three-dimensional Navier-Stroke equations in the CFD-ACE+ software, respectively, changed dramatically after stent placement. Flow fields showed a complex three-dimensional spiral motion due to arterial tortuosity. The corresponding wall shear stresses, pressure gradient, and flow field all varied significantly after stent placement. Combined angiography and CFD techniques allow more detailed investigation of flow patterns in various segments. The implanted stent(s) may be quantitatively studied from the proposed hemodynamic modeling approach.

The Evolution of Oblique Impact Flow Fields Using Maxwell's Z Model

NASA Technical Reports Server (NTRS)

Anderson, J. L. B.; Schultz, P. H.; Heineck, J. T.

2003-01-01

Oblique impacts are the norm rather than the exception for impact craters on planetary surfaces. This work focuses on the excavation of experimental oblique impact craters using the NASA Ames Vertical Gun Range (AVGR). Three-dimensional particle image velocimetry (3D PIV) is used to obtain quantitative data on ejection positions, three dimensional velocities and angles. These data are then used to constrain Maxwell's Z Model and follow the subsurface evolution of the excavation-stage flow-field center during oblique impacts.

[Differential diagnosis of papillary carcinomas of the thyroid, using image analysis and three dimensional reconstruction from serial sections].

PubMed

Holschbach, A; Kriete, A; Schäffer, R

1990-01-01

Papillae with fibrovascular cores are characteristic of papillary carcinoma of the thyroid. Papillae may be found in diffuse hyperplasia, nodular hyperplasia, Hashimoto's disease and follicular adenoma. Tissues from ten benign hyperplasias and ten papillary carcinomas were reconstructed from serial sections with three dimensional reconstruction programs. Significant qualitative and quantitative differences were found between the hyperplasia and the carcinoma. The principal differences between papillae of papillary carcinoma and hyperplasia were more clearly seen in the three dimensional reconstruction, than by means of morphometric methods. Certain criteria, e.g. the volume of papillae, were useful only with regard to the third dimension. Nevertheless, three dimensional reconstruction of biological tissue is a time consuming procedure which is not yet suitable for routine examination.

Fracture mechanics by three-dimensional crack-tip synchrotron X-ray microscopy

PubMed Central

Withers, P. J.

2015-01-01

To better understand the relationship between the nucleation and growth of defects and the local stresses and phase changes that cause them, we need both imaging and stress mapping. Here, we explore how this can be achieved by bringing together synchrotron X-ray diffraction and tomographic imaging. Conventionally, these are undertaken on separate synchrotron beamlines; however, instruments capable of both imaging and diffraction are beginning to emerge, such as ID15 at the European Synchrotron Radiation Facility and JEEP at the Diamond Light Source. This review explores the concept of three-dimensional crack-tip X-ray microscopy, bringing them together to probe the crack-tip behaviour under realistic environmental and loading conditions and to extract quantitative fracture mechanics information about the local crack-tip environment. X-ray diffraction provides information about the crack-tip stress field, phase transformations, plastic zone and crack-face tractions and forces. Time-lapse CT, besides providing information about the three-dimensional nature of the crack and its local growth rate, can also provide information as to the activation of extrinsic toughening mechanisms such as crack deflection, crack-tip zone shielding, crack bridging and crack closure. It is shown how crack-tip microscopy allows a quantitative measure of the crack-tip driving force via the stress intensity factor or the crack-tip opening displacement. Finally, further opportunities for synchrotron X-ray microscopy are explored. PMID:25624521

Comparison of Mars Science Laboratory Reaction Control System Jet Computations With Flow Visualization and Velocimetry

NASA Technical Reports Server (NTRS)

Bathel, Brett F.; Danehy, Paul M.; Johansen, Craig T.; Ashcraft, Scott W.; Novak, Luke A.

2013-01-01

Numerical predictions of the Mars Science Laboratory reaction control system jets interacting with a Mach 10 hypersonic flow are compared to experimental nitric oxide planar laser-induced fluorescence data. The steady Reynolds Averaged Navier Stokes equations using the Baldwin-Barth one-equation turbulence model were solved using the OVERFLOW code. The experimental fluorescence data used for comparison consists of qualitative two-dimensional visualization images, qualitative reconstructed three-dimensional flow structures, and quantitative two-dimensional distributions of streamwise velocity. Through modeling of the fluorescence signal equation, computational flow images were produced and directly compared to the qualitative fluorescence data.

Quantitative multi-modality imaging analysis of a bioabsorbable poly-L-lactic acid stent design in the acute phase: a comparison between 2- and 3D-QCA, QCU and QMSCT-CA.

PubMed

Bruining, Nico; Tanimoto, Shuzou; Otsuka, Masato; Weustink, Annick; Ligthart, Jurgen; de Winter, Sebastiaan; van Mieghem, Carlos; Nieman, Koen; de Feyter, Pim J; van Domburg, Ron T; Serruys, Patrick W

2008-08-01

To investigate if three-dimensional (3D) based quantitative techniques are comparable to each other and to explore possible differences with respect to the reference method of 2D-QCA in the acute phase and to study whether non-invasive MSCT could potentially be applied to quantify luminal dimensions of a stented coronary segment with a novel bioabsorable drug-eluting stent made of poly-l-lactic-acid (PLLA). Quantitative imaging data derived from 16 patients enrolled at our institution in a first-in-man trial (ABSORB) receiving a biodegradable stent and who were imaged with standard coronary angiography and intravascular ultrasound were compared. Shortly, after stenting the patients also underwent a MSCT procedure. Standard 2D-QCA showed significant smaller stent lengths (p < 0.01). Although, the absolute measured stent diameters and areas by 2D-QCA tend to be smaller, the differences failed to be statistically different when compared to the 3D based quantitative modalities. Measurements made by non-invasive QMSCT-CA of implanted PLLA stents appeared to be comparable to the other 3D modalities without significant differences. Three-dimensional based quantitative analyses showed similar results quantifying luminal dimensions as compared to 2D-QCA during an evaluation of a new bioabsorbable coronary stent design in the acute phase. Furthermore, in biodegradable stents made of PLLA, non-invasive QMSCT-CA can be used to quantify luminal dimensions.

Stochastic optical reconstruction microscopy-based relative localization analysis (STORM-RLA) for quantitative nanoscale assessment of spatial protein organization.

PubMed

Veeraraghavan, Rengasayee; Gourdie, Robert G

2016-11-07

The spatial association between proteins is crucial to understanding how they function in biological systems. Colocalization analysis of fluorescence microscopy images is widely used to assess this. However, colocalization analysis performed on two-dimensional images with diffraction-limited resolution merely indicates that the proteins are within 200-300 nm of each other in the xy-plane and within 500-700 nm of each other along the z-axis. Here we demonstrate a novel three-dimensional quantitative analysis applicable to single-molecule positional data: stochastic optical reconstruction microscopy-based relative localization analysis (STORM-RLA). This method offers significant advantages: 1) STORM imaging affords 20-nm resolution in the xy-plane and <50 nm along the z-axis; 2) STORM-RLA provides a quantitative assessment of the frequency and degree of overlap between clusters of colabeled proteins; and 3) STORM-RLA also calculates the precise distances between both overlapping and nonoverlapping clusters in three dimensions. Thus STORM-RLA represents a significant advance in the high-throughput quantitative assessment of the spatial organization of proteins. © 2016 Veeraraghavan and Gourdie. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Quantification of mitral valve morphology with three-dimensional echocardiography--can measurement lead to better management?

PubMed

Lee, Alex Pui-Wai; Fang, Fang; Jin, Chun-Na; Kam, Kevin Ka-Ho; Tsui, Gary K W; Wong, Kenneth K Y; Looi, Jen-Li; Wong, Randolph H L; Wan, Song; Sun, Jing Ping; Underwood, Malcolm J; Yu, Cheuk-Man

2014-01-01

The mitral valve (MV) has complex 3-dimensional (3D) morphology and motion. Advance in real-time 3D echocardiography (RT3DE) has revolutionized clinical imaging of the MV by providing clinicians with realistic visualization of the valve. Thus far, RT3DE of the MV structure and dynamics has adopted an approach that depends largely on subjective and qualitative interpretation of the 3D images of the valve, rather than objective and reproducible measurement. RT3DE combined with image-processing computer techniques provides precise segmentation and reliable quantification of the complex 3D morphology and rapid motion of the MV. This new approach to imaging may provide additional quantitative descriptions that are useful in diagnostic and therapeutic decision-making. Quantitative analysis of the MV using RT3DE has increased our understanding of the pathologic mechanism of degenerative, ischemic, functional, and rheumatic MV disease. Most recently, 3D morphologic quantification has entered into clinical use to provide more accurate diagnosis of MV disease and for planning surgery and transcatheter interventions. Current limitations of this quantitative approach to MV imaging include labor-intensiveness during image segmentation and lack of a clear definition of the clinical significance of many of the morphologic parameters. This review summarizes the current development and applications of quantitative analysis of the MV morphology using RT3DE.

Lateral resolution testing of a novel developed confocal microscopic imaging system

NASA Astrophysics Data System (ADS)

Zhang, Xin; Zhang, Yunhai; Chang, Jian; Huang, Wei; Xue, Xiaojun; Xiao, Yun

2015-10-01

Laser scanning confocal microscope has been widely used in biology, medicine and material science owing to its advantages of high resolution and tomographic imaging. Based on a set of confirmatory experiments and system design, a novel confocal microscopic imaging system is developed. The system is composed of a conventional fluorescence microscope and a confocal scanning unit. In the scanning unit a laser beam coupling module provides four different wavelengths 405nm 488nm 561nm and 638nm which can excite a variety of dyes. The system works in spot-to-spot scanning mode with a two-dimensional galvanometer. A 50 microns pinhole is used to guarantee that stray light is blocked and only the fluorescence signal from the focal point can be received . The three-channel spectral splitter is used to perform fluorescence imaging at three different working wavelengths simultaneously. The rat kidney tissue slice is imaged using the developed confocal microscopic imaging system. Nucleues labeled by DAPI and kidney spherule curved pipe labeled by Alexa Fluor 488 can be imaged clearly and respectively, realizing the distinction between the different components of mouse kidney tissue. The three-dimensional tomographic imaging of mouse kidney tissue is reconstructed by several two-dimensional images obtained in different depths. At last the resolution of the confocal microscopic imaging system is tested quantitatively. The experimental result shows that the system can achieve lateral resolution priority to 230nm.

Optical computed tomography for spatially isotropic four-dimensional imaging of live single cells

PubMed Central

Kelbauskas, Laimonas; Shetty, Rishabh; Cao, Bin; Wang, Kuo-Chen; Smith, Dean; Wang, Hong; Chao, Shi-Hui; Gangaraju, Sandhya; Ashcroft, Brian; Kritzer, Margaret; Glenn, Honor; Johnson, Roger H.; Meldrum, Deirdre R.

2017-01-01

Quantitative three-dimensional (3D) computed tomography (CT) imaging of living single cells enables orientation-independent morphometric analysis of the intricacies of cellular physiology. Since its invention, x-ray CT has become indispensable in the clinic for diagnostic and prognostic purposes due to its quantitative absorption-based imaging in true 3D that allows objects of interest to be viewed and measured from any orientation. However, x-ray CT has not been useful at the level of single cells because there is insufficient contrast to form an image. Recently, optical CT has been developed successfully for fixed cells, but this technology called Cell-CT is incompatible with live-cell imaging due to the use of stains, such as hematoxylin, that are not compatible with cell viability. We present a novel development of optical CT for quantitative, multispectral functional 4D (three spatial + one spectral dimension) imaging of living single cells. The method applied to immune system cells offers truly isotropic 3D spatial resolution and enables time-resolved imaging studies of cells suspended in aqueous medium. Using live-cell optical CT, we found a heterogeneous response to mitochondrial fission inhibition in mouse macrophages and differential basal remodeling of small (0.1 to 1 fl) and large (1 to 20 fl) nuclear and mitochondrial structures on a 20- to 30-s time scale in human myelogenous leukemia cells. Because of its robust 3D measurement capabilities, live-cell optical CT represents a powerful new tool in the biomedical research field. PMID:29226240

Thymidine Kinase PET Reporter Gene Imaging of Cancer Cells In Vivo.

PubMed

McCracken, Melissa N

2018-01-01

Positron emission tomography (PET) is a three dimensional imaging modality that detects the accumulation of radiolabeled isotopes in vivo. Ectopic expression of a thymidine kinase reporter gene allows for the specific detection of reporter cells in vivo by imaging with the reporter specific probe. PET reporter imaging is sensitive, quantitative and can be scaled into larger tumors or animals with little to no tissue diffraction. Here, we describe how thymidine kinase PET reporter genes can be used to noninvasively image cancer cells in vivo.

Quantitative characterization of 3D deformations of cell interactions with soft biomaterials

NASA Astrophysics Data System (ADS)

Franck, Christian

In recent years, the importance of mechanical forces in directing cellular function has been recognized as a significant factor in biological and physiological processes. In fact, these physical forces are now viewed equally as important as biochemical stimuli in controlling cellular response. Not only do these cellular forces, or cell tractions, play an important role in cell migration, they are also significant to many other physiological and pathological processes, both at the tissue and organ level, including wound healing, inflammation, angiogenesis, and embryogenesis. A complete quantification of cell tractions during cell-material interactions can lead to a deeper understanding of the fundamental role these forces play in cell biology. Thus, understanding the function and role of a cell from a mechanical framework can have important implications towards the development of new implant materials and drug treatments. Previous research has contributed significant descriptions of cell-tissue interactions by quantifying cell tractions in two-dimensional environments; however, most physiological processes are three-dimensional in nature. Recent studies have shown morphological differences in cells cultured on two-dimensional substrates versus three-dimensional matrices, and that the intrinsic extracellular matrix interactions and migration behavior are different in three dimensions versus two dimensions. Hence, measurement techniques are needed to investigate cellular behavior in all three dimensions. This thesis presents a full-field imaging technique capable of quantitatively measuring cell traction forces in all three spatial dimensions, and hence addresses the need of a three-dimensional quantitative imaging technique to gain insight into the fundamental role of physical forces in biological processes. The technique combines laser scanning confocal microscopy (LSCM) with digital volume correlation (DVC) to track the motion of fluorescent particles during cell-induced or externally applied deformations. This method is validated by comparing experimentally measured non-uniform deformation fields near hard and soft spherical inclusions under uniaxial compression with the corresponding analytical solution. Utilization of a newly developed computationally efficient stretch-correlation and deconvolution algorithm is shown to improve the overall measurement accuracy, in particular under large deformations. Using this technique, the full three-dimensional substrate displacement fields are experimentally determined during the migration of individual fibroblast cells on polyacrylamide gels. This is the first study to show the highly three-dimensional structure of cell-induced displacement and traction fields. These new findings suggest a three-dimensional push-pull cell motility, which differs from the traditional theories based on two-dimensional data. These results provide new insight into the dynamic cell-matrix force exchange or mechanotransduction of migrating cells, and will aid in the development of new three-dimensional cell motility and adhesion models. As this study reveals, the mechanical interactions of cells and their extracellular matrix appear to be highly three-dimensional. It also shows that the LSCM-DVC technique is well suited for investigating the mechanics of cell-matrix interactions while providing a platform to access detailed information of the intricate biomechanical coupling for many cellular responses. Thus, this method has the capability to provide direct quantitative experimental data showing how cells interact with their surroundings in three dimensions and might stimulate new avenues of scientific thought in understanding the fundamental role physical forces play in regulating cell behavior.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.; Park, YongKeun

2014-01-01

We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

PubMed Central

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.

2013-01-01

Abstract. We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated. PMID:23797986

Imaging challenges in biomaterials and tissue engineering

PubMed Central

Appel, Alyssa A.; Anastasio, Mark A.; Larson, Jeffery C.; Brey, Eric M.

2013-01-01

Biomaterials are employed in the fields of tissue engineering and regenerative medicine (TERM) in order to enhance the regeneration or replacement of tissue function and/or structure. The unique environments resulting from the presence of biomaterials, cells, and tissues result in distinct challenges in regards to monitoring and assessing the results of these interventions. Imaging technologies for three-dimensional (3D) analysis have been identified as a strategic priority in TERM research. Traditionally, histological and immunohistochemical techniques have been used to evaluate engineered tissues. However, these methods do not allow for an accurate volume assessment, are invasive, and do not provide information on functional status. Imaging techniques are needed that enable non-destructive, longitudinal, quantitative, and three-dimensional analysis of TERM strategies. This review focuses on evaluating the application of available imaging modalities for assessment of biomaterials and tissue in TERM applications. Included is a discussion of limitations of these techniques and identification of areas for further development. PMID:23768903

A high-throughput three-dimensional cell migration assay for toxicity screening with mobile device-based macroscopic image analysis

PubMed Central

Timm, David M.; Chen, Jianbo; Sing, David; Gage, Jacob A.; Haisler, William L.; Neeley, Shane K.; Raphael, Robert M.; Dehghani, Mehdi; Rosenblatt, Kevin P.; Killian, T. C.; Tseng, Hubert; Souza, Glauco R.

2013-01-01

There is a growing demand for in vitro assays for toxicity screening in three-dimensional (3D) environments. In this study, 3D cell culture using magnetic levitation was used to create an assay in which cells were patterned into 3D rings that close over time. The rate of closure was determined from time-lapse images taken with a mobile device and related to drug concentration. Rings of human embryonic kidney cells (HEK293) and tracheal smooth muscle cells (SMCs) were tested with ibuprofen and sodium dodecyl sulfate (SDS). Ring closure correlated with the viability and migration of cells in two dimensions (2D). Images taken using a mobile device were similar in analysis to images taken with a microscope. Ring closure may serve as a promising label-free and quantitative assay for high-throughput in vivo toxicity in 3D cultures. PMID:24141454

The research of statistical properties of colorimetric features of screens with a three-component color formation principle

NASA Astrophysics Data System (ADS)

Zharinov, I. O.; Zharinov, O. O.

2017-12-01

The problem of the research is concerned with quantitative analysis of influence of technological variation of the screen color profile parameters on chromaticity coordinates of the displayed image. Some mathematical expressions which approximate the two-dimensional distribution of chromaticity coordinates of an image, which is displayed on the screen with a three-component color formation principle were proposed. Proposed mathematical expressions show the way to development of correction techniques to improve reproducibility of the colorimetric features of displays.

The Evolution of Oblique Impact Flow Fields Using Maxwell's Z Model

NASA Technical Reports Server (NTRS)

Anderson, J. L. B.; Schultz, P. H.; Heineck, J. T.

2003-01-01

Oblique impacts are the norm rather than the exception for impact craters on planetary surfaces. This work focuses on the excavation of experimental oblique impact craters using the NASA Ames Vertical Gun Range (AVGR). Three-dimensional particle image velocimetry (3D PIV) is used to obtain quantitative data on ejection positions, three-dimensional velocities and angles. These data are then used to test the applicability and limitations of Maxwell's Z Model in representing the subsurface evolution of the excavation-stage flow-field center during vertical and oblique impacts.

Quantitative imaging of fibrotic and morphological changes in liver of non-alcoholic steatohepatitis (NASH) model mice by second harmonic generation (SHG) and auto-fluorescence (AF) imaging using two-photon excitation microscopy (TPEM).

PubMed

Yamamoto, Shin; Oshima, Yusuke; Saitou, Takashi; Watanabe, Takao; Miyake, Teruki; Yoshida, Osamu; Tokumoto, Yoshio; Abe, Masanori; Matsuura, Bunzo; Hiasa, Yoichi; Imamura, Takeshi

2016-12-01

Non-alcoholic steatohepatitis (NASH) is a common liver disorder caused by fatty liver. Because NASH is associated with fibrotic and morphological changes in liver tissue, a direct imaging technique is required for accurate staging of liver tissue. For this purpose, in this study we took advantage of two label-free optical imaging techniques, second harmonic generation (SHG) and auto-fluorescence (AF), using two-photon excitation microscopy (TPEM). Three-dimensional ex vivo imaging of tissues from NASH model mice, followed by image processing, revealed that SHG and AF are sufficient to quantitatively characterize the hepatic capsule at an early stage and parenchymal morphologies associated with liver disease progression, respectively.

Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.

PubMed

Davatzikos, Christos; Rathore, Saima; Bakas, Spyridon; Pati, Sarthak; Bergman, Mark; Kalarot, Ratheesh; Sridharan, Patmaa; Gastounioti, Aimilia; Jahani, Nariman; Cohen, Eric; Akbari, Hamed; Tunc, Birkan; Doshi, Jimit; Parker, Drew; Hsieh, Michael; Sotiras, Aristeidis; Li, Hongming; Ou, Yangming; Doot, Robert K; Bilello, Michel; Fan, Yong; Shinohara, Russell T; Yushkevich, Paul; Verma, Ragini; Kontos, Despina

2018-01-01

The growth of multiparametric imaging protocols has paved the way for quantitative imaging phenotypes that predict treatment response and clinical outcome, reflect underlying cancer molecular characteristics and spatiotemporal heterogeneity, and can guide personalized treatment planning. This growth has underlined the need for efficient quantitative analytics to derive high-dimensional imaging signatures of diagnostic and predictive value in this emerging era of integrated precision diagnostics. This paper presents cancer imaging phenomics toolkit (CaPTk), a new and dynamically growing software platform for analysis of radiographic images of cancer, currently focusing on brain, breast, and lung cancer. CaPTk leverages the value of quantitative imaging analytics along with machine learning to derive phenotypic imaging signatures, based on two-level functionality. First, image analysis algorithms are used to extract comprehensive panels of diverse and complementary features, such as multiparametric intensity histogram distributions, texture, shape, kinetics, connectomics, and spatial patterns. At the second level, these quantitative imaging signatures are fed into multivariate machine learning models to produce diagnostic, prognostic, and predictive biomarkers. Results from clinical studies in three areas are shown: (i) computational neuro-oncology of brain gliomas for precision diagnostics, prediction of outcome, and treatment planning; (ii) prediction of treatment response for breast and lung cancer, and (iii) risk assessment for breast cancer.

Three-dimensional organization of vestibular related eye movements to rotational motion in pigeons

NASA Technical Reports Server (NTRS)

Dickman, J. D.; Beyer, M.; Hess, B. J.

2000-01-01

During rotational motions, compensatory eye movement adjustments must continually occur in order to maintain objects of visual interest as stable images on the retina. In the present study, the three-dimensional organization of the vestibulo-ocular reflex in pigeons was quantitatively examined. Rotations about different head axes produced horizontal, vertical, and torsional eye movements, whose component magnitude was dependent upon the cosine of the stimulus axis relative to the animal's visual axis. Thus, the three-dimensional organization of the VOR in pigeons appears to be compensatory for any direction of head rotation. Frequency responses of the horizontal, vertical, and torsional slow phase components exhibited high pass filter properties with dominant time constants of approximately 3 s.

Noninvasive Quantitative Imaging of Collagen Microstructure in Three-Dimensional Hydrogels Using High-Frequency Ultrasound

PubMed Central

Mercado, Karla P.; Helguera, María; Hocking, Denise C.

2015-01-01

Collagen I is widely used as a natural component of biomaterials for both tissue engineering and regenerative medicine applications. The physical and biological properties of fibrillar collagens are strongly tied to variations in collagen fiber microstructure. The goal of this study was to develop the use of high-frequency quantitative ultrasound to assess collagen microstructure within three-dimensional (3D) hydrogels noninvasively and nondestructively. The integrated backscatter coefficient (IBC) was employed as a quantitative ultrasound parameter to detect, image, and quantify spatial variations in collagen fiber density and diameter. Collagen fiber microstructure was varied by fabricating hydrogels with different collagen concentrations or polymerization temperatures. IBC values were computed from measurements of the backscattered radio-frequency ultrasound signals collected using a single-element transducer (38-MHz center frequency, 13–47 MHz bandwidth). The IBC increased linearly with increasing collagen concentration and decreasing polymerization temperature. Parametric 3D images of the IBC were generated to visualize and quantify regional variations in collagen microstructure throughout the volume of hydrogels fabricated in standard tissue culture plates. IBC parametric images of corresponding cell-embedded collagen gels showed cell accumulation within regions having elevated collagen IBC values. The capability of this ultrasound technique to noninvasively detect and quantify spatial differences in collagen microstructure offers a valuable tool to monitor the structural properties of collagen scaffolds during fabrication, to detect functional differences in collagen microstructure, and to guide fundamental research on the interactions of cells and collagen matrices. PMID:25517512

Noninvasive Quantitative Imaging of Collagen Microstructure in Three-Dimensional Hydrogels Using High-Frequency Ultrasound.

PubMed

Mercado, Karla P; Helguera, María; Hocking, Denise C; Dalecki, Diane

2015-07-01

Collagen I is widely used as a natural component of biomaterials for both tissue engineering and regenerative medicine applications. The physical and biological properties of fibrillar collagens are strongly tied to variations in collagen fiber microstructure. The goal of this study was to develop the use of high-frequency quantitative ultrasound to assess collagen microstructure within three-dimensional (3D) hydrogels noninvasively and nondestructively. The integrated backscatter coefficient (IBC) was employed as a quantitative ultrasound parameter to detect, image, and quantify spatial variations in collagen fiber density and diameter. Collagen fiber microstructure was varied by fabricating hydrogels with different collagen concentrations or polymerization temperatures. IBC values were computed from measurements of the backscattered radio-frequency ultrasound signals collected using a single-element transducer (38-MHz center frequency, 13-47 MHz bandwidth). The IBC increased linearly with increasing collagen concentration and decreasing polymerization temperature. Parametric 3D images of the IBC were generated to visualize and quantify regional variations in collagen microstructure throughout the volume of hydrogels fabricated in standard tissue culture plates. IBC parametric images of corresponding cell-embedded collagen gels showed cell accumulation within regions having elevated collagen IBC values. The capability of this ultrasound technique to noninvasively detect and quantify spatial differences in collagen microstructure offers a valuable tool to monitor the structural properties of collagen scaffolds during fabrication, to detect functional differences in collagen microstructure, and to guide fundamental research on the interactions of cells and collagen matrices.

Non-invasive microstructure and morphology investigation of the mouse lung: qualitative description and quantitative measurement.

PubMed

Zhang, Lu; Li, Dongyue; Luo, Shuqian

2011-02-25

Early detection of lung cancer is known to improve the chances of successful treatment. However, lungs are soft tissues with complex three-dimensional configuration. Conventional X-ray imaging is based purely on absorption resulting in very low contrast when imaging soft tissues without contrast agents. It is difficult to obtain adequate information of lung lesions from conventional X-ray imaging. In this study, a recently emerged imaging technique, in-line X-ray phase contrast imaging (IL-XPCI) was used. This powerful technique enabled high-resolution investigations of soft tissues without contrast agents. We applied IL-XPCI to observe the lungs in an intact mouse for the purpose of defining quantitatively the micro-structures in lung. The three-dimensional model of the lung was successfully established, which provided an excellent view of lung airways. We highlighted the use of IL-XPCI in the visualization and assessment of alveoli which had rarely been studied in three dimensions (3D). The precise view of individual alveolus was achieved. The morphological parameters, such as diameter and alveolar surface area were measured. These parameters were of great importance in the diagnosis of diseases related to alveolus and alveolar scar. Our results indicated that IL-XPCI had the ability to represent complex anatomical structures in lung. This offered a new perspective on the diagnosis of respiratory disease and may guide future work in the study of respiratory mechanism on the alveoli level.

Measuring the Nonuniform Evaporation Dynamics of Sprayed Sessile Microdroplets with Quantitative Phase Imaging.

PubMed

Edwards, Chris; Arbabi, Amir; Bhaduri, Basanta; Wang, Xiaozhen; Ganti, Raman; Yunker, Peter J; Yodh, Arjun G; Popescu, Gabriel; Goddard, Lynford L

2015-10-13

We demonstrate real-time quantitative phase imaging as a new optical approach for measuring the evaporation dynamics of sessile microdroplets. Quantitative phase images of various droplets were captured during evaporation. The images enabled us to generate time-resolved three-dimensional topographic profiles of droplet shape with nanometer accuracy and, without any assumptions about droplet geometry, to directly measure important physical parameters that characterize surface wetting processes. Specifically, the time-dependent variation of the droplet height, volume, contact radius, contact angle distribution along the droplet's perimeter, and mass flux density for two different surface preparations are reported. The studies clearly demonstrate three phases of evaporation reported previously: pinned, depinned, and drying modes; the studies also reveal instances of partial pinning. Finally, the apparatus is employed to investigate the cooperative evaporation of the sprayed droplets. We observe and explain the neighbor-induced reduction in evaporation rate, that is, as compared to predictions for isolated droplets. In the future, the new experimental methods should stimulate the exploration of colloidal particle dynamics on the gas-liquid-solid interface.

Cardiovascular and pulmonary dynamics by quantitative imaging

NASA Technical Reports Server (NTRS)

Wood, E. H.

1976-01-01

The accuracy and range of studies on cardiovascular and pulmonary functions can be greatly facilitated if the motions of the underlying organ systems throughout individual cycles can be directly visualized and readily measured with minimum or preferably no effect on these motions. Achievement of this objective requires development of techniques for quantitative noninvasive or minimally invasive dynamic and stop-action imaging of the organ systems. A review of advances in dynamic quantitative imaging of moving organs reveals that the revolutionary value of cross-sectional and three-dimensional images produced by various types of radiant energy such as X-rays and gamma rays, positrons, electrons, protons, light, and ultrasound for clinical diagnostic and biomedical research applications is just beginning to be realized. The fabrication of a clinically useful cross-section reconstruction device with sensing capabilities for both anatomical structural composition and chemical composition may be possible and awaits future development.

Three-dimensional imaging and remote sensing imaging; Proceedings of the Meeting, Los Angeles, CA, Jan. 14, 15, 1988

NASA Astrophysics Data System (ADS)

Robbins, Woodrow E.

1988-01-01

The present conference discusses topics in novel technologies and techniques of three-dimensional imaging, human factors-related issues in three-dimensional display system design, three-dimensional imaging applications, and image processing for remote sensing. Attention is given to a 19-inch parallactiscope, a chromostereoscopic CRT-based display, the 'SpaceGraph' true three-dimensional peripheral, advantages of three-dimensional displays, holographic stereograms generated with a liquid crystal spatial light modulator, algorithms and display techniques for four-dimensional Cartesian graphics, an image processing system for automatic retina diagnosis, the automatic frequency control of a pulsed CO2 laser, and a three-dimensional display of magnetic resonance imaging of the spine.

Three-dimensional surface profile intensity correction for spatially modulated imaging

NASA Astrophysics Data System (ADS)

Gioux, Sylvain; Mazhar, Amaan; Cuccia, David J.; Durkin, Anthony J.; Tromberg, Bruce J.; Frangioni, John V.

2009-05-01

We describe a noncontact profile correction technique for quantitative, wide-field optical measurement of tissue absorption (μa) and reduced scattering (μs') coefficients, based on geometric correction of the sample's Lambertian (diffuse) reflectance intensity. Because the projection of structured light onto an object is the basis for both phase-shifting profilometry and modulated imaging, we were able to develop a single instrument capable of performing both techniques. In so doing, the surface of the three-dimensional object could be acquired and used to extract the object's optical properties. The optical properties of flat polydimethylsiloxane (silicone) phantoms with homogenous tissue-like optical properties were extracted, with and without profilometry correction, after vertical translation and tilting of the phantoms at various angles. Objects having a complex shape, including a hemispheric silicone phantom and human fingers, were acquired and similarly processed, with vascular constriction of a finger being readily detectable through changes in its optical properties. Using profilometry correction, the accuracy of extracted absorption and reduced scattering coefficients improved from two- to ten-fold for surfaces having height variations as much as 3 cm and tilt angles as high as 40 deg. These data lay the foundation for employing structured light for quantitative imaging during surgery.

Analyzing Remodeling of Cardiac Tissue: A Comprehensive Approach Based on Confocal Microscopy and 3D Reconstructions

PubMed Central

Sachse, F. B.

2015-01-01

Microstructural characterization of cardiac tissue and its remodeling in disease is a crucial step in many basic research projects. We present a comprehensive approach for three-dimensional characterization of cardiac tissue at the submicrometer scale. We developed a compression-free mounting method as well as labeling and imaging protocols that facilitate acquisition of three-dimensional image stacks with scanning confocal microscopy. We evaluated the approach with normal and infarcted ventricular tissue. We used the acquired image stacks for segmentation, quantitative analysis and visualization of important tissue components. In contrast to conventional mounting, compression-free mounting preserved cell shapes, capillary lumens and extracellular laminas. Furthermore, the new approach and imaging protocols resulted in high signal-to-noise ratios at depths up to 60 μm. This allowed extensive analyses revealing major differences in volume fractions and distribution of cardiomyocytes, blood vessels, fibroblasts, myofibroblasts and extracellular space in control versus infarct border zone. Our results show that the developed approach yields comprehensive data on microstructure of cardiac tissue and its remodeling in disease. In contrast to other approaches, it allows quantitative assessment of all major tissue components. Furthermore, we suggest that the approach will provide important data for physiological models of cardiac tissue at the submicrometer scale. PMID:26399990

Quantitative Three-Dimensional Imaging of Heterogeneous Materials by Thermal Tomography

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

Sun, J. G.

2016-07-19

Infrared thermal imaging based on active thermal excitations has been widely used for nondestructive evaluation ( NDE) of materials. While the experimental systems have remained essentially the same during the last few decades, development of advanced data-processing methods has significantly improved the capabilities of this technology. However, many limitations still exist. One fundamental limitation is the requirement, either explicitly or implicitly, of the tested material to be homogeneous such that detected thermal contrasts may be used to determine an average material property or attributed to flaws. In this paper, a new thermal tomography ( TT) method is introduced, which formore » the first time can evaluate heterogeneous materials by directly imaging their thermal-property variations with space. It utilizes one-sided flash thermal-imaging data to construct the three-dimensional ( 3D) distribution of thermal effusivity in the entire volume of a test sample. Theoretical analyses for single and multilayer material systems were conducted to validate its formulation and to demonstrate its performance. Experimental results for a ceramic composite plate and a thermal barrier coating ( TBC) sample are also presented. It was shown that thermal diffusion is the primary factor that degrades the spatial resolution with depth for TT; the spatial resolutions in the lateral and axial directions were quantitatively evaluated.« less

An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes

NASA Astrophysics Data System (ADS)

Guldner, Ian H.; Yang, Lin; Cowdrick, Kyle R.; Wang, Qingfei; Alvarez Barrios, Wendy V.; Zellmer, Victoria R.; Zhang, Yizhe; Host, Misha; Liu, Fang; Chen, Danny Z.; Zhang, Siyuan

2016-04-01

Metastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining, and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis, and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.

In vivo, high-resolution, three-dimensional imaging of port wine stain microvasculature in human skin.

PubMed

Liu, Gangjun; Jia, Wangcun; Nelson, J Stuart; Chen, Zhongping

2013-12-01

Port-wine stain (PWS) is a congenital, progressive vascular malformation of the dermis. The use of optical coherence tomography (OCT) for the characterization of blood vessels in PWS skin has been demonstrated by several groups. In the past few years, advances in OCT technology have greatly increased imaging speed. Sophisticated numerical algorithms have improved the sensitivity of Doppler OCT dramatically. These improvements have enabled the noninvasive, high-resolution, three-dimensional functional imaging of PWS skin. Here, we demonstrate high-resolution, three-dimensional, microvasculature imaging of PWS and normal skin using Doppler OCT technique. The OCT system uses a swept source laser which has a central wavelength of 1,310 nm, an A-line rate of 50 kHz and a total average power of 16 mW. The system uses a handheld imaging probe and has an axial resolution of 9.3 µm in air and a lateral resolution of approximately 15 µm. Images were acquired from PWS subjects at the Beckman Laser Institute and Medical Clinic. Microvasculature of the PWS skin and normal skin were obtained from the PWS subject. High-resolution, three-dimensional microvasculature of PWS and normal skin were obtained. Many enlarged PWS vessels are detected in the dermis down to 1.0 mm below the PWS skin surface. In one subject, the blood vessel diameters range from 40 to 90 µm at the epidermal-dermal junction and increase up to 300-500 µm at deeper regions 700-1,000 µm below skin surface. The blood vessels close to the epidermal-dermal junction are more uniform, in terms of diameter. The more tortuous and dilated PWS blood vessels are located at deeper regions 600-1,000 µm below the skin surface. In another subject example, the PWS skin blood vessels are dilated at very superficial layers at a depth less than 500 µm below the skin surface. The PWS skin vessel diameters range from 60 to 650 µm, with most vessels having a diameter of around 200 µm. OCT can be used to quantitatively image in vivo skin micro-vasculature. Analysis of the PWS and normal skin blood vessels were performed and the results can provide quantitative information to optimize laser treatment on an individual patient basis. © 2013 Wiley Periodicals, Inc.

A low-cost tracked C-arm (TC-arm) upgrade system for versatile quantitative intraoperative imaging.

PubMed

Amiri, Shahram; Wilson, David R; Masri, Bassam A; Anglin, Carolyn

2014-07-01

C-arm fluoroscopy is frequently used in clinical applications as a low-cost and mobile real-time qualitative assessment tool. C-arms, however, are not widely accepted for applications involving quantitative assessments, mainly due to the lack of reliable and low-cost position tracking methods, as well as adequate calibration and registration techniques. The solution suggested in this work is a tracked C-arm (TC-arm) which employs a low-cost sensor tracking module that can be retrofitted to any conventional C-arm for tracking the individual joints of the device. Registration and offline calibration methods were developed that allow accurate tracking of the gantry and determination of the exact intrinsic and extrinsic parameters of the imaging system for any acquired fluoroscopic image. The performance of the system was evaluated in comparison to an Optotrak[Formula: see text] motion tracking system and by a series of experiments on accurately built ball-bearing phantoms. Accuracies of the system were determined for 2D-3D registration, three-dimensional landmark localization, and for generating panoramic stitched views in simulated intraoperative applications. The system was able to track the center point of the gantry with an accuracy of [Formula: see text] mm or better. Accuracies of 2D-3D registrations were [Formula: see text] mm and [Formula: see text]. Three-dimensional landmark localization had an accuracy of [Formula: see text] of the length (or [Formula: see text] mm) on average, depending on whether the landmarks were located along, above, or across the table. The overall accuracies of the two-dimensional measurements conducted on stitched panoramic images of the femur and lumbar spine were 2.5 [Formula: see text] 2.0 % [Formula: see text] and [Formula: see text], respectively. The TC-arm system has the potential to achieve sophisticated quantitative fluoroscopy assessment capabilities using an existing C-arm imaging system. This technology may be useful to improve the quality of orthopedic surgery and interventional radiology.

DIGE Analysis of Human Tissues.

PubMed

Gelfi, Cecilia; Capitanio, Daniele

2018-01-01

Two-dimensional difference gel electrophoresis (2-D DIGE) is an advanced and elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2-DE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The two-dye or three-dye systems can be adopted and their choice depends on specific applications. Furthermore, the use of an internal pooled standard makes 2-D DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. The image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.

Prior-knowledge Fitting of Accelerated Five-dimensional Echo Planar J-resolved Spectroscopic Imaging: Effect of Nonlinear Reconstruction on Quantitation.

PubMed

Iqbal, Zohaib; Wilson, Neil E; Thomas, M Albert

2017-07-24

1 H Magnetic Resonance Spectroscopic imaging (SI) is a powerful tool capable of investigating metabolism in vivo from mul- tiple regions. However, SI techniques are time consuming, and are therefore difficult to implement clinically. By applying non-uniform sampling (NUS) and compressed sensing (CS) reconstruction, it is possible to accelerate these scans while re- taining key spectral information. One recently developed method that utilizes this type of acceleration is the five-dimensional echo planar J-resolved spectroscopic imaging (5D EP-JRESI) sequence, which is capable of obtaining two-dimensional (2D) spectra from three spatial dimensions. The prior-knowledge fitting (ProFit) algorithm is typically used to quantify 2D spectra in vivo, however the effects of NUS and CS reconstruction on the quantitation results are unknown. This study utilized a simulated brain phantom to investigate the errors introduced through the acceleration methods. Errors (normalized root mean square error >15%) were found between metabolite concentrations after twelve-fold acceleration for several low concentra- tion (<2 mM) metabolites. The Cramér Rao lower bound% (CRLB%) values, which are typically used for quality control, were not reflective of the increased quantitation error arising from acceleration. Finally, occipital white (OWM) and gray (OGM) human brain matter were quantified in vivo using the 5D EP-JRESI sequence with eight-fold acceleration.

Plenoptic Imaging for Three-Dimensional Particle Field Diagnostics.

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

Guildenbecher, Daniel Robert; Hall, Elise Munz

2017-06-01

Plenoptic imaging is a promising emerging technology for single-camera, 3D diagnostics of particle fields. In this work, recent developments towards quantitative measurements of particle size, positions, and velocities are discussed. First, the technique is proven viable with measurements of the particle field generated by the impact of a water drop on a thin film of water. Next, well cont rolled experiments are used to verify diagnostic uncertainty. Finally, an example is presented of 3D plenoptic imaging of a laboratory scale, explosively generated fragment field.

Tomographic diffractive microscopy with agile illuminations for imaging targets in a noisy background.

PubMed

Zhang, T; Godavarthi, C; Chaumet, P C; Maire, G; Giovannini, H; Talneau, A; Prada, C; Sentenac, A; Belkebir, K

2015-02-15

Tomographic diffractive microscopy is a marker-free optical digital imaging technique in which three-dimensional samples are reconstructed from a set of holograms recorded under different angles of incidence. We show experimentally that, by processing the holograms with singular value decomposition, it is possible to image objects in a noisy background that are invisible with classical wide-field microscopy and conventional tomographic reconstruction procedure. The targets can be further characterized with a selective quantitative inversion.

Spatiotemporal dynamics of oscillatory cellular patterns in three-dimensional directional solidification.

PubMed

Bergeon, N; Tourret, D; Chen, L; Debierre, J-M; Guérin, R; Ramirez, A; Billia, B; Karma, A; Trivedi, R

2013-05-31

We report results of directional solidification experiments conducted on board the International Space Station and quantitative phase-field modeling of those experiments. The experiments image for the first time in situ the spatially extended dynamics of three-dimensional cellular array patterns formed under microgravity conditions where fluid flow is suppressed. Experiments and phase-field simulations reveal the existence of oscillatory breathing modes with time periods of several 10's of minutes. Oscillating cells are usually noncoherent due to array disorder, with the exception of small areas where the array structure is regular and stable.

Investigation of iterative image reconstruction in three-dimensional optoacoustic tomography

PubMed Central

Wang, Kun; Su, Richard; Oraevsky, Alexander A; Anastasio, Mark A

2012-01-01

Iterative image reconstruction algorithms for optoacoustic tomography (OAT), also known as photoacoustic tomography, have the ability to improve image quality over analytic algorithms due to their ability to incorporate accurate models of the imaging physics, instrument response, and measurement noise. However, to date, there have been few reported attempts to employ advanced iterative image reconstruction algorithms for improving image quality in three-dimensional (3D) OAT. In this work, we implement and investigate two iterative image reconstruction methods for use with a 3D OAT small animal imager: namely, a penalized least-squares (PLS) method employing a quadratic smoothness penalty and a PLS method employing a total variation norm penalty. The reconstruction algorithms employ accurate models of the ultrasonic transducer impulse responses. Experimental data sets are employed to compare the performances of the iterative reconstruction algorithms to that of a 3D filtered backprojection (FBP) algorithm. By use of quantitative measures of image quality, we demonstrate that the iterative reconstruction algorithms can mitigate image artifacts and preserve spatial resolution more effectively than FBP algorithms. These features suggest that the use of advanced image reconstruction algorithms can improve the effectiveness of 3D OAT while reducing the amount of data required for biomedical applications. PMID:22864062

Development of quantitative analysis method for stereotactic brain image: assessment of reduced accumulation in extent and severity using anatomical segmentation.

PubMed

Mizumura, Sunao; Kumita, Shin-ichiro; Cho, Keiichi; Ishihara, Makiko; Nakajo, Hidenobu; Toba, Masahiro; Kumazaki, Tatsuo

2003-06-01

Through visual assessment by three-dimensional (3D) brain image analysis methods using stereotactic brain coordinates system, such as three-dimensional stereotactic surface projections and statistical parametric mapping, it is difficult to quantitatively assess anatomical information and the range of extent of an abnormal region. In this study, we devised a method to quantitatively assess local abnormal findings by segmenting a brain map according to anatomical structure. Through quantitative local abnormality assessment using this method, we studied the characteristics of distribution of reduced blood flow in cases with dementia of the Alzheimer type (DAT). Using twenty-five cases with DAT (mean age, 68.9 years old), all of whom were diagnosed as probable Alzheimer's disease based on NINCDS-ADRDA, we collected I-123 iodoamphetamine SPECT data. A 3D brain map using the 3D-SSP program was compared with the data of 20 cases in the control group, who age-matched the subject cases. To study local abnormalities on the 3D images, we divided the whole brain into 24 segments based on anatomical classification. We assessed the extent of an abnormal region in each segment (rate of the coordinates with a Z-value that exceeds the threshold value, in all coordinates within a segment), and severity (average Z-value of the coordinates with a Z-value that exceeds the threshold value). This method clarified orientation and expansion of reduced accumulation, through classifying stereotactic brain coordinates according to the anatomical structure. This method was considered useful for quantitatively grasping distribution abnormalities in the brain and changes in abnormality distribution.

Spatiotemporal Characterization of a Fibrin Clot Using Quantitative Phase Imaging

PubMed Central

Gannavarpu, Rajshekhar; Bhaduri, Basanta; Tangella, Krishnarao; Popescu, Gabriel

2014-01-01

Studying the dynamics of fibrin clot formation and its morphology is an important problem in biology and has significant impact for several scientific and clinical applications. We present a label-free technique based on quantitative phase imaging to address this problem. Using quantitative phase information, we characterized fibrin polymerization in real-time and present a mathematical model describing the transition from liquid to gel state. By exploiting the inherent optical sectioning capability of our instrument, we measured the three-dimensional structure of the fibrin clot. From this data, we evaluated the fractal nature of the fibrin network and extracted the fractal dimension. Our non-invasive and speckle-free approach analyzes the clotting process without the need for external contrast agents. PMID:25386701

Fast Two-Dimensional Bubble Analysis of Biopolymer Filamentous Networks Pore Size from Confocal Microscopy Thin Data Stacks

PubMed Central

Molteni, Matteo; Magatti, Davide; Cardinali, Barbara; Rocco, Mattia; Ferri, Fabio

2013-01-01

The average pore size ξ0 of filamentous networks assembled from biological macromolecules is one of the most important physical parameters affecting their biological functions. Modern optical methods, such as confocal microscopy, can noninvasively image such networks, but extracting a quantitative estimate of ξ0 is a nontrivial task. We present here a fast and simple method based on a two-dimensional bubble approach, which works by analyzing one by one the (thresholded) images of a series of three-dimensional thin data stacks. No skeletonization or reconstruction of the full geometry of the entire network is required. The method was validated by using many isotropic in silico generated networks of different structures, morphologies, and concentrations. For each type of network, the method provides accurate estimates (a few percent) of the average and the standard deviation of the three-dimensional distribution of the pore sizes, defined as the diameters of the largest spheres that can be fit into the pore zones of the entire gel volume. When applied to the analysis of real confocal microscopy images taken on fibrin gels, the method provides an estimate of ξ0 consistent with results from elastic light scattering data. PMID:23473499

Investigations on the change of texture of plant cells due to preservative treatments by digital holographic microscopy

NASA Astrophysics Data System (ADS)

Vora, Priyanka; Anand, Arun

2014-10-01

Texture change is observed in preserved fruits and vegetables. Responsible factors for texture change during preservative treatments are cell morphology, cell wall structure, cell turger, water content and some biochemical components, and also the environmental conditions. Digital Holographic microscopy (DHM) is a quantitative phase contrast imaging technique, which provides three dimensional optical thickness profiles of transparent specimen. Using DHM the morphology of plant cells preserved by refrigeration or stored in vinegar or in sodium chloride can be obtained. This information about the spatio-temporal evolution of optical volume and thickness can be an important tool in area of food processing. Also from the three dimensional images, the texture of the cell can be retrieved and can be investigated under varying conditions.

The perception of three-dimensionality across continuous surfaces

NASA Technical Reports Server (NTRS)

Stevens, Kent A.

1989-01-01

The apparent three-dimensionality of a viewed surface presumably corresponds to several internal preceptual quantities, such as surface curvature, local surface orientation, and depth. These quantities are mathematically related for points within the silhouette bounds of a smooth, continuous surface. For instance, surface curvature is related to the rate of change of local surface orientation, and surface orientation is related to the local gradient of distance. It is not clear to what extent these 3D quantities are determined directly from image information rather than indirectly from mathematically related forms, by differentiation or by integration within boundary constraints. An open empirical question, for example, is to what extent surface curvature is perceived directly, and to what extent it is quantitative rather than qualitative. In addition to surface orientation and curvature, one derives an impression of depth, i.e., variations in apparent egocentric distance. A static orthographic image is essentially devoid of depth information, and any quantitative depth impression must be inferred from surface orientation and other sources. Such conversion of orientation to depth does appear to occur, and even to prevail over stereoscopic depth information under some circumstances.

X-ray Phase Contrast Allows Three Dimensional, Quantitative Imaging of Hydrogel Implants

PubMed Central

Appel, Alyssa A.; Larson, Jeffery C.; Jiang, Bin; Zhong, Zhong; Anastasio, Mark A.; Brey, Eric M.

2015-01-01

Three dimensional imaging techniques are needed for the evaluation and assessment of biomaterials used for tissue engineering and drug delivery applications. Hydrogels are a particularly popular class of materials for medical applications but are difficult to image in tissue using most available imaging modalities. Imaging techniques based on X-ray Phase Contrast (XPC) have shown promise for tissue engineering applications due to their ability to provide image contrast based on multiple X-ray properties. In this manuscript, we investigate the use of XPC for imaging a model hydrogel and soft tissue structure. Porous fibrin loaded poly(ethylene glycol) hydrogels were synthesized and implanted in a rodent subcutaneous model. Samples were explanted and imaged with an analyzer-based XPC technique and processed and stained for histology for comparison. Both hydrogel and soft tissues structures could be identified in XPC images. Structure in skeletal muscle adjacent could be visualized and invading fibrovascular tissue could be quantified. There were no differences between invading tissue measurements from XPC and the gold-standard histology. These results provide evidence of the significant potential of techniques based on XPC for 3D imaging of hydrogel structure and local tissue response. PMID:26487123

Evaluation of simulation-based scatter correction for 3-D PET cardiac imaging

NASA Astrophysics Data System (ADS)

Watson, C. C.; Newport, D.; Casey, M. E.; deKemp, R. A.; Beanlands, R. S.; Schmand, M.

1997-02-01

Quantitative imaging of the human thorax poses one of the most difficult challenges for three-dimensional (3-D) (septaless) positron emission tomography (PET), due to the strong attenuation of the annihilation radiation and the large contribution of scattered photons to the data. In [/sup 18/F] fluorodeoxyglucose (FDG) studies of the heart with the patient's arms in the field of view, the contribution of scattered events can exceed 50% of the total detected coincidences. Accurate correction for this scatter component is necessary for meaningful quantitative image analysis and tracer kinetic modeling. For this reason, the authors have implemented a single-scatter simulation technique for scatter correction in positron volume imaging. Here, they describe this algorithm and present scatter correction results from human and chest phantom studies.

Analysis of x-ray tomography data of an extruded low density styrenic foam: an image analysis study

NASA Astrophysics Data System (ADS)

Lin, Jui-Ching; Heeschen, William

2016-10-01

Extruded styrenic foams are low density foams that are widely used for thermal insulation. It is difficult to precisely characterize the structure of the cells in low density foams by traditional cross-section viewing due to the frailty of the walls of the cells. X-ray computed tomography (CT) is a non-destructive, three dimensional structure characterization technique that has great potential for structure characterization of styrenic foams. Unfortunately the intrinsic artifacts of the data and the artifacts generated during image reconstruction are often comparable in size and shape to the thin walls of the foam, making robust and reliable analysis of cell sizes challenging. We explored three different image processing methods to clean up artifacts in the reconstructed images, thus allowing quantitative three dimensional determination of cell size in a low density styrenic foam. Three image processing approaches - an intensity based approach, an intensity variance based approach, and a machine learning based approach - are explored in this study, and the machine learning image feature classification method was shown to be the best. Individual cells are segmented within the images after the images were cleaned up using the three different methods and the cell sizes are measured and compared in the study. Although the collected data with the image analysis methods together did not yield enough measurements for a good statistic of the measurement of cell sizes, the problem can be resolved by measuring multiple samples or increasing imaging field of view.

Seeing Below the Drop: Direct Nano-to-microscale Imaging of Complex Interfaces involving Solid, Liquid, and Gas Phases

NASA Astrophysics Data System (ADS)

Rykaczewski, Konrad; Landin, Trevan; Walker, Marlon L.; Scott, John Henry J.; Varanasi, Kripa K.

2012-11-01

Nanostructured surfaces with special wetting properties have the potential to transform number of industries, including power generation, water desalination, gas and oil production, and microelectronics thermal management. Predicting the wetting properties of these surfaces requires detailed knowledge of the geometry and the composition of the contact volume linking the droplet to the underlying substrate. Surprisingly, a general nano-to-microscale method for direct imaging of such interfaces has previously not been developed. Here we introduce a three dimensional imaging method which resolves this one-hundred-year-old metrology gap in wetting research. Specifically, we demonstrate direct nano-to-microscale imaging of complex fluidic interfaces using cryofixation in combination with cryo-FIB/SEM. We show that application of this method yields previously unattainable quantitative information about the interfacial geometry of water condensed on silicon nanowire forests with hydrophilic and hydrophobic surface termination in the presence or absence of an intermediate water repelling oil. We also discuss imaging artifacts and the advantages of secondary and backscatter electron imaging, Energy Dispersive Spectrometry (EDS), and three dimensional FIB/SEM tomography.

Noncontact three-dimensional evaluation of surface alterations and wear in NiTi endodontic instruments.

PubMed

Ferreira, Fabiano Guerra; Barbosa, Igor Bastos; Scelza, Pantaleo; Montagnana, Marcello Bulhões; Russano, Daniel; Neff, John; Scelza, Miriam Zaccaro

2017-09-28

The aim of this study was to undertake a qualitative and quantitative assessment of nanoscale alterations and wear on the surfaces of nickel-titanium (NiTi) endodontic instruments, before and after use, through a high-resolution, noncontact, three-dimensional optical profiler, and to verify the accuracy of the evaluation method. Cutting blade surfaces of two different brands of NiTi endodontic instruments, Reciproc R25 (n = 5) and WaveOne Primary (n = 5), were examined and compared before and after two uses in simulated root canals made in clear resin blocks. The analyses were performed on three-dimensional images which were obtained from surface areas measuring 211 × 211 µm, located 3 mm from their tips. The quantitative evaluation of the samples was conducted before and after the first and second usage, by the recordings of three amplitude parameters. The data were subjected to statistical analysis at a 5% level of significance. The results revealed statistically significant increases in the surface wear of both instruments groups after the second use. The presence of irregularities was found on the surface topography of all the instruments, before and after use. Regardless of the evaluation stage, most of the defects were observed in the WaveOne instruments. The three-dimensional technique was suitable and effective for the accurate investigation of the same surfaces of the instruments in different periods of time.

CUBIC pathology: three-dimensional imaging for pathological diagnosis.

PubMed

Nojima, Satoshi; Susaki, Etsuo A; Yoshida, Kyotaro; Takemoto, Hiroyoshi; Tsujimura, Naoto; Iijima, Shohei; Takachi, Ko; Nakahara, Yujiro; Tahara, Shinichiro; Ohshima, Kenji; Kurashige, Masako; Hori, Yumiko; Wada, Naoki; Ikeda, Jun-Ichiro; Kumanogoh, Atsushi; Morii, Eiichi; Ueda, Hiroki R

2017-08-24

The examination of hematoxylin and eosin (H&E)-stained tissues on glass slides by conventional light microscopy is the foundation for histopathological diagnosis. However, this conventional method has some limitations in x-y axes due to its relatively narrow range of observation area and in z-axis due to its two-dimensionality. In this study, we applied a CUBIC pipeline, which is the most powerful tissue-clearing and three-dimensional (3D)-imaging technique, to clinical pathology. CUBIC was applicable to 3D imaging of both normal and abnormal patient-derived, human lung and lymph node tissues. Notably, the combination of deparaffinization and CUBIC enabled 3D imaging of specimens derived from paraffin-embedded tissue blocks, allowing quantitative evaluation of nuclear and structural atypia of an archival malignant lymphoma tissue. Furthermore, to examine whether CUBIC can be applied to practical use in pathological diagnosis, we performed a histopathological screening of a lymph node metastasis based on CUBIC, which successfully improved the sensitivity in detecting minor metastatic carcinoma nodules in lymph nodes. Collectively, our results indicate that CUBIC significantly contributes to retrospective and prospective clinicopathological diagnosis, which might lead to the establishment of a novel field of medical science based on 3D histopathology.

Quantitative Oxygenation Venography from MRI Phase

PubMed Central

Fan, Audrey P.; Bilgic, Berkin; Gagnon, Louis; Witzel, Thomas; Bhat, Himanshu; Rosen, Bruce R.; Adalsteinsson, Elfar

2014-01-01

Purpose To demonstrate acquisition and processing methods for quantitative oxygenation venograms that map in vivo oxygen saturation (SvO2) along cerebral venous vasculature. Methods Regularized quantitative susceptibility mapping (QSM) is used to reconstruct susceptibility values and estimate SvO2 in veins. QSM with ℓ1 and ℓ2 regularization are compared in numerical simulations of vessel structures with known magnetic susceptibility. Dual-echo, flow-compensated phase images are collected in three healthy volunteers to create QSM images. Bright veins in the susceptibility maps are vectorized and used to form a three-dimensional vascular mesh, or venogram, along which to display SvO2 values from QSM. Results Quantitative oxygenation venograms that map SvO2 along brain vessels of arbitrary orientation and geometry are shown in vivo. SvO2 values in major cerebral veins lie within the normal physiological range reported by 15O positron emission tomography. SvO2 from QSM is consistent with previous MR susceptometry methods for vessel segments oriented parallel to the main magnetic field. In vessel simulations, ℓ1 regularization results in less than 10% SvO2 absolute error across all vessel tilt orientations and provides more accurate SvO2 estimation than ℓ2 regularization. Conclusion The proposed analysis of susceptibility images enables reliable mapping of quantitative SvO2 along venograms and may facilitate clinical use of venous oxygenation imaging. PMID:24006229

Hyper-spectrum scanning laser optical tomography

NASA Astrophysics Data System (ADS)

Chen, Lingling; Li, Guiye; Li, Yingchao; Liu, Lina; Liu, Ang; Hu, Xuejuan; Ruan, Shuangchen

2018-02-01

We describe a quantitative fluorescence projection tomography technique which measures the three-dimensional fluorescence spectrum in biomedical samples with size up to several millimeters. This is achieved by acquiring a series of hyperspectral images, by using laser scanning scheme, at different projection angles. We demonstrate that this technique provide a quantitative measure of the fluorescence signal by comparing the spectrum and intensity profile of a fluorescent bead phantom and also demonstrate its application to differentiating the extrinsic label and the autofluorescence in a mouse embryo.

Effects of the approximations of light propagation on quantitative photoacoustic tomography using two-dimensional photon diffusion equation and linearization

NASA Astrophysics Data System (ADS)

Okawa, Shinpei; Hirasawa, Takeshi; Kushibiki, Toshihiro; Ishihara, Miya

2017-12-01

Quantitative photoacoustic tomography (QPAT) employing a light propagation model will play an important role in medical diagnoses by quantifying the concentration of hemoglobin or a contrast agent. However, QPAT by the light propagation model with the three-dimensional (3D) radiative transfer equation (RTE) requires a huge computational load in the iterative forward calculations involved in the updating process to reconstruct the absorption coefficient. The approximations of the light propagation improve the efficiency of the image reconstruction for the QPAT. In this study, we compared the 3D/two-dimensional (2D) photon diffusion equation (PDE) approximating 3D RTE with the Monte Carlo simulation based on 3D RTE. Then, the errors in a 2D PDE-based linearized image reconstruction caused by the approximations were quantitatively demonstrated and discussed in the numerical simulations. It was clearly observed that the approximations affected the reconstructed absorption coefficient. The 2D PDE-based linearized algorithm succeeded in the image reconstruction of the region with a large absorption coefficient in the 3D phantom. The value reconstructed in the phantom experiment agreed with that in the numerical simulation, so that it was validated that the numerical simulation of the image reconstruction predicted the relationship between the true absorption coefficient of the target in the 3D medium and the reconstructed value with the 2D PDE-based linearized algorithm. Moreover, the the true absorption coefficient in 3D medium was estimated from the 2D reconstructed image on the basis of the prediction by the numerical simulation. The estimation was successful in the phantom experiment, although some limitations were revealed.

Quantitative analysis of in vivo mucosal bacterial biofilms.

PubMed

Singhal, Deepti; Boase, Sam; Field, John; Jardeleza, Camille; Foreman, Andrew; Wormald, Peter-John

2012-01-01

Quantitative assays of mucosal biofilms on ex vivo samples are challenging using the currently applied specialized microscopic techniques to identify them. The COMSTAT2 computer program has been applied to in vitro biofilm models for quantifying biofilm structures seen on confocal scanning laser microscopy (CSLM). The aim of this study was to quantify Staphylococcus aureus (S. aureus) biofilms seen via CSLM on ex situ samples of sinonasal mucosa, using the COMSTAT2 program. S. aureus biofilms were grown in frontal sinuses of 4 merino sheep as per a previously standardized sheep sinusitis model for biofilms. Two sinonasal mucosal samples, 10 mm × 10 mm in size, from each of the 2 sinuses of the 4 sheep were analyzed for biofilm presence with Baclight stain and CSLM. Two random image stacks of mucosa with S. aureus biofilm were recorded from each sample, and analyzed using COMSTAT2 software that translates image stacks into a simplified 3-dimensional matrix of biofilm mass by eliminating surrounding host tissue. Three independent observers analyzed images using COMSTAT2 and 3 repeated rounds of analyses were done to calculate biofilm biomass. The COMSTAT2 application uses an observer-dependent threshold setting to translate CSLM biofilm images into a simplified 3-dimensional output for quantitative analysis. Intraclass correlation coefficient (ICC) between thresholds set by the 3 observers for each image stacks was 0.59 (p = 0.0003). Threshold values set at different points of time by a single observer also showed significant correlation as seen by ICC of 0.80 (p < 0.001). COMSTAT2 can be applied to quantify and study the complex 3-dimensional biofilm structures that are recorded via CSLM on mucosal tissue like the sinonasal mucosa. Copyright © 2011 American Rhinologic Society-American Academy of Otolaryngic Allergy, LLC.

Reproducibility and Prognosis of Quantitative Features Extracted from CT Images12

PubMed Central

Balagurunathan, Yoganand; Gu, Yuhua; Wang, Hua; Kumar, Virendra; Grove, Olya; Hawkins, Sam; Kim, Jongphil; Goldgof, Dmitry B; Hall, Lawrence O; Gatenby, Robert A; Gillies, Robert J

2014-01-01

We study the reproducibility of quantitative imaging features that are used to describe tumor shape, size, and texture from computed tomography (CT) scans of non-small cell lung cancer (NSCLC). CT images are dependent on various scanning factors. We focus on characterizing image features that are reproducible in the presence of variations due to patient factors and segmentation methods. Thirty-two NSCLC nonenhanced lung CT scans were obtained from the Reference Image Database to Evaluate Response data set. The tumors were segmented using both manual (radiologist expert) and ensemble (software-automated) methods. A set of features (219 three-dimensional and 110 two-dimensional) was computed, and quantitative image features were statistically filtered to identify a subset of reproducible and nonredundant features. The variability in the repeated experiment was measured by the test-retest concordance correlation coefficient (CCCTreT). The natural range in the features, normalized to variance, was measured by the dynamic range (DR). In this study, there were 29 features across segmentation methods found with CCCTreT and DR ≥ 0.9 and R2Bet ≥ 0.95. These reproducible features were tested for predicting radiologist prognostic score; some texture features (run-length and Laws kernels) had an area under the curve of 0.9. The representative features were tested for their prognostic capabilities using an independent NSCLC data set (59 lung adenocarcinomas), where one of the texture features, run-length gray-level nonuniformity, was statistically significant in separating the samples into survival groups (P ≤ .046). PMID:24772210

Optimal Anesthetic Regime for Motionless Three-Dimensional Image Acquisition During Longitudinal Studies of Adult Nonpigmented Zebrafish.

PubMed

Lockwood, Nicola; Parker, Jennifer; Wilson, Carole; Frankel, Paul

2017-04-01

With many live imaging techniques, it is crucial that a deep level of anesthesia is reached and maintained throughout image acquisition without reducing zebrafish viability. This is particularly true for three-dimensional tomographic imaging modalities. Currently, the most commonly used anesthetic in the zebrafish community, MS-222 (tricaine methanesulfonate), does not allow this. We show, using a combination of both MS-222 and isoflurane, that we can significantly improve the anesthetic regime required for motionless image acquisition of live adult zebrafish. We have benchmarked this against the requirements of our novel quantitative imaging platform, compressive sensing optical projection tomography. Using nonpigmented transgenic zebrafish, we show that a combination of 175 ppm of both anesthetics improves the maintenance of deep anesthesia for prolonged periods of time and it can be used repeatedly to enable longitudinal imaging. Importantly, it does not affect the health or viability of the adult zebrafish. We also show that nonpigmented fish, with a mutated form of the gene transparent, took significantly longer to reach deep anesthesia. The anesthetic regime presented in this study should lead to significant improvements in accuracy and information achievable from imaging live adult zebrafish and in its application to longitudinal studies.

The contribution of synchrotron X-ray computed microtomography to understanding volcanic processes.

PubMed

Polacci, Margherita; Mancini, Lucia; Baker, Don R

2010-03-01

A series of computed microtomography experiments are reported which were performed by using a third-generation synchrotron radiation source on volcanic rocks from various active hazardous volcanoes in Italy and other volcanic areas in the world. The applied technique allowed the internal structure of the investigated material to be accurately imaged at the micrometre scale and three-dimensional views of the investigated samples to be produced as well as three-dimensional quantitative measurements of textural features. The geometry of the vesicle (gas-filled void) network in volcanic products of both basaltic and trachytic compositions were particularly focused on, as vesicle textures are directly linked to the dynamics of volcano degassing. This investigation provided novel insights into modes of gas exsolution, transport and loss in magmas that were not recognized in previous studies using solely conventional two-dimensional imaging techniques. The results of this study are important to understanding the behaviour of volcanoes and can be combined with other geosciences disciplines to forecast their future activity.

Quantitative imaging reveals heterogeneous growth dynamics and treatment-dependent residual tumor distributions in a three-dimensional ovarian cancer model

NASA Astrophysics Data System (ADS)

Celli, Jonathan P.; Rizvi, Imran; Evans, Conor L.; Abu-Yousif, Adnan O.; Hasan, Tayyaba

2010-09-01

Three-dimensional tumor models have emerged as valuable in vitro research tools, though the power of such systems as quantitative reporters of tumor growth and treatment response has not been adequately explored. We introduce an approach combining a 3-D model of disseminated ovarian cancer with high-throughput processing of image data for quantification of growth characteristics and cytotoxic response. We developed custom MATLAB routines to analyze longitudinally acquired dark-field microscopy images containing thousands of 3-D nodules. These data reveal a reproducible bimodal log-normal size distribution. Growth behavior is driven by migration and assembly, causing an exponential decay in spatial density concomitant with increasing mean size. At day 10, cultures are treated with either carboplatin or photodynamic therapy (PDT). We quantify size-dependent cytotoxic response for each treatment on a nodule by nodule basis using automated segmentation combined with ratiometric batch-processing of calcein and ethidium bromide fluorescence intensity data (indicating live and dead cells, respectively). Both treatments reduce viability, though carboplatin leaves micronodules largely structurally intact with a size distribution similar to untreated cultures. In contrast, PDT treatment disrupts micronodular structure, causing punctate regions of toxicity, shifting the distribution toward smaller sizes, and potentially increasing vulnerability to subsequent chemotherapeutic treatment.

Three-dimensional atlas of iron, copper, and zinc in the mouse cerebrum and brainstem.

PubMed

Hare, Dominic J; Lee, Jason K; Beavis, Alison D; van Gramberg, Amanda; George, Jessica; Adlard, Paul A; Finkelstein, David I; Doble, Philip A

2012-05-01

Atlases depicting molecular and functional features of the brain are becoming an integral part of modern neuroscience. In this study we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICPMS) to quantitatively measure iron (Fe), copper (Cu), and zinc (Zn) levels in a serially sectioned C57BL/6 mouse brain (cerebrum and brainstem). Forty-six sections were analyzed in a single experiment of approximately 158 h in duration. We constructed a 46-plate reference atlas by aligning quantified images of metal distribution with corresponding coronal sections from the Allen Mouse Brain Reference Atlas. The 46 plates were also used to construct three-dimensional models of Fe, Cu, and Zn distribution. This atlas represents the first reconstruction of quantitative trace metal distribution through the brain by LA-ICPMS and will facilitate the study of trace metals in the brain and help to elucidate their role in neurobiology.

Three-dimensional ophthalmic optical coherence tomography with a refraction correction algorithm

NASA Astrophysics Data System (ADS)

Zawadzki, Robert J.; Leisser, Christoph; Leitgeb, Rainer; Pircher, Michael; Fercher, Adolf F.

2003-10-01

We built an optical coherence tomography (OCT) system with a rapid scanning optical delay (RSOD) line, which allows probing full axial eye length. The system produces Three-dimensional (3D) data sets that are used to generate 3D tomograms of the model eye. The raw tomographic data were processed by an algorithm, which is based on Snell"s law to correct the interface positions. The Zernike polynomials representation of the interfaces allows quantitative wave aberration measurements. 3D images of our results are presented to illustrate the capabilities of the system and the algorithm performance. The system allows us to measure intra-ocular distances.

Visible/Infrared Optical Depths of Cirrus as Seen by Satellite and Scanning Lidar

NASA Technical Reports Server (NTRS)

Wylie, Donald; Wolf, Walt; Piironen, Paivi; Eloranta, Edwin

1996-01-01

The High Spectral Resolution Lidar (HSRL) and the Volume Imaging Lidar (VIL) were combined to produce a quantitative image of the visible optical depth of cirrus clouds. The HSRL was used to calibrate the VIL signal into backscatter cross sections of particulates. The backscatter cross sections were related to extinction by a constant backscatter phase function determined from the HSRL data. This produced a three dimensional image of visual extinction in the cirrus clouds over a one hour period. Two lidar images were constructed from one hour VIL cross section records.

Imaging of pharmacokinetic rates of indocyanine green in mouse liver with a hybrid fluorescence molecular tomography/x-ray computed tomography system.

PubMed

Zhang, Guanglei; Liu, Fei; Zhang, Bin; He, Yun; Luo, Jianwen; Bai, Jing

2013-04-01

Pharmacokinetic rates have the potential to provide quantitative physiological and pathological information for biological studies and drug development. Fluorescence molecular tomography (FMT) is an attractive imaging tool for three-dimensionally resolving fluorophore distribution in small animals. In this letter, pharmacokinetic rates of indocyanine green (ICG) in mouse liver are imaged with a hybrid FMT and x-ray computed tomography (XCT) system. A recently developed FMT method using structural priors from an XCT system is adopted to improve the quality of FMT reconstruction. In the in vivo experiments, images of uptake and excretion rates of ICG in mouse liver are obtained, which can be used to quantitatively evaluate liver function. The accuracy of the results is validated by a fiber-based fluorescence measurement system.

Living specimen tomography by digital holographic microscopy: morphometry of testate amoeba

NASA Astrophysics Data System (ADS)

Charrière, Florian; Pavillon, Nicolas; Colomb, Tristan; Depeursinge, Christian; Heger, Thierry J.; Mitchell, Edward A. D.; Marquet, Pierre; Rappaz, Benjamin

2006-08-01

This paper presents an optical diffraction tomography technique based on digital holographic microscopy. Quantitative 2-dimensional phase images are acquired for regularly-spaced angular positions of the specimen covering a total angle of π, allowing to built 3-dimensional quantitative refractive index distributions by an inverse Radon transform. A 20x magnification allows a resolution better than 3 μm in all three dimensions, with accuracy better than 0.01 for the refractive index measurements. This technique is for the first time to our knowledge applied to living specimen (testate amoeba, Protista). Morphometric measurements are extracted from the tomographic reconstructions, showing that the commonly used method for testate amoeba biovolume evaluation leads to systematic under evaluations by about 50%.

[Three-dimensional reconstruction of functional brain images].

PubMed

Inoue, M; Shoji, K; Kojima, H; Hirano, S; Naito, Y; Honjo, I

1999-08-01

We consider PET (positron emission tomography) measurement with SPM (Statistical Parametric Mapping) analysis to be one of the most useful methods to identify activated areas of the brain involved in language processing. SPM is an effective analytical method that detects markedly activated areas over the whole brain. However, with the conventional presentations of these functional brain images, such as horizontal slices, three directional projection, or brain surface coloring, makes understanding and interpreting the positional relationships among various brain areas difficult. Therefore, we developed three-dimensionally reconstructed images from these functional brain images to improve the interpretation. The subjects were 12 normal volunteers. The following three types of images were constructed: 1) routine images by SPM, 2) three-dimensional static images, and 3) three-dimensional dynamic images, after PET images were analyzed by SPM during daily dialog listening. The creation of images of both the three-dimensional static and dynamic types employed the volume rendering method by VTK (The Visualization Toolkit). Since the functional brain images did not include original brain images, we synthesized SPM and MRI brain images by self-made C++ programs. The three-dimensional dynamic images were made by sequencing static images with available software. Images of both the three-dimensional static and dynamic types were processed by a personal computer system. Our newly created images showed clearer positional relationships among activated brain areas compared to the conventional method. To date, functional brain images have been employed in fields such as neurology or neurosurgery, however, these images may be useful even in the field of otorhinolaryngology, to assess hearing and speech. Exact three-dimensional images based on functional brain images are important for exact and intuitive interpretation, and may lead to new developments in brain science. Currently, the surface model is the most common method of three-dimensional display. However, the volume rendering method may be more effective for imaging regions such as the brain.

3D Filament Network Segmentation with Multiple Active Contours

NASA Astrophysics Data System (ADS)

Xu, Ting; Vavylonis, Dimitrios; Huang, Xiaolei

2014-03-01

Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and microtubules. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate quantitative, reproducible and objective analysis of the image data, we developed a semi-automated method to extract actin networks and retrieve their topology in 3D. Our method uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then evolve along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. The proposed approach is generally applicable to images of curvilinear networks with low SNR. We demonstrate its potential by extracting the centerlines of synthetic meshwork images, actin networks in 2D TIRF Microscopy images, and 3D actin cable meshworks of live fission yeast cells imaged by spinning disk confocal microscopy.

Quantitative facial asymmetry: using three-dimensional photogrammetry to measure baseline facial surface symmetry.

PubMed

Taylor, Helena O; Morrison, Clinton S; Linden, Olivia; Phillips, Benjamin; Chang, Johnny; Byrne, Margaret E; Sullivan, Stephen R; Forrest, Christopher R

2014-01-01

Although symmetry is hailed as a fundamental goal of aesthetic and reconstructive surgery, our tools for measuring this outcome have been limited and subjective. With the advent of three-dimensional photogrammetry, surface geometry can be captured, manipulated, and measured quantitatively. Until now, few normative data existed with regard to facial surface symmetry. Here, we present a method for reproducibly calculating overall facial symmetry and present normative data on 100 subjects. We enrolled 100 volunteers who underwent three-dimensional photogrammetry of their faces in repose. We collected demographic data on age, sex, and race and subjectively scored facial symmetry. We calculated the root mean square deviation (RMSD) between the native and reflected faces, reflecting about a plane of maximum symmetry. We analyzed the interobserver reliability of the subjective assessment of facial asymmetry and the quantitative measurements and compared the subjective and objective values. We also classified areas of greatest asymmetry as localized to the upper, middle, or lower facial thirds. This cluster of normative data was compared with a group of patients with subtle but increasing amounts of facial asymmetry. We imaged 100 subjects by three-dimensional photogrammetry. There was a poor interobserver correlation between subjective assessments of asymmetry (r = 0.56). There was a high interobserver reliability for quantitative measurements of facial symmetry RMSD calculations (r = 0.91-0.95). The mean RMSD for this normative population was found to be 0.80 ± 0.24 mm. Areas of greatest asymmetry were distributed as follows: 10% upper facial third, 49% central facial third, and 41% lower facial third. Precise measurement permitted discrimination of subtle facial asymmetry within this normative group and distinguished norms from patients with subtle facial asymmetry, with placement of RMSDs along an asymmetry ruler. Facial surface symmetry, which is poorly assessed subjectively, can be easily and reproducibly measured using three-dimensional photogrammetry. The RMSD for facial asymmetry of healthy volunteers clusters at approximately 0.80 ± 0.24 mm. Patients with facial asymmetry due to a pathologic process can be differentiated from normative facial asymmetry based on their RMSDs.

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.

Quantitative power Doppler ultrasound measures of peripheral joint synovitis in poor prognosis early rheumatoid arthritis predict radiographic progression.

PubMed

Sreerangaiah, Dee; Grayer, Michael; Fisher, Benjamin A; Ho, Meilien; Abraham, Sonya; Taylor, Peter C

2016-01-01

To assess the value of quantitative vascular imaging by power Doppler US (PDUS) as a tool that can be used to stratify patient risk of joint damage in early seropositive RA while still biologic naive but on synthetic DMARD treatment. Eighty-five patients with seropositive RA of <3 years duration had clinical, laboratory and imaging assessments at 0 and 12 months. Imaging assessments consisted of radiographs of the hands and feet, two-dimensional (2D) high-frequency and PDUS imaging of 10 MCP joints that were scored for erosions and vascularity and three-dimensional (3D) PDUS of MCP joints and wrists that were scored for vascularity. Severe deterioration on radiographs and ultrasonography was seen in 45 and 28% of patients, respectively. The 3D power Doppler volume and 2D vascularity scores were the most useful US predictors of deterioration. These variables were modelled in two equations that estimate structural damage over 12 months. The equations had a sensitivity of 63.2% and specificity of 80.9% for predicting radiographic structural damage and a sensitivity of 54.2% and specificity of 96.7% for predicting structural damage on ultrasonography. In seropositive early RA, quantitative vascular imaging by PDUS has clinical utility in predicting which patients will derive benefit from early use of biologic therapy. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Determination of mouse skeletal muscle architecture using three-dimensional diffusion tensor imaging.

PubMed

Heemskerk, Anneriet M; Strijkers, Gustav J; Vilanova, Anna; Drost, Maarten R; Nicolay, Klaas

2005-06-01

Muscle architecture is the main determinant of the mechanical behavior of skeletal muscles. This study explored the feasibility of diffusion tensor imaging (DTI) and fiber tracking to noninvasively determine the in vivo three-dimensional (3D) architecture of skeletal muscle in mouse hind leg. In six mice, the hindlimb was imaged with a diffusion-weighted (DW) 3D fast spin-echo (FSE) sequence followed by the acquisition of an exercise-induced, T(2)-enhanced data set. The data showed the expected fiber organization, from which the physiological cross-sectional area (PCSA), fiber length, and pennation angle for the tibialis anterior (TA) were obtained. The values of these parameters ranged from 5.4-9.1 mm(2), 5.8-7.8 mm, and 21-24 degrees , respectively, which is in agreement with values obtained previously with the use of invasive methods. This study shows that 3D DT acquisition and fiber tracking is feasible for the skeletal muscle of mice, and thus enables the quantitative determination of muscle architecture.

Three-dimensional digital mapping of the optic nerve head cupping in glaucoma

NASA Astrophysics Data System (ADS)

Mitra, Sunanda; Ramirez, Manuel; Morales, Jose

1992-08-01

Visualization of the optic nerve head cupping is clinically achieved by stereoscopic viewing of a fundus image pair of the suspected eye. A novel algorithm for three-dimensional digital surface representation of the optic nerve head, using fusion of stereo depth map with a linearly stretched intensity image of a stereo fundus image pair, is presented. Prior to depth map acquisition, a number of preprocessing tasks including feature extraction, registration by cepstral analysis, and correction for intensity variations are performed. The depth map is obtained by using a coarse to fine strategy for obtaining disparities between corresponding areas. The required matching techniques to obtain the translational differences in every step, uses cepstral analysis and correlation-like scanning technique in the spatial domain for the finest details. The quantitative and precise representation of the optic nerve head surface topography following this algorithm is not computationally intensive and should provide more useful information than just qualitative stereoscopic viewing of the fundus as one of the diagnostic criteria for diagnosis of glaucoma.

Does a 3D Image Improve Laparoscopic Motor Skills?

PubMed

Folaranmi, Semiu Eniola; Partridge, Roland W; Brennan, Paul M; Hennessey, Iain A M

2016-08-01

To quantitatively determine whether a three-dimensional (3D) image improves laparoscopic performance compared with a two-dimensional (2D) image. This is a prospective study with two groups of participants: novices (5) and experts (5). Individuals within each group undertook a validated laparoscopic task on a box simulator, alternating between 2D and a 3D laparoscopic image until they had repeated the task five times with each imaging modality. A dedicated motion capture camera was used to determine the time taken to complete the task (seconds) and instrument distance traveled (meters). Among the experts, the mean time taken to perform the task on the 3D image was significantly quicker than on the 2D image, 40.2 seconds versus 51.2 seconds, P < .0001. Among the novices, the mean task time again was significantly quicker on the 3D image, 56.4 seconds versus 82.7 seconds, P < .0001. There was no significant difference in the mean time it took a novice to perform the task using a 3D camera compared with an expert on a 2D camera, 56.4 seconds versus 51.3 seconds, P = .3341. The use of a 3D image confers a significant performance advantage over a 2D camera in quantitatively measured laparoscopic skills for both experts and novices. The use of a 3D image appears to improve a novice's performance to the extent that it is not statistically different from an expert using a 2D image.

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.

A Measure of the Effectiveness of Incorporating 3D Human Anatomy into an Online Undergraduate Laboratory

ERIC Educational Resources Information Center

Hilbelink, Amy J.

2009-01-01

Results of a study designed to determine the effectiveness of implementing three-dimensional (3D) stereo images of a human skull in an undergraduate human anatomy online laboratory were gathered and analysed. Mental model theory and its applications to 3D relationships are discussed along with the research results. Quantitative results on 62 pairs…

Automatic detection and quantitative analysis of cells in the mouse primary motor cortex

NASA Astrophysics Data System (ADS)

Meng, Yunlong; He, Yong; Wu, Jingpeng; Chen, Shangbin; Li, Anan; Gong, Hui

2014-09-01

Neuronal cells play very important role on metabolism regulation and mechanism control, so cell number is a fundamental determinant of brain function. Combined suitable cell-labeling approaches with recently proposed three-dimensional optical imaging techniques, whole mouse brain coronal sections can be acquired with 1-μm voxel resolution. We have developed a completely automatic pipeline to perform cell centroids detection, and provided three-dimensional quantitative information of cells in the primary motor cortex of C57BL/6 mouse. It involves four principal steps: i) preprocessing; ii) image binarization; iii) cell centroids extraction and contour segmentation; iv) laminar density estimation. Investigations on the presented method reveal promising detection accuracy in terms of recall and precision, with average recall rate 92.1% and average precision rate 86.2%. We also analyze laminar density distribution of cells from pial surface to corpus callosum from the output vectorizations of detected cell centroids in mouse primary motor cortex, and find significant cellular density distribution variations in different layers. This automatic cell centroids detection approach will be beneficial for fast cell-counting and accurate density estimation, as time-consuming and error-prone manual identification is avoided.

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain

PubMed Central

Osechinskiy, Sergey; Kruggel, Frithjof

2011-01-01

Registration of histological images to three-dimensional imaging modalities is an important step in quantitative analysis of brain structure, in architectonic mapping of the brain, and in investigation of the pathology of a brain disease. Reconstruction of histology volume from serial sections is a well-established procedure, but it does not address registration of individual slices from sparse sections, which is the aim of the slice-to-volume approach. This study presents a flexible framework for intensity-based slice-to-volume nonrigid registration algorithms with a geometric transformation deformation field parametrized by various classes of spline functions: thin-plate splines (TPS), Gaussian elastic body splines (GEBS), or cubic B-splines. Algorithms are applied to cross-modality registration of histological and magnetic resonance images of the human brain. Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions. For a particular case of histological data, best results are obtained with a TPS three-dimensional (3D) warp, a new unconstrained optimization algorithm (NEWUOA), and a correlation-coefficient-based cost function. PMID:22567290

Fast determination of three-dimensional fibril orientation of type-I collagen via macroscopic chirality

NASA Astrophysics Data System (ADS)

Zhuo, Guan-Yu; Chen, Mei-Yu; Yeh, Chao-Yuan; Guo, Chin-Lin; Kao, Fu-Jen

2017-01-01

Polarization-resolved second harmonic generation (SHG) microscopy is appealing for studying structural proteins and well-organized biophotonic nanostructures, due to its highly sensitized structural specificity. In recent years, it has been used to investigate the chiroptical effect, particularly SHG circular dichroism (SHG-CD) in biological tissues. Although SHG-CD attributed to macromolecular structures has been demonstrated, the corresponding quantitative analysis and interpretation on how SHG correlates with second-order susceptibility χ(2) under circularly polarized excitations remains unclear. In this study, we demonstrate a method based on macroscopic chirality to elucidate the correlation between SHG-CD and the orientation angle of the molecular structure. By exploiting this approach, three-dimensional (3D) molecular orientation of type-I collagen is revealed with only two cross polarized SHG images (i.e., interactions of left and right circular polarizations) without acquiring an image stack of varying polarization.

Three dimensional identification card and applications

NASA Astrophysics Data System (ADS)

Zhou, Changhe; Wang, Shaoqing; Li, Chao; Li, Hao; Liu, Zhao

2016-10-01

Three dimensional Identification Card, with its three-dimensional personal image displayed and stored for personal identification, is supposed be the advanced version of the present two-dimensional identification card in the future [1]. Three dimensional Identification Card means that there are three-dimensional optical techniques are used, the personal image on ID card is displayed to be three-dimensional, so we can see three dimensional personal face. The ID card also stores the three-dimensional face information in its inside electronics chip, which might be recorded by using two-channel cameras, and it can be displayed in computer as three-dimensional images for personal identification. Three-dimensional ID card might be one interesting direction to update the present two-dimensional card in the future. Three-dimension ID card might be widely used in airport custom, entrance of hotel, school, university, as passport for on-line banking, registration of on-line game, etc...

Stereo imaging velocimetry for microgravity applications

NASA Technical Reports Server (NTRS)

Miller, Brian B.; Meyer, Maryjo B.; Bethea, Mark D.

1994-01-01

Stereo imaging velocimetry is the quantitative measurement of three-dimensional flow fields using two sensors recording data from different vantage points. The system described in this paper, under development at NASA Lewis Research Center in Cleveland, Ohio, uses two CCD cameras placed perpendicular to one another, laser disk recorders, an image processing substation, and a 586-based computer to record data at standard NTSC video rates (30 Hertz) and reduce it offline. The flow itself is marked with seed particles, hence the fluid must be transparent. The velocimeter tracks the motion of the particles, and from these we deduce a multipoint (500 or more), quantitative map of the flow. Conceptually, the software portion of the velocimeter can be divided into distinct modules. These modules are: camera calibration, particle finding (image segmentation) and centroid location, particle overlap decomposition, particle tracking, and stereo matching. We discuss our approach to each module, and give our currently achieved speed and accuracy for each where available.

Reconstruction 3-dimensional image from 2-dimensional image of status optical coherence tomography (OCT) for analysis of changes in retinal thickness

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

Arinilhaq,; Widita, Rena

2014-09-30

Optical Coherence Tomography is often used in medical image acquisition to diagnose that change due easy to use and low price. Unfortunately, this type of examination produces a two-dimensional retinal image of the point of acquisition. Therefore, this study developed a method that combines and reconstruct 2-dimensional retinal images into three-dimensional images to display volumetric macular accurately. The system is built with three main stages: data acquisition, data extraction and 3-dimensional reconstruction. At data acquisition step, Optical Coherence Tomography produced six *.jpg images of each patient were further extracted with MATLAB 2010a software into six one-dimensional arrays. The six arraysmore » are combined into a 3-dimensional matrix using a kriging interpolation method with SURFER9 resulting 3-dimensional graphics of macula. Finally, system provides three-dimensional color graphs based on the data distribution normal macula. The reconstruction system which has been designed produces three-dimensional images with size of 481 × 481 × h (retinal thickness) pixels.« less

[Measurement of the frontal and prefrontal lobe volumes in children with malnutrition by three dimensional magnetic resonance imaging scan].

PubMed

Kanemura, Hideaki; Aihara, Masao; Nakazawa, Shinpei

2002-09-01

To evaluate the effects of malnutrition in early life on the growth of the frontal and prefrontal lobes, we quantitatively measured the volumes of the frontal and prefrontal lobes by three dimensional (3-D) MRI in three children (1 year 2 months to 2 years 5 months) with malnutrition. The 3-D MRI data were acquired by the fast spoiled gradient recalled (SPGR) sequence using a 1.5T MR imager. The frontal and prefrontal lobe volumes were measured by the volume measurement function of the Workstation. The data obtained were compared with those of 16 normal subjects (13 children aged 5 months to 14 years, and 3 adults aged 27 to 39 years). The volumes of the frontal and prefrontal lobes in the subjects were smaller compared with age matched controls. The results suggest that malnutrition in early life affects the growth of the frontal and prefrontal lobes.

Utility of three-dimensional and multiplanar reformatted computed tomography for evaluation of pediatric congenital spine abnormalities.

PubMed

Newton, Peter O; Hahn, Gregory W; Fricka, Kevin B; Wenger, Dennis R

2002-04-15

A retrospective radiographic review of 31 patients with congenital spine abnormalities who underwent conventional radiography and advanced imaging studies was conducted. To analyze the utility of three-dimensional computed tomography with multiplanar reformatted images for congenital spine anomalies, as compared with plain radiographs and axial two-dimensional computed tomography imaging. Conventional radiographic imaging for congenital spine disorders often are difficult to interpret because of the patient's small size, the complexity of the disorder, a deformity not in the plane of the radiographs, superimposed structures, and difficulty in forming a mental three-dimensional image. Multiplanar reformatted and three-dimensional computed tomographic imaging offers many potential advantages for defining congenital spine anomalies including visualization of the deformity in any plane, from any angle, with the overlying structures subtracted. The imaging studies of patients who had undergone a three-dimensional computed tomography for congenital deformities of the spine between 1992 and 1998 were reviewed (31 cases). All plain radiographs and axial two-dimensional computed tomography images performed before the three-dimensional computed tomography were reviewed and the findings documented. This was repeated for the three-dimensional reconstructions and, when available, the multiplanar reformatted images (15 cases). In each case, the utility of the advanced imaging was graded as one of the following: Grade A (substantial new information obtained), Grade B (confirmatory with improved visualization and understanding of the deformity), and Grade C (no added useful information obtained). In 17 of 31 cases, the multiplanar reformatted and three-dimensional images allowed identification of unrecognized malformations. In nine additional cases, the advanced imaging was helpful in better visualizing and understanding previously identified deformities. In five cases, no new information was gained. The standard and curved multiplanar reformatted images were best for defining the occiput-C1-C2 anatomy and the extent of segmentation defects. The curved multiplanar reformatted images were especially helpful in keeping the spine from "coming in" and "going out" of the plane of the image when there was significant spine deformity in the sagittal or coronal plane. The three-dimensional reconstructions proved valuable in defining failures of formation. Advanced computed tomography imaging (three-dimensional computed tomography and curved/standard multiplanar reformatted images) allows better definition of congenital spine anomalies. More than 50% of the cases showed additional abnormalities not appreciated on plain radiographs or axial two-dimensional computed tomography images. Curved multiplanar reformatted images allowed imaging in the coronal and sagittal planes of the entire deformity.

Differential diagnosis of lung carcinoma with three-dimensional quantitative molecular vibrational imaging

NASA Astrophysics Data System (ADS)

Gao, Liang; Hammoudi, Ahmad A.; Li, Fuhai; Thrall, Michael J.; Cagle, Philip T.; Chen, Yuanxin; Yang, Jian; Xia, Xiaofeng; Fan, Yubo; Massoud, Yehia; Wang, Zhiyong; Wong, Stephen T. C.

2012-06-01

The advent of molecularly targeted therapies requires effective identification of the various cell types of non-small cell lung carcinomas (NSCLC). Currently, cell type diagnosis is performed using small biopsies or cytology specimens that are often insufficient for molecular testing after morphologic analysis. Thus, the ability to rapidly recognize different cancer cell types, with minimal tissue consumption, would accelerate diagnosis and preserve tissue samples for subsequent molecular testing in targeted therapy. We report a label-free molecular vibrational imaging framework enabling three-dimensional (3-D) image acquisition and quantitative analysis of cellular structures for identification of NSCLC cell types. This diagnostic imaging system employs superpixel-based 3-D nuclear segmentation for extracting such disease-related features as nuclear shape, volume, and cell-cell distance. These features are used to characterize cancer cell types using machine learning. Using fresh unstained tissue samples derived from cell lines grown in a mouse model, the platform showed greater than 97% accuracy for diagnosis of NSCLC cell types within a few minutes. As an adjunct to subsequent histology tests, our novel system would allow fast delineation of cancer cell types with minimum tissue consumption, potentially facilitating on-the-spot diagnosis, while preserving specimens for additional tests. Furthermore, 3-D measurements of cellular structure permit evaluation closer to the native state of cells, creating an alternative to traditional 2-D histology specimen evaluation, potentially increasing accuracy in diagnosing cell type of lung carcinomas.

Automated Recovery of Three-Dimensional Models of Plant Shoots from Multiple Color Images1[C][W][OPEN

PubMed Central

Pound, Michael P.; French, Andrew P.; Murchie, Erik H.; Pridmore, Tony P.

2014-01-01

Increased adoption of the systems approach to biological research has focused attention on the use of quantitative models of biological objects. This includes a need for realistic three-dimensional (3D) representations of plant shoots for quantification and modeling. Previous limitations in single-view or multiple-view stereo algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. We present a fully automatic approach to image-based 3D plant reconstruction that can be achieved using a single low-cost camera. The reconstructed plants are represented as a series of small planar sections that together model the more complex architecture of the leaf surfaces. The boundary of each leaf patch is refined using the level-set method, optimizing the model based on image information, curvature constraints, and the position of neighboring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed and, as such, is applicable to a wide variety of plant species and topologies and can be extended to canopy-scale imaging. We demonstrate the effectiveness of our approach on data sets of wheat (Triticum aestivum) and rice (Oryza sativa) plants as well as a unique virtual data set that allows us to compute quantitative measures of reconstruction accuracy. The output is a 3D mesh structure that is suitable for modeling applications in a format that can be imported in the majority of 3D graphics and software packages. PMID:25332504

Quantitative three-dimensional confocal imaging of the cornea in situ and in vivo: system design and calibration.

PubMed

Petroll, W M; Jester, J V; Cavanagh, H D

1996-01-01

A new depth encoding system (DES) is presented, which makes it possible to calculate, display, and record the z-axis position continuously during in vivo imaging using tandem scanning confocal microscopy (TSCM). In order to verify the accuracy of the DES for calculating the position of the focal plane in the cornea both in vitro and in vivo, we compared TSCM measurements of corneal thickness to measurements made using an ultrasonic pachymeter (UP, a standard clinical instrument) in both enucleated rabbit, cat, and human eyes (n = 15), and in both human patients (n = 7). Very close agreement was found between the UP and TSCM measurements in enucleated eyes; the mean percent difference was 0.50 +/- 2.58% (mean +/- SD, not significant). A significant correlation (R = 0.995, n = 15, p < 0.01) was found between UP and TSCM measurements. These results verify that the theoretical equation for calculating focal depth provided by the TSCM manufacturer is accurate for corneal imaging. Similarly, close agreement was found between the in vivo UP and TSCM measurements; the mean percent differences was 1.67 +/- 1.38% (not significant), confirming that z-axis drift can be minimized with proper applanation of the objective. These results confirm the accuracy of the DES for imaging of the cornea both ex vivo and in vivo. This system should be of great utility for applications where quantitation of the three-dimensional location of cellular structures is needed.

A web service system supporting three-dimensional post-processing of medical images based on WADO protocol.

PubMed

He, Longjun; Xu, Lang; Ming, Xing; Liu, Qian

2015-02-01

Three-dimensional post-processing operations on the volume data generated by a series of CT or MR images had important significance on image reading and diagnosis. As a part of the DIOCM standard, WADO service defined how to access DICOM objects on the Web, but it didn't involve three-dimensional post-processing operations on the series images. This paper analyzed the technical features of three-dimensional post-processing operations on the volume data, and then designed and implemented a web service system for three-dimensional post-processing operations of medical images based on the WADO protocol. In order to improve the scalability of the proposed system, the business tasks and calculation operations were separated into two modules. As results, it was proved that the proposed system could support three-dimensional post-processing service of medical images for multiple clients at the same moment, which met the demand of accessing three-dimensional post-processing operations on the volume data on the web.

Quantification of bone marrow water and lipid composition in anterior cruciate ligament-injured and osteoarthritic knees using three-dimensional magnetic resonance spectroscopic imaging.

PubMed

Tufts, Lauren S; Shet, Keerthi; Liang, Fei; Majumdar, Sharmila; Li, Xiaojuan

2016-06-01

To quantitatively evaluate longitudinal changes in water and lipid in knee bone marrow with and without bone marrow edema-like lesions (BMELs) in subjects with acutely ruptured anterior cruciate ligaments (ACLs) or osteoarthritis (OA) using three-dimensional magnetic resonance spectroscopic imaging (3D MRSI). Ten ACL and 10 OA subjects who presented with BMEL and seven BMEL-free controls were scanned at 3T. All ACL and OA subjects had one-year follow-up scans. 3D MRSI was acquired in BMEL and adjacent bone marrow, and water content (WC) and unsaturated lipid index (UI) were calculated in each region of interest. At baseline, ACL BMEL WC was significantly higher than ACL non-BMEL, OA BMEL, and control WC; ACL non-BMEL WC, ACL BMEL UI, and OA BMEL WC were significantly higher than control. ACL BMEL WC decreased significantly one year post-reconstruction; UI decreased non-significantly (p=0.09). No significant changes in OA BMEL or ACL and OA non-BMEL WC and UI were observed. 3D MRSI is a powerful method of quantitatively assessing the biochemical composition of bone marrow in OA and ACL-injured knees, which may serve as imaging markers to improve comprehension of primary and secondary OA pathology. Copyright © 2016 Elsevier Inc. All rights reserved.

Photogrammetry Applied to Wind Tunnel Testing

NASA Technical Reports Server (NTRS)

Liu, Tian-Shu; Cattafesta, L. N., III; Radeztsky, R. H.; Burner, A. W.

2000-01-01

In image-based measurements, quantitative image data must be mapped to three-dimensional object space. Analytical photogrammetric methods, which may be used to accomplish this task, are discussed from the viewpoint of experimental fluid dynamicists. The Direct Linear Transformation (DLT) for camera calibration, used in pressure sensitive paint, is summarized. An optimization method for camera calibration is developed that can be used to determine the camera calibration parameters, including those describing lens distortion, from a single image. Combined with the DLT method, this method allows a rapid and comprehensive in-situ camera calibration and therefore is particularly useful for quantitative flow visualization and other measurements such as model attitude and deformation in production wind tunnels. The paper also includes a brief description of typical photogrammetric applications to temperature- and pressure-sensitive paint measurements and model deformation measurements in wind tunnels.

Cornea and ocular lens visualized with three-dimensional confocal microscopy

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1992-08-01

This paper demonstrates the advantages of three-dimensional reconstruction of the cornea and the ocular crystalline lens by confocal microscopy and volume rendering computer techniques. The advantages of noninvasive observation of ocular structures in living, unstained, unfixed tissue include the following: the tissue is in a natural living state without the artifacts of fixation, mechanical sectioning, and staining; the three-dimensional structure can be observed from any view point and quantitatively analyzed; the dynamics of morphological changes can be studied; and the use of confocal microscopic observation results in a reduction of the number of animals required for ocular morphometric studies. The main advantage is that the dynamic morphology of ocular structures can be investigated in living ocular tissue. A laser scanning confocal microscope was used in the reflected light mode to obtain the two- dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with 488 nm wavelength. The microscope objective was a Leitz 25X, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133, three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The under sampling resulted in a three-dimensional visualization rendering in which the corneal thickness (z-axis) is compressed. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their `beaded' cell borders, basal lamina, nerve plexus, nerve fibers, free nerve endings in the basal epithelial cells, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in-situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers.

Positron emission tomography

NASA Astrophysics Data System (ADS)

Yamamoto, Y. Lucas; Thompson, Christopher J.; Diksic, Mirko; Meyer, Ernest; Feindel, William H.

One of the most exciting new technologies introduced in the last 10 yr is positron emission tomography (PET). PET provides quantitative, three-dimensional images for the study of specific biochemical and physiological processes in the human body. This approach is analogous to quantitative in-vivo autoradiography but has the added advantage of permitting non-invasive in vivo studies. PET scanning requires a small cyclotron to produce short-lived positron emitting isotopes such as oxygen-15, carbon-11, nitrogen-13 and fluorine-18. Proper radiochemical facilities and advanced computer equipment are also needed. Most important, PET requires a multidisciplinary scientific team of physicists, radiochemists, mathematicians, biochemists and physicians. This review analyzes the most recent trends in the imaging technology, radiochemistry, methodology and clinical applications of positron emission tomography.

Multicellular tumor spheroids as an in vivo-like tumor model for three-dimensional imaging of chemotherapeutic and nano material cellular penetration.

PubMed

Ma, Hui-li; Jiang, Qiao; Han, Siyuan; Wu, Yan; Cui Tomshine, Jin; Wang, Dongliang; Gan, Yaling; Zou, Guozhang; Liang, Xing-Jie

2012-01-01

We present a flexible and highly reproducible method using three-dimensional (3D) multicellular tumor spheroids to quantify chemotherapeutic and nanoparticle penetration properties in vitro. We generated HeLa cell-derived spheroids using the liquid overlay method. To properly characterize HeLa spheroids, scanning electron microscopy, transmission electron microscopy, and multiphoton microscopy were used to obtain high-resolution 3D images of HeLa spheroids. Next, pairing high-resolution optical characterization techniques with flow cytometry, we quantitatively compared the penetration of doxorubicin, quantum dots, and synthetic micelles into 3D HeLa spheroid versus HeLa cells grown in a traditional two-dimensional culturing system. Our data revealed that 3D cultured HeLa cells acquired several clinically relevant morphologic and cellular characteristics (such as resistance to chemotherapeutics) often found in human solid tumors. These characteristic, however, could not be captured using conventional two-dimensional cell culture techniques. This study demonstrated the remarkable versatility of HeLa spheroid 3D imaging. In addition, our results revealed the capability of HeLa spheroids to function as a screening tool for nanoparticles or synthetic micelles that, due to their inherent size, charge, and hydrophobicity, can penetrate into solid tumors and act as delivery vehicles for chemotherapeutics. The development of this image-based, reproducible, and quantifiable in vitro HeLa spheroid screening tool will greatly aid future exploration of chemotherapeutics and nanoparticle delivery into solid tumors.

Three-Dimensional Reflectance Traction Microscopy

PubMed Central

Jones, Christopher A. R.; Groves, Nicholas Scott; Sun, Bo

2016-01-01

Cells in three-dimensional (3D) environments exhibit very different biochemical and biophysical phenotypes compared to the behavior of cells in two-dimensional (2D) environments. As an important biomechanical measurement, 2D traction force microscopy can not be directly extended into 3D cases. In order to quantitatively characterize the contraction field, we have developed 3D reflectance traction microscopy which combines confocal reflection imaging and partial volume correlation postprocessing. We have measured the deformation field of collagen gel under controlled mechanical stress. We have also characterized the deformation field generated by invasive breast cancer cells of different morphologies in 3D collagen matrix. In contrast to employ dispersed tracing particles or fluorescently-tagged matrix proteins, our methods provide a label-free, computationally effective strategy to study the cell mechanics in native 3D extracellular matrix. PMID:27304456

Anisotropic shrinkage of insect air sacs revealed in vivo by X-ray microtomography

NASA Astrophysics Data System (ADS)

Xu, Liang; Chen, Rongchang; Du, Guohao; Yang, Yiming; Wang, Feixiang; Deng, Biao; Xie, Honglan; Xiao, Tiqiao

2016-09-01

Air sacs are thought to be the bellows for insect respiration. However, their exact mechanism of action as a bellows remains unclear. A direct way to investigate this problem is in vivo observation of the changes in their three-dimensional structures. Therefore, four-dimensional X-ray phase contrast microtomography is employed to solve this puzzle. Quantitative analysis of three-dimensional image series reveals that the compression of the air sac during respiration in bell crickets exhibits obvious anisotropic characteristics both longitudinally and transversely. Volumetric changes of the tracheal trunks in the prothorax further strengthen the evidence of this finding. As a result, we conclude that the shrinkage and expansion of the insect air sac is anisotropic, contrary to the hypothesis of isotropy, thereby providing new knowledge for further research on the insect respiratory system.

Three-Dimensional Computer Graphics Brain-Mapping Project.

DTIC Science & Technology

1987-03-15

NEUROQUANT . This package was directed towards quantitative microneuroanatomic data acquisition and analysis. Using this interface, image frames captured...populations of brains. This would have been aprohibitive task if done manually with a densitometer and film, due to user error and bias. NEUROQUANT functioned...of cells were of interest. NEUROQUANT is presently being implemented with a more fully automatic method of localizing the cell bodies directly

Lens-free computational imaging of capillary morphogenesis within three-dimensional substrates

NASA Astrophysics Data System (ADS)

Weidling, John; Isikman, Serhan O.; Greenbaum, Alon; Ozcan, Aydogan; Botvinick, Elliot

2012-12-01

Endothelial cells cultured in three-dimensional (3-D) extracellular matrices spontaneously form microvessels in response to soluble and matrix-bound factors. Such cultures are common for the study of angiogenesis and may find widespread use in drug discovery. Vascular networks are imaged over weeks to measure the distribution of vessel morphogenic parameters. Measurements require micron-scale spatial resolution, which for light microscopy comes at the cost of limited field-of-view (FOV) and shallow depth-of-focus (DOF). Small FOVs and DOFs necessitate lateral and axial mechanical scanning, thus limiting imaging throughput. We present a lens-free holographic on-chip microscopy technique to rapidly image microvessels within a Petri dish over a large volume without any mechanical scanning. This on-chip method uses partially coherent illumination and a CMOS sensor to record in-line holographic images of the sample. For digital reconstruction of the measured holograms, we implement a multiheight phase recovery method to obtain phase images of capillary morphogenesis over a large FOV (24 mm2) with ˜1.5 μm spatial resolution. On average, measured capillary length in our method was within approximately 2% of lengths measured using a 10× microscope objective. These results suggest lens-free on-chip imaging is a useful toolset for high-throughput monitoring and quantitative analysis of microvascular 3-D networks.

Dimension-Factorized Range Migration Algorithm for Regularly Distributed Array Imaging

PubMed Central

Guo, Qijia; Wang, Jie; Chang, Tianying

2017-01-01

The two-dimensional planar MIMO array is a popular approach for millimeter wave imaging applications. As a promising practical alternative, sparse MIMO arrays have been devised to reduce the number of antenna elements and transmitting/receiving channels with predictable and acceptable loss in image quality. In this paper, a high precision three-dimensional imaging algorithm is proposed for MIMO arrays of the regularly distributed type, especially the sparse varieties. Termed the Dimension-Factorized Range Migration Algorithm, the new imaging approach factorizes the conventional MIMO Range Migration Algorithm into multiple operations across the sparse dimensions. The thinner the sparse dimensions of the array, the more efficient the new algorithm will be. Advantages of the proposed approach are demonstrated by comparison with the conventional MIMO Range Migration Algorithm and its non-uniform fast Fourier transform based variant in terms of all the important characteristics of the approaches, especially the anti-noise capability. The computation cost is analyzed as well to evaluate the efficiency quantitatively. PMID:29113083

Tomographic particle image velocimetry of desert locust wakes: instantaneous volumes combine to reveal hidden vortex elements and rapid wake deformation

PubMed Central

Bomphrey, Richard J.; Henningsson, Per; Michaelis, Dirk; Hollis, David

2012-01-01

Aerodynamic structures generated by animals in flight are unstable and complex. Recent progress in quantitative flow visualization has advanced our understanding of animal aerodynamics, but measurements have hitherto been limited to flow velocities at a plane through the wake. We applied an emergent, high-speed, volumetric fluid imaging technique (tomographic particle image velocimetry) to examine segments of the wake of desert locusts, capturing fully three-dimensional instantaneous flow fields. We used those flow fields to characterize the aerodynamic footprint in unprecedented detail and revealed previously unseen wake elements that would have gone undetected by two-dimensional or stereo-imaging technology. Vortex iso-surface topographies show the spatio-temporal signature of aerodynamic force generation manifest in the wake of locusts, and expose the extent to which animal wakes can deform, potentially leading to unreliable calculations of lift and thrust when using conventional diagnostic methods. We discuss implications for experimental design and analysis as volumetric flow imaging becomes more widespread. PMID:22977102

Computer-aided light sheet flow visualization using photogrammetry

NASA Technical Reports Server (NTRS)

Stacy, Kathryn; Severance, Kurt; Childers, Brooks A.

1994-01-01

A computer-aided flow visualization process has been developed to analyze video images acquired from rotating and translating light sheet visualization systems. The computer process integrates a mathematical model for image reconstruction, advanced computer graphics concepts, and digital image processing to provide a quantitative and a visual analysis capability. The image reconstruction model, based on photogrammetry, uses knowledge of the camera and light sheet locations and orientations to project two-dimensional light sheet video images into three-dimensional space. A sophisticated computer visualization package, commonly used to analyze computational fluid dynamics (CFD) results, was chosen to interactively display the reconstructed light sheet images with the numerical surface geometry for the model or aircraft under study. The photogrammetric reconstruction technique and the image processing and computer graphics techniques and equipment are described. Results of the computer-aided process applied to both a wind tunnel translating light sheet experiment and an in-flight rotating light sheet experiment are presented. The capability to compare reconstructed experimental light sheet images with CFD solutions in the same graphics environment is also demonstrated.

Computer-Aided Light Sheet Flow Visualization

NASA Technical Reports Server (NTRS)

Stacy, Kathryn; Severance, Kurt; Childers, Brooks A.

1993-01-01

A computer-aided flow visualization process has been developed to analyze video images acquired from rotating and translating light sheet visualization systems. The computer process integrates a mathematical model for image reconstruction, advanced computer graphics concepts, and digital image processing to provide a quantitative and visual analysis capability. The image reconstruction model, based on photogrammetry, uses knowledge of the camera and light sheet locations and orientations to project two-dimensional light sheet video images into three-dimensional space. A sophisticated computer visualization package, commonly used to analyze computational fluid dynamics (CFD) data sets, was chosen to interactively display the reconstructed light sheet images, along with the numerical surface geometry for the model or aircraft under study. A description is provided of the photogrammetric reconstruction technique, and the image processing and computer graphics techniques and equipment. Results of the computer aided process applied to both a wind tunnel translating light sheet experiment and an in-flight rotating light sheet experiment are presented. The capability to compare reconstructed experimental light sheet images and CFD solutions in the same graphics environment is also demonstrated.

Computer-aided light sheet flow visualization

NASA Technical Reports Server (NTRS)

Stacy, Kathryn; Severance, Kurt; Childers, Brooks A.

1993-01-01

A computer-aided flow visualization process has been developed to analyze video images acquired from rotating and translating light sheet visualization systems. The computer process integrates a mathematical model for image reconstruction, advanced computer graphics concepts, and digital image processing to provide a quantitative and visual analysis capability. The image reconstruction model, based on photogrammetry, uses knowledge of the camera and light sheet locations and orientations to project two-dimensional light sheet video images into three-dimensional space. A sophisticated computer visualization package, commonly used to analyze computational fluid dynamics (CFD) data sets, was chosen to interactively display the reconstructed light sheet images, along with the numerical surface geometry for the model or aircraft under study. A description is provided of the photogrammetric reconstruction technique, and the image processing and computer graphics techniques and equipment. Results of the computer aided process applied to both a wind tunnel translating light sheet experiment and an in-flight rotating light sheet experiment are presented. The capability to compare reconstructed experimental light sheet images and CFD solutions in the same graphics environment is also demonstrated.

Pursuing Mirror Image Reconstruction in Unilateral Microtia: Customizing Auricular Framework by Application of Three-Dimensional Imaging and Three-Dimensional Printing.

PubMed

Chen, Hsin-Yu; Ng, Li-Shia; Chang, Chun-Shin; Lu, Ting-Chen; Chen, Ning-Hung; Chen, Zung-Chung

2017-06-01

Advances in three-dimensional imaging and three-dimensional printing technology have expanded the frontier of presurgical design for microtia reconstruction from two-dimensional curved lines to three-dimensional perspectives. This study presents an algorithm for combining three-dimensional surface imaging, computer-assisted design, and three-dimensional printing to create patient-specific auricular frameworks in unilateral microtia reconstruction. Between January of 2015 and January of 2016, six patients with unilateral microtia were enrolled. The average age of the patients was 7.6 years. A three-dimensional image of the patient's head was captured by 3dMDcranial, and virtual sculpture carried out using Geomagic Freeform software and a Touch X Haptic device for fabrication of the auricular template. Each template was tailored according to the patient's unique auricular morphology. The final construct was mirrored onto the defective side and printed out with biocompatible acrylic material. During the surgery, the prefabricated customized template served as a three-dimensional guide for surgical simulation and sculpture of the MEDPOR framework. Average follow-up was 10.3 months. Symmetric and good aesthetic results with regard to auricular shape, projection, and orientation were obtained. One case with severe implant exposure was salvaged with free temporoparietal fascia transfer and skin grafting. The combination of three-dimensional imaging and manufacturing technology with the malleability of MEDPOR has surpassed existing limitations resulting from the use of autologous materials and the ambiguity of two-dimensional planning. This approach allows surgeons to customize the auricular framework in a highly precise and sophisticated manner, taking a big step closer to the goal of mirror-image reconstruction for unilateral microtia patients. Therapeutic, IV.

Breast segmentation in MR images using three-dimensional spiral scanning and dynamic programming

NASA Astrophysics Data System (ADS)

Jiang, Luan; Lian, Yanyun; Gu, Yajia; Li, Qiang

2013-03-01

Magnetic resonance (MR) imaging has been widely used for risk assessment and diagnosis of breast cancer in clinic. To develop a computer-aided diagnosis (CAD) system, breast segmentation is the first important and challenging task. The accuracy of subsequent quantitative measurement of breast density and abnormalities depends on accurate definition of the breast area in the images. The purpose of this study is to develop and evaluate a fully automated method for accurate segmentation of breast in three-dimensional (3-D) MR images. A fast method was developed to identify bounding box, i.e., the volume of interest (VOI), for breasts. A 3-D spiral scanning method was used to transform the VOI of each breast into a single two-dimensional (2-D) generalized polar-coordinate image. Dynamic programming technique was applied to the transformed 2-D image for delineating the "optimal" contour of the breast. The contour of the breast in the transformed 2-D image was utilized to reconstruct the segmentation results in the 3-D MR images using interpolation and lookup table. The preliminary results on 17 cases show that the proposed method can obtain accurate segmentation of the breast based on subjective observation. By comparing with the manually delineated region of 16 breasts in 8 cases, an overlap index of 87.6% +/- 3.8% (mean +/- SD), and a volume agreement of 93.4% +/- 4.5% (mean +/- SD) were achieved, respectively. It took approximately 3 minutes for our method to segment the breast in an MR scan of 256 slices.

Quantitative Live-Cell Confocal Imaging of 3D Spheroids in a High-Throughput Format.

PubMed

Leary, Elizabeth; Rhee, Claire; Wilks, Benjamin T; Morgan, Jeffrey R

2018-06-01

Accurately predicting the human response to new compounds is critical to a wide variety of industries. Standard screening pipelines (including both in vitro and in vivo models) often lack predictive power. Three-dimensional (3D) culture systems of human cells, a more physiologically relevant platform, could provide a high-throughput, automated means to test the efficacy and/or toxicity of novel substances. However, the challenge of obtaining high-magnification, confocal z stacks of 3D spheroids and understanding their respective quantitative limitations must be overcome first. To address this challenge, we developed a method to form spheroids of reproducible size at precise spatial locations across a 96-well plate. Spheroids of variable radii were labeled with four different fluorescent dyes and imaged with a high-throughput confocal microscope. 3D renderings of the spheroid had a complex bowl-like appearance. We systematically analyzed these confocal z stacks to determine the depth of imaging and the effect of spheroid size and dyes on quantitation. Furthermore, we have shown that this loss of fluorescence can be addressed through the use of ratio imaging. Overall, understanding both the limitations of confocal imaging and the tools to correct for these limits is critical for developing accurate quantitative assays using 3D spheroids.

Generating standardized image data for testing and calibrating quantification of volumes, surfaces, lengths, and object counts in fibrous and porous materials using X-ray microtomography.

PubMed

Jiřík, Miroslav; Bartoš, Martin; Tomášek, Petr; Malečková, Anna; Kural, Tomáš; Horáková, Jana; Lukáš, David; Suchý, Tomáš; Kochová, Petra; Hubálek Kalbáčová, Marie; Králíčková, Milena; Tonar, Zbyněk

2018-06-01

Quantification of the structure and composition of biomaterials using micro-CT requires image segmentation due to the low contrast and overlapping radioopacity of biological materials. The amount of bias introduced by segmentation procedures is generally unknown. We aim to develop software that generates three-dimensional models of fibrous and porous structures with known volumes, surfaces, lengths, and object counts in fibrous materials and to provide a software tool that calibrates quantitative micro-CT assessments. Virtual image stacks were generated using the newly developed software TeIGen, enabling the simulation of micro-CT scans of unconnected tubes, connected tubes, and porosities. A realistic noise generator was incorporated. Forty image stacks were evaluated using micro-CT, and the error between the true known and estimated data was quantified. Starting with geometric primitives, the error of the numerical estimation of surfaces and volumes was eliminated, thereby enabling the quantification of volumes and surfaces of colliding objects. Analysis of the sensitivity of the thresholding upon parameters of generated testing image sets revealed the effects of decreasing resolution and increasing noise on the accuracy of the micro-CT quantification. The size of the error increased with decreasing resolution when the voxel size exceeded 1/10 of the typical object size, which simulated the effect of the smallest details that could still be reliably quantified. Open-source software for calibrating quantitative micro-CT assessments by producing and saving virtually generated image data sets with known morphometric data was made freely available to researchers involved in morphometry of three-dimensional fibrillar and porous structures in micro-CT scans. © 2018 Wiley Periodicals, Inc.

Quantitative analysis of three-dimensional biological cells using interferometric microscopy

NASA Astrophysics Data System (ADS)

Shaked, Natan T.; Wax, Adam

2011-06-01

Live biological cells are three-dimensional microscopic objects that constantly adjust their sizes, shapes and other biophysical features. Wide-field digital interferometry (WFDI) is a holographic technique that is able to record the complex wavefront of the light which has interacted with in-vitro cells in a single camera exposure, where no exogenous contrast agents are required. However, simple quasi-three-dimensional holographic visualization of the cell phase profiles need not be the end of the process. Quantitative analysis should permit extraction of numerical parameters which are useful for cytology or medical diagnosis. Using a transmission-mode setup, the phase profile represents the multiplication between the integral refractive index and the thickness of the sample. These coupled variables may not be distinct when acquiring the phase profiles of dynamic cells. Many morphological parameters which are useful for cell biologists are based on the cell thickness profile rather than on its phase profile. We first overview methods to decouple the cell thickness and its refractive index using the WFDI-based phase profile. Then, we present a whole-cell-imaging approach which is able to extract useful numerical parameters on the cells even in cases where decoupling of cell thickness and refractive index is not possible or desired.

Differentiation of Benign and Malignant Breast Tumors by In-Vivo Three-Dimensional Parallel-Plate Diffuse Optical Tomography

PubMed Central

Choe, Regine; Konecky, Soren D.; Corlu, Alper; Lee, Kijoon; Durduran, Turgut; Busch, David R.; Pathak, Saurav; Czerniecki, Brian J.; Tchou, Julia; Fraker, Douglas L.; DeMichele, Angela; Chance, Britton; Arridge, Simon R.; Schweiger, Martin; Culver, Joseph P.; Schnall, Mitchell D.; Putt, Mary E.; Rosen, Mark A.; Yodh, Arjun G.

2009-01-01

We have developed a novel parallel-plate diffuse optical tomography (DOT) system for three-dimensional in vivo imaging of human breast tumor based on large optical data sets. Images of oxy-, deoxy-, total-hemoglobin concentration, blood oxygen saturation, and tissue scattering were reconstructed. Tumor margins were derived using the optical data with guidance from radiology reports and Magnetic Resonance Imaging. Tumor-to-normal ratios of these endogenous physiological parameters and an optical index were computed for 51 biopsy-proven lesions from 47 subjects. Malignant cancers (N=41) showed statistically significant higher total hemoglobin, oxy-hemoglobin concentration, and scattering compared to normal tissue. Furthermore, malignant lesions exhibited a two-fold average increase in optical index. The influence of core biopsy on DOT results was also explored; the difference between the malignant group measured before core biopsy and the group measured more than one week after core biopsy was not significant. Benign tumors (N=10) did not exhibit statistical significance in the tumor-to-normal ratios of any parameter. Optical index and tumor-to-normal ratios of total hemoglobin, oxy-hemoglobin concentration, and scattering exhibited high area under the receiver operating characteristic curve values from 0.90 to 0.99, suggesting good discriminatory power. The data demonstrate that benign and malignant lesions can be distinguished by quantitative three-dimensional DOT. PMID:19405750

Hindered diffusion of high molecular weight compounds in brain extracellular microenvironment measured with integrative optical imaging.

PubMed

Nicholson, C; Tao, L

1993-12-01

This paper describes the theory of an integrative optical imaging system and its application to the analysis of the diffusion of 3-, 10-, 40-, and 70-kDa fluorescent dextran molecules in agarose gel and brain extracellular microenvironment. The method uses a precisely defined source of fluorescent molecules pressure ejected from a micropipette, and a detailed theory of the intensity contributions from out-of-focus molecules in a three-dimensional medium to a two-dimensional image. Dextrans tagged with either tetramethylrhodamine or Texas Red were ejected into 0.3% agarose gel or rat cortical slices maintained in a perfused chamber at 34 degrees C and imaged using a compound epifluorescent microscope with a 10 x water-immersion objective. About 20 images were taken at 2-10-s intervals, recorded with a cooled CCD camera, then transferred to a 486 PC for quantitative analysis. The diffusion coefficient in agarose gel, D, and the apparent diffusion coefficient, D*, in brain tissue were determined by fitting an integral expression relating the measured two-dimensional image intensity to the theoretical three-dimensional dextran concentration. The measurements in dilute agarose gel provided a reference value of D and validated the method. Values of the tortuosity, lambda = (D/D*)1/2, for the 3- and 10-kDa dextrans were 1.70 and 1.63, respectively, which were consistent with previous values derived from tetramethylammonium measurements in cortex. Tortuosities for the 40- and 70-kDa dextrans had significantly larger values of 2.16 and 2.25, respectively. This suggests that the extracellular space may have local constrictions that hinder the diffusion of molecules above a critical size that lies in the range of many neurotrophic compounds.

Four dimensional observations of clouds from geosynchronous orbit using stereo display and measurement techniques on an interactive information processing system

NASA Technical Reports Server (NTRS)

Hasler, A. F.; Desjardins, M.; Shenk, W. E.

1979-01-01

Simultaneous Geosynchronous Operational Environmental Satellite (GOES) 1 km resolution visible image pairs can provide quantitative three dimensional measurements of clouds. These data have great potential for severe storms research and as a basic parameter measurement source for other areas of meteorology (e.g. climate). These stereo cloud height measurements are not subject to the errors and ambiguities caused by unknown cloud emissivity and temperature profiles that are associated with infrared techniques. This effort describes the display and measurement of stereo data using digital processing techniques.

Mitral Annular Dynamics in Mitral Annular Calcification: A Three-Dimensional Imaging Study.

PubMed

Pressman, Gregg S; Movva, Rajesh; Topilsky, Yan; Clavel, Marie-Annick; Saldanha, Jason A; Watanabe, Nozomi; Enriquez-Sarano, Maurice

2015-07-01

The mitral annulus displays complex conformational changes during the cardiac cycle that can now be quantified by three-dimensional echocardiography. Mitral annular calcification (MAC) is increasingly encountered, but its structural and dynamic consequences are largely unexplored. The objective of this study was to describe alterations in mitral annular dimensions and dynamics in patients with MAC. Transthoracic three-dimensional echocardiography was performed in 43 subjects with MAC and 36 age- and sex-matched normal control subjects. Mitral annular dimensions were quantified, using dedicated software, at six time points (three diastolic, three systolic) during the cardiac cycle. In diastole, the calcified annulus was larger and flatter than normal, with increased anteroposterior diameter (29.4 ± 0.6 vs 27.8 ± 0.6 mm, P = .046), reduced height (2.8 ± 0.2 vs 3.6 ± 0.2 mm, P = .006), and decreased saddle shape (8.9 ± 0.6% vs 11.4 ± 0.6%, P = .005). In systole, patients with MAC had greater annular area at all time points (P < .05 for each) compared with control subjects, because of reduced contraction along the anteroposterior diameter (P < .001). Saddle shape increased in early systole (from 10.5% to 13.5%, P = .04) in control subjects but not in those with MAC (P = NS). Valvular alterations were also noted; although mitral valve tent length decreased during systole in both groups, decreases were less in patients with MAC (P < .05 for mid- and late systole). For certain parameters (e.g., annular area), changes were confined largely to those patients with moderate to severe MAC (P = .006 vs control subjects, but nonsignificant for patients with mild MAC). Quantitative three-dimensional echocardiography provides new insights into the dynamic consequences of MAC. This imaging technique demonstrates that the mitral annulus is not made smaller by calcification. However, there is loss of annular contraction, particularly along the anteroposterior diameter, and loss of early systolic folding along the intercommissural diameter. Associated valvular alterations include smaller than usual declines in tenting during systole. These quantitative three-dimensional echocardiographic data provide new insights into the dynamic physiology of the calcified mitral annulus. Copyright © 2015 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Objective assessment of skin tightening in Asians using a water-filtered near-infrared (1,000–1,800 nm) device with contact-cooling and freezer-stored gel

PubMed Central

Tanaka, Yohei; Tsunemi, Yuichiro; Kawashima, Makoto; Tatewaki, Naoto; Nishida, Hiroshi

2013-01-01

Background Near-infrared has been shown to penetrate deeper than optical light sources independent of skin color, allowing safer treatment for the Asian skin type. Many studies have indicated the efficacy of various types of devices, but have not included a sufficiently objective evaluation. In this study, we used three-dimensional imaging for objective evaluation of facial skin tightening using a water-filtered near-infrared device. Methods Twenty Japanese patients were treated with the water-filtered near-infrared (1,000–1,800 nm) device using a contact-cooling and nonfreezing gel stored in a freezer. Three-dimensional imaging was performed, and quantitative volume measurements were taken to evaluate the change in post-treatment volume. The patients then provided their subjective assessments. Results Objective assessments of the treated cheek volume evaluated by a three-dimensional color schematic representation with quantitative volume measurements showed significant improvement 3 months after treatment. The mean volume reduction at the last post-treatment visit was 2.554 ± 0.999 mL. The post-treatment volume was significantly reduced compared with the pretreatment volume in all patients (P < 0.0001). Eighty-five percent of patients reported satisfaction with the improvement of skin laxity, and 80% of patients reported satisfaction with improvement of rhytids, such as the nasolabial folds. Side effects, such as epidermal burns and scar formation, were not observed throughout the study. Conclusion The advantages of this water-filtered near-infrared treatment are its high efficacy for skin tightening, associated with a minimal level of discomfort and minimal side effects. Together, these characteristics facilitate our ability to administer repeated treatments and provide alternative or adjunctive treatment for patients, with improved results. This study provides a qualitative and quantitative volumetric assessment, establishing the ability of this technology to reduce volume through noninvasive skin tightening. PMID:23837000

Three-Dimensional Analysis of Long-Term Midface Volume Change After Vertical Vector Deep-Plane Rhytidectomy.

PubMed

Jacono, Andrew A; Malone, Melanie H; Talei, Benjamin

2015-07-01

Facial aging is a complicated process that includes volume loss and soft tissue descent. This study provides quantitative 3-dimensional (3D) data on the long-term effect of vertical vector deep-plane rhytidectomy on restoring volume to the midface. To determine if primary vertical vector deep-plane rhytidectomy resulted in long-term volume change in the midface. We performed a prospective study on patients undergoing primary vertical vector deep-plane rhytidectomy to quantitate 3D volume changes in the midface. Quantitative analysis of volume changes was made using the Vectra 3D imaging software (Canfield Scientific, Inc, Fairfield, New Jersey) at a minimum follow-up of 1 year. Forty-three patients (86 hemifaces) were analyzed. The average volume gained in each hemi-midface after vertical vector deep-plane rhytidectomy was 3.2 mL. Vertical vector deep-plane rhytidectomy provides significant long-term augmentation of volume in the midface. These quantitative data demonstrate that some midface volume loss is related to gravitational descent of the cheek fat compartments and that vertical vector deep-plane rhytidectomy may obviate the need for other volumization procedures such as autologous fat grafting in selected cases. 4 Therapeutic. © 2015 The American Society for Aesthetic Plastic Surgery, Inc. Reprints and permission: journals.permissions@oup.com.

3D Reconstruction of the Retinal Arterial Tree Using Subject-Specific Fundus Images

NASA Astrophysics Data System (ADS)

Liu, D.; Wood, N. B.; Xu, X. Y.; Witt, N.; Hughes, A. D.; Samcg, Thom

Systemic diseases, such as hypertension and diabetes, are associated with changes in the retinal microvasculature. Although a number of studies have been performed on the quantitative assessment of the geometrical patterns of the retinal vasculature, previous work has been confined to 2 dimensional (2D) analyses. In this paper, we present an approach to obtain a 3D reconstruction of the retinal arteries from a pair of 2D retinal images acquired in vivo. A simple essential matrix based self-calibration approach was employed for the "fundus camera-eye" system. Vessel segmentation was performed using a semi-automatic approach and correspondence between points from different images was calculated. The results of 3D reconstruction show the centreline of retinal vessels and their 3D curvature clearly. Three-dimensional reconstruction of the retinal vessels is feasible and may be useful in future studies of the retinal vasculature in disease.

Ventilation inhomogeneity in obstructive lung diseases measured by electrical impedance tomography: a simulation study.

PubMed

Schullcke, B; Krueger-Ziolek, S; Gong, B; Jörres, R A; Mueller-Lisse, U; Moeller, K

2017-10-10

Electrical impedance tomography (EIT) has mostly been used in the Intensive Care Unit (ICU) to monitor ventilation distribution but is also promising for the diagnosis in spontaneously breathing patients with obstructive lung diseases. Beside tomographic images, several numerical measures have been proposed to quantitatively assess the lung state. In this study two common measures, the 'Global Inhomogeneity Index' and the 'Coefficient of Variation' were compared regarding their capability to reflect the severity of lung obstruction. A three-dimensional simulation model was used to simulate obstructed lungs, whereby images were reconstructed on a two-dimensional domain. Simulations revealed that minor obstructions are not adequately recognized in the reconstructed images and that obstruction above and below the electrode plane may result in misleading values of inhomogeneity measures. EIT measurements on several electrode planes are necessary to apply these measures in patients with obstructive lung diseases in a promising manner.

Influence of region-of-interest designs on quantitative measurement of multimodal imaging of MR non-enhancing gliomas.

PubMed

Takano, Koji; Kinoshita, Manabu; Arita, Hideyuki; Okita, Yoshiko; Chiba, Yasuyoshi; Kagawa, Naoki; Watanabe, Yoshiyuki; Shimosegawa, Eku; Hatazawa, Jun; Hashimoto, Naoya; Fujimoto, Yasunori; Kishima, Haruhiko

2018-05-01

A number of studies have revealed the usefulness of multimodal imaging in gliomas. Although the results have been heavily affected by the method used for region of interest (ROI) design, the most discriminatory method for setting the ROI remains unclear. The aim of the present study was to determine the most suitable ROI design for 18 F-fluorodeoxyglucose (FDG) and 11 C-methionine (MET) positron emission tomography (PET), apparent diffusion coefficient (ADC), and fractional anisotropy (FA) obtained by diffusion tensor imaging (DTI) from the viewpoint of grades of non-enhancing gliomas. A total of 31 consecutive patients with newly diagnosed, histologically confirmed magnetic resonance (MR) non-enhancing gliomas who underwent FDG-PET, MET-PET and DTI were retrospectively investigated. Quantitative measurements were performed using four different ROIs; hotspot/tumor center and whole tumor, constructed in either two-dimensional (2D) or three-dimensional (3D). Histopathological grading of the tumor was considered as empirical truth and the quantitative measurements obtained from each ROI was correlated with the grade of the tumor. The most discriminating ROI for non-enhancing glioma grading was different according to the different imaging modalities. 2D-hotspot/center ROI was most discriminating for FDG-PET (P=0.087), ADC map (P=0.0083), and FA map (P=0.25), whereas 3D-whole tumor ROI was best for MET-PET (P=0.0050). In the majority of scenarios, 2D-ROIs performed better than 3D-ROIs. Results from the image analysis using FDG-PET, MET-PET, ADC and FA may be affected by ROI design and the most discriminating ROI for non-enhancing glioma grading was different according to the imaging modality.

Implementation of a computationally efficient least-squares algorithm for highly under-determined three-dimensional diffuse optical tomography problems.

PubMed

Yalavarthy, Phaneendra K; Lynch, Daniel R; Pogue, Brian W; Dehghani, Hamid; Paulsen, Keith D

2008-05-01

Three-dimensional (3D) diffuse optical tomography is known to be a nonlinear, ill-posed and sometimes under-determined problem, where regularization is added to the minimization to allow convergence to a unique solution. In this work, a generalized least-squares (GLS) minimization method was implemented, which employs weight matrices for both data-model misfit and optical properties to include their variances and covariances, using a computationally efficient scheme. This allows inversion of a matrix that is of a dimension dictated by the number of measurements, instead of by the number of imaging parameters. This increases the computation speed up to four times per iteration in most of the under-determined 3D imaging problems. An analytic derivation, using the Sherman-Morrison-Woodbury identity, is shown for this efficient alternative form and it is proven to be equivalent, not only analytically, but also numerically. Equivalent alternative forms for other minimization methods, like Levenberg-Marquardt (LM) and Tikhonov, are also derived. Three-dimensional reconstruction results indicate that the poor recovery of quantitatively accurate values in 3D optical images can also be a characteristic of the reconstruction algorithm, along with the target size. Interestingly, usage of GLS reconstruction methods reduces error in the periphery of the image, as expected, and improves by 20% the ability to quantify local interior regions in terms of the recovered optical contrast, as compared to LM methods. Characterization of detector photo-multiplier tubes noise has enabled the use of the GLS method for reconstructing experimental data and showed a promise for better quantification of target in 3D optical imaging. Use of these new alternative forms becomes effective when the ratio of the number of imaging property parameters exceeds the number of measurements by a factor greater than 2.

Time-efficient high-resolution whole-brain three-dimensional macromolecular proton fraction mapping

PubMed Central

Yarnykh, Vasily L.

2015-01-01

Purpose Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole-brain MPF mapping technique utilizing a minimal possible number of source images for scan time reduction. Methods The described technique is based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole-brain three-dimensional MPF mapping with isotropic 1.25×1.25×1.25 mm3 voxel size and scan time of 20 minutes. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from 8 healthy subjects. Results Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (<2%). High-resolution MPF maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details including gray matter structures with high iron content. Conclusions Synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. PMID:26102097

Three-dimensional DNA image cytometry by optical projection tomographic microscopy for early cancer diagnosis.

PubMed

Agarwal, Nitin; Biancardi, Alberto M; Patten, Florence W; Reeves, Anthony P; Seibel, Eric J

2014-04-01

Aneuploidy is typically assessed by flow cytometry (FCM) and image cytometry (ICM). We used optical projection tomographic microscopy (OPTM) for assessing cellular DNA content using absorption and fluorescence stains. OPTM combines some of the attributes of both FCM and ICM and generates isometric high-resolution three-dimensional (3-D) images of single cells. Although the depth of field of the microscope objective was in the submicron range, it was 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. These projections were later reconstructed using computed tomography methods to form a 3-D image. We also present an automated method for 3-D nuclear segmentation. Nuclei of chicken, trout, and triploid trout erythrocyte were used to calibrate OPTM. Ratios of integrated optical densities extracted from 50 images of each standard were compared to ratios of DNA indices from FCM. A comparison of mean square errors with thionin, hematoxylin, Feulgen, and SYTOX green was done. Feulgen technique was preferred as it showed highest stoichiometry, least variance, and preserved nuclear morphology in 3-D. The addition of this quantitative biomarker could further strengthen existing classifiers and improve early diagnosis of cancer using 3-D microscopy.

Synchrotron X-ray computed laminography of the three-dimensional anatomy of tomato leaves.

PubMed

Verboven, Pieter; Herremans, Els; Helfen, Lukas; Ho, Quang T; Abera, Metadel; Baumbach, Tilo; Wevers, Martine; Nicolaï, Bart M

2015-01-01

Synchrotron radiation computed laminography (SR-CL) is presented as an imaging method for analyzing the three-dimensional (3D) anatomy of leaves. The SR-CL method was used to provide 3D images of 1-mm² samples of intact leaves at a pixel resolution of 750 nm. The method allowed visualization and quantitative analysis of palisade and spongy mesophyll cells, and showed local venation patterns, aspects of xylem vascular structure and stomata. The method failed to image subcellular organelles such as chloroplasts. We constructed 3D computer models of leaves that can provide a basis for calculating gas exchange, light penetration and water and solute transport. The leaf anatomy of two different tomato genotypes grown in saturating light conditions was compared by 3D analysis. Differences were found in calculated values of tissue porosity, cell number density, cell area to volume ratio and cell volume and cell shape distributions of palisade and spongy cell layers. In contrast, the exposed cell area to leaf area ratio in mesophyll, a descriptor that correlates to the maximum rate of photosynthesis in saturated light conditions, was no different between spongy and palisade cells or between genotypes. The use of 3D image processing avoids many of the limitations of anatomical analysis with two-dimensional sections. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

Quantitative three-dimensional dynamic imaging of structure and function of the cardiopulmonary and circulatory systems in all regions of the body

NASA Technical Reports Server (NTRS)

Sturm, R. E.; Ritman, E. L.; Wood, E. H.

1975-01-01

The background for, and design of a third generation, general purpose, all electronic spatial scanning system, the DSR is described. Its specified performance capabilities provide dynamic and stop action three dimensional spatial reconstructions of any portion of the body based on a minimum exposure time of 0.01 second for each 28 multiplanar 180 deg scanning set, a maximum scan repetition rate of sixty 28 multiplane scan sets per second, each scan set consisting of a maximum of 240 parallel cross sections of a minimum thickness of 0.9 mm, and encompassing a maximum cylindrical volume about 23 cm in length and up to 38 cm in diameter.

The third dimension bridges the gap between cell culture and live tissue.

PubMed

Pampaloni, Francesco; Reynaud, Emmanuel G; Stelzer, Ernst H K

2007-10-01

Moving from cell monolayers to three-dimensional (3D) cultures is motivated by the need to work with cellular models that mimic the functions of living tissues. Essential cellular functions that are present in tissues are missed by 'petri dish'-based cell cultures. This limits their potential to predict the cellular responses of real organisms. However, establishing 3D cultures as a mainstream approach requires the development of standard protocols, new cell lines and quantitative analysis methods, which include well-suited three-dimensional imaging techniques. We believe that 3D cultures will have a strong impact on drug screening and will also decrease the use of laboratory animals, for example, in the context of toxicity assays.

Three-Dimensional Multiscale Modeling of Dendritic Spacing Selection During Al-Si Directional Solidification

NASA Astrophysics Data System (ADS)

Tourret, Damien; Clarke, Amy J.; Imhoff, Seth D.; Gibbs, Paul J.; Gibbs, John W.; Karma, Alain

2015-08-01

We present a three-dimensional extension of the multiscale dendritic needle network (DNN) model. This approach enables quantitative simulations of the unsteady dynamics of complex hierarchical networks in spatially extended dendritic arrays. We apply the model to directional solidification of Al-9.8 wt.%Si alloy and directly compare the model predictions with measurements from experiments with in situ x-ray imaging. We focus on the dynamical selection of primary spacings over a range of growth velocities, and the influence of sample geometry on the selection of spacings. Simulation results show good agreement with experiments. The computationally efficient DNN model opens new avenues for investigating the dynamics of large dendritic arrays at scales relevant to solidification experiments and processes.

Three-dimensional image acquisition and reconstruction system on a mobile device based on computer-generated integral imaging.

PubMed

Erdenebat, Munkh-Uchral; Kim, Byeong-Jun; Piao, Yan-Ling; Park, Seo-Yeon; Kwon, Ki-Chul; Piao, Mei-Lan; Yoo, Kwan-Hee; Kim, Nam

2017-10-01

A mobile three-dimensional image acquisition and reconstruction system using a computer-generated integral imaging technique is proposed. A depth camera connected to the mobile device acquires the color and depth data of a real object simultaneously, and an elemental image array is generated based on the original three-dimensional information for the object, with lens array specifications input into the mobile device. The three-dimensional visualization of the real object is reconstructed on the mobile display through optical or digital reconstruction methods. The proposed system is implemented successfully and the experimental results certify that the system is an effective and interesting method of displaying real three-dimensional content on a mobile device.

Three-dimensional architecture of the whole human soleus muscle in vivo

PubMed Central

Finni, Taija; D’Souza, Arkiev; Eguchi, Junya; Clarke, Elizabeth C.; Herbert, Robert D.

2018-01-01

Background Most data on the architecture of the human soleus muscle have been obtained from cadaveric dissection or two-dimensional ultrasound imaging. We present the first comprehensive, quantitative study on the three-dimensional anatomy of the human soleus muscle in vivo using diffusion tensor imaging (DTI) techniques. Methods We report three-dimensional fascicle lengths, pennation angles, fascicle curvatures, physiological cross-sectional areas and volumes in four compartments of the soleus at ankle joint angles of 69 ± 12° (plantarflexion, short muscle length; average ± SD across subjects) and 108 ± 7° (dorsiflexion, long muscle length) of six healthy young adults. Microdissection and three-dimensional digitisation on two cadaveric muscles corroborated the compartmentalised structure of the soleus, and confirmed the validity of DTI-based muscle fascicle reconstructions. Results The posterior compartments of the soleus comprised 80 ± 5% of the total muscle volume (356 ± 58 cm3). At the short muscle length, the average fascicle length, pennation angle and curvature was 37 ± 8 mm, 31 ± 3° and 17 ± 4 /m, respectively. We did not find differences in fascicle lengths between compartments. However, pennation angles were on average 12° larger (p < 0.01) in the posterior compartments than in the anterior compartments. For every centimetre that the muscle-tendon unit lengthened, fascicle lengths increased by 3.7 ± 0.8 mm, pennation angles decreased by −3.2 ± 0.9° and curvatures decreased by −2.7 ± 0.8 /m. Fascicles in the posterior compartments rotated almost twice as much as in the anterior compartments during passive lengthening. Discussion The homogeneity in fascicle lengths and inhomogeneity in pennation angles of the soleus may indicate a functionally different role for the anterior and posterior compartments. The data and techniques presented here demonstrate how DTI can be used to obtain detailed, quantitative measurements of the anatomy of complex skeletal muscles in living humans. PMID:29682414

The application of time series models to cloud field morphology analysis

NASA Technical Reports Server (NTRS)

Chin, Roland T.; Jau, Jack Y. C.; Weinman, James A.

1987-01-01

A modeling method for the quantitative description of remotely sensed cloud field images is presented. A two-dimensional texture modeling scheme based on one-dimensional time series procedures is adopted for this purpose. The time series procedure used is the seasonal autoregressive, moving average (ARMA) process in Box and Jenkins. Cloud field properties such as directionality, clustering and cloud coverage can be retrieved by this method. It has been demonstrated that a cloud field image can be quantitatively defined by a small set of parameters and synthesized surrogates can be reconstructed from these model parameters. This method enables cloud climatology to be studied quantitatively.

Magnetic resonance imaging reveals functional anatomy and biomechanics of a living dragon tree

PubMed Central

Hesse, Linnea; Masselter, Tom; Leupold, Jochen; Spengler, Nils; Speck, Thomas; Korvink, Jan Gerrit

2016-01-01

Magnetic resonance imaging (MRI) was used to gain in vivo insight into load-induced displacements of inner plant tissues making a non-invasive and non-destructive stress and strain analysis possible. The central aim of this study was the identification of a possible load-adapted orientation of the vascular bundles and their fibre caps as the mechanically relevant tissue in branch-stem-attachments of Dracaena marginata. The complex three-dimensional deformations that occur during mechanical loading can be analysed on the basis of quasi-three-dimensional data representations of the outer surface, the inner tissue arrangement (meristem and vascular system), and the course of single vascular bundles within the branch-stem-attachment region. In addition, deformations of vascular bundles could be quantified manually and by using digital image correlation software. This combination of qualitative and quantitative stress and strain analysis leads to an improved understanding of the functional morphology and biomechanics of D. marginata, a plant that is used as a model organism for optimizing branched technical fibre-reinforced lightweight trusses in order to increase their load bearing capacity. PMID:27604526

Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data.

PubMed

Suresh, Niraj; Stephens, Sean A; Adams, Lexor; Beck, Anthon N; McKinney, Adriana L; Varga, Tamas

2016-04-26

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and crop management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving plants. X-ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. We aimed to develop a costless and efficient tool that approximates the surface and volume of the root regardless of its shape from three-dimensional (3D) tomography data. The root structure of a Prairie dropseed (Sporobolus heterolepis) specimen was imaged using XCT. The root was reconstructed, and the primary root structure was extracted from the data using a combination of licensed and open-source software. An isosurface polygonal mesh was then created for ease of analysis. We have developed the standalone application imeshJ, generated in MATLAB(1), to calculate root volume and surface area from the mesh. The outputs of imeshJ are surface area (in mm(2)) and the volume (in mm(3)). The process, utilizing a unique combination of tools from imaging to quantitative root analysis, is described. A combination of XCT and open-source software proved to be a powerful combination to noninvasively image plant root samples, segment root data, and extract quantitative information from the 3D data. This methodology of processing 3D data should be applicable to other material/sample systems where there is connectivity between components of similar X-ray attenuation and difficulties arise with segmentation.

Multicenter study of quantitative computed tomography analysis using a computer-aided three-dimensional system in patients with idiopathic pulmonary fibrosis.

PubMed

Iwasawa, Tae; Kanauchi, Tetsu; Hoshi, Toshiko; Ogura, Takashi; Baba, Tomohisa; Gotoh, Toshiyuki; Oba, Mari S

2016-01-01

To evaluate the feasibility of automated quantitative analysis with a three-dimensional (3D) computer-aided system (i.e., Gaussian histogram normalized correlation, GHNC) of computed tomography (CT) images from different scanners. Each institution's review board approved the research protocol. Informed patient consent was not required. The participants in this multicenter prospective study were 80 patients (65 men, 15 women) with idiopathic pulmonary fibrosis. Their mean age was 70.6 years. Computed tomography (CT) images were obtained by four different scanners set at different exposures. We measured the extent of fibrosis using GHNC, and used Pearson's correlation analysis, Bland-Altman plots, and kappa analysis to directly compare the GHNC results with manual scoring by radiologists. Multiple linear regression analysis was performed to determine the association between the CT data and forced vital capacity (FVC). For each scanner, the extent of fibrosis as determined by GHNC was significantly correlated with the radiologists' score. In multivariate analysis, the extent of fibrosis as determined by GHNC was significantly correlated with FVC (p < 0.001). There was no significant difference between the results obtained using different CT scanners. Gaussian histogram normalized correlation was feasible, irrespective of the type of CT scanner used.

Modeling susceptibility difference artifacts produced by metallic implants in magnetic resonance imaging with point-based thin-plate spline image registration.

PubMed

Pauchard, Y; Smith, M; Mintchev, M

2004-01-01

Magnetic resonance imaging (MRI) suffers from geometric distortions arising from various sources. One such source are the non-linearities associated with the presence of metallic implants, which can profoundly distort the obtained images. These non-linearities result in pixel shifts and intensity changes in the vicinity of the implant, often precluding any meaningful assessment of the entire image. This paper presents a method for correcting these distortions based on non-rigid image registration techniques. Two images from a modelled three-dimensional (3D) grid phantom were subjected to point-based thin-plate spline registration. The reference image (without distortions) was obtained from a grid model including a spherical implant, and the corresponding test image containing the distortions was obtained using previously reported technique for spatial modelling of magnetic susceptibility artifacts. After identifying the nonrecoverable area in the distorted image, the calculated spline model was able to quantitatively account for the distortions, thus facilitating their compensation. Upon the completion of the compensation procedure, the non-recoverable area was removed from the reference image and the latter was compared to the compensated image. Quantitative assessment of the goodness of the proposed compensation technique is presented.

Space Radar Image of Kilauea Volcano, Hawaii

NASA Image and Video Library

1999-05-01

This three-dimensional image of the volcano Kilauea was generated based on interferometric fringes derived from two X-band Synthetic Aperture Radar data takes on April 13, 1994 and October 4, 1994. The altitude lines are based on quantitative interpolation of the topographic fringes. The level difference between neighboring altitude lines is 20 meters (66 feet). The ground area covers 12 kilometers by 4 kilometers (7.5 miles by 2.5 miles). The altitude difference in the image is about 500 meters (1,640 feet). The volcano is located around 19.58 degrees north latitude and 155.55 degrees west longitude. http://photojournal.jpl.nasa.gov/catalog/PIA01761

Three-dimensional imaging technology offers promise in medicine.

PubMed

Karako, Kenji; Wu, Qiong; Gao, Jianjun

2014-04-01

Medical imaging plays an increasingly important role in the diagnosis and treatment of disease. Currently, medical equipment mainly has two-dimensional (2D) imaging systems. Although this conventional imaging largely satisfies clinical requirements, it cannot depict pathologic changes in 3 dimensions. The development of three-dimensional (3D) imaging technology has encouraged advances in medical imaging. Three-dimensional imaging technology offers doctors much more information on a pathology than 2D imaging, thus significantly improving diagnostic capability and the quality of treatment. Moreover, the combination of 3D imaging with augmented reality significantly improves surgical navigation process. The advantages of 3D imaging technology have made it an important component of technological progress in the field of medical imaging.

Multiview echocardiography fusion using an electromagnetic tracking system.

PubMed

Punithakumar, Kumaradevan; Hareendranathan, Abhilash R; Paakkanen, Riitta; Khan, Nehan; Noga, Michelle; Boulanger, Pierre; Becher, Harald

2016-08-01

Three-dimensional ultrasound is an emerging modality for the assessment of complex cardiac anatomy and function. The advantages of this modality include lack of ionizing radiation, portability, low cost, and high temporal resolution. Major limitations include limited field-of-view, reliance on frequently limited acoustic windows, and poor signal to noise ratio. This study proposes a novel approach to combine multiple views into a single image using an electromagnetic tracking system in order to improve the field-of-view. The novel method has several advantages: 1) it does not rely on image information for alignment, and therefore, the method does not require image overlap; 2) the alignment accuracy of the proposed approach is not affected by any poor image quality as in the case of image registration based approaches; 3) in contrast to previous optical tracking based system, the proposed approach does not suffer from line-of-sight limitation; and 4) it does not require any initial calibration. In this pilot project, we were able to show that using a heart phantom, our method can fuse multiple echocardiographic images and improve the field-of view. Quantitative evaluations showed that the proposed method yielded a nearly optimal alignment of image data sets in three-dimensional space. The proposed method demonstrates the electromagnetic system can be used for the fusion of multiple echocardiography images with a seamless integration of sensors to the transducer.

Three dimensional characterization of laser ablation craters using high resolution X-ray computed tomography

NASA Astrophysics Data System (ADS)

Galmed, A. H.; du Plessis, A.; le Roux, S. G.; Hartnick, E.; Von Bergmann, H.; Maaza, M.

2018-01-01

Laboratory X-ray computed tomography is an emerging technology for the 3D characterization and dimensional analysis of many types of materials. In this work we demonstrate the usefulness of this characterization method for the full three dimensional analysis of laser ablation craters, in the context of a laser induced breakdown spectroscopy setup. Laser induced breakdown spectroscopy relies on laser ablation for sampling the material of interest. We demonstrate here qualitatively (in images) and quantitatively (in terms of crater cone angles, depths, diameters and volume) laser ablation crater analysis in 3D for metal (aluminum) and rock (false gold ore). We show the effect of a Gaussian beam profile on the resulting crater geometry, as well as the first visual evidence of undercutting in the rock sample, most likely due to ejection of relatively large grains. The method holds promise for optimization of laser ablation setups especially for laser induced breakdown spectroscopy.

3D Actin Network Centerline Extraction with Multiple Active Contours

PubMed Central

Xu, Ting; Vavylonis, Dimitrios; Huang, Xiaolei

2013-01-01

Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and actin cables. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate quantitative, reproducible and objective analysis of the image data, we propose a semi-automated method to extract actin networks and retrieve their topology in 3D. Our method uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then evolve along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. The proposed approach is generally applicable to images of curvilinear networks with low SNR. We demonstrate its potential by extracting the centerlines of synthetic meshwork images, actin networks in 2D Total Internal Reflection Fluorescence Microscopy images, and 3D actin cable meshworks of live fission yeast cells imaged by spinning disk confocal microscopy. Quantitative evaluation of the method using synthetic images shows that for images with SNR above 5.0, the average vertex error measured by the distance between our result and ground truth is 1 voxel, and the average Hausdorff distance is below 10 voxels. PMID:24316442

Comparison of three‐dimensional analysis and stereological techniques for quantifying lithium‐ion battery electrode microstructures

PubMed Central

TAIWO, OLUWADAMILOLA O.; FINEGAN, DONAL P.; EASTWOOD, DAVID S.; FIFE, JULIE L.; BROWN, LEON D.; DARR, JAWWAD A.; LEE, PETER D.; BRETT, DANIEL J.L.

2016-01-01

Summary Lithium‐ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium‐ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3‐D imaging techniques, quantitative assessment of 3‐D microstructures from 2‐D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two‐dimensional (2‐D) data sets. In this study, stereological prediction and three‐dimensional (3‐D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium‐ion battery electrodes were imaged using synchrotron‐based X‐ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2‐D image sections generated from tomographic imaging, whereas direct 3‐D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2‐D image sections is bound to be associated with ambiguity and that volume‐based 3‐D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially‐dependent parameters, such as tortuosity and pore‐phase connectivity. PMID:26999804

Ultrahigh-Resolution 3-Dimensional Seismic Imaging of Seeps from the Continental Slope of the Northern Gulf of Mexico: Subsurface, Seafloor and Into the Water Column

NASA Astrophysics Data System (ADS)

Brookshire, B. N., Jr.; Mattox, B. A.; Parish, A. E.; Burks, A. G.

2016-02-01

Utilizing recently advanced ultrahigh-resolution 3-dimensional (UHR3D) seismic tools we have imaged the seafloor geomorphology and associated subsurface aspects of seep related expulsion features along the continental slope of the northern Gulf of Mexico with unprecedented clarity and continuity. Over an area of approximately 400 km2, over 50 discrete features were identified and three general seafloor geomorphologies indicative of seep activity including mounds, depressions and bathymetrically complex features were quantitatively characterized. Moreover, areas of high seafloor reflectivity indicative of mineralization and areas of coherent seismic amplitude anomalies in the near-seafloor water column indicative of active gas expulsion were identified. In association with these features, shallow source gas accumulations and migration pathways based on salt related stratigraphic uplift and faulting were imaged. Shallow, bottom simulating reflectors (BSRs) interpreted to be free gas trapped under near seafloor gas hydrate accumulations were very clearly imaged.

Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine

NASA Astrophysics Data System (ADS)

Candeo, Alessia; Sana, Ilenia; Ferrari, Eleonora; Maiuri, Luigi; D'Andrea, Cosimo; Valentini, Gianluca; Bassi, Andrea

2016-05-01

Light sheet fluorescence microscopy has proven to be a powerful tool to image fixed and chemically cleared samples, providing in depth and high resolution reconstructions of intact mouse organs. We applied light sheet microscopy to image the mouse intestine. We found that large portions of the sample can be readily visualized, assessing the organ status and highlighting the presence of regions with impaired morphology. Yet, three-dimensional (3-D) sectioning of the intestine leads to a large dataset that produces unnecessary storage and processing overload. We developed a routine that extracts the relevant information from a large image stack and provides quantitative analysis of the intestine morphology. This result was achieved by a three step procedure consisting of: (1) virtually unfold the 3-D reconstruction of the intestine; (2) observe it layer-by-layer; and (3) identify distinct villi and statistically analyze multiple samples belonging to different intestinal regions. Even if the procedure has been developed for the murine intestine, most of the underlying concepts have a general applicability.

Biodynamic profiling of three-dimensional tissue growth techniques

NASA Astrophysics Data System (ADS)

Sun, Hao; Merrill, Dan; Turek, John; Nolte, David

2016-03-01

Three-dimensional tissue culture presents a more biologically relevant environment in which to perform drug development than conventional two-dimensional cell culture. However, obtaining high-content information from inside three dimensional tissue has presented an obstacle to rapid adoption of 3D tissue culture for pharmaceutical applications. Biodynamic imaging is a high-content three-dimensional optical imaging technology based on low-coherence interferometry and digital holography that uses intracellular dynamics as high-content image contrast. In this paper, we use biodynamic imaging to compare pharmaceutical responses to Taxol of three-dimensional multicellular spheroids grown by three different growth techniques: rotating bioreactor, hanging-drop and plate-grown spheroids. The three growth techniques have systematic variations among tissue cohesiveness and intracellular activity and consequently display different pharmacodynamics under identical drug dose conditions. The in vitro tissue cultures are also compared to ex vivo living biopsies. These results demonstrate that three-dimensional tissue cultures are not equivalent, and that drug-response studies must take into account the growth method.

Denoised ordered subset statistically penalized algebraic reconstruction technique (DOS-SPART) in digital breast tomosynthesis

NASA Astrophysics Data System (ADS)

Garrett, John; Li, Yinsheng; Li, Ke; Chen, Guang-Hong

2017-03-01

Digital breast tomosynthesis (DBT) is a three dimensional (3D) breast imaging modality in which projections are acquired over a limited angular span around the compressed breast and reconstructed into image slices parallel to the detector. DBT has been shown to help alleviate the breast tissue overlapping issues of two dimensional (2D) mammography. Since the overlapping tissues may simulate cancer masses or obscure true cancers, this improvement is critically important for improved breast cancer screening and diagnosis. In this work, a model-based image reconstruction method is presented to show that spatial resolution in DBT volumes can be maintained while dose is reduced using the presented method when compared to that of a state-of-the-art commercial reconstruction technique. Spatial resolution was measured in phantom images and subjectively in a clinical dataset. Noise characteristics were explored in a cadaver study. In both the quantitative and subjective results the image sharpness was maintained and overall image quality was maintained at reduced doses when the model-based iterative reconstruction was used to reconstruct the volumes.

A meta-classifier for detecting prostate cancer by quantitative integration of in vivo magnetic resonance spectroscopy and magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Viswanath, Satish; Tiwari, Pallavi; Rosen, Mark; Madabhushi, Anant

2008-03-01

Recently, in vivo Magnetic Resonance Imaging (MRI) and Magnetic Resonance Spectroscopy (MRS) have emerged as promising new modalities to aid in prostate cancer (CaP) detection. MRI provides anatomic and structural information of the prostate while MRS provides functional data pertaining to biochemical concentrations of metabolites such as creatine, choline and citrate. We have previously presented a hierarchical clustering scheme for CaP detection on in vivo prostate MRS and have recently developed a computer-aided method for CaP detection on in vivo prostate MRI. In this paper we present a novel scheme to develop a meta-classifier to detect CaP in vivo via quantitative integration of multimodal prostate MRS and MRI by use of non-linear dimensionality reduction (NLDR) methods including spectral clustering and locally linear embedding (LLE). Quantitative integration of multimodal image data (MRI and PET) involves the concatenation of image intensities following image registration. However multimodal data integration is non-trivial when the individual modalities include spectral and image intensity data. We propose a data combination solution wherein we project the feature spaces (image intensities and spectral data) associated with each of the modalities into a lower dimensional embedding space via NLDR. NLDR methods preserve the relationships between the objects in the original high dimensional space when projecting them into the reduced low dimensional space. Since the original spectral and image intensity data are divorced from their original physical meaning in the reduced dimensional space, data at the same spatial location can be integrated by concatenating the respective embedding vectors. Unsupervised consensus clustering is then used to partition objects into different classes in the combined MRS and MRI embedding space. Quantitative results of our multimodal computer-aided diagnosis scheme on 16 sets of patient data obtained from the ACRIN trial, for which corresponding histological ground truth for spatial extent of CaP is known, show a marginally higher sensitivity, specificity, and positive predictive value compared to corresponding CAD results with the individual modalities.

Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors

PubMed Central

Rey-Villamizar, Nicolas; Merouane, Amine; Lu, Yanbin; Mukherjee, Amit; Trett, Kristen; Chong, Peter; Harris, Carolyn; Shain, William; Roysam, Badrinath

2015-01-01

Motivation: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions. Results: Thick rat brain sections (100–300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni’s L-measure. Coifman’s harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances. Availability and implementation: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors Contact: broysam@central.uh.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701570

[Bone drilling simulation by three-dimensional imaging].

PubMed

Suto, Y; Furuhata, K; Kojima, T; Kurokawa, T; Kobayashi, M

1989-06-01

The three-dimensional display technique has a wide range of medical applications. Pre-operative planning is one typical application: in orthopedic surgery, three-dimensional image processing has been used very successfully. We have employed this technique in pre-operative planning for orthopedic surgery, and have developed a simulation system for bone-drilling. Positive results were obtained by pre-operative rehearsal; when a region of interest is indicated by means of a mouse on the three-dimensional image displayed on the CRT, the corresponding region appears on the slice image which is displayed simultaneously. Consequently, the status of the bone-drilling is constantly monitored. In developing this system, we have placed emphasis on the quality of the reconstructed three-dimensional images, on fast processing, and on the easy operation of the surgical planning simulation.

A novel method to acquire 3D data from serial 2D images of a dental cast

NASA Astrophysics Data System (ADS)

Yi, Yaxing; Li, Zhongke; Chen, Qi; Shao, Jun; Li, Xinshe; Liu, Zhiqin

2007-05-01

This paper introduced a newly developed method to acquire three-dimensional data from serial two-dimensional images of a dental cast. The system consists of a computer and a set of data acquiring device. The data acquiring device is used to take serial pictures of the a dental cast; an artificial neural network works to translate two-dimensional pictures to three-dimensional data; then three-dimensional image can reconstruct by the computer. The three-dimensional data acquiring of dental casts is the foundation of computer-aided diagnosis and treatment planning in orthodontics.

Quantitative 3-d diagnostic ultrasound imaging using a modified transducer array and an automated image tracking technique.

PubMed

Hossack, John A; Sumanaweera, Thilaka S; Napel, Sandy; Ha, Jun S

2002-08-01

An approach for acquiring dimensionally accurate three-dimensional (3-D) ultrasound data from multiple 2-D image planes is presented. This is based on the use of a modified linear-phased array comprising a central imaging array that acquires multiple, essentially parallel, 2-D slices as the transducer is translated over the tissue of interest. Small, perpendicularly oriented, tracking arrays are integrally mounted on each end of the imaging transducer. As the transducer is translated in an elevational direction with respect to the central imaging array, the images obtained by the tracking arrays remain largely coplanar. The motion between successive tracking images is determined using a minimum sum of absolute difference (MSAD) image matching technique with subpixel matching resolution. An initial phantom scanning-based test of a prototype 8 MHz array indicates that linear dimensional accuracy of 4.6% (2 sigma) is achievable. This result compares favorably with those obtained using an assumed average velocity [31.5% (2 sigma) accuracy] and using an approach based on measuring image-to-image decorrelation [8.4% (2 sigma) accuracy]. The prototype array and imaging system were also tested in a clinical environment, and early results suggest that the approach has the potential to enable a low cost, rapid, screening method for detecting carotid artery stenosis. The average time for performing a screening test for carotid stenosis was reduced from an average of 45 minutes using 2-D duplex Doppler to 12 minutes using the new 3-D scanning approach.

Computer-generated 3D ultrasound images of the carotid artery

NASA Technical Reports Server (NTRS)

Selzer, Robert H.; Lee, Paul L.; Lai, June Y.; Frieden, Howard J.; Blankenhorn, David H.

1989-01-01

A method is under development to measure carotid artery lesions from a computer-generated three-dimensional ultrasound image. For each image, the position of the transducer in six coordinates (x, y, z, azimuth, elevation, and roll) is recorded and used to position each B-mode picture element in its proper spatial position in a three-dimensional memory array. After all B-mode images have been assembled in the memory, the three-dimensional image is filtered and resampled to produce a new series of parallel-plane two-dimensional images from which arterial boundaries are determined using edge tracking methods.

Computer-generated 3D ultrasound images of the carotid artery

NASA Astrophysics Data System (ADS)

Selzer, Robert H.; Lee, Paul L.; Lai, June Y.; Frieden, Howard J.; Blankenhorn, David H.

A method is under development to measure carotid artery lesions from a computer-generated three-dimensional ultrasound image. For each image, the position of the transducer in six coordinates (x, y, z, azimuth, elevation, and roll) is recorded and used to position each B-mode picture element in its proper spatial position in a three-dimensional memory array. After all B-mode images have been assembled in the memory, the three-dimensional image is filtered and resampled to produce a new series of parallel-plane two-dimensional images from which arterial boundaries are determined using edge tracking methods.

Three dimensional quantitative characterization of magnetite nanoparticles embedded in mesoporous silicon: local curvature, demagnetizing factors and magnetic Monte Carlo simulations.

PubMed

Uusimäki, Toni; Margaris, Georgios; Trohidou, Kalliopi; Granitzer, Petra; Rumpf, Klemens; Sezen, Meltem; Kothleitner, Gerald

2013-12-07

Magnetite nanoparticles embedded within the pores of a mesoporous silicon template have been characterized using electron tomography. Linear least squares optimization was used to fit an arbitrary ellipsoid to each segmented particle from the three dimensional reconstruction. It was then possible to calculate the demagnetizing factors and the direction of the shape anisotropy easy axis for every particle. The demagnetizing factors, along with the knowledge of spatial and volume distribution of the superparamagnetic nanoparticles, were used as a model for magnetic Monte Carlo simulations, yielding zero field cooling/field cooling and magnetic hysteresis curves, which were compared to the measured ones. Additionally, the local curvature of the magnetite particles' docking site within the mesoporous silicon's surface was obtained in two different ways and a comparison will be given. A new iterative semi-automatic image alignment program was written and the importance of image segmentation for a truly objective analysis is also addressed.

Measurement of cell death by oxidative stress in three-dimensional spheroids from trophoblast and in fragments of decidua tissue.

PubMed

Theuerkauf, Regine-Susanne; Ahammer, Helmut; Siwetz, Monika; Helige, Christine; Dohr, Gottfried; Walcher, Wolfgang; Palacio, José Ramón; Martinez, Paz; Sedlmayr, Peter

2010-05-01

We report a new morphometric method for measurement of the amount of cell death in three-dimensional multicellular spheroids of the trophoblast-like cell line AC1-M59 and of cultured pieces of decidua tissue (decidua spheroids) in response to a cytotoxic agent. The viability of the spheroids was assessed by adding propidium iodide to the culture medium at the end of the toxic treatment. On fluorescence and brightfield images of serial cryosections the areas of propidium iodide fluorescence and the entire corresponding spheroids were measured by applying digital image processing and ratiometrical quantification. As an example, we evaluated the cytotoxic effect of hydrogen peroxide on both types of spheroids. The relative potency of hydrogen peroxide to induce tissue damage was assessed quantitatively for determination of the minimal concentration that leads to an increase in cytotoxicity. The method presented suggests general applicability for in vitro determination of toxicity against tissues. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

Quantitative 3D imaging of yeast by hard X-ray tomography.

PubMed

Zheng, Ting; Li, Wenjie; Guan, Yong; Song, Xiangxia; Xiong, Ying; Liu, Gang; Tian, Yangchao

2012-05-01

Full-field hard X-ray tomography could be used to obtain three-dimensional (3D) nanoscale structures of biological samples. The image of the fission yeast, Schizosaccharomyces pombe, was clearly visualized based on Zernike phase contrast imaging technique and heavy metal staining method at a spatial resolution better than 50 nm at the energy of 8 keV. The distributions and shapes of the organelles during the cell cycle were clearly visualized and two types of organelle were distinguished. The results for cells during various phases were compared and the ratios of organelle volume to cell volume can be analyzed quantitatively. It showed that the ratios remained constant between growth and division phase and increased strongly in stationary phase, following the shape and size of two types of organelles changes. Our results demonstrated that hard X-ray microscopy was a complementary method for imaging and revealing structural information for biological samples. Copyright © 2011 Wiley Periodicals, Inc.

[Study of the reliability in one dimensional size measurement with digital slit lamp microscope].

PubMed

Wang, Tao; Qi, Chaoxiu; Li, Qigen; Dong, Lijie; Yang, Jiezheng

2010-11-01

To study the reliability of digital slit lamp microscope as a tool for quantitative analysis in one dimensional size measurement. Three single-blinded observers acquired and repeatedly measured the images with a size of 4.00 mm and 10.00 mm on the vernier caliper, which simulatated the human eye pupil and cornea diameter under China-made digital slit lamp microscope in the objective magnification of 4 times, 10 times, 16 times, 25 times, 40 times and 4 times, 10 times, 16 times, respectively. The correctness and precision of measurement were compared. The images with 4 mm size were measured by three investigators and the average values were located between 3.98 to 4.06. For the images with 10.00 mm size, the average values fell within 10.00 ~ 10.04. Measurement results of 4.00 mm images showed, except A4, B25, C16 and C25, significant difference was noted between the measured value and the true value. Regarding measurement results of 10.00 mm iamges indicated, except A10, statistical significance was found between the measured value and the true value. In terms of comparing the results of the same size measured at different magnifications by the same investigator, except for investigators A's measurements of 10.00 mm dimension, the measurement results by all the remaining investigators presented statistical significance at different magnifications. Compared measurements of the same size with different magnifications, measurements of 4.00 mm in 4-fold magnification had no significant difference among the investigators', the remaining results were statistically significant. The coefficient of variation of all measurement results were less than 5%; as magnification increased, the coefficient of variation decreased. The measurement of digital slit lamp microscope in one-dimensional size has good reliability,and should be performed for reliability analysis before used for quantitative analysis to reduce systematic errors.

Photogrammetry of the Human Brain: A Novel Method for Three-Dimensional Quantitative Exploration of the Structural Connectivity in Neurosurgery and Neurosciences.

PubMed

De Benedictis, Alessandro; Nocerino, Erica; Menna, Fabio; Remondino, Fabio; Barbareschi, Mattia; Rozzanigo, Umberto; Corsini, Francesco; Olivetti, Emanuele; Marras, Carlo Efisio; Chioffi, Franco; Avesani, Paolo; Sarubbo, Silvio

2018-04-13

Anatomic awareness of the structural connectivity of the brain is mandatory for neurosurgeons, to select the most effective approaches for brain resections. Although standard microdissection is a validated technique to investigate the different white matter (WM) pathways and to verify the results of tractography, the possibility of interactive exploration of the specimens and reliable acquisition of quantitative information has not been described. Photogrammetry is a well-established technique allowing an accurate metrology on highly defined three-dimensional (3D) models. The aim of this work is to propose the application of the photogrammetric technique for supporting the 3D exploration and the quantitative analysis on the cerebral WM connectivity. The main perisylvian pathways, including the superior longitudinal fascicle and the arcuate fascicle were exposed using the Klingler technique. The photogrammetric acquisition followed each dissection step. The point clouds were registered to a reference magnetic resonance image of the specimen. All the acquisitions were coregistered into an open-source model. We analyzed 5 steps, including the cortical surface, the short intergyral fibers, the indirect posterior and anterior superior longitudinal fascicle, and the arcuate fascicle. The coregistration between the magnetic resonance imaging mesh and the point clouds models was highly accurate. Multiple measures of distances between specific cortical landmarks and WM tracts were collected on the photogrammetric model. Photogrammetry allows an accurate 3D reproduction of WM anatomy and the acquisition of unlimited quantitative data directly on the real specimen during the postdissection analysis. These results open many new promising neuroscientific and educational perspectives and also optimize the quality of neurosurgical treatments. Copyright © 2018 Elsevier Inc. All rights reserved.

Clinical utility of three-dimensional contrast-enhanced ultrasound in the differentiation between noninvasive and invasive neoplasms of urinary bladder.

PubMed

Li, Qiu-yang; Tang, Jie; He, En-hui; Li, Yan-mi; Zhou, Yun; Zhang, Xu; Chen, Guangfu

2012-11-01

The purpose of this study was to evaluate the effectiveness of three-dimensional contrast-enhanced ultrasound in differentiating invasive and noninvasive neoplasms of urinary bladder. A total of 60 lesions in 60 consecutive patients with bladder tumors received three dimensional ultrasonography, low acoustic power contrast enhanced ultrasonography and low acoustic power three-dimensional contrast-enhanced ultrasound examination. The IU22 ultrasound scanner and a volume transducer were used and the ultrasound contrast agent was SonoVue. The contrast-specific sonographic imaging modes were PI (pulse inversion) and PM (power modulation). The three dimensional ultrasonography, contrast enhanced ultrasonography, and three-dimensional contrast-enhanced ultrasound images were independently reviewed by two readers who were not in the images acquisition. Images were analyzed off-site. A level of confidence in the diagnosis of tumor invasion of the muscle layer was assigned on a 5° scale. Receiver operating characteristic analysis was used to assess overall confidence in the diagnosis of muscle invasion by tumor. Kappa values were used to assess inter-readers agreement. Histologic diagnosis was obtained for all patients. Final pathologic staging revealed 44 noninvasive tumors and 16 invasive tumors. Three-dimensional contrast-enhanced ultrasound depicted all 16 muscle-invasive tumors. The diagnostic performance of three-dimensional contrast-enhanced ultrasound was better than those of three dimensional ultrasonography and contrast enhanced ultrasonography. The receiver operating characteristic curves were 0.976 and 0.967 for three-dimensional contrast-enhanced ultrasound, those for three dimensional ultrasonography were 0.881 and 0.869, those for contrast enhanced ultrasonography were 0.927 and 0.929. The kappa values in the three dimensional ultrasonography, contrast enhanced ultrasonography and three-dimensional contrast-enhanced ultrasound for inter-reader agreements were 0.717, 0.794 and 0.914. Three-dimensional contrast-enhanced ultrasound imaging, with contrast-enhanced spatial visualization is clinical useful for differentiating invasive and noninvasive neoplasms of urinary bladder objectively. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Three-Dimensional Imaging in Rhinoplasty: A Comparison of the Simulated versus Actual Result.

PubMed

Persing, Sarah; Timberlake, Andrew; Madari, Sarika; Steinbacher, Derek

2018-05-22

Computer imaging has become increasingly popular for rhinoplasty. Three-dimensional (3D) analysis permits a more comprehensive view from multiple vantage points. However, the predictability and concordance between the simulated and actual result have not been morphometrically studied. The purpose of this study was to aesthetically and quantitatively compare the simulated to actual rhinoplasty result. A retrospective review of 3D images (VECTRA, Canfield) for rhinoplasty patients was performed. Images (preop, simulated, and actual) were randomized. A blinded panel of physicians rated the images (1 = poor, 5 = excellent). The image series considered "best" was also recorded. A quantitative assessment of nasolabial angle and tip projection was compared. Paired and two-sample t tests were performed for statistical analysis (P < 0.05 as significant). Forty patients were included. 67.5% of preoperative images were rated as poor (mean = 1.7). The simulation received a mean score of 2.9 (good in 60% of cases). 82.5% of actual cases were rated good to excellent (mean 3.4) (P < 0.001). Overall, the panel significantly preferred the actual postoperative result in 77.5% of cases compared to the simulation in 22.5% of cases (P < 0.001). The actual nasal tip was more projected compared to the simulations for both males and females. There was no significant difference in nasal tip rotation between simulated and postoperative groups. 3D simulation is a powerful communication and planning tool in rhinoplasty. In this study, the actual result was deemed more aesthetic than the simulated image. Surgeon experience is important to translate the plan and achieve favorable postoperative results. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

A novel image processing technique for 3D volumetric analysis of severely resorbed alveolar sockets with CBCT.

PubMed

Manavella, Valeria; Romano, Federica; Garrone, Federica; Terzini, Mara; Bignardi, Cristina; Aimetti, Mario

2017-06-01

The aim of this study was to present and validate a novel procedure for the quantitative volumetric assessment of extraction sockets that combines cone-beam computed tomography (CBCT) and image processing techniques. The CBCT dataset of 9 severely resorbed extraction sockets was analyzed by means of two image processing software, Image J and Mimics, using manual and automated segmentation techniques. They were also applied on 5-mm spherical aluminum markers of known volume and on a polyvinyl chloride model of one alveolar socket scanned with Micro-CT to test the accuracy. Statistical differences in alveolar socket volume were found between the different methods of volumetric analysis (P<0.0001). The automated segmentation using Mimics was the most reliable and accurate method with a relative error of 1.5%, considerably smaller than the error of 7% and of 10% introduced by the manual method using Mimics and by the automated method using ImageJ. The currently proposed automated segmentation protocol for the three-dimensional rendering of alveolar sockets showed more accurate results, excellent inter-observer similarity and increased user friendliness. The clinical application of this method enables a three-dimensional evaluation of extraction socket healing after the reconstructive procedures and during the follow-up visits.

Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition.

PubMed

Mathew, B; Schmitz, A; Muñoz-Descalzo, S; Ansari, N; Pampaloni, F; Stelzer, E H K; Fischer, S C

2015-06-08

Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological specimens cell nuclei are densely packed and appear to touch one another in the images. Therefore, a major difficulty of three-dimensional cell nuclei segmentation is the decomposition of cell nuclei that apparently touch each other. Current methods are highly adapted to a certain biological specimen or a specific microscope. They do not ensure similarly accurate segmentation performance, i.e. their robustness for different datasets is not guaranteed. Hence, these methods require elaborate adjustments to each dataset. We present an advanced three-dimensional cell nuclei segmentation algorithm that is accurate and robust. Our approach combines local adaptive pre-processing with decomposition based on Lines-of-Sight (LoS) to separate apparently touching cell nuclei into approximately convex parts. We demonstrate the superior performance of our algorithm using data from different specimens recorded with different microscopes. The three-dimensional images were recorded with confocal and light sheet-based fluorescence microscopes. The specimens are an early mouse embryo and two different cellular spheroids. We compared the segmentation accuracy of our algorithm with ground truth data for the test images and results from state-of-the-art methods. The analysis shows that our method is accurate throughout all test datasets (mean F-measure: 91%) whereas the other methods each failed for at least one dataset (F-measure≤69%). Furthermore, nuclei volume measurements are improved for LoS decomposition. The state-of-the-art methods required laborious adjustments of parameter values to achieve these results. Our LoS algorithm did not require parameter value adjustments. The accurate performance was achieved with one fixed set of parameter values. We developed a novel and fully automated three-dimensional cell nuclei segmentation method incorporating LoS decomposition. LoS are easily accessible features that ensure correct splitting of apparently touching cell nuclei independent of their shape, size or intensity. Our method showed superior performance compared to state-of-the-art methods, performing accurately for a variety of test images. Hence, our LoS approach can be readily applied to quantitative evaluation in drug testing, developmental and cell biology.

Rectification of curved document images based on single view three-dimensional reconstruction.

PubMed

Kang, Lai; Wei, Yingmei; Jiang, Jie; Bai, Liang; Lao, Songyang

2016-10-01

Since distortions in camera-captured document images significantly affect the accuracy of optical character recognition (OCR), distortion removal plays a critical role for document digitalization systems using a camera for image capturing. This paper proposes a novel framework that performs three-dimensional (3D) reconstruction and rectification of camera-captured document images. While most existing methods rely on additional calibrated hardware or multiple images to recover the 3D shape of a document page, or make a simple but not always valid assumption on the corresponding 3D shape, our framework is more flexible and practical since it only requires a single input image and is able to handle a general locally smooth document surface. The main contributions of this paper include a new iterative refinement scheme for baseline fitting from connected components of text line, an efficient discrete vertical text direction estimation algorithm based on convex hull projection profile analysis, and a 2D distortion grid construction method based on text direction function estimation using 3D regularization. In order to examine the performance of our proposed method, both qualitative and quantitative evaluation and comparison with several recent methods are conducted in our experiments. The experimental results demonstrate that the proposed method outperforms relevant approaches for camera-captured document image rectification, in terms of improvements on both visual distortion removal and OCR accuracy.

Three-dimensional representation of curved nanowires.

PubMed

Huang, Z; Dikin, D A; Ding, W; Qiao, Y; Chen, X; Fridman, Y; Ruoff, R S

2004-12-01

Nanostructures, such as nanowires, nanotubes and nanocoils, can be described in many cases as quasi one-dimensional curved objects projecting in three-dimensional space. A parallax method to construct the correct three-dimensional geometry of such one-dimensional nanostructures is presented. A series of scanning electron microscope images was acquired at different view angles, thus providing a set of image pairs that were used to generate three-dimensional representations using a matlab program. An error analysis as a function of the view angle between the two images is presented and discussed. As an example application, the importance of knowing the true three-dimensional shape of boron nanowires is demonstrated; without the nanowire's correct length and diameter, mechanical resonance data cannot provide an accurate estimate of Young's modulus.

Local facet approximation for image stitching

NASA Astrophysics Data System (ADS)

Li, Jing; Lai, Shiming; Liu, Yu; Wang, Zhengming; Zhang, Maojun

2018-01-01

Image stitching aims at eliminating multiview parallax and generating a seamless panorama given a set of input images. This paper proposes a local adaptive stitching method, which could achieve both accurate and robust image alignments across the whole panorama. A transformation estimation model is introduced by approximating the scene as a combination of neighboring facets. Then, the local adaptive stitching field is constructed using a series of linear systems of the facet parameters, which enables the parallax handling in three-dimensional space. We also provide a concise but effective global projectivity preserving technique that smoothly varies the transformations from local adaptive to global planar. The proposed model is capable of stitching both normal images and fisheye images. The efficiency of our method is quantitatively demonstrated in the comparative experiments on several challenging cases.

Quantitative analysis of a reconstruction method for fully three-dimensional PET.

PubMed

Suckling, J; Ott, R J; Deehan, B J

1992-03-01

The major advantage of positron emission tomography (PET) using large area planar detectors over scintillator-based commercial ring systems is the potentially larger (by a factor of two or three) axial field-of-view (FOV). However, to achieve the space invariance of the point spread function necessary for Fourier filtering a polar angle rejection criterion is applied to the data during backprojection resulting in a trade-off between FOV size and sensitivity. A new algorithm due to Defrise and co-workers developed for list-mode data overcomes this problem with a solution involving the division of the image into several subregions. A comparison between the existing backprojection-then-filter algorithm and the new method (with three subregions) has been made using both simulated and real data collected from the MUP-PET positron camera. Signal-to-noise analysis reveals that improvements of up to a factor of 1.4 are possible resulting from an increased data usage of up to a factor of 2.5 depending on the axial extent of the imaged object. Quantitation is also improved.

Polarization sensitive optical coherence tomography – a review [Invited

PubMed Central

de Boer, Johannes F.; Hitzenberger, Christoph K.; Yasuno, Yoshiaki

2017-01-01

Optical coherence tomography (OCT) is now a well-established modality for high-resolution cross-sectional and three-dimensional imaging of transparent and translucent samples and tissues. Conventional, intensity based OCT, however, does not provide a tissue-specific contrast, causing an ambiguity with image interpretation in several cases. Polarization sensitive (PS) OCT draws advantage from the fact that several materials and tissues can change the light’s polarization state, adding an additional contrast channel and providing quantitative information. In this paper, we review basic and advanced methods of PS-OCT and demonstrate its use in selected biomedical applications. PMID:28663869

Modified Faraday cup

DOEpatents

Elmer, J.W.; Teruya, A.T.; O`Brien, D.W.

1996-09-10

A tomographic technique for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams is disclosed. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees from 0{degree} to 360{degree} and the waveforms are recorded by a digitizing storage oscilloscope. Two-dimensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment. 12 figs.

System for tomographic determination of the power distribution in electron beams

DOEpatents

Elmer, John W.; Teruya, Alan T.; O'Brien, Dennis W.

1995-01-01

A tomographic technique for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0.degree. to 360.degree. and the waveforms are recorded by a digitizing storage oscilloscope. Two-dimensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment.

System for tomographic determination of the power distribution in electron beams

DOEpatents

Elmer, J.W.; Teruya, A.T.; O`Brien, D.W.

1995-11-21

A tomographic technique for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0{degree} to 360{degree} and the waveforms are recorded by a digitizing storage oscilloscope. Two-dimensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment. 12 figs.

Three-dimensional multiscale modeling of dendritic spacing selection during Al-Si directional solidification

DOE PAGES

Tourret, Damien; Clarke, Amy J.; Imhoff, Seth D.; ...

2015-05-27

We present a three-dimensional extension of the multiscale dendritic needle network (DNN) model. This approach enables quantitative simulations of the unsteady dynamics of complex hierarchical networks in spatially extended dendritic arrays. We apply the model to directional solidification of Al-9.8 wt.%Si alloy and directly compare the model predictions with measurements from experiments with in situ x-ray imaging. The focus is on the dynamical selection of primary spacings over a range of growth velocities, and the influence of sample geometry on the selection of spacings. Simulation results show good agreement with experiments. The computationally efficient DNN model opens new avenues formore » investigating the dynamics of large dendritic arrays at scales relevant to solidification experiments and processes.« less

Noncontact three-dimensional quantitative profiling of fast aspheric lenses by optical coherence tomography

NASA Astrophysics Data System (ADS)

Goud, Bujagouni Karthik; Udupa, Dinesh Venkatesh; Prathap, Chilakala; Shinde, Deepak Dilip; Rao, Kompalli Divakar; Sahoo, Naba Kishore

2016-12-01

The use of optical coherence tomography (OCT) for noncontact three-dimensional aspheric lens profiling and retrieval of aspheric surface parameters is demonstrated. Two commercially available aspheric lenses with different focal length-to-diameter ratio have been imaged using OCT, and the measured optical path length distribution has been least square fitted with the aspheric lens surface retrieving the radius of curvature, aspheric constant, and conic constants. The refractive index of these lenses has also been measured referencing with a standard Zerodur glass flat. The fitted aspheric surface coefficients of the lenses are in close agreement with the manufacturer's values, thus, envisaging the potential of OCT in rapid screening, testing of aspheric lenses, and other micro-optical components such as those used in illumination optics.

SU-C-207A-03: Development of Proton CT Imaging System Using Thick Scintillator and CCD Camera

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

Tanaka, S; Uesaka, M; Nishio, T

2016-06-15

Purpose: In the treatment planning of proton therapy, Water Equivalent Length (WEL), which is the parameter for the calculation of dose and the range of proton, is derived by X-ray CT (xCT) image and xCT-WEL conversion. However, about a few percent error in the accuracy of proton range calculation through this conversion has been reported. The purpose of this study is to construct a proton CT (pCT) imaging system for an evaluation of the error. Methods: The pCT imaging system was constructed with a thick scintillator and a cooled CCD camera, which acquires the two-dimensional image of integrated value ofmore » the scintillation light toward the beam direction. The pCT image is reconstructed by FBP method using a correction between the light intensity and residual range of proton beam. An experiment for the demonstration of this system was performed with 70-MeV proton beam provided by NIRS cyclotron. The pCT image of several objects reconstructed from the experimental data was evaluated quantitatively. Results: Three-dimensional pCT images of several objects were reconstructed experimentally. A finestructure of approximately 1 mm was clearly observed. The position resolution of pCT image was almost the same as that of xCT image. And the error of proton CT pixel value was up to 4%. The deterioration of image quality was caused mainly by the effect of multiple Coulomb scattering. Conclusion: We designed and constructed the pCT imaging system using a thick scintillator and a CCD camera. And the system was evaluated with the experiment by use of 70-MeV proton beam. Three-dimensional pCT images of several objects were acquired by the system. This work was supported by JST SENTAN Grant Number 13A1101 and JSPS KAKENHI Grant Number 15H04912.« less

Real-time in situ three-dimensional integral videography and surgical navigation using augmented reality: a pilot study

PubMed Central

Suenaga, Hideyuki; Hoang Tran, Huy; Liao, Hongen; Masamune, Ken; Dohi, Takeyoshi; Hoshi, Kazuto; Mori, Yoshiyuki; Takato, Tsuyoshi

2013-01-01

To evaluate the feasibility and accuracy of a three-dimensional augmented reality system incorporating integral videography for imaging oral and maxillofacial regions, based on preoperative computed tomography data. Three-dimensional surface models of the jawbones, based on the computed tomography data, were used to create the integral videography images of a subject's maxillofacial area. The three-dimensional augmented reality system (integral videography display, computed tomography, a position tracker and a computer) was used to generate a three-dimensional overlay that was projected on the surgical site via a half-silvered mirror. Thereafter, a feasibility study was performed on a volunteer. The accuracy of this system was verified on a solid model while simulating bone resection. Positional registration was attained by identifying and tracking the patient/surgical instrument's position. Thus, integral videography images of jawbones, teeth and the surgical tool were superimposed in the correct position. Stereoscopic images viewed from various angles were accurately displayed. Change in the viewing angle did not negatively affect the surgeon's ability to simultaneously observe the three-dimensional images and the patient, without special glasses. The difference in three-dimensional position of each measuring point on the solid model and augmented reality navigation was almost negligible (<1 mm); this indicates that the system was highly accurate. This augmented reality system was highly accurate and effective for surgical navigation and for overlaying a three-dimensional computed tomography image on a patient's surgical area, enabling the surgeon to understand the positional relationship between the preoperative image and the actual surgical site, with the naked eye. PMID:23703710

Chemotaxis of cancer cells in three-dimensional environment monitored label-free by quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Schnekenburger, Jürgen; Ketelhut, Steffi

2017-02-01

We investigated the capabilities of digital holographic microscopy (DHM) for label-free quantification of the response of living single cells to chemical stimuli in 3D assays. Fibro sarcoma cells were observed in a collagen matrix inside 3D chemotaxis chambers with a Mach-Zehnder interferometer-based DHM setup. From the obtained series of quantitative phase images, the migration trajectories of single cells were retrieved by automated cell tracking and subsequently analyzed for maximum migration distance and motility. Our results demonstrate DHM as a highly reliable and efficient tool for label-free quantification of chemotaxis in 2D and 3D environments.

A new holistic 3D non-invasive analysis of cellular distribution and motility on fibroin-alginate microcarriers using light sheet fluorescent microscopy

PubMed Central

Pierini, Michela; Bevilacqua, Alessandro; Torre, Maria Luisa; Lucarelli, Enrico

2017-01-01

Cell interaction with biomaterials is one of the keystones to developing medical devices for tissue engineering applications. Biomaterials are the scaffolds that give three-dimensional support to the cells, and are vectors that deliver the cells to the injured tissue requiring repair. Features of biomaterials can influence the behaviour of the cells and consequently the efficacy of the tissue-engineered product. The adhesion, distribution and motility of the seeded cells onto the scaffold represent key aspects, and must be evaluated in vitro during the product development, especially when the efficacy of a specific tissue-engineered product depends on viable and functional cell loading. In this work, we propose a non-invasive and non-destructive imaging analysis for investigating motility, viability and distribution of Mesenchymal Stem Cells (MSCs) on silk fibroin-based alginate microcarriers, to test the adhesion capacity of the fibroin coating onto alginate which is known to be unsuitable for cell adhesion. However, in depth characterization of the biomaterial is beyond the scope of this paper. Scaffold-loaded MSCs were stained with Calcein-AM and Ethidium homodimer-1 to detect live and dead cells, respectively, and counterstained with Hoechst to label cell nuclei. Time-lapse Light Sheet Fluorescent Microscopy (LSFM) was then used to produce three-dimensional images of the entire cells-loaded fibroin/alginate microcarriers. In order to quantitatively track the cell motility over time, we also developed an open source user friendly software tool called Fluorescent Cell Tracker in Three-Dimensions (F-Tracker3D). Combining LSFM with F-Tracker3D we were able for the first time to assess the distribution and motility of stem cells in a non-invasive, non-destructive, quantitative, and three-dimensional analysis of the entire surface of the cell-loaded scaffold. We therefore propose this imaging technique as an innovative holistic tool for monitoring cell-biomaterial interactions, and as a tool for the design, fabrication and functionalization of a scaffold as a medical device. PMID:28817694

Early Changes in Facial Profile Following Structured Filler Rhinoplasty: An Anthropometric Analysis Using a 3-Dimensional Imaging System.

PubMed

Rho, Nark Kyoung; Park, Je Young; Youn, Choon Shik; Lee, Soo-Keun; Kim, Hei Sung

2017-02-01

Quantitative measurements are important for objective evaluation of postprocedural outcomes. Three-dimensional (3D) imaging is known as an objective, accurate, and reliable system for quantifying the soft tissue dimensions of the face. To compare the preprocedural and acute postprocedural nasofrontal, nasofacial, nasolabial, and nasomental angles, early changes in the height and length of the nose, and nasal volume using a 3D surface imaging with a light-emitting diode. The 3D imaging analysis of 40 Korean women who underwent structured nonsurgical rhinoplasty was conducted. The 3D assessment was performed before, immediately after, 1 day, and 2 weeks after filler rhinoplasty with a Morpheus 3D scanner (Morpheus Co., Seoul, Korea). There were significant early changes in facial profile following nonsurgical rhinoplasty with a hyaluronic acid filler. An average increase of 6.03° in the nasofrontal angle, an increase of 3.79° in the nasolabial angle, increase of 0.88° in the nasomental angle, and a reduction of 0.83° in the nasofacial angle was observed at 2 weeks of follow-up. Increment in nasal volume and nose height was also found after 2 weeks. Side effects, such as hematoma, nodules, and skin necrosis, were not observed. The 3D surface imaging quantitatively demonstrated the early changes in facial profile after structured filler rhinoplasty. The study results describe significant acute spatial changes in nose shape following treatment.

High-resolution x-ray guided three-dimensional diffuse optical tomography of joint tissues in hand osteoarthritis: Morphological and functional assessments

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

Yuan Zhen; Zhang Qizhi; Sobel, Eric S.

Purpose: The aim of this study was to investigate the potential use of multimodality functional imaging techniques to identify the quantitative optical findings that can be used to distinguish between osteoarthritic and normal finger joints. Methods: Between 2006 and 2009, the distal interphalangeal finger joints from 40 female subjects including 22 patients and 18 healthy controls were examined clinically and scanned by a hybrid imaging system. This system integrated x-ray tomosynthetic setup with a diffuse optical imaging system. Optical absorption and scattering images were recovered based on a regularization-based hybrid reconstruction algorithm. A receiver operating characteristic curve was used tomore » calculate the statistical significance of specific optical features obtained from osteoarthritic and healthy joints groups. Results: The three-dimensional optical and x-ray images captured made it possible to quantify optical properties and joint space width of finger joints. Based on the recovered optical absorption and scattering parameters, the authors observed statistically significant differences between healthy and osteoarthritis finger joints. Conclusions: The statistical results revealed that sensitivity and specificity values up to 92% and 100%, respectively, can be achieved when optical properties of joint tissues were used as classifiers. This suggests that these optical imaging parameters are possible indicators for diagnosing osteoarthritis and monitoring its progression.« less

Three-dimensional imaging of porous media using confocal laser scanning microscopy.

PubMed

Shah, S M; Crawshaw, J P; Boek, E S

2017-02-01

In the last decade, imaging techniques capable of reconstructing three-dimensional (3-D) pore-scale model have played a pivotal role in the study of fluid flow through complex porous media. In this study, we present advances in the application of confocal laser scanning microscopy (CLSM) to image, reconstruct and characterize complex porous geological materials with hydrocarbon reservoir and CO 2 storage potential. CLSM has a unique capability of producing 3-D thin optical sections of a material, with a wide field of view and submicron resolution in the lateral and axial planes. However, CLSM is limited in the depth (z-dimension) that can be imaged in porous materials. In this study, we introduce a 'grind and slice' technique to overcome this limitation. We discuss the practical and technical aspects of the confocal imaging technique with application to complex rock samples including Mt. Gambier and Ketton carbonates. We then describe the complete workflow of image processing to filtering and segmenting the raw 3-D confocal volumetric data into pores and grains. Finally, we use the resulting 3-D pore-scale binarized confocal data obtained to quantitatively determine petrophysical pore-scale properties such as total porosity, macro- and microporosity and single-phase permeability using lattice Boltzmann (LB) simulations, validated by experiments. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Efficient Segmentation of a Breast in B-Mode Ultrasound Tomography Using Three-Dimensional GrabCut (GC3D)

PubMed Central

Wu, Shibin; Zhuang, Ling; Wei, Xinhua; Sak, Mark; Neb, Duric; Hu, Jiani; Xie, Yaoqin

2017-01-01

As an emerging modality for whole breast imaging, ultrasound tomography (UST), has been adopted for diagnostic purposes. Efficient segmentation of an entire breast in UST images plays an important role in quantitative tissue analysis and cancer diagnosis, while major existing methods suffer from considerable time consumption and intensive user interaction. This paper explores three-dimensional GrabCut (GC3D) for breast isolation in thirty reflection (B-mode) UST volumetric images. The algorithm can be conveniently initialized by localizing points to form a polygon, which covers the potential breast region. Moreover, two other variations of GrabCut and an active contour method were compared. Algorithm performance was evaluated from volume overlap ratios (TO, target overlap; MO, mean overlap; FP, false positive; FN, false negative) and time consumption. Experimental results indicate that GC3D considerably reduced the work load and achieved good performance (TO = 0.84; MO = 0.91; FP = 0.006; FN = 0.16) within an average of 1.2 min per volume. Furthermore, GC3D is not only user friendly, but also robust to various inputs, suggesting its great potential to facilitate clinical applications during whole-breast UST imaging. In the near future, the implemented GC3D can be easily automated to tackle B-mode UST volumetric images acquired from the updated imaging system. PMID:28786946

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

Volcano collapse promoted by hydrothermal alteration and edifice shape, Mount Rainier, Washington

USGS Publications Warehouse

Reid, M.E.; Sisson, T.W.; Brien, D.L.

2001-01-01

Catastrophic collapses of steep volcano flanks threaten many populated regions, and understanding factors that promote collapse could save lives and property. Large collapses of hydrothermally altered parts of Mount Rainier have generated far-traveled debris flows; future flows would threaten densely populated parts of the Puget Sound region. We evaluate edifice collapse hazards at Mount Rainier using a new three-dimensional slope stability method incorporating detailed geologic mapping and subsurface geophysical imaging to determine distributions of strong (fresh) and weak (altered) rock. Quantitative three-dimensional slope stability calculations reveal that sizeable flank collapse (>0.1 km3) is promoted by voluminous, weak, hydrothermally altered rock situated high on steep slopes. These conditions exist only on Mount Rainier's upper west slope, consistent with the Holocene debris-flow history. Widespread alteration on lower flanks or concealed in regions of gentle slope high on the edifice does not greatly facilitate collapse. Our quantitative stability assessment method can also provide useful hazard predictions using reconnaissance geologic information and is a potentially rapid and inexpensive new tool for aiding volcano hazard assessments.

Automatic 3D segmentation of multiphoton images: a key step for the quantification of human skin.

PubMed

Decencière, Etienne; Tancrède-Bohin, Emmanuelle; Dokládal, Petr; Koudoro, Serge; Pena, Ana-Maria; Baldeweck, Thérèse

2013-05-01

Multiphoton microscopy has emerged in the past decade as a useful noninvasive imaging technique for in vivo human skin characterization. However, it has not been used until now in evaluation clinical trials, mainly because of the lack of specific image processing tools that would allow the investigator to extract pertinent quantitative three-dimensional (3D) information from the different skin components. We propose a 3D automatic segmentation method of multiphoton images which is a key step for epidermis and dermis quantification. This method, based on the morphological watershed and graph cuts algorithms, takes into account the real shape of the skin surface and of the dermal-epidermal junction, and allows separating in 3D the epidermis and the superficial dermis. The automatic segmentation method and the associated quantitative measurements have been developed and validated on a clinical database designed for aging characterization. The segmentation achieves its goals for epidermis-dermis separation and allows quantitative measurements inside the different skin compartments with sufficient relevance. This study shows that multiphoton microscopy associated with specific image processing tools provides access to new quantitative measurements on the various skin components. The proposed 3D automatic segmentation method will contribute to build a powerful tool for characterizing human skin condition. To our knowledge, this is the first 3D approach to the segmentation and quantification of these original images. © 2013 John Wiley & Sons A/S. Published by Blackwell Publishing Ltd.

High-performance thin-layer chromatography and three-dimensional image analysis for the determination of rutin in pharmaceutical preparations.

PubMed

Soponar, Florin; Moţ, Augustin C; Sârbu, Costel

2010-01-01

A novel HPTLC method was developed for fast and simple quantitative determination of rutin in pharmaceutical preparations. The proposed method combines the advantages of HPTLC with the comfort and the convenience of digital processing of images. For the separation of rutin, silica gel with attached amino groups was used as the stationary phase and ethyl acetate-formic acid-methanol-water (10 + 0.9 + 1.1 + 1.7, v/v/v/v) as the mobile phase. The chromatographic plate was sprayed with 2-aminoethyldiphenyl borate solution for visual detection of the spots. For the construction of a three-dimensional chromatogram, Melanie 7.0 software was used together with an HP flatbed scanner that allowed capture of the images on chromatographic plates. The calibration curve was linear within the range of 0.95-4.78 microg/spot with an r value of 0.9984. The RSD for six replicates at three concentration levels was less than 3%, while the recovery was between 97.28 and 103.27%. The proposed method was found to be simple, precise, sensitive, and accurate and has been applied for the determination of rutin in two commercial drugs. The results were compared with the results of other techniques that generate bidimensional chromatograms and validated by UV-Vis spectrophotometry.

Three-dimensional imaging of the craniofacial complex.

PubMed

Nguyen, Can X.; Nissanov, Jonathan; Öztürk, Cengizhan; Nuveen, Michiel J.; Tuncay, Orhan C.

2000-02-01

Orthodontic treatment requires the rearrangement of craniofacial complex elements in three planes of space, but oddly the diagnosis is done with two-dimensional images. Here we report on a three-dimensional (3D) imaging system that employs the stereoimaging method of structured light to capture the facial image. The images can be subsequently integrated with 3D cephalometric tracings derived from lateral and PA films (www.clinorthodres.com/cor-c-070). The accuracy of the reconstruction obtained with this inexpensive system is about 400 µ.

Application of 3D and 2D quantitative shear wave elastography (SWE) to differentiate between benign and malignant breast masses.

PubMed

Tian, Jie; Liu, Qianqi; Wang, Xi; Xing, Ping; Yang, Zhuowen; Wu, Changjun

2017-01-20

As breast cancer tissues are stiffer than normal tissues, shear wave elastography (SWE) can locally quantify tissue stiffness and provide histological information. Moreover, tissue stiffness can be observed on three-dimensional (3D) colour-coded elasticity maps. Our objective was to evaluate the diagnostic performances of quantitative features in differentiating breast masses by two-dimensional (2D) and 3D SWE. Two hundred ten consecutive women with 210 breast masses were examined with B-mode ultrasound (US) and SWE. Quantitative features of 3D and 2D SWE were assessed, including elastic modulus standard deviation (E SD E ) measured on SWE mode images and E SD U measured on B-mode images, as well as maximum elasticity (E max ). Adding quantitative features to B-mode US improved the diagnostic performance (p < 0.05) and reduced false-positive biopsies (p < 0.0001). The area under the receiver operating characteristic curve (AUC) of 3D SWE was similar to that of 2D SWE for E SD E (p = 0.026) and E SD U (p = 0.159) but inferior to that of 2D SWE for E max (p = 0.002). Compared with E SD U , E SD E showed a higher AUC on 2D (p = 0.0038) and 3D SWE (p = 0.0057). Our study indicates that quantitative features of 3D and 2D SWE can significantly improve the diagnostic performance of B-mode US, especially 3D SWE E SD E , which shows considerable clinical value.

A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

PubMed Central

Morales-Navarrete, Hernán; Segovia-Miranda, Fabián; Klukowski, Piotr; Meyer, Kirstin; Nonaka, Hidenori; Marsico, Giovanni; Chernykh, Mikhail; Kalaidzidis, Alexander; Zerial, Marino; Kalaidzidis, Yannis

2015-01-01

A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness. DOI: http://dx.doi.org/10.7554/eLife.11214.001 PMID:26673893

Evolution of the three-dimensional collagen structure in vascular walls during deformation: an in situ mechanical testing under multiphoton microscopy observation.

PubMed

Nierenberger, Mathieu; Fargier, Guillaume; Ahzi, Saïd; Rémond, Yves

2015-08-01

The collagen fibers' three-dimensional architecture has a strong influence on the mechanical behavior of biological tissues. To accurately model this behavior, it is necessary to get some knowledge about the structure of the collagen network. In the present paper, we focus on the in situ characterization of the collagenous structure, which is present in porcine jugular vein walls. An observation of the vessel wall is first proposed in an unloaded configuration. The vein is then put into a mechanical tensile testing device. As the vein is stretched, three-dimensional images of its collagenous structure are acquired using multiphoton microscopy. Orientation analyses are provided for the multiple images recorded during the mechanical test. From these analyses, the reorientation of the two families of collagen fibers existing in the vein wall is quantified. We noticed that the reorientation of the fibers stops as the tissue stiffness starts decreasing, corresponding to the onset of damage. Besides, no relevant evolutions of the out of plane collagen orientations were observed. Due to the applied loading, our analysis also allowed for linking the stress relaxation within the tissue to its internal collagenous structure. Finally, this analysis constitutes the first mechanical test performed under a multiphoton microscope with a continuous three-dimensional observation of the tissue structure all along the test. It allows for a quantitative evaluation of microstructural parameters combined with a measure of the global mechanical behavior. Such data are useful for the development of structural mechanical models for living tissues.

Diagnosing common bile duct obstruction: comparison of image quality and diagnostic performance of three-dimensional magnetic resonance cholangiopancreatography with and without compressed sensing.

PubMed

Kwon, Heejin; Reid, Scott; Kim, Dongeun; Lee, Sangyun; Cho, Jinhan; Oh, Jongyeong

2018-01-04

This study aimed to evaluate image quality and diagnostic performance of a recently developed navigated three-dimensional magnetic resonance cholangiopancreatography (3D-MRCP) with compressed sensing (CS) based on parallel imaging (PI) and conventional 3D-MRCP with PI only in patients with abnormal bile duct dilatation. This institutional review board-approved study included 45 consecutive patients [non-malignant common bile duct lesions (n = 21) and malignant common bile duct lesions (n = 24)] who underwent MRCP of the abdomen to evaluate bile duct dilatation. All patients were imaged at 3T (MR 750, GE Healthcare, Waukesha, WI) including two kinds of 3D-MRCP using 352 × 288 matrices with and without CS based on PI. Two radiologists independently and blindly assessed randomized images. CS acceleration reduced the acquisition time on average 5 min and 6 s to a total of 2 min and 56 s. The all CS cine image quality was significantly higher than standard cine MR image for all quantitative measurements. Diagnostic accuracy for benign and malignant lesions is statistically different between standard and CS 3D-MRCP. Total image quality and diagnostic accuracy at biliary obstruction evaluation demonstrates that CS-accelerated 3D-MRCP sequences can provide superior quality of diagnostic information in 42.5% less time. This has the potential to reduce motion-related artifacts and improve diagnostic efficacy.

Dimensional metrology of lab-on-a-chip internal structures: a comparison of optical coherence tomography with confocal fluorescence microscopy.

PubMed

Reyes, D R; Halter, M; Hwang, J

2015-07-01

The characterization of internal structures in a polymeric microfluidic device, especially of a final product, will require a different set of optical metrology tools than those traditionally used for microelectronic devices. We demonstrate that optical coherence tomography (OCT) imaging is a promising technique to characterize the internal structures of poly(methyl methacrylate) devices where the subsurface structures often cannot be imaged by conventional wide field optical microscopy. The structural details of channels in the devices were imaged with OCT and analyzed with an in-house written ImageJ macro in an effort to identify the structural details of the channel. The dimensional values obtained with OCT were compared with laser-scanning confocal microscopy images of channels filled with a fluorophore solution. Attempts were also made using confocal reflectance and interferometry microscopy to measure the channel dimensions, but artefacts present in the images precluded quantitative analysis. OCT provided the most accurate estimates for the channel height based on an analysis of optical micrographs obtained after destructively slicing the channel with a microtome. OCT may be a promising technique for the future of three-dimensional metrology of critical internal structures in lab-on-a-chip devices because scans can be performed rapidly and noninvasively prior to their use. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Three-dimensional Imaging Methods for Quantitative Analysis of Facial Soft Tissues and Skeletal Morphology in Patients with Orofacial Clefts: A Systematic Review

PubMed Central

Kuijpers, Mette A. R.; Chiu, Yu-Ting; Nada, Rania M.; Carels, Carine E. L.; Fudalej, Piotr S.

2014-01-01

Background Current guidelines for evaluating cleft palate treatments are mostly based on two-dimensional (2D) evaluation, but three-dimensional (3D) imaging methods to assess treatment outcome are steadily rising. Objective To identify 3D imaging methods for quantitative assessment of soft tissue and skeletal morphology in patients with cleft lip and palate. Data sources Literature was searched using PubMed (1948–2012), EMBASE (1980–2012), Scopus (2004–2012), Web of Science (1945–2012), and the Cochrane Library. The last search was performed September 30, 2012. Reference lists were hand searched for potentially eligible studies. There was no language restriction. Study selection We included publications using 3D imaging techniques to assess facial soft tissue or skeletal morphology in patients older than 5 years with a cleft lip with/or without cleft palate. We reviewed studies involving the facial region when at least 10 subjects in the sample size had at least one cleft type. Only primary publications were included. Data extraction Independent extraction of data and quality assessments were performed by two observers. Results Five hundred full text publications were retrieved, 144 met the inclusion criteria, with 63 high quality studies. There were differences in study designs, topics studied, patient characteristics, and success measurements; therefore, only a systematic review could be conducted. Main 3D-techniques that are used in cleft lip and palate patients are CT, CBCT, MRI, stereophotogrammetry, and laser surface scanning. These techniques are mainly used for soft tissue analysis, evaluation of bone grafting, and changes in the craniofacial skeleton. Digital dental casts are used to evaluate treatment and changes over time. Conclusion Available evidence implies that 3D imaging methods can be used for documentation of CLP patients. No data are available yet showing that 3D methods are more informative than conventional 2D methods. Further research is warranted to elucidate it. Systematic review registration International Prospective Register of Systematic Reviews, PROSPERO CRD42012002041 PMID:24710215

CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution.

PubMed

Gross, Colin A; Reddy, Chandan K; Dazzo, Frank B

2010-02-01

Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system's uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance of the color segmentation algorithm evaluated on 26 complex micrographs at single pixel resolution had an overall pixel classification accuracy of 99+%. Several applications illustrate how this improved computing technology can successfully resolve numerous challenges of complex color segmentation in order to produce images from which quantitative information can be accurately extracted, thereby gain new perspectives on the in situ ecology of microorganisms. Examples include improvements in the quantitative analysis of (1) microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities, (2) cell viability, (3) spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms, and (4) biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization. The stand-alone executable file plus user manual and tutorial images for this color segmentation computing application are freely available at http://cme.msu.edu/cmeias/ . This improved computing technology opens new opportunities of imaging applications where discriminating colors really matter most, thereby strengthening quantitative microscopy-based approaches to advance microbial ecology in situ at individual single-cell resolution.

Attenuation correction with region growing method used in the positron emission mammography imaging system

NASA Astrophysics Data System (ADS)

Gu, Xiao-Yue; Li, Lin; Yin, Peng-Fei; Yun, Ming-Kai; Chai, Pei; Huang, Xian-Chao; Sun, Xiao-Li; Wei, Long

2015-10-01

The Positron Emission Mammography imaging system (PEMi) provides a novel nuclear diagnosis method dedicated for breast imaging. With a better resolution than whole body PET, PEMi can detect millimeter-sized breast tumors. To address the requirement of semi-quantitative analysis with a radiotracer concentration map of the breast, a new attenuation correction method based on a three-dimensional seeded region growing image segmentation (3DSRG-AC) method has been developed. The method gives a 3D connected region as the segmentation result instead of image slices. The continuity property of the segmentation result makes this new method free of activity variation of breast tissues. The threshold value chosen is the key process for the segmentation method. The first valley in the grey level histogram of the reconstruction image is set as the lower threshold, which works well in clinical application. Results show that attenuation correction for PEMi improves the image quality and the quantitative accuracy of radioactivity distribution determination. Attenuation correction also improves the probability of detecting small and early breast tumors. Supported by Knowledge Innovation Project of The Chinese Academy of Sciences (KJCX2-EW-N06)

Biodistribution and Clearance of Human Mesenchymal Stem Cells by Quantitative Three-Dimensional Cryo-Imaging After Intravenous Infusion in a Rat Lung Injury Model.

PubMed

Schmuck, Eric G; Koch, Jill M; Centanni, John M; Hacker, Timothy A; Braun, Rudolf K; Eldridge, Marlowe; Hei, Derek J; Hematti, Peiman; Raval, Amish N

2016-12-01

: Cell tracking is a critical component of the safety and efficacy evaluation of therapeutic cell products. To date, cell-tracking modalities have been hampered by poor resolution, low sensitivity, and inability to track cells beyond the shortterm. Three-dimensional (3D) cryo-imaging coregisters fluorescent and bright-field microcopy images and allows for single-cell quantification within a 3D organ volume. We hypothesized that 3D cryo-imaging could be used to measure cell biodistribution and clearance after intravenous infusion in a rat lung injury model compared with normal rats. A bleomycin lung injury model was established in Sprague-Dawley rats (n = 12). Human mesenchymal stem cells (hMSCs) labeled with QTracker655 were infused via jugular vein. After 2, 4, or 8 days, a second dose of hMSCs labeled with QTracker605 was infused, and animals were euthanized after 60, 120, or 240 minutes. Lungs, liver, spleen, heart, kidney, testis, and intestine were cryopreserved, followed by 3D cryo-imaging of each organ. At 60 minutes, 82% ± 9.7% of cells were detected; detection decreased to 60% ± 17% and 66% ± 22% at 120 and 240 minutes, respectively. At day 2, 0.06% of cells were detected, and this level remained constant at days 4 and 8 postinfusion. At 60, 120, and 240 minutes, 99.7% of detected cells were found in the liver, lungs, and spleen, with cells primarily retained in the liver. This is the first study using 3D cryo-imaging to track hMSCs in a rat lung injury model. hMSCs were retained primarily in the liver, with fewer detected in lungs and spleen. Effective bench-to-bedside clinical translation of cellular therapies requires careful understanding of cell fate through tracking. Tracking cells is important to measure cell retention so that delivery methods and cell dose can be optimized and so that biodistribution and clearance can be defined to better understand potential off-target toxicity and redosing strategies. This article demonstrates, for the first time, the use of three-dimensional cryo-imaging for single-cell quantitative tracking of intravenous infused clinical-grade mesenchymal stem cells in a clinically relevant model of lung injury. The important information learned in this study will help guide future clinical and translational stem cell therapies for lung injuries. ©AlphaMed Press.

Data representation for joint kinematics simulation of the lower limb within an educational context.

PubMed

Van Sint Jan, Serge; Hilal, Isam; Salvia, Patrick; Sholukha, Victor; Poulet, Pascal; Kirokoya, Ibrahim; Rooze, Marcel

2003-04-01

Three-dimensional (3D) visualization is becoming increasingly frequent in both qualitative and quantitative biomechanical studies of anatomical structures involving multiple data sources (e.g. morphological data and kinematics data). For many years, this kind of experiment was limited to the use of bi-dimensional images due to a lack of accurate 3D data. However, recent progress in medical imaging and computer graphics has forged new perspectives. Indeed, new techniques allow the development of an interactive interface for the simulation of human motions combining data from both medical imaging (i.e., morphology) and biomechanical studies (i.e., kinematics). Fields of application include medical education, biomechanical research and clinical research. This paper presents an experimental protocol for the development of anatomically realistic joint simulation within a pedagogical context. Results are shown for the lower limb. Extension to other joints is straightforward. This work is part of the Virtual Animation of the Kinematics of the Human project (VAKHUM) (http://www.ulb.ac.be/project/vakhum).

Three-dimensional ultrasound-based texture analysis of the effect of atorvastatin on carotid atherosclerosis

NASA Astrophysics Data System (ADS)

Awad, Joseph; Krasinski, Adam; Spence, David; Parraga, Grace; Fenster, Aaron

2010-03-01

Carotid atherosclerosis is the major cause of ischemic stroke, a leading cause of death and disability. This is driving the development of image analysis methods to quantitatively evaluate local arterial effects of potential treatments of carotid disease. Here we investigate the use of novel texture analysis tools to detect potential changes in the carotid arteries after statin therapy. Three-dimensional (3D) carotid ultrasound images were acquired from the left and right carotid arteries of 35 subjects (16 treated with 80 mg atorvastatin and 19 treated with placebo) at baseline and after 3 months of treatment. Two-hundred and seventy texture features were extracted from 3D ultrasound carotid artery images. These images previously had their vessel walls (VW) manually segmented. Highly ranked individual texture features were selected and compared to the VW volume (VWV) change using 3 measures: distance between classes, Wilcoxon rank sum test, and accuracy of the classifiers. Six classifiers were used. Using texture feature (L7R7) increases the average accuracy and area under the ROC curve to 74.4% and 0.72 respectively compared to 57.2% and 0.61 using VWV change. Thus, the results demonstrate that texture features are more sensitive in detecting drug effects on the carotid vessel wall than VWV change.

Feasibility of free-breathing dynamic contrast-enhanced MRI of gastric cancer using a golden-angle radial stack-of-stars VIBE sequence: comparison with the conventional contrast-enhanced breath-hold 3D VIBE sequence.

PubMed

Li, Huan-Huan; Zhu, Hui; Yue, Lei; Fu, Yi; Grimm, Robert; Stemmer, Alto; Fu, Cai-Xia; Peng, Wei-Jun

2018-05-01

To investigate the feasibility and diagnostic value of free-breathing, radial, stack-of-stars three-dimensional (3D) gradient echo (GRE) sequence ("golden angle") on dynamic contrast-enhanced (DCE) MRI of gastric cancer. Forty-three gastric cancer patients were divided into cooperative and uncooperative groups. Respiratory fluctuation was observed using an abdominal respiratory gating sensor. Those who breath-held for more than 15 s were placed in the cooperative group and the remainder in the uncooperative group. The 3-T MRI scanning protocol included 3D GRE and conventional breath-hold VIBE (volume-interpolated breath-hold examination) sequences, comparing images quantitatively and qualitatively. DCE-MRI parameters from VIBE images of normal gastric wall and malignant lesions were compared. For uncooperative patients, 3D GRE scored higher qualitatively, and had higher SNRs (signal-to-noise ratios) and CNRs (contrast-to-noise ratios) than conventional VIBE quantitatively. Though 3D GRE images scored lower in qualitative parameters compared with conventional VIBE for cooperative patients, it provided images with fewer artefacts. DCE parameters differed significantly between normal gastric wall and lesions, with higher Ve (extracellular volume) and lower Kep (reflux constant) in gastric cancer. The free-breathing, golden-angle, radial stack-of-stars 3D GRE technique is feasible for DCE-MRI of gastric cancer. Dynamic enhanced images can be used for quantitative analysis of this malignancy. • Golden-angle radial stack-of-stars VIBE aids gastric cancer MRI diagnosis. • The 3D GRE technique is suitable for patients unable to suspend respiration. • Method scored higher in the qualitative evaluation for uncooperative patients. • The technique produced images with fewer artefacts than conventional VIBE sequence. • Dynamic enhanced images can be used for quantitative analysis of gastric cancer.

Electric Potential and Electric Field Imaging with Dynamic Applications: 2017 Research Award Innovation

NASA Technical Reports Server (NTRS)

Generazio, Ed

2017-01-01

The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field may be used for illuminating volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e- Sensor enhancements (ephemeral e-Sensor) are discussed. Critical design elements of current linear and real-time two-dimensional (2D) measurement systems are highlighted, and the development of a three dimensional (3D) EFI system is presented. Demonstrations for structural, electronic, human, and memory applications are shown. Recent work demonstrates that phonons may be used to create and annihilate electric dipoles within structures. Phonon induced dipoles are ephemeral and their polarization, strength, and location may be quantitatively characterized by EFI providing a new subsurface Phonon-EFI imaging technology. Initial results from real-time imaging of combustion and ion flow, and their measurement complications, will be discussed. These new EFI capabilities are demonstrated to characterize electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, crime scene forensics, design and materials selection for advanced sensors, combustion science, on-orbit space potential, container inspection, remote characterization of electronic circuits and level of activation, dielectric morphology of structures, tether integrity, organic molecular memory, atmospheric science, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

Dynamic three-dimensional display of common congenital cardiac defects from reconstruction of two-dimensional echocardiographic images.

PubMed

Hsieh, K S; Lin, C C; Liu, W S; Chen, F L

1996-01-01

Two-dimensional echocardiography had long been a standard diagnostic modality for congenital heart disease. Further attempts of three-dimensional reconstruction using two-dimensional echocardiographic images to visualize stereotypic structure of cardiac lesions have been successful only recently. So far only very few studies have been done to display three-dimensional anatomy of the heart through two-dimensional image acquisition because such complex procedures were involved. This study introduced a recently developed image acquisition and processing system for dynamic three-dimensional visualization of various congenital cardiac lesions. From December 1994 to April 1995, 35 cases were selected in the Echo Laboratory here from about 3000 Echo examinations completed. Each image was acquired on-line with specially designed high resolution image grazmber with EKG and respiratory gating technique. Off-line image processing using a window-architectured interactive software package includes construction of 2-D ehcocardiographic pixel to 3-D "voxel" with conversion of orthogonal to rotatory axial system, interpolation, extraction of region of interest, segmentation, shading and, finally, 3D rendering. Three-dimensional anatomy of various congenital cardiac defects was shown, including four cases with ventricular septal defects, two cases with atrial septal defects, and two cases with aortic stenosis. Dynamic reconstruction of a "beating heart" is recorded as vedio tape with video interface. The potential application of 3D display of the reconstruction from 2D echocardiographic images for the diagnosis of various congenital heart defects has been shown. The 3D display was able to improve the diagnostic ability of echocardiography, and clear-cut display of the various congenital cardiac defects and vavular stenosis could be demonstrated. Reinforcement of current techniques will expand future application of 3D display of conventional 2D images.

Development of 3D microwave imaging technology for damage assessment of concrete bridge.

DOT National Transportation Integrated Search

2003-11-01

An innovative microwave 3-dimensional (3D) sub-surface imaging technology is developed for : detecting and quantitatively assessing internal damage of concrete structures. This technology is : based on reconstruction of dielectric profile (image) of ...

Statistical assessment of normal mitral annular geometry using automated three-dimensional echocardiographic analysis.

PubMed

Pouch, Alison M; Vergnat, Mathieu; McGarvey, Jeremy R; Ferrari, Giovanni; Jackson, Benjamin M; Sehgal, Chandra M; Yushkevich, Paul A; Gorman, Robert C; Gorman, Joseph H

2014-01-01

The basis of mitral annuloplasty ring design has progressed from qualitative surgical intuition to experimental and theoretical analysis of annular geometry with quantitative imaging techniques. In this work, we present an automated three-dimensional (3D) echocardiographic image analysis method that can be used to statistically assess variability in normal mitral annular geometry to support advancement in annuloplasty ring design. Three-dimensional patient-specific models of the mitral annulus were automatically generated from 3D echocardiographic images acquired from subjects with normal mitral valve structure and function. Geometric annular measurements including annular circumference, annular height, septolateral diameter, intercommissural width, and the annular height to intercommissural width ratio were automatically calculated. A mean 3D annular contour was computed, and principal component analysis was used to evaluate variability in normal annular shape. The following mean ± standard deviations were obtained from 3D echocardiographic image analysis: annular circumference, 107.0 ± 14.6 mm; annular height, 7.6 ± 2.8 mm; septolateral diameter, 28.5 ± 3.7 mm; intercommissural width, 33.0 ± 5.3 mm; and annular height to intercommissural width ratio, 22.7% ± 6.9%. Principal component analysis indicated that shape variability was primarily related to overall annular size, with more subtle variation in the skewness and height of the anterior annular peak, independent of annular diameter. Patient-specific 3D echocardiographic-based modeling of the human mitral valve enables statistical analysis of physiologically normal mitral annular geometry. The tool can potentially lead to the development of a new generation of annuloplasty rings that restore the diseased mitral valve annulus back to a truly normal geometry. Copyright © 2014 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Near-field three-dimensional radar imaging techniques and applications.

PubMed

Sheen, David; McMakin, Douglas; Hall, Thomas

2010-07-01

Three-dimensional radio frequency imaging techniques have been developed for a variety of near-field applications, including radar cross-section imaging, concealed weapon detection, ground penetrating radar imaging, through-barrier imaging, and nondestructive evaluation. These methods employ active radar transceivers that operate at various frequency ranges covering a wide range, from less than 100 MHz to in excess of 350 GHz, with the frequency range customized for each application. Computational wavefront reconstruction imaging techniques have been developed that optimize the resolution and illumination quality of the images. In this paper, rectilinear and cylindrical three-dimensional imaging techniques are described along with several application results.

Three-dimensional T1rho-weighted MRI at 1.5 Tesla.

PubMed

Borthakur, Arijitt; Wheaton, Andrew; Charagundla, Sridhar R; Shapiro, Erik M; Regatte, Ravinder R; Akella, Sarma V S; Kneeland, J Bruce; Reddy, Ravinder

2003-06-01

To design and implement a magnetic resonance imaging (MRI) pulse sequence capable of performing three-dimensional T(1rho)-weighted MRI on a 1.5-T clinical scanner, and determine the optimal sequence parameters, both theoretically and experimentally, so that the energy deposition by the radiofrequency pulses in the sequence, measured as the specific absorption rate (SAR), does not exceed safety guidelines for imaging human subjects. A three-pulse cluster was pre-encoded to a three-dimensional gradient-echo imaging sequence to create a three-dimensional, T(1rho)-weighted MRI pulse sequence. Imaging experiments were performed on a GE clinical scanner with a custom-built knee-coil. We validated the performance of this sequence by imaging articular cartilage of a bovine patella and comparing T(1rho) values measured by this sequence to those obtained with a previously tested two-dimensional imaging sequence. Using a previously developed model for SAR calculation, the imaging parameters were adjusted such that the energy deposition by the radiofrequency pulses in the sequence did not exceed safety guidelines for imaging human subjects. The actual temperature increase due to the sequence was measured in a phantom by a MRI-based temperature mapping technique. Following these experiments, the performance of this sequence was demonstrated in vivo by obtaining T(1rho)-weighted images of the knee joint of a healthy individual. Calculated T(1rho) of articular cartilage in the specimen was similar for both and three-dimensional and two-dimensional methods (84 +/- 2 msec and 80 +/- 3 msec, respectively). The temperature increase in the phantom resulting from the sequence was 0.015 degrees C, which is well below the established safety guidelines. Images of the human knee joint in vivo demonstrate a clear delineation of cartilage from surrounding tissues. We developed and implemented a three-dimensional T(1rho)-weighted pulse sequence on a 1.5-T clinical scanner. Copyright 2003 Wiley-Liss, Inc.

Quantitative 3D electromagnetic field determination of 1D nanostructures from single projection

DOE PAGES

Phatak, C.; Knoop, L. de; Houdellier, F.; ...

2016-05-01

One-dimensional (1D) nanostructures have been regarded as the most promising building blocks for nanoelectronics and nanocomposite material systems as well as for alternative energy applications. Although they result in confinement of a material, their properties and interactions with other nanostructures are still very much three-dimensional (3D) in nature. In this work, we present a novel method for quantitative determination of the 3D electromagnetic fields in and around 1D nanostructures using a single electron wave phase image, thereby eliminating the cumbersome acquisition of tomographic data. Using symmetry arguments, we have reconstructed the 3D magnetic field of a nickel nanowire as wellmore » as the 3D electric field around a carbon nanotube field emitter, from one single projection. The accuracy of quantitative values determined here is shown to be a better fit to the physics at play than the value obtained by conventional analysis. Moreover the 3D reconstructions can then directly be visualized and used in the design of functional 3D architectures built using 1D nanostructures.« less

Quantitative 3D electromagnetic field determination of 1D nanostructures from single projection

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

Phatak, C.; Knoop, L. de; Houdellier, F.

One-dimensional (1D) nanostructures have been regarded as the most promising building blocks for nanoelectronics and nanocomposite material systems as well as for alternative energy applications. Although they result in confinement of a material, their properties and interactions with other nanostructures are still very much three-dimensional (3D) in nature. In this work, we present a novel method for quantitative determination of the 3D electromagnetic fields in and around 1D nanostructures using a single electron wave phase image, thereby eliminating the cumbersome acquisition of tomographic data. Using symmetry arguments, we have reconstructed the 3D magnetic field of a nickel nanowire as wellmore » as the 3D electric field around a carbon nanotube field emitter, from one single projection. The accuracy of quantitative values determined here is shown to be a better fit to the physics at play than the value obtained by conventional analysis. Moreover the 3D reconstructions can then directly be visualized and used in the design of functional 3D architectures built using 1D nanostructures.« less

A new method of morphological comparison for bony reconstructive surgery: maxillary reconstruction using scapular tip bone

NASA Astrophysics Data System (ADS)

Chan, Harley; Gilbert, Ralph W.; Pagedar, Nitin A.; Daly, Michael J.; Irish, Jonathan C.; Siewerdsen, Jeffrey H.

2010-02-01

esthetic appearance is one of the most important factors for reconstructive surgery. The current practice of maxillary reconstruction chooses radial forearm, fibula or iliac rest osteocutaneous to recreate three-dimensional complex structures of the palate and maxilla. However, these bone flaps lack shape similarity to the palate and result in a less satisfactory esthetic. Considering similarity factors and vasculature advantages, reconstructive surgeons recently explored the use of scapular tip myo-osseous free flaps to restore the excised site. We have developed a new method that quantitatively evaluates the morphological similarity of the scapula tip bone and palate based on a diagnostic volumetric computed tomography (CT) image. This quantitative result was further interpreted as a color map that rendered on the surface of a three-dimensional computer model. For surgical planning, this color interpretation could potentially assist the surgeon to maximize the orientation of the bone flaps for best fit of the reconstruction site. With approval from the Research Ethics Board (REB) of the University Health Network, we conducted a retrospective analysis with CT image obtained from 10 patients. Each patient had a CT scans including the maxilla and chest on the same day. Based on this image set, we simulated total, subtotal and hemi palate reconstruction. The procedure of simulation included volume segmentation, conversing the segmented volume to a stereo lithography (STL) model, manual registration, computation of minimum geometric distances and curvature between STL model. Across the 10 patients data, we found the overall root-mean-square (RMS) conformance was 3.71+/- 0.16 mm

ECAT: A New Computerized Tomographic Imaging System for Position-Emitting Radiopharmaceuticals

DOE R&D Accomplishments Database

Phelps, M. E.; Hoffman, E. J.; Huang, S. C.; Kuhl, D. E.

1977-01-01

The ECAT was designed and developed as a complete computerized positron radionuclide imaging system capable of providing high contrast, high resolution, quantitative images in 2 dimensional and tomographic formats. Flexibility, in its various image mode options, allows it to be used for a wide variety of imaging problems.

Quantitative intact specimen magnetic resonance microscopy at 3.0 T.

PubMed

Bath, Kevin G; Voss, Henning U; Jing, Deqiang; Anderson, Stewart; Hempstead, Barbara; Lee, Francis S; Dyke, Jonathan P; Ballon, Douglas J

2009-06-01

In this report, we discuss the application of a methodology for high-contrast, high-resolution magnetic resonance microscopy (MRM) of murine tissue using a 3.0-T imaging system. We employed a threefold strategy that included customized specimen preparation to maximize image contrast, three-dimensional data acquisition to minimize scan time and custom radiofrequency resonator design to maximize signal sensitivity. Images had a resolution of 100 x 78 x 78 microm(3) with a signal-to-noise ratio per voxel greater than 25:1 and excellent contrast-to-noise ratios over a 30-min acquisition. We quantitatively validated the methods through comparisons of neuroanatomy across two lines of genetically engineered mice. Specifically, we were able to detect volumetric differences of as little as 9% between genetically engineered mouse strains in multiple brain regions that were predictive of underlying impairments in brain development. The overall methodology was straightforward to implement and provides ready access to basic MRM at field strengths that are widely available in both the laboratory and the clinic.

Amide proton transfer imaging of brain tumors using a self-corrected 3D fast spin-echo dixon method: Comparison With separate B0 correction.

PubMed

Togao, Osamu; Keupp, Jochen; Hiwatashi, Akio; Yamashita, Koji; Kikuchi, Kazufumi; Yoneyama, Masami; Honda, Hiroshi

2017-06-01

To assess the quantitative performance of three-dimensional (3D) fast spin-echo (FSE) Dixon amide proton transfer (APT) imaging of brain tumors compared with B 0 correction with separate mapping methods. Twenty-two patients with brain tumors (54.2 ± 18.7 years old, 12 males and 10 females) were scanned at 3 Tesla (T). Z-spectra were obtained at seven different frequency offsets at ±3.1 ppm, ± 3.5 ppm, ± 3.9 ppm, and -1560 ppm. The scan was repeated three times at +3.5 ppm with echo shifts for Dixon B 0 mapping. The APT image corrected by a three-point Dixon-type B 0 map from the same scan (3D-Dixon) or a separate B 0 map (2D-separate and 3D-separate), and an uncorrected APT image (3D-uncorrected) were generated. We compared the APT-weighted signals within a tumor obtained with each 3D method with those obtained with 2D-separate as a reference standard. Excellent agreements and correlations with the 2D-separate were obtained by the 3D-Dixon method for both mean (ICC = 0.964, r = 0.93, P < 0.0001) and 90th-percentile (ICC = 0.972, r = 0.95, P < 0.0001) APT-weighted signals. These agreements and correlations for 3D-Dixon were better than those obtained by the 3D-uncorrected and 3D-separate methods. The 3D FSE Dixon APT method with intrinsic B 0 correction offers a quantitative performance that is similar to that of established two-dimensional (2D) methods. Magn Reson Med 77:2272-2279, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Inverse methods for 3D quantitative optical coherence elasticity imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Dong, Li; Wijesinghe, Philip; Hugenberg, Nicholas; Sampson, David D.; Munro, Peter R. T.; Kennedy, Brendan F.; Oberai, Assad A.

2017-02-01

In elastography, quantitative elastograms are desirable as they are system and operator independent. Such quantification also facilitates more accurate diagnosis, longitudinal studies and studies performed across multiple sites. In optical elastography (compression, surface-wave or shear-wave), quantitative elastograms are typically obtained by assuming some form of homogeneity. This simplifies data processing at the expense of smearing sharp transitions in elastic properties, and/or introducing artifacts in these regions. Recently, we proposed an inverse problem-based approach to compression OCE that does not assume homogeneity, and overcomes the drawbacks described above. In this approach, the difference between the measured and predicted displacement field is minimized by seeking the optimal distribution of elastic parameters. The predicted displacements and recovered elastic parameters together satisfy the constraint of the equations of equilibrium. This approach, which has been applied in two spatial dimensions assuming plane strain, has yielded accurate material property distributions. Here, we describe the extension of the inverse problem approach to three dimensions. In addition to the advantage of visualizing elastic properties in three dimensions, this extension eliminates the plane strain assumption and is therefore closer to the true physical state. It does, however, incur greater computational costs. We address this challenge through a modified adjoint problem, spatially adaptive grid resolution, and three-dimensional decomposition techniques. Through these techniques the inverse problem is solved on a typical desktop machine within a wall clock time of 20 hours. We present the details of the method and quantitative elasticity images of phantoms and tissue samples.

3D in-vivo imaging of GFP-expressing T-cells in mice with non-contact fluorescence molecular tomography (Invited Paper)

NASA Astrophysics Data System (ADS)

Garofalakis, Anikitos; Meyer, Heiko; Zacharakis, Giannis; Economou, Eleftherios N.; Mamalaki, Clio; Papamatheakis, Joseph; Ntziachristos, Vasilis; Ripoll, Jorge

2005-06-01

Optical imaging and tomography in tissues can facilitate the quantitative study of several important chromophores and fluorophores in-vivo. Due to this fact, there has been great interest in developing imaging systems offering quantitative information on the location and concentration of chromophores and fluorescent probes. In this study we present a novel imaging system that enables three dimensional (3D) imaging of fluorescent signals in bodies of arbitrary shapes in a non-contact geometry, in combination with a 3D surface reconstruction algorithm, which is appropriate for in-vivo small animal imaging of fluorescent probes. The system consists of a rotating sample holder and a lens coupled Charge Coupled Device (CCD) camera in combination with a fiber coupled laser scanning device. An Argon ion laser is used as the source and different filters are used for the detection of various fluorophores or fluorescing proteins. With this new setup a large measurements dataset can be achieved while the use of inversion models give a high capacity for quantitative 3D reconstruction of fluorochrome distributions as well as high spatial resolution. The system has already been tested in the observation of the distribution of Green Fluorescent Protein (GFP) expressing T-lymphocytes in order to study the function of the immune system in a murine model, which can then be related to the function of the human immune system.

Associative image analysis: a method for automated quantification of 3D multi-parameter images of brain tissue

PubMed Central

Bjornsson, Christopher S; Lin, Gang; Al-Kofahi, Yousef; Narayanaswamy, Arunachalam; Smith, Karen L; Shain, William; Roysam, Badrinath

2009-01-01

Brain structural complexity has confounded prior efforts to extract quantitative image-based measurements. We present a systematic ‘divide and conquer’ methodology for analyzing three-dimensional (3D) multi-parameter images of brain tissue to delineate and classify key structures, and compute quantitative associations among them. To demonstrate the method, thick (~100 μm) slices of rat brain tissue were labeled using 3 – 5 fluorescent signals, and imaged using spectral confocal microscopy and unmixing algorithms. Automated 3D segmentation and tracing algorithms were used to delineate cell nuclei, vasculature, and cell processes. From these segmentations, a set of 23 intrinsic and 8 associative image-based measurements was computed for each cell. These features were used to classify astrocytes, microglia, neurons, and endothelial cells. Associations among cells and between cells and vasculature were computed and represented as graphical networks to enable further analysis. The automated results were validated using a graphical interface that permits investigator inspection and corrective editing of each cell in 3D. Nuclear counting accuracy was >89%, and cell classification accuracy ranged from 81–92% depending on cell type. We present a software system named FARSIGHT implementing our methodology. Its output is a detailed XML file containing measurements that may be used for diverse quantitative hypothesis-driven and exploratory studies of the central nervous system. PMID:18294697

System for tomographic determination of the power distribution in electron beams

DOEpatents

Elmer, J.W.; Teruya, A.T.; O'Brien, D.W.

1995-01-17

A tomographic technique is disclosed for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0[degree] to 360[degree] and the waveforms are recorded by a digitizing storage oscilloscope. Two-dimensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment. 12 figures.

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

PubMed

Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

2017-03-03

Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6  cells/mm 3 . Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

Electric Potential and Electric Field Imaging with Dynamic Applications & Extensions

NASA Technical Reports Server (NTRS)

Generazio, Ed

2017-01-01

The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field made be used for volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e- Sensor enhancements (ephemeral e-Sensor) are discussed. Critical design elements of current linear and real-time two-dimensional (2D) measurement systems are highlighted, and the development of a three dimensional (3D) EFI system is presented. Demonstrations for structural, electronic, human, and memory applications are shown. Recent work demonstrates that phonons may be used to create and annihilate electric dipoles within structures. Phonon induced dipoles are ephemeral and their polarization, strength, and location may be quantitatively characterized by EFI providing a new subsurface Phonon-EFI imaging technology. Results from real-time imaging of combustion and ion flow, and their measurement complications, will be discussed. Extensions to environment, Space and subterranean applications will be presented, and initial results for quantitative characterizing material properties are shown. A wearable EFI system has been developed by using fundamental EFI concepts. These new EFI capabilities are demonstrated to characterize electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, manufacturing quality control, crime scene forensics, design and materials selection for advanced sensors, combustion science, on-orbit space potential, container inspection, remote characterization of electronic circuits and level of activation, dielectric morphology of structures, tether integrity, organic molecular memory, atmospheric science, weather prediction, earth quake prediction, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

Cerebral cortex three-dimensional profiling in human fetuses by magnetic resonance imaging

PubMed Central

Sbarbati, Andrea; Pizzini, Francesca; Fabene, Paolo F; Nicolato, Elena; Marzola, Pasquina; Calderan, Laura; Simonati, Alessandro; Longo, Laura; Osculati, Antonio; Beltramello, Alberto

2004-01-01

Seven human fetuses of crown/rump length corresponding to gestational ages ranging from the 12th to the 16th week were studied using a paradigm based on three-dimensional reconstruction of the brain obtained by magnetic resonance imaging (MRI). The aim of the study was to evaluate brain morphology in situ and to describe developmental dynamics during an important period of fetal morphogenesis. Three-dimensional MRI showed the increasing degree of maturation of the brains; fronto-occipital distance, bitemporal distance and occipital angle were examined in all the fetuses. The data were interpreted by correlation with the internal structure as visualized using high-spatial-resolution MRI, acquired using a 4.7-T field intensity magnet with a gradient power of 20 G cm−1. The spatial resolution was sufficient for a detailed detection of five layers, and the contrast was optimized using sequences with different degrees of T1 and T2 weighting. Using the latter, it was possible to visualize the subplate and marginal zones. The cortical thickness was mapped on to the hemispheric surface, describing the thickness gradient from the insular cortex to the periphery of the hemispheres. The study demonstrates the utility of MRI for studying brain development. The method provides a quantitative profiling of the brain, which allows the calculation of important morphological parameters, and it provides informative regarding transient features of the developing brain. PMID:15198688

SedCT: MATLAB™ tools for standardized and quantitative processing of sediment core computed tomography (CT) data collected using a medical CT scanner

NASA Astrophysics Data System (ADS)

Reilly, B. T.; Stoner, J. S.; Wiest, J.

2017-08-01

Computed tomography (CT) of sediment cores allows for high-resolution images, three-dimensional volumes, and down core profiles. These quantitative data are generated through the attenuation of X-rays, which are sensitive to sediment density and atomic number, and are stored in pixels as relative gray scale values or Hounsfield units (HU). We present a suite of MATLAB™ tools specifically designed for routine sediment core analysis as a means to standardize and better quantify the products of CT data collected on medical CT scanners. SedCT uses a graphical interface to process Digital Imaging and Communications in Medicine (DICOM) files, stitch overlapping scanned intervals, and create down core HU profiles in a manner robust to normal coring imperfections. Utilizing a random sampling technique, SedCT reduces data size and allows for quick processing on typical laptop computers. SedCTimage uses a graphical interface to create quality tiff files of CT slices that are scaled to a user-defined HU range, preserving the quantitative nature of CT images and easily allowing for comparison between sediment cores with different HU means and variance. These tools are presented along with examples from lacustrine and marine sediment cores to highlight the robustness and quantitative nature of this method.

Three-Dimensional Anatomic Evaluation of the Anterior Cruciate Ligament for Planning Reconstruction

PubMed Central

Hoshino, Yuichi; Kim, Donghwi; Fu, Freddie H.

2012-01-01

Anatomic study related to the anterior cruciate ligament (ACL) reconstruction surgery has been developed in accordance with the progress of imaging technology. Advances in imaging techniques, especially the move from two-dimensional (2D) to three-dimensional (3D) image analysis, substantially contribute to anatomic understanding and its application to advanced ACL reconstruction surgery. This paper introduces previous research about image analysis of the ACL anatomy and its application to ACL reconstruction surgery. Crucial bony landmarks for the accurate placement of the ACL graft can be identified by 3D imaging technique. Additionally, 3D-CT analysis of the ACL insertion site anatomy provides better and more consistent evaluation than conventional “clock-face” reference and roentgenologic quadrant method. Since the human anatomy has a complex three-dimensional structure, further anatomic research using three-dimensional imaging analysis and its clinical application by navigation system or other technologies is warranted for the improvement of the ACL reconstruction. PMID:22567310

Positron emission reconstruction tomography for the assessment of regional myocardial metabolism by the administration of substrates labeled with cyclotron produced radionuclides

NASA Technical Reports Server (NTRS)

Ter-Pogossian, M. M.; Hoffman, E. J.; Weiss, E. S.; Coleman, R. E.; Phelps, M. E.; Welch, M. J.; Sobel, B. E.

1975-01-01

A positron emission transverse tomograph device was developed which provides transaxial sectional images of the distribution of positron-emitting radionuclides in the heart. The images provide a quantitative three-dimensional map of the distribution of activity unencumbered by the superimposition of activity originating from regions overlying and underlying the plane of interest. PETT is used primarily with the cyclotron-produced radionuclides oxygen-15, nitrogen-13 and carbon-11. Because of the participation of these atoms in metabolism, they can be used to label metabolic substrates and intermediary molecules incorporated in myocardial metabolism.

Correction of motion artifacts in endoscopic optical coherence tomography and autofluorescence images based on azimuthal en face image registration.

PubMed

Abouei, Elham; Lee, Anthony M D; Pahlevaninezhad, Hamid; Hohert, Geoffrey; Cua, Michelle; Lane, Pierre; Lam, Stephen; MacAulay, Calum

2018-01-01

We present a method for the correction of motion artifacts present in two- and three-dimensional in vivo endoscopic images produced by rotary-pullback catheters. This method can correct for cardiac/breathing-based motion artifacts and catheter-based motion artifacts such as nonuniform rotational distortion (NURD). This method assumes that en face tissue imaging contains slowly varying structures that are roughly parallel to the pullback axis. The method reduces motion artifacts using a dynamic time warping solution through a cost matrix that measures similarities between adjacent frames in en face images. We optimize and demonstrate the suitability of this method using a real and simulated NURD phantom and in vivo endoscopic pulmonary optical coherence tomography and autofluorescence images. Qualitative and quantitative evaluations of the method show an enhancement of the image quality. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

An evaluation of three-dimensional sensors for the extravehicular activity helper/retreiver

NASA Technical Reports Server (NTRS)

Magee, Michael

1993-01-01

The Extravehicular Activity Retriever/Helper (EVAHR) is a robotic device currently under development at the NASA Johnson Space Center that is designed to fetch objects or to assist in retrieving an astronaut who may have become inadvertently de-tethered. The EVAHR will be required to exhibit a high degree of intelligent autonomous operation and will base much of its reasoning upon information obtained from one or more three-dimensional sensors that it will carry and control. At the highest level of visual cognition and reasoning, the EVAHR will be required to detect objects, recognize them, and estimate their spatial orientation and location. The recognition phase and estimation of spatial pose will depend on the ability of the vision system to reliably extract geometric features of the objects such as whether the surface topologies observed are planar or curved and the spatial relationships between the component surfaces. In order to achieve these tasks, accurate sensing of the operational environment and objects in the environment will therefore be critical. The qualitative and quantitative results of empirical studies of three sensors that are capable of providing three-dimensional information to the EVAHR, but using completely different hardware approaches are documented. The first of these devices is a phase shift laser with an effective operating range (ambiguity interval) of approximately 15 meters. The second sensor is a laser triangulation system designed to operate at much closer range and to provide higher resolution images. The third sensor is a dual camera stereo imaging system from which range images can also be obtained. The remainder of the report characterizes the strengths and weaknesses of each of these systems relative to quality of data extracted and how different object characteristics affect sensor operation.

Designing It Smart With SIV

NASA Technical Reports Server (NTRS)

2003-01-01

When research staff at NASA s Glenn Research Center developed and patented Stereo Imaging Velocimetry (SIV), the world s first three-dimensional (3-D), full-field quantitative and qualitative analysis tool to investigate flow velocities, experiments that were previously impossible became a reality. Seizing the opportunity to commercialize NASA s breakthrough invention, Digital Interface Systems (DIS), Inc., of North Olmsted, Ohio, acquired an exclusive license to market SIV, which has a range of applications from improving the aerodynamics of aircraft and automobiles to avoiding "no flow" regions in artificial hearts.

The use of computer imaging techniques to visualize cardiac muscle cells in three dimensions.

PubMed

Marino, T A; Cook, P N; Cook, L T; Dwyer, S J

1980-11-01

Atrial muscle cells and atrioventricular bundle cells were reconstructed using a computer-assisted three-dimensional reconstruction system. This reconstruction technique permitted these cells to be viewed from any direction. The cell surfaces were approximated using triangular tiles, and this optimization technique for cell reconstruction allowed for the computation of cell surface area and cell volume. A transparent mode is described which enables the investigator to examine internal cellular features such as the shape and location of the nucleus. In addition, more than one cell can be displayed simultaneously, and, therefore, spatial relationships are preserved and intercellular relationships viewed directly. The use of computer imaging techniques allows for a more complete collection of quantitative morphological data and also the visualization of the morphological information gathered.

The dynamic micro computed tomography at SSRF

NASA Astrophysics Data System (ADS)

Chen, R.; Xu, L.; Du, G.; Deng, B.; Xie, H.; Xiao, T.

2018-05-01

Synchrotron radiation micro-computed tomography (SR-μCT) is a critical technique for quantitative characterizing the 3D internal structure of samples, recently the dynamic SR-μCT has been attracting vast attention since it can evaluate the three-dimensional structure evolution of a sample. A dynamic μCT method, which is based on monochromatic beam, was developed at the X-ray Imaging and Biomedical Application Beamline at Shanghai Synchrotron Radiation Facility, by combining the compressed sensing based CT reconstruction algorithm and hardware upgrade. The monochromatic beam based method can achieve quantitative information, and lower dose than the white beam base method in which the lower energy beam is absorbed by the sample rather than contribute to the final imaging signal. The developed method is successfully used to investigate the compression of the air sac during respiration in a bell cricket, providing new knowledge for further research on the insect respiratory system.

Detection of brain tumor margins using optical coherence tomography

NASA Astrophysics Data System (ADS)

Juarez-Chambi, Ronald M.; Kut, Carmen; Rico-Jimenez, Jesus; Campos-Delgado, Daniel U.; Quinones-Hinojosa, Alfredo; Li, Xingde; Jo, Javier

2018-02-01

In brain cancer surgery, it is critical to achieve extensive resection without compromising adjacent healthy, noncancerous regions. Various technological advances have made major contributions in imaging, including intraoperative magnetic imaging (MRI) and computed tomography (CT). However, these technologies have pros and cons in providing quantitative, real-time and three-dimensional (3D) continuous guidance in brain cancer detection. Optical Coherence Tomography (OCT) is a non-invasive, label-free, cost-effective technique capable of imaging tissue in three dimensions and real time. The purpose of this study is to reliably and efficiently discriminate between non-cancer and cancerinfiltrated brain regions using OCT images. To this end, a mathematical model for quantitative evaluation known as the Blind End-Member and Abundances Extraction method (BEAE). This BEAE method is a constrained optimization technique which extracts spatial information from volumetric OCT images. Using this novel method, we are able to discriminate between cancerous and non-cancerous tissues and using logistic regression as a classifier for automatic brain tumor margin detection. Using this technique, we are able to achieve excellent performance using an extensive cross-validation of the training dataset (sensitivity 92.91% and specificity 98.15%) and again using an independent, blinded validation dataset (sensitivity 92.91% and specificity 86.36%). In summary, BEAE is well-suited to differentiate brain tissue which could support the guiding surgery process for tissue resection.

Detection of brain tumor margins using optical coherence tomography

NASA Astrophysics Data System (ADS)

Juarez-Chambi, Ronald M.; Kut, Carmen; Rico-Jimenez, Jesus; Campos-Delgado, Daniel U.; Quinones-Hinojosa, Alfredo; Li, Xingde; Jo, Javier

2018-02-01

In brain cancer surgery, it is critical to achieve extensive resection without compromising adjacent healthy, non-cancerous regions. Various technological advances have made major contributions in imaging, including intraoperative magnetic imaging (MRI) and computed tomography (CT). However, these technologies have pros and cons in providing quantitative, real-time and three-dimensional (3D) continuous guidance in brain cancer detection. Optical Coherence Tomography (OCT) is a non-invasive, label-free, cost-effective technique capable of imaging tissue in three dimensions and real time. The purpose of this study is to reliably and efficiently discriminate between non-cancer and cancer-infiltrated brain regions using OCT images. To this end, a mathematical model for quantitative evaluation known as the Blind End- Member and Abundances Extraction method (BEAE). This BEAE method is a constrained optimization technique which extracts spatial information from volumetric OCT images. Using this novel method, we are able to discriminate between cancerous and non-cancerous tissues and using logistic regression as a classifier for automatic brain tumor margin detection. Using this technique, we are able to achieve excellent performance using an extensive cross-validation of the training dataset (sensitivity 92.91% and specificity 98.15%) and again using an independent, blinded validation dataset (sensitivity 92.91% and specificity 86.36%). In summary, BEAE is well-suited to differentiate brain tissue which could support the guiding surgery process for tissue resection.

Light ray field capture using focal plane sweeping and its optical reconstruction using 3D displays.

PubMed

Park, Jae-Hyeung; Lee, Sung-Keun; Jo, Na-Young; Kim, Hee-Jae; Kim, Yong-Soo; Lim, Hong-Gi

2014-10-20

We propose a method to capture light ray field of three-dimensional scene using focal plane sweeping. Multiple images are captured using a usual camera at different focal distances, spanning the three-dimensional scene. The captured images are then back-projected to four-dimensional spatio-angular space to obtain the light ray field. The obtained light ray field can be visualized either using digital processing or optical reconstruction using various three-dimensional display techniques including integral imaging, layered display, and holography.

Neuronavigation using three-dimensional proton magnetic resonance spectroscopy data.

PubMed

Kanberoglu, Berkay; Moore, Nina Z; Frakes, David; Karam, Lina J; Debbins, Josef P; Preul, Mark C

2014-01-01

Applications in clinical medicine can benefit from fusion of spectroscopy data with anatomical imagery. For example, new 3-dimensional (3D) spectroscopy techniques allow for improved correlation of metabolite profiles with specific regions of interest in anatomical tumor images, which can be useful in characterizing and treating heterogeneous tumors that appear structurally homogeneous. We sought to develop a clinical workflow and uniquely capable custom software tool to integrate advanced 3-tesla 3D proton magnetic resonance spectroscopic imaging ((1)H-MRSI) into industry standard image-guided neuronavigation systems, especially for use in brain tumor surgery. (1)H-MRSI spectra from preoperative scanning on 15 patients with recurrent or newly diagnosed meningiomas were processed and analyzed, and specific voxels were selected based on their chemical contents. 3D neuronavigation overlays were then generated and applied to anatomical image data in the operating room. The proposed 3D methods fully account for scanner calibration and comprise tools that we have now made publicly available. The new methods were quantitatively validated through a phantom study and applied successfully to mitigate biopsy uncertainty in a clinical study of meningiomas. The proposed methods improve upon the current state of the art in neuronavigation through the use of detailed 3D (1)H-MRSI data. Specifically, 3D MRSI-based overlays provide comprehensive, quantitative visual cues and location information during neurosurgery, enabling a progressive new form of online spectroscopy-guided neuronavigation. © 2014 S. Karger AG, Basel.

Assessment of Normal Eyeball Protrusion Using Computed Tomographic Imaging and Three-Dimensional Reconstruction in Korean Adults.

PubMed

Shin, Kang-Jae; Gil, Young-Chun; Lee, Shin-Hyo; Kim, Jeong-Nam; Yoo, Ja-Young; Kim, Soon-Heum; Choi, Hyun-Gon; Shin, Hyun Jin; Koh, Ki-Seok; Song, Wu-Chul

2017-01-01

The aim of the present study was to assess normal eyeball protrusion from the orbital rim using two- and three-dimensional images and demonstrate the better suitability of CT images for assessment of exophthalmos. The facial computed tomographic (CT) images of Korean adults were acquired in sagittal and transverse views. The CT images were used in reconstructing three-dimensional volume of faces using computer software. The protrusion distances from orbital rims and the diameters of eyeballs were measured in the two views of the CT image and three-dimensional volume of the face. Relative exophthalmometry was calculated by the difference in protrusion distance between the right and left sides. The eyeball protrusion was 4.9 and 12.5 mm in sagittal and transverse views, respectively. The protrusion distances were 2.9 mm in the three-dimensional volume of face. There were no significant differences between right and left sides in the degree of protrusion, and the difference was within 2 mm in more than 90% of the subjects. The results of the present study will provide reliable criteria for precise diagnosis and postoperative monitoring using CT imaging of diseases such as thyroid-associated ophthalmopathy and orbital tumors.

Reflection imaging of China ink-perfused brain vasculature using confocal laser-scanning microscopy after clarification of brain tissue by the Spalteholz method.

PubMed

Gutierre, R C; Vannucci Campos, D; Mortara, R A; Coppi, A A; Arida, R M

2017-04-01

Confocal laser-scanning microscopy is a useful tool for visualizing neurons and glia in transparent preparations of brain tissue from laboratory animals. Currently, imaging capillaries and venules in transparent brain tissues requires the use of fluorescent proteins. Here, we show that vessels can be imaged by confocal laser-scanning microscopy in transparent cortical, hippocampal and cerebellar preparations after clarification of China ink-injected specimens by the Spalteholz method. This method may be suitable for global, three-dimensional, quantitative analyses of vessels, including stereological estimations of total volume and length and of surface area of vessels, which constitute indirect approaches to investigate angiogenesis. © 2017 Anatomical Society.

Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison.

PubMed

Wegel, Eva; Göhler, Antonia; Lagerholm, B Christoffer; Wainman, Alan; Uphoff, Stephan; Kaufmann, Rainer; Dobbie, Ian M

2016-06-06

Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques.

Out-of-Sample Extrapolation utilizing Semi-Supervised Manifold Learning (OSE-SSL): Content Based Image Retrieval for Histopathology Images

PubMed Central

Sparks, Rachel; Madabhushi, Anant

2016-01-01

Content-based image retrieval (CBIR) retrieves database images most similar to the query image by (1) extracting quantitative image descriptors and (2) calculating similarity between database and query image descriptors. Recently, manifold learning (ML) has been used to perform CBIR in a low dimensional representation of the high dimensional image descriptor space to avoid the curse of dimensionality. ML schemes are computationally expensive, requiring an eigenvalue decomposition (EVD) for every new query image to learn its low dimensional representation. We present out-of-sample extrapolation utilizing semi-supervised ML (OSE-SSL) to learn the low dimensional representation without recomputing the EVD for each query image. OSE-SSL incorporates semantic information, partial class label, into a ML scheme such that the low dimensional representation co-localizes semantically similar images. In the context of prostate histopathology, gland morphology is an integral component of the Gleason score which enables discrimination between prostate cancer aggressiveness. Images are represented by shape features extracted from the prostate gland. CBIR with OSE-SSL for prostate histology obtained from 58 patient studies, yielded an area under the precision recall curve (AUPRC) of 0.53 ± 0.03 comparatively a CBIR with Principal Component Analysis (PCA) to learn a low dimensional space yielded an AUPRC of 0.44 ± 0.01. PMID:27264985

Optofluidic bioimaging platform for quantitative phase imaging of lab on a chip devices using digital holographic microscopy.

PubMed

Pandiyan, Vimal Prabhu; John, Renu

2016-01-20

We propose a versatile 3D phase-imaging microscope platform for real-time imaging of optomicrofluidic devices based on the principle of digital holographic microscopy (DHM). Lab-on-chip microfluidic devices fabricated on transparent polydimethylsiloxane (PDMS) and glass substrates have attained wide popularity in biological sensing applications. However, monitoring, visualization, and characterization of microfluidic devices, microfluidic flows, and the biochemical kinetics happening in these devices is difficult due to the lack of proper techniques for real-time imaging and analysis. The traditional bright-field microscopic techniques fail in imaging applications, as the microfluidic channels and the fluids carrying biological samples are transparent and not visible in bright light. Phase-based microscopy techniques that can image the phase of the microfluidic channel and changes in refractive indices due to the fluids and biological samples present in the channel are ideal for imaging the fluid flow dynamics in a microfluidic channel at high resolutions. This paper demonstrates three-dimensional imaging of a microfluidic device with nanometric depth precisions and high SNR. We demonstrate imaging of microelectrodes of nanometric thickness patterned on glass substrate and the microfluidic channel. Three-dimensional imaging of a transparent PDMS optomicrofluidic channel, fluid flow, and live yeast cell flow in this channel has been demonstrated using DHM. We also quantify the average velocity of fluid flow through the channel. In comparison to any conventional bright-field microscope, the 3D depth information in the images illustrated in this work carry much information about the biological system under observation. The results demonstrated in this paper prove the high potential of DHM in imaging optofluidic devices; detection of pathogens, cells, and bioanalytes on lab-on-chip devices; and in studying microfluidic dynamics in real time based on phase changes.

Study on the application of MRF and the D-S theory to image segmentation of the human brain and quantitative analysis of the brain tissue

NASA Astrophysics Data System (ADS)

Guan, Yihong; Luo, Yatao; Yang, Tao; Qiu, Lei; Li, Junchang

2012-01-01

The features of the spatial information of Markov random field image was used in image segmentation. It can effectively remove the noise, and get a more accurate segmentation results. Based on the fuzziness and clustering of pixel grayscale information, we find clustering center of the medical image different organizations and background through Fuzzy cmeans clustering method. Then we find each threshold point of multi-threshold segmentation through two dimensional histogram method, and segment it. The features of fusing multivariate information based on the Dempster-Shafer evidence theory, getting image fusion and segmentation. This paper will adopt the above three theories to propose a new human brain image segmentation method. Experimental result shows that the segmentation result is more in line with human vision, and is of vital significance to accurate analysis and application of tissues.

Low-temperature magnetic resonance imaging with 2.8 μm isotropic resolution

NASA Astrophysics Data System (ADS)

Chen, Hsueh-Ying; Tycko, Robert

2018-02-01

We demonstrate the feasibility of high-resolution 1H magnetic resonance imaging (MRI) at low temperatures by obtaining an MRI image of 20 μm diameter glass beads in glycerol/water at 28 K with 2.8 μm isotropic resolution. The experiments use a recently-described MRI apparatus (Moore and Tycko, 2015) with minor modifications. The sample is contained within a radio-frequency microcoil with 150 μm inner diameter. Sensitivity is additionally enhanced by paramagnetic doping, optimization of the sample temperature, three-dimensional phase-encoding of k-space data, pulsed spin-lock detection of 1H nuclear magnetic resonance signals, and spherical sampling of k-space. We verify that the actual image resolution is 2.7 ± 0.3 μm by quantitative comparisons of experimental and calculated images. Our imaging approach is compatible with dynamic nuclear polarization, providing a path to significantly higher resolution in future experiments.

Polarization analysis for magnetic field imaging at RADEN in J-PARC/MLF

NASA Astrophysics Data System (ADS)

Shinohara, Takenao; Hiroi, Kosuke; Su, Yuhua; Kai, Tetsuya; Nakatani, Takeshi; Oikawa, Kenichi; Segawa, Mariko; Hayashida, Hirotoshi; Parker, Joseph D.; Matsumoto, Yoshihiro; Zhang, Shuoyuan; Kiyanagi, Yoshiaki

2017-06-01

Polarized neutron imaging is an attractive method for visualizing magnetic fields in a bulk object or in free space. In this technique polarization of neutrons transmitted through a sample is analyzed position by position to produce an image of the polarization distribution. In particular, the combination of three-dimensional spin analysis and the use of a pulsed neutron beam is very effective for the quantitative evaluation of both field strength and direction by means of the analysis of the wavelength dependent polarization vector. Recently a new imaging instrument “RADEN” has been constructed at the beam line of BL22 of the Materials and Life Science Experimental Facility (MLF) at J-PARC, which is dedicated to energy-resolved neutron imaging experiments. We have designed a polarization analysis apparatus for magnetic field imaging at the RADEN instrument and have evaluated its performance.

Validation of two-dimensional and three-dimensional measurements of subpleural alveolar size parameters by optical coherence tomography

PubMed Central

Warger, William C.; Hostens, Jeroen; Namati, Eman; Birngruber, Reginald; Bouma, Brett E.; Tearney, Guillermo J.

2012-01-01

Abstract. Optical coherence tomography (OCT) has been increasingly used for imaging pulmonary alveoli. Only a few studies, however, have quantified individual alveolar areas, and the validity of alveolar volumes represented within OCT images has not been shown. To validate quantitative measurements of alveoli from OCT images, we compared the cross-sectional area, perimeter, volume, and surface area of matched subpleural alveoli from microcomputed tomography (micro-CT) and OCT images of fixed air-filled swine samples. The relative change in size between different alveoli was extremely well correlated (r>0.9, P<0.0001), but OCT images underestimated absolute sizes compared to micro-CT by 27% (area), 7% (perimeter), 46% (volume), and 25% (surface area) on average. We hypothesized that the differences resulted from refraction at the tissue–air interfaces and developed a ray-tracing model that approximates the reconstructed alveolar size within OCT images. Using this model and OCT measurements of the refractive index for lung tissue (1.41 for fresh, 1.53 for fixed), we derived equations to obtain absolute size measurements of superellipse and circular alveoli with the use of predictive correction factors. These methods and results should enable the quantification of alveolar sizes from OCT images in vivo. PMID:23235834

Validation of two-dimensional and three-dimensional measurements of subpleural alveolar size parameters by optical coherence tomography

NASA Astrophysics Data System (ADS)

Unglert, Carolin I.; Warger, William C.; Hostens, Jeroen; Namati, Eman; Birngruber, Reginald; Bouma, Brett E.; Tearney, Guillermo J.

2012-12-01

Optical coherence tomography (OCT) has been increasingly used for imaging pulmonary alveoli. Only a few studies, however, have quantified individual alveolar areas, and the validity of alveolar volumes represented within OCT images has not been shown. To validate quantitative measurements of alveoli from OCT images, we compared the cross-sectional area, perimeter, volume, and surface area of matched subpleural alveoli from microcomputed tomography (micro-CT) and OCT images of fixed air-filled swine samples. The relative change in size between different alveoli was extremely well correlated (r>0.9, P<0.0001), but OCT images underestimated absolute sizes compared to micro-CT by 27% (area), 7% (perimeter), 46% (volume), and 25% (surface area) on average. We hypothesized that the differences resulted from refraction at the tissue-air interfaces and developed a ray-tracing model that approximates the reconstructed alveolar size within OCT images. Using this model and OCT measurements of the refractive index for lung tissue (1.41 for fresh, 1.53 for fixed), we derived equations to obtain absolute size measurements of superellipse and circular alveoli with the use of predictive correction factors. These methods and results should enable the quantification of alveolar sizes from OCT images in vivo.

Crack Modelling for Radiography

NASA Astrophysics Data System (ADS)

Chady, T.; Napierała, L.

2010-02-01

In this paper, possibility of creation of three-dimensional crack models, both random type and based on real-life radiographic images is discussed. Method for storing cracks in a number of two-dimensional matrices, as well algorithm for their reconstruction into three-dimensional objects is presented. Also the possibility of using iterative algorithm for matching simulated images of cracks to real-life radiographic images is discussed.

A software package to improve image quality and isolation of objects of interest for quantitative stereology studies of rat hepatocarcinogenesis.

PubMed

Xu, Yihua; Pitot, Henry C

2006-03-01

In the studies of quantitative stereology of rat hepatocarcinogenesis, we have used image analysis technology (automatic particle analysis) to obtain data such as liver tissue area, size and location of altered hepatic focal lesions (AHF), and nuclei counts. These data are then used for three-dimensional estimation of AHF occurrence and nuclear labeling index analysis. These are important parameters for quantitative studies of carcinogenesis, for screening and classifying carcinogens, and for risk estimation. To take such measurements, structures or cells of interest should be separated from the other components based on the difference of color and density. Common background problems seen on the captured sample image such as uneven light illumination or color shading can cause severe problems in the measurement. Two application programs (BK_Correction and Pixel_Separator) have been developed to solve these problems. With BK_Correction, common background problems such as incorrect color temperature setting, color shading, and uneven light illumination background, can be corrected. With Pixel_Separator different types of objects can be separated from each other in relation to their color, such as seen with different colors in immunohistochemically stained slides. The resultant images of such objects separated from other components are then ready for particle analysis. Objects that have the same darkness but different colors can be accurately differentiated in a grayscale image analysis system after application of these programs.

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

NASA Technical Reports Server (NTRS)

Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

2001-01-01

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

Image intensifier-based volume tomographic angiography imaging system: system evaluation

NASA Astrophysics Data System (ADS)

Ning, Ruola; Wang, Xiaohui; Shen, Jianjun; Conover, David L.

1995-05-01

An image intensifier-based rotational volume tomographic angiography imaging system has been constructed. The system consists of an x-ray tube and an image intensifier that are separately mounted on a gantry. This system uses an image intensifier coupled to a TV camera as a two-dimensional detector so that a set of two-dimensional projections can be acquired for a direct three-dimensional reconstruction (3D). This system has been evaluated with two phantoms: a vascular phantom and a monkey head cadaver. One hundred eighty projections of each phantom were acquired with the system. A set of three-dimensional images were directly reconstructed from the projection data. The experimental results indicate that good imaging quality can be obtained with this system.

Laser interference fringe tomography: a novel 3D imaging technique for pathology

NASA Astrophysics Data System (ADS)

Kazemzadeh, Farnoud; Haylock, Thomas M.; Chifman, Lev M.; Hajian, Arsen R.; Behr, Bradford B.; Cenko, Andrew T.; Meade, Jeff T.; Hendrikse, Jan

2011-03-01

Laser interference fringe tomography (LIFT) is within the class of optical imaging devices designed for in vivo and ex vivo medical imaging applications. LIFT is a very simple and cost-effective three-dimensional imaging device with performance rivaling some of the leading three-dimensional imaging devices used for histology. Like optical coherence tomography (OCT), it measures the reflectivity as a function of depth within a sample and is capable of producing three-dimensional images from optically scattering media. LIFT has the potential capability to produce high spectral resolution, full-color images. The optical design of LIFT along with the planned iterations for improvements and miniaturization are presented and discussed in addition to the theoretical concepts and preliminary imaging results of the device.

Brain MR imaging at ultra-low radiofrequency power.

PubMed

Sarkar, Subhendra N; Alsop, David C; Madhuranthakam, Ananth J; Busse, Reed F; Robson, Philip M; Rofsky, Neil M; Hackney, David B

2011-05-01

To explore the lower limits for radiofrequency (RF) power-induced specific absorption rate (SAR) achievable at 1.5 T for brain magnetic resonance (MR) imaging without loss of tissue signal or contrast present in high-SAR clinical imaging in order to create a potentially viable MR method at ultra-low RF power to image tissues containing implanted devices. An institutional review board-approved HIPAA-compliant prospective MR study design was used, with written informed consent from all subjects prior to MR sessions. Seven healthy subjects were imaged prospectively at 1.5 T with ultra-low-SAR optimized three-dimensional (3D) fast spin-echo (FSE) and fluid-attenuated inversion-recovery (FLAIR) T2-weighted sequences and an ultra-low-SAR 3D spoiled gradient-recalled acquisition in the steady state T1-weighted sequence. Corresponding high-SAR two-dimensional (2D) clinical sequences were also performed. In addition to qualitative comparisons, absolute signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs) for multicoil, parallel imaging acquisitions were generated by using a Monte Carlo method for quantitative comparison between ultra-low-SAR and high-SAR results. There were minor to moderate differences in the absolute tissue SNR and CNR values and in qualitative appearance of brain images obtained by using ultra-low-SAR and high-SAR techniques. High-SAR 2D T2-weighted imaging produced slightly higher SNR, while ultra-low-SAR 3D technique not only produced higher SNR for T1-weighted and FLAIR images but also higher CNRs for all three sequences for most of the brain tissues. The 3D techniques adopted here led to a decrease in the absorbed RF power by two orders of magnitude at 1.5 T, and still the image quality was preserved within clinically acceptable imaging times. RSNA, 2011

Mean apparent propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure.

PubMed

Özarslan, Evren; Koay, Cheng Guan; Shepherd, Timothy M; Komlosh, Michal E; İrfanoğlu, M Okan; Pierpaoli, Carlo; Basser, Peter J

2013-09-01

Diffusion-weighted magnetic resonance (MR) signals reflect information about underlying tissue microstructure and cytoarchitecture. We propose a quantitative, efficient, and robust mathematical and physical framework for representing diffusion-weighted MR imaging (MRI) data obtained in "q-space," and the corresponding "mean apparent propagator (MAP)" describing molecular displacements in "r-space." We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework. We describe efficient analytical representation of the three-dimensional q-space MR signal in a series expansion of basis functions that accurately describes diffusion in many complex geometries. The lowest order term in this expansion contains a diffusion tensor that characterizes the Gaussian displacement distribution, equivalent to diffusion tensor MRI (DTI). Inclusion of higher order terms enables the reconstruction of the true average propagator whose projection onto the unit "displacement" sphere provides an orientational distribution function (ODF) that contains only the orientational dependence of the diffusion process. The representation characterizes novel features of diffusion anisotropy and the non-Gaussian character of the three-dimensional diffusion process. Other important measures this representation provides include the return-to-the-origin probability (RTOP), and its variants for diffusion in one- and two-dimensions-the return-to-the-plane probability (RTPP), and the return-to-the-axis probability (RTAP), respectively. These zero net displacement probabilities measure the mean compartment (pore) volume and cross-sectional area in distributions of isolated pores irrespective of the pore shape. MAP-MRI represents a new comprehensive framework to model the three-dimensional q-space signal and transform it into diffusion propagators. Experiments on an excised marmoset brain specimen demonstrate that MAP-MRI provides several novel, quantifiable parameters that capture previously obscured intrinsic features of nervous tissue microstructure. This should prove helpful for investigating the functional organization of normal and pathologic nervous tissue. Copyright © 2013 Elsevier Inc. All rights reserved.

Three-dimensional magnetic resonance angiography of vascular lesions in children.

PubMed

Katayama, H; Shimizu, T; Tanaka, Y; Narabayashi, I; Tamai, H

2000-01-01

We applied three-dimensional (3D) magnetic resonance (MR) angiography to vascular lesions in children and evaluated the clinical usefulness of this technique. Ten patients, whose ages ranged from 1 month to 16 years, underwent 3D MR angiography for 12 vascular lesions, including lesions in seven pulmonary arteries, two thoracic aortae, a pair of renal arteries, and one iliac artery. Three-dimensional MR angiography was performed with body-or pelvic-phased array coils on a 1.5-T scanner using fast spoiled gradient echo sequence. Data were acquired with the following parameters: TE, 1.9 ms; TR, 10.1 ms; flip angle, 20-60 degrees ; 1 or 2 NEX; field of view, 24-48 x 18-40 cm; matrix, 256 or 512 x 128 or 256; slice thickness, 1.2-7.5 mm; and 12, 28, or 60 partitions. Vascular imaging was enhanced with 20% gadolinium-diethylenetriaminepentaacetic acid. The examination was performed under breath-holding in six patients and with shallow breathing in four patients. In a comparative study with other noninvasive methods, 3D MR angiography was superior in seven of nine cases to other noninvasive examinations and in two cases, all methods evaluated the lesions. Furthermore, six cases were compared with conventional angiography. In five of the six cases, both methods depicted the lesions similarly, and in one case, MR angiography was more effective. A quantitative comparison of vascular diameter in the MR image was made with that in the conventional angiographic image. The correlation between them was excellent: y = 1.145x-2.090 (r = 0.987; P < 0.0001), where x is the diameter in the conventional angiographic images, y is the diameter in the MR images, and r is the correlation coefficient. In conclusion, 3D MR angiography is useful for depicting peripheral vascular lesions in children.

In Situ Three-Dimensional Reciprocal-Space Mapping of Diffuse Scattering Intensity Distribution and Data Analysis for Precursor Phenomenon in Shape-Memory Alloy

NASA Astrophysics Data System (ADS)

Cheng, Tian-Le; Ma, Fengde D.; Zhou, Jie E.; Jennings, Guy; Ren, Yang; Jin, Yongmei M.; Wang, Yu U.

2012-01-01

Diffuse scattering contains rich information on various structural disorders, thus providing a useful means to study the nanoscale structural deviations from the average crystal structures determined by Bragg peak analysis. Extraction of maximal information from diffuse scattering requires concerted efforts in high-quality three-dimensional (3D) data measurement, quantitative data analysis and visualization, theoretical interpretation, and computer simulations. Such an endeavor is undertaken to study the correlated dynamic atomic position fluctuations caused by thermal vibrations (phonons) in precursor state of shape-memory alloys. High-quality 3D diffuse scattering intensity data around representative Bragg peaks are collected by using in situ high-energy synchrotron x-ray diffraction and two-dimensional digital x-ray detector (image plate). Computational algorithms and codes are developed to construct the 3D reciprocal-space map of diffuse scattering intensity distribution from the measured data, which are further visualized and quantitatively analyzed to reveal in situ physical behaviors. Diffuse scattering intensity distribution is explicitly formulated in terms of atomic position fluctuations to interpret the experimental observations and identify the most relevant physical mechanisms, which help set up reduced structural models with minimal parameters to be efficiently determined by computer simulations. Such combined procedures are demonstrated by a study of phonon softening phenomenon in precursor state and premartensitic transformation of Ni-Mn-Ga shape-memory alloy.

Quantitative 3D reconstruction of airway and pulmonary vascular trees using HRCT

NASA Astrophysics Data System (ADS)

Wood, Susan A.; Hoford, John D.; Hoffman, Eric A.; Zerhouni, Elias A.; Mitzner, Wayne A.

1993-07-01

Accurate quantitative measurements of airway and vascular dimensions are essential to evaluate function in the normal and diseased lung. In this report, a novel method is described for three-dimensional extraction and analysis of pulmonary tree structures using data from High Resolution Computed Tomography (HRCT). Serially scanned two-dimensional slices of the lower left lobe of isolated dog lungs were stacked to create a volume of data. Airway and vascular trees were three-dimensionally extracted using a three dimensional seeded region growing algorithm based on difference in CT number between wall and lumen. To obtain quantitative data, we reduced each tree to its central axis. From the central axis, branch length is measured as the distance between two successive branch points, branch angle is measured as the angle produced by two daughter branches, and cross sectional area is measured from a plane perpendicular to the central axis point. Data derived from these methods can be used to localize and quantify structural differences both during changing physiologic conditions and in pathologic lungs.

Two-dimensional auto-correlation analysis and Fourier-transform analysis of second-harmonic-generation image for quantitative analysis of collagen fiber in human facial skin

NASA Astrophysics Data System (ADS)

Ogura, Yuki; Tanaka, Yuji; Hase, Eiji; Yamashita, Toyonobu; Yasui, Takeshi

2018-02-01

We compare two-dimensional auto-correlation (2D-AC) analysis and two-dimensional Fourier transform (2D-FT) for evaluation of age-dependent structural change of facial dermal collagen fibers caused by intrinsic aging and extrinsic photo-aging. The age-dependent structural change of collagen fibers for female subjects' cheek skin in their 20s, 40s, and 60s were more noticeably reflected in 2D-AC analysis than in 2D-FT analysis. Furthermore, 2D-AC analysis indicated significantly higher correlation with the skin elasticity measured by Cutometer® than 2D-AC analysis. 2D-AC analysis of SHG image has a high potential for quantitative evaluation of not only age-dependent structural change of collagen fibers but also skin elasticity.

Feasibility of Obtaining Quantitative 3-Dimensional Information Using Conventional Endoscope: A Pilot Study

PubMed Central

Hyun, Jong Jin; Keum, Bora; Seo, Yeon Seok; Kim, Yong Sik; Jeen, Yoon Tae; Lee, Hong Sik; Um, Soon Ho; Kim, Chang Duck; Ryu, Ho Sang; Lim, Jong-Wook; Woo, Dong-Gi; Kim, Young-Joong; Lim, Myo-Taeg

2012-01-01

Background/Aims Three-dimensional (3D) imaging is gaining popularity and has been partly adopted in laparoscopic surgery or robotic surgery but has not been applied to gastrointestinal endoscopy. As a first step, we conducted an experiment to evaluate whether images obtained by conventional gastrointestinal endoscopy could be used to acquire quantitative 3D information. Methods Two endoscopes (GIF-H260) were used in a Borrmann type I tumor model made of clay. The endoscopes were calibrated by correcting the barrel distortion and perspective distortion. Obtained images were converted to gray-level image, and the characteristics of the images were obtained by edge detection. Finally, data on 3D parameters were measured by using epipolar geometry, two view geometry, and pinhole camera model. Results The focal length (f) of endoscope at 30 mm was 258.49 pixels. Two endoscopes were fixed at predetermined distance, 12 mm (d12). After matching and calculating disparity (v2-v1), which was 106 pixels, the calculated length between the camera and object (L) was 29.26 mm. The height of the object projected onto the image (h) was then applied to the pinhole camera model, and the result of H (height and width) was 38.21 mm and 41.72 mm, respectively. Measurements were conducted from 2 different locations. The measurement errors ranged from 2.98% to 7.00% with the current Borrmann type I tumor model. Conclusions It was feasible to obtain parameters necessary for 3D analysis and to apply the data to epipolar geometry with conventional gastrointestinal endoscope to calculate the size of an object. PMID:22977798

[Clinical effect of three dimensional human body scanning system BurnCalc in the evaluation of burn wound area].

PubMed

Lu, J; Wang, L; Zhang, Y C; Tang, H T; Xia, Z F

2017-10-20

Objective: To validate the clinical effect of three dimensional human body scanning system BurnCalc developed by our research team in the evaluation of burn wound area. Methods: A total of 48 burn patients treated in the outpatient department of our unit from January to June 2015, conforming to the study criteria, were enrolled in. For the first 12 patients, one wound on the limbs or torso was selected from each patient. The stability of the system was tested by 3 attending physicians using three dimensional human body scanning system BurnCalc to measure the area of wounds individually. For the following 36 patients, one wound was selected from each patient, including 12 wounds on limbs, front torso, and side torso, respectively. The area of wounds was measured by the same attending physician using transparency tracing method, National Institutes of Health (NIH) Image J method, and three dimensional human body scanning system BurnCalc, respectively. The time for getting information of 36 wounds by three methods was recorded by stopwatch. The stability among the testers was evaluated by the intra-class correlation coefficient (ICC). Data were processed with randomized blocks analysis of variance and Bonferroni test. Results: (1) Wound area of patients measured by three physicians using three dimensional human body scanning system BurnCalc was (122±95), (121±95), and (123±96) cm(2,) respectively, and there was no statistically significant difference among them ( F =1.55, P >0.05). The ICC among 3 physicians was 0.999. (2) The wound area of limbs of patients measured by transparency tracing method, NIH Image J method, and three dimensional human body scanning system BurnCalc was (84±50), (76±46), and (84±49) cm(2,) respectively. There was no statistically significant difference in the wound area of limbs of patients measured by transparency tracing method and three dimensional human body scanning system BurnCalc ( P >0.05). The wound area of limbs of patients measured by NIH Image J method was smaller than that measured by transparency tracing method and three dimensional human body scanning system BurnCalc (with P values below 0.05). There was no statistically significant difference in the wound area of front torso of patients measured by transparency tracing method, NIH Image J method, and three dimensional human body scanning system BurnCalc ( F =0.33, P >0.05). The wound area of side torso of patients measured by transparency tracing method, NIH Image J method, and three dimensional human body scanning system BurnCalc was (169±88), (150±80), and (169±86) cm(2,) respectively. There was no statistically significant difference in the wound area of side torso of patients measured by transparency tracing method and three dimensional human body scanning system BurnCalc ( P >0.05). The wound area of side torso of patients measured by NIH Image J method was smaller than that measured by transparency tracing method and three dimensional human body scanning system BurnCalc (with P values below 0.05). (3) The time for getting information of wounds of patients by transparency tracing method, NIH Image J method, and three dimensional human body scanning system BurnCalc was (77±14), (10±3), and (9±3) s, respectively. The time for getting information of wounds of patients by transparency tracing method was longer than that by NIH Image J method and three dimensional human body scanning system BurnCalc (with P values below 0.05). The time for getting information of wounds of patients by three dimensional human body scanning system BurnCalc was close to that by NIH Image J method ( P >0.05). Conclusions: The three dimensional human body scanning system BurnCalc is stable and can accurately evaluate the wound area on limbs and torso of burn patients.

Ultrahigh resolution optical coherence tomography for quantitative topographic mapping of retinal and intraretinal architectural morphology

NASA Astrophysics Data System (ADS)

Ko, Tony H.; Hartl, Ingmar; Drexler, Wolfgang; Ghanta, Ravi K.; Fujimoto, James G.

2002-06-01

Quantitative, three-dimensional mapping of retinal architectural morphology was achieved using an ultrahigh resolution ophthalmic OCT system. This OCT system utilizes a broad bandwidth titanium-sapphire laser light source generating bandwidths of up to 300 nm near 800 nm center wavelength. The system enables real-time cross-sectional imaging of the retina with ~3 micrometers axial resolution. The macula and the papillomacular axis of a normal human subject were systematically mapped using a series of linear scans. Edge detection and segmentation algorithms were developed to quantify retinal and intraretinal thicknesses. Topographic mapping of the total retinal thickness and the total ganglion cell/inner plexiform layer thickness was achieved around the macula. A topographic mapping quantifying the progressive thickening of the nerve fiber layer (NFL) nasally approaching the optic disk was also demonstrated. The ability to create three-dimensional topographic mapping of retinal architectural morphology at ~3 micrometers axial resolution will be relevant for the diagnosis of many retinal diseases. The topographic quantification of these structures can serve as a powerful tool for developing algorithms and clinical scanning protocols for the screening and staging of ophthalmic diseases such as glaucoma.

Three-dimensional modeling of tea-shoots using images and models.

PubMed

Wang, Jian; Zeng, Xianyin; Liu, Jianbing

2011-01-01

In this paper, a method for three-dimensional modeling of tea-shoots with images and calculation models is introduced. The process is as follows: the tea shoots are photographed with a camera, color space conversion is conducted, using an improved algorithm that is based on color and regional growth to divide the tea shoots in the images, and the edges of the tea shoots extracted with the help of edge detection; after that, using the divided tea-shoot images, the three-dimensional coordinates of the tea shoots are worked out and the feature parameters extracted, matching and calculation conducted according to the model database, and finally the three-dimensional modeling of tea-shoots is completed. According to the experimental results, this method can avoid a lot of calculations and has better visual effects and, moreover, performs better in recovering the three-dimensional information of the tea shoots, thereby providing a new method for monitoring the growth of and non-destructive testing of tea shoots.

Quantitative Analysis of Three-Dimensional Human Mammary Epithelial Tissue Architecture Reveals a Role for Tenascin-C in Regulating c-Met Function

PubMed Central

Taraseviciute, Agne; Vincent, Benjamin T.; Schedin, Pepper; Jones, Peter Lloyd

2010-01-01

Remodeling of the stromal extracellular matrix and elevated expression of specific proto-oncogenes within the adjacent epithelium represent cardinal features of breast cancer, yet how these events become integrated is not fully understood. To address this question, we focused on tenascin-C (TN-C), a stromal extracellular matrix glycoprotein whose expression increases with disease severity. Initially, nonmalignant human mammary epithelial cells (MCF-10A) were cultured within a reconstituted basement membrane (BM) where they formed three-dimensional (3-D) polarized, growth-attenuated, multicellular acini, enveloped by a continuous endogenous BM. In the presence of TN-C, however, acini failed to generate a normal BM, and net epithelial cell proliferation increased. To quantify how TN-C alters 3-D tissue architecture and function, we developed a computational image analysis algorithm, which showed that although TN-C disrupted acinar surface structure, it had no effect on their volume. Thus, TN-C promoted epithelial cell proliferation leading to luminal filling, a process that we hypothesized involved c-met, a proto-oncogene amplified in breast tumors that promotes intraluminal filling. Indeed, TN-C increased epithelial c-met expression and promoted luminal filling, whereas blockade of c-met function reversed this phenotype, resulting in normal BM deposition, proper lumen formation, and decreased cell proliferation. Collectively, these studies, combining a novel quantitative image analysis tool with 3-D organotypic cultures, demonstrate that stromal changes associated with breast cancer can control proto-oncogene function. PMID:20042668

Three-dimensional imaging of dislocation dynamics during the hydriding phase transformation

NASA Astrophysics Data System (ADS)

Ulvestad, A.; Welland, M. J.; Cha, W.; Liu, Y.; Kim, J. W.; Harder, R.; Maxey, E.; Clark, J. N.; Highland, M. J.; You, H.; Zapol, P.; Hruszkewycz, S. O.; Stephenson, G. B.

2017-05-01

Crystallographic imperfections significantly alter material properties and their response to external stimuli, including solute-induced phase transformations. Despite recent progress in imaging defects using electron and X-ray techniques, in situ three-dimensional imaging of defect dynamics remains challenging. Here, we use Bragg coherent diffractive imaging to image defects during the hydriding phase transformation of palladium nanocrystals. During constant-pressure experiments we observe that the phase transformation begins after dislocation nucleation close to the phase boundary in particles larger than 300 nm. The three-dimensional phase morphology suggests that the hydrogen-rich phase is more similar to a spherical cap on the hydrogen-poor phase than to the core-shell model commonly assumed. We substantiate this using three-dimensional phase field modelling, demonstrating how phase morphology affects the critical size for dislocation nucleation. Our results reveal how particle size and phase morphology affects transformations in the PdH system.

Segmentation and Quantitative Analysis of Apoptosis of Chinese Hamster Ovary Cells from Fluorescence Microscopy Images.

PubMed

Du, Yuncheng; Budman, Hector M; Duever, Thomas A

2017-06-01

Accurate and fast quantitative analysis of living cells from fluorescence microscopy images is useful for evaluating experimental outcomes and cell culture protocols. An algorithm is developed in this work to automatically segment and distinguish apoptotic cells from normal cells. The algorithm involves three steps consisting of two segmentation steps and a classification step. The segmentation steps are: (i) a coarse segmentation, combining a range filter with a marching square method, is used as a prefiltering step to provide the approximate positions of cells within a two-dimensional matrix used to store cells' images and the count of the number of cells for a given image; and (ii) a fine segmentation step using the Active Contours Without Edges method is applied to the boundaries of cells identified in the coarse segmentation step. Although this basic two-step approach provides accurate edges when the cells in a given image are sparsely distributed, the occurrence of clusters of cells in high cell density samples requires further processing. Hence, a novel algorithm for clusters is developed to identify the edges of cells within clusters and to approximate their morphological features. Based on the segmentation results, a support vector machine classifier that uses three morphological features: the mean value of pixel intensities in the cellular regions, the variance of pixel intensities in the vicinity of cell boundaries, and the lengths of the boundaries, is developed for distinguishing apoptotic cells from normal cells. The algorithm is shown to be efficient in terms of computational time, quantitative analysis, and differentiation accuracy, as compared with the use of the active contours method without the proposed preliminary coarse segmentation step.

X-ray microbeam three-dimensional topography for dislocation strain-field analysis of 4H-SiC

NASA Astrophysics Data System (ADS)

Tanuma, R.; Mori, D.; Kamata, I.; Tsuchida, H.

2013-07-01

This paper describes the strain-field analysis of threading edge dislocations (TEDs) and basal-plane dislocations (BPDs) in 4H-SiC using x-ray microbeam three-dimensional (3D) topography. This 3D topography enables quantitative strain-field analysis, which measures images of effective misorientations (Δω maps) around the dislocations. A deformation-matrix-based simulation algorithm is developed to theoretically evaluate the Δω mapping. Systematic linear calculations can provide simulated Δω maps (Δωsim maps) of dislocations with different Burgers vectors, directions, and reflection vectors for the desired cross-sections. For TEDs and BPDs, Δω maps are compared with Δωsim maps, and their excellent correlation is demonstrated. Two types of asymmetric reflections, high- and low-angle incidence types, are compared. Strain analyses are also conducted to investigate BPD-TED conversion near an epilayer/substrate interface in 4H-SiC.

Automated fiber tracking and tissue characterization of the anterior cruciate ligament with optical coherence tomography

NASA Astrophysics Data System (ADS)

Balasubramanian, Priya S.; Guo, Jiaqi; Yao, Xinwen; Qu, Dovina; Lu, Helen H.; Hendon, Christine P.

2017-02-01

The directionality of collagen fibers across the anterior cruciate ligament (ACL) as well as the insertion of this key ligament into bone are important for understanding the mechanical integrity and functionality of this complex tissue. Quantitative analysis of three-dimensional fiber directionality is of particular interest due to the physiological, mechanical, and biological heterogeneity inherent across the ACL-to-bone junction, the behavior of the ligament under mechanical stress, and the usefulness of this information in designing tissue engineered grafts. We have developed an algorithm to characterize Optical Coherence Tomography (OCT) image volumes of the ACL. We present an automated algorithm for measuring ligamentous fiber angles, and extracting attenuation and backscattering coefficients of ligament, interface, and bone regions within mature and immature bovine ACL insertion samples. Future directions include translating this algorithm for real time processing to allow three-dimensional volumetric analysis within dynamically moving samples.

Three dimensional fabric evolution of sheared sand

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

Hasan, Alsidqi; Alshibli, Khalid

2012-10-24

Granular particles undergo translation and rolling when they are sheared. This paper presents a three-dimensional (3D) experimental assessment of fabric evolution of sheared sand at the particle level. F-75 Ottawa sand specimen was tested under an axisymmetric triaxial loading condition. It measured 9.5 mm in diameter and 20 mm in height. The quantitative evaluation was conducted by analyzing 3D high-resolution x-ray synchrotron micro-tomography images of the specimen at eight axial strain levels. The analyses included visualization of particle translation and rotation, and quantification of fabric orientation as shearing continued. Representative individual particles were successfully tracked and visualized to assess themore » mode of interaction between them. This paper discusses fabric evolution and compares the evolution of particles within and outside the shear band as shearing continues. Changes in particle orientation distributions are presented using fabric histograms and fabric tensor.« less

Three-dimensional Dendritic Needle Network model with application to Al-Cu directional solidification experiments

NASA Astrophysics Data System (ADS)

Tourret, D.; Karma, A.; Clarke, A. J.; Gibbs, P. J.; Imhoff, S. D.

2015-06-01

We present a three-dimensional (3D) extension of a previously proposed multi-scale Dendritic Needle Network (DNN) approach for the growth of complex dendritic microstructures. Using a new formulation of the DNN dynamics equations for dendritic paraboloid-branches of a given thickness, one can directly extend the DNN approach to 3D modeling. We validate this new formulation against known scaling laws and analytical solutions that describe the early transient and steady-state growth regimes, respectively. Finally, we compare the predictions of the model to in situ X-ray imaging of Al-Cu alloy solidification experiments. The comparison shows a very good quantitative agreement between 3D simulations and thin sample experiments. It also highlights the importance of full 3D modeling to accurately predict the primary dendrite arm spacing that is significantly over-estimated by 2D simulations.

Quantitative three-dimensional ice roughness from scanning electron microscopy

NASA Astrophysics Data System (ADS)

Butterfield, Nicholas; Rowe, Penny M.; Stewart, Emily; Roesel, David; Neshyba, Steven

2017-03-01

We present a method for inferring surface morphology of ice from scanning electron microscope images. We first develop a novel functional form for the backscattered electron intensity as a function of ice facet orientation; this form is parameterized using smooth ice facets of known orientation. Three-dimensional representations of rough surfaces are retrieved at approximately micrometer resolution using Gauss-Newton inversion within a Bayesian framework. Statistical analysis of the resulting data sets permits characterization of ice surface roughness with a much higher statistical confidence than previously possible. A survey of results in the range -39°C to -29°C shows that characteristics of the roughness (e.g., Weibull parameters) are sensitive not only to the degree of roughening but also to the symmetry of the roughening. These results suggest that roughening characteristics obtained by remote sensing and in situ measurements of atmospheric ice clouds can potentially provide more facet-specific information than has previously been appreciated.

Three-dimensional Dendritic Needle Network model with application to Al-Cu directional solidification experiments

DOE PAGES

Tourret, D.; Karma, A.; Clarke, A. J.; ...

2015-06-11

We present a three-dimensional (3D) extension of a previously proposed multi-scale Dendritic Needle Network (DNN) approach for the growth of complex dendritic microstructures. Using a new formulation of the DNN dynamics equations for dendritic paraboloid-branches of a given thickness, one can directly extend the DNN approach to 3D modeling. We validate this new formulation against known scaling laws and analytical solutions that describe the early transient and steady-state growth regimes, respectively. Finally, we compare the predictions of the model to in situ X-ray imaging of Al-Cu alloy solidification experiments. The comparison shows a very good quantitative agreement between 3D simulationsmore » and thin sample experiments. It also highlights the importance of full 3D modeling to accurately predict the primary dendrite arm spacing that is significantly over-estimated by 2D simulations.« less

Self-assembled three-dimensional nanocrown array.

PubMed

Hong, Soongweon; Kang, Taewook; Choi, Dukhyun; Choi, Yeonho; Lee, Luke P

2012-07-24

Although an ordered nanoplasmonic probe array will have a huge impact on light harvesting, selective frequency response (i.e., nanoantenna), and quantitative molecular/cellular imaging, the realization of such an array is still limited by conventional techniques due to the serial processing or resolution limit by light diffraction. Here, we demonstrate a thermodynamically driven, self-assembled three-dimensional nanocrown array that consists of a core and six satellite gold nanoparticles (GNPs). Our ordered nanoprobe array is fabricated over a large area by thermal dewetting of thin gold film on hexagonally ordered porous anodic alumina (PAA). During thermal dewetting, the structural order of the PAA template dictates the periodic arrangement of gold nanoparticles, rendering the array of gold nanocrown. Because of its tunable size (i.e., 50 nm core and 20 nm satellite GNPs), arrangement, and periodicity, the nanocrown array shows multiple optical resonance frequencies at visible wavelengths as well as angle-dependent optical properties.

Enabling three-dimensional densitometric measurements using laboratory source X-ray micro-computed tomography

NASA Astrophysics Data System (ADS)

Pankhurst, M. J.; Fowler, R.; Courtois, L.; Nonni, S.; Zuddas, F.; Atwood, R. C.; Davis, G. R.; Lee, P. D.

2018-01-01

We present new software allowing significantly improved quantitative mapping of the three-dimensional density distribution of objects using laboratory source polychromatic X-rays via a beam characterisation approach (c.f. filtering or comparison to phantoms). One key advantage is that a precise representation of the specimen material is not required. The method exploits well-established, widely available, non-destructive and increasingly accessible laboratory-source X-ray tomography. Beam characterisation is performed in two stages: (1) projection data are collected through a range of known materials utilising a novel hardware design integrated into the rotation stage; and (2) a Python code optimises a spectral response model of the system. We provide hardware designs for use with a rotation stage able to be tilted, yet the concept is easily adaptable to virtually any laboratory system and sample, and implicitly corrects the image artefact known as beam hardening.

Isotropic-resolution linear-array-based photoacoustic computed tomography through inverse Radon transform

NASA Astrophysics Data System (ADS)

Li, Guo; Xia, Jun; Li, Lei; Wang, Lidai; Wang, Lihong V.

2015-03-01

Linear transducer arrays are readily available for ultrasonic detection in photoacoustic computed tomography. They offer low cost, hand-held convenience, and conventional ultrasonic imaging. However, the elevational resolution of linear transducer arrays, which is usually determined by the weak focus of the cylindrical acoustic lens, is about one order of magnitude worse than the in-plane axial and lateral spatial resolutions. Therefore, conventional linear scanning along the elevational direction cannot provide high-quality three-dimensional photoacoustic images due to the anisotropic spatial resolutions. Here we propose an innovative method to achieve isotropic resolutions for three-dimensional photoacoustic images through combined linear and rotational scanning. In each scan step, we first elevationally scan the linear transducer array, and then rotate the linear transducer array along its center in small steps, and scan again until 180 degrees have been covered. To reconstruct isotropic three-dimensional images from the multiple-directional scanning dataset, we use the standard inverse Radon transform originating from X-ray CT. We acquired a three-dimensional microsphere phantom image through the inverse Radon transform method and compared it with a single-elevational-scan three-dimensional image. The comparison shows that our method improves the elevational resolution by up to one order of magnitude, approaching the in-plane lateral-direction resolution. In vivo rat images were also acquired.

Single-Shot, Volumetrically Illuminated, Three-Dimensional, Tomographic Laser-Induced-Fluorescence Imaging in a Gaseous Free Jet

DTIC Science & Technology

2016-04-28

Single- shot , volumetrically illuminated, three- dimensional, tomographic laser-induced- fluorescence imaging in a gaseous free jet Benjamin R. Halls...us.af.mil Abstract: Single- shot , tomographic imaging of the three-dimensional concentration field is demonstrated in a turbulent gaseous free jet in co-flow...2001). 6. K. M. Tacina and W. J. A. Dahm, “Effects of heat release on turbulent shear flows, Part 1. A general equivalence principle for non-buoyant

Three Dimensional Imaging of Paraffin Embedded Human Lung Tissue Samples by Micro-Computed Tomography

PubMed Central

Scott, Anna E.; Vasilescu, Dragos M.; Seal, Katherine A. D.; Keyes, Samuel D.; Mavrogordato, Mark N.; Hogg, James C.; Sinclair, Ian; Warner, Jane A.; Hackett, Tillie-Louise; Lackie, Peter M.

2015-01-01

Background Understanding the three-dimensional (3-D) micro-architecture of lung tissue can provide insights into the pathology of lung disease. Micro computed tomography (µCT) has previously been used to elucidate lung 3D histology and morphometry in fixed samples that have been stained with contrast agents or air inflated and dried. However, non-destructive microstructural 3D imaging of formalin-fixed paraffin embedded (FFPE) tissues would facilitate retrospective analysis of extensive tissue archives of lung FFPE lung samples with linked clinical data. Methods FFPE human lung tissue samples (n = 4) were scanned using a Nikon metrology µCT scanner. Semi-automatic techniques were used to segment the 3D structure of airways and blood vessels. Airspace size (mean linear intercept, Lm) was measured on µCT images and on matched histological sections from the same FFPE samples imaged by light microscopy to validate µCT imaging. Results The µCT imaging protocol provided contrast between tissue and paraffin in FFPE samples (15mm x 7mm). Resolution (voxel size 6.7 µm) in the reconstructed images was sufficient for semi-automatic image segmentation of airways and blood vessels as well as quantitative airspace analysis. The scans were also used to scout for regions of interest, enabling time-efficient preparation of conventional histological sections. The Lm measurements from µCT images were not significantly different to those from matched histological sections. Conclusion We demonstrated how non-destructive imaging of routinely prepared FFPE samples by laboratory µCT can be used to visualize and assess the 3D morphology of the lung including by morphometric analysis. PMID:26030902

Quantitative Restoration of the Evolution of Mantle Structures Using Data Assimilation

NASA Astrophysics Data System (ADS)

Ismail-Zadeh, A.; Schubert, G.; Tsepelev, I.

2008-12-01

Rapid progress in imaging deep Earth structures and in studies of physical and chemical properties of mantle rocks facilitates research in assimilation of data related to mantle dynamics. We present a quantitative approach to assimilation of geophysical and geodetic data, which allows for incorporating observations and unknown initial conditions for mantle temperature and flow into a three-dimensional dynamic model in order to determine the initial conditions in the geological past. Once the conditions are determined the evolution of mantle structures can be restore backward in time. We apply data assimilation techniques to model the evolution of mantle plumes and lithospheric slabs. We show that the geometry of the mantle structures changes with time diminishing the degree of surface curvature of the structures, because the heat conduction smoothes the complex thermal surfaces of mantle bodies with time. Present seismic tomography images of mantle structures do not allow definition of the sharp shapes of these structures. Assimilation of mantle temperature and flow to the geological past instead provides a quantitative tool to restore thermal shapes of prominent structures in the past from their diffusive shapes at present.

Evaluation of three-dimensional virtual perception of garments

NASA Astrophysics Data System (ADS)

Aydoğdu, G.; Yeşilpinar, S.; Erdem, D.

2017-10-01

In recent years, three-dimensional design, dressing and simulation programs came into prominence in the textile industry. By these programs, the need to produce clothing samples for every design in design process has been eliminated. Clothing fit, design, pattern, fabric and accessory details and fabric drape features can be evaluated easily. Also, body size of virtual mannequin can be adjusted so more realistic simulations can be created. Moreover, three-dimensional virtual garment images created by these programs can be used while presenting the product to end-user instead of two-dimensional photograph images. In this study, a survey was carried out to investigate the visual perception of consumers. The survey was conducted for three different garment types, separately. Questions about gender, profession etc. was asked to the participants and expected them to compare real samples and artworks or three-dimensional virtual images of garments. When survey results were analyzed statistically, it is seen that demographic situation of participants does not affect visual perception and three-dimensional virtual garment images reflect the real sample characteristics better than artworks for each garment type. Also, it is reported that there is no perception difference depending on garment type between t-shirt, sweatshirt and tracksuit bottom.

Depth Perception and the History of Three-Dimensional Art: Who Produced the First Stereoscopic Images?

PubMed Central

2017-01-01

The history of the expression of three-dimensional structure in art can be traced from the use of occlusion in Palaeolithic cave paintings, through the use of shadow in classical art, to the development of perspective during the Renaissance. However, the history of the use of stereoscopic techniques is controversial. Although the first undisputed stereoscopic images were presented by Wheatstone in 1838, it has been claimed that two sketches by Jacopo Chimenti da Empoli (c. 1600) can be to be fused to yield an impression of stereoscopic depth, while others suggest that Leonardo da Vinci’s Mona Lisa is the world’s first stereogram. Here, we report the first quantitative study of perceived depth in these works, in addition to more recent works by Salvador Dalí. To control for the contribution of monocular depth cues, ratings of the magnitude and coherence of depth were recorded for both stereoscopic and pseudoscopic presentations, with a genuine contribution of stereoscopic cues revealed by a difference between these scores. Although effects were clear for Wheatstone and Dalí’s images, no such effects could be found for works produced earlier. As such, we have no evidence to reject the conventional view that the first producer of stereoscopic imagery was Sir Charles Wheatstone. PMID:28203349

Depth Perception and the History of Three-Dimensional Art: Who Produced the First Stereoscopic Images?

PubMed

Brooks, Kevin R

2017-01-01

The history of the expression of three-dimensional structure in art can be traced from the use of occlusion in Palaeolithic cave paintings, through the use of shadow in classical art, to the development of perspective during the Renaissance. However, the history of the use of stereoscopic techniques is controversial. Although the first undisputed stereoscopic images were presented by Wheatstone in 1838, it has been claimed that two sketches by Jacopo Chimenti da Empoli (c. 1600) can be to be fused to yield an impression of stereoscopic depth, while others suggest that Leonardo da Vinci's Mona Lisa is the world's first stereogram. Here, we report the first quantitative study of perceived depth in these works, in addition to more recent works by Salvador Dalí. To control for the contribution of monocular depth cues, ratings of the magnitude and coherence of depth were recorded for both stereoscopic and pseudoscopic presentations, with a genuine contribution of stereoscopic cues revealed by a difference between these scores. Although effects were clear for Wheatstone and Dalí's images, no such effects could be found for works produced earlier. As such, we have no evidence to reject the conventional view that the first producer of stereoscopic imagery was Sir Charles Wheatstone.

Quantitative Evaluation of Adult Subglottic Stenosis Using Intraoperative Long-range Optical Coherence Tomography

PubMed Central

Sharma, Giriraj K.; Loy, Anthony Chin; Su, Erica; Jing, Joe; Chen, Zhongping; Wong, Brian J-F.; Verma, Sunil

2016-01-01

Objectives To determine the feasibility of long-range optical coherence tomography (LR-OCT) as a tool to intraoperatively image and measure the subglottis and trachea during suspension microlaryngoscopy before and after endoscopic treatment of subglottic stenosis (SGS). Methods Long-range optical coherence tomography of the adult subglottis and trachea was performed during suspension microlaryngoscopy before and after endoscopic treatment for SGS. The anteroposterior and transverse diameters, cross-sectional area (CSA), distance from the vocal cords, and length of the SGS were measured using a MATLAB software. Pre-intervention and postintervention airway dimensions were compared. Three-dimensional volumetric airway reconstructions were generated using medical image processing software (MIMICS). Results Intraoperative LR-OCT imaging was performed in 3 patients undergoing endoscopic management of SGS. Statistically significant differences in mean anteroposterior diameter (P < .01), transverse diameter (P < .001), and CSA (P < .001) were noted between pre-intervention and postintervention data. Three-dimensional airway models were viewed in cross-sectional format and via virtual “fly through” bronchoscopy. Conclusions This is the first report of intraoperative LR-OCT of the subglottic and tracheal airway before and after surgical management of SGS in humans. Long-range optical coherence tomography offers a practical means to measure the dimensions of SGS and acquire objective data on the response to endoscopic treatment of SGS. PMID:27354215

Incremental Value of Three-Dimensional Transesophageal Echocardiography over the Two-Dimensional Technique in the Assessment of a Thrombus in Transit through a Patent Foramen Ovale.

PubMed

Thind, Munveer; Ahmed, Mustafa I; Gok, Gulay; Joson, Marisa; Elsayed, Mahmoud; Tuck, Benjamin C; Townsley, Matthew M; Klas, Berthold; McGiffin, David C; Nanda, Navin C

2015-05-01

We report a case of a right atrial thrombus traversing a patent foramen ovale into the left atrium, where three-dimensional transesophageal echocardiography provided considerable incremental value over two-dimensional transesophageal echocardiography in its assessment. As well as allowing us to better spatially characterize the thrombus, three-dimensional transesophageal echocardiography provided a more quantitative assessment through estimation of total thrombus burden. © 2015, Wiley Periodicals, Inc.

Incremental value of live/real time three-dimensional transesophageal echocardiography over the two-dimensional technique in the assessment of primary cardiac malignant fibrous histiocytoma.

PubMed

Gok, Gulay; Elsayed, Mahmoud; Thind, Munveer; Uygur, Begum; Abtahi, Firoozeh; Chahwala, Jugal R; Yıldırımtürk, Özlem; Kayacıoğlu, İlyas; Pehlivanoğlu, Seçkin; Nanda, Navin C

2015-07-01

We describe a case of primary cardiac malignant fibrous histiocytoma where live/real time three-dimensional transesophageal echocardiography added incremental value to the two-dimensional modalities. Specifically, the three-dimensional technique allowed us to delineate the true extent and infiltration of the tumor, to identify characteristics of the tumor mass suggestive of its malignant nature, and to quantitatively assess the total tumor burden. © 2015, Wiley Periodicals, Inc.

Three Dimensional Imaging with Multiple Wavelength Speckle Interferometry

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

Bernacki, Bruce E.; Cannon, Bret D.; Schiffern, John T.

2014-05-28

We present the design, modeling, construction, and results of a three-dimensional imager based upon multiple-wavelength speckle interferometry. A surface under test is illuminated with tunable laser light in a Michelson interferometer configuration while a speckled image is acquired at each laser frequency step. The resulting hypercube is Fourier transformed in the frequency dimension and the beat frequencies that result map the relative offsets of surface features. Synthetic wavelengths resulting from the laser tuning can probe features ranging from 18 microns to hundreds of millimeters. Three dimensional images will be presented along with modeling results.

Three-dimensional visualization of geographical terrain data using temporal parallax difference induction

NASA Astrophysics Data System (ADS)

Mayhew, Christopher A.; Mayhew, Craig M.

2009-02-01

Vision III Imaging, Inc. (the Company) has developed Parallax Image Display (PIDTM) software tools to critically align and display aerial images with parallax differences. Terrain features are rendered obvious to the viewer when critically aligned images are presented alternately at 4.3 Hz. The recent inclusion of digital elevation models in geographic data browsers now allows true three-dimensional parallax to be acquired from virtual globe programs like Google Earth. The authors have successfully developed PID methods and code that allow three-dimensional geographical terrain data to be visualized using temporal parallax differences.

Textural analysis of optical coherence tomography skin images: quantitative differentiation between healthy and cancerous tissues

NASA Astrophysics Data System (ADS)

Adabi, Saba; Conforto, Silvia; Hosseinzadeh, Matin; Noe, Shahryar; Daveluy, Steven; Mehregan, Darius; Nasiriavanaki, Mohammadreza

2017-02-01

Optical Coherence Tomography (OCT) offers real-time high-resolution three-dimensional images of tissue microstructures. In this study, we used OCT skin images acquired from ten volunteers, neither of whom had any skin conditions addressing the features of their anatomic location. OCT segmented images are analyzed based on their optical properties (attenuation coefficient) and textural image features e.g., contrast, correlation, homogeneity, energy, entropy, etc. Utilizing the information and referring to their clinical insight, we aim to make a comprehensive computational model for the healthy skin. The derived parameters represent the OCT microstructural morphology and might provide biological information for generating an atlas of normal skin from different anatomic sites of human skin and may allow for identification of cell microstructural changes in cancer patients. We then compared the parameters of healthy samples with those of abnormal skin and classified them using a linear Support Vector Machines (SVM) with 82% accuracy.

Super-resolution Imaging of Chemical Synapses in the Brain

PubMed Central

Dani, Adish; Huang, Bo; Bergan, Joseph; Dulac, Catherine; Zhuang, Xiaowei

2010-01-01

Determination of the molecular architecture of synapses requires nanoscopic image resolution and specific molecular recognition, a task that has so far defied many conventional imaging approaches. Here we present a super-resolution fluorescence imaging method to visualize the molecular architecture of synapses in the brain. Using multicolor, three-dimensional stochastic optical reconstruction microscopy, the distributions of synaptic proteins can be measured with nanometer precision. Furthermore, the wide-field, volumetric imaging method enables high-throughput, quantitative analysis of a large number of synapses from different brain regions. To demonstrate the capabilities of this approach, we have determined the organization of ten protein components of the presynaptic active zone and the postsynaptic density. Variations in synapse morphology, neurotransmitter receptor composition, and receptor distribution were observed both among synapses and across different brain regions. Combination with optogenetics further allowed molecular events associated with synaptic plasticity to be resolved at the single-synapse level. PMID:21144999

Quantitative 4D Transcatheter Intraarterial Perfusion MR Imaging as a Method to Standardize Angiographic Chemoembolization Endpoints

PubMed Central

Jin, Brian; Wang, Dingxin; Lewandowski, Robert J.; Ryu, Robert K.; Sato, Kent T.; Larson, Andrew C.; Salem, Riad; Omary, Reed A.

2011-01-01

PURPOSE We aimed to test the hypothesis that subjective angiographic endpoints during transarterial chemoembolization (TACE) of hepatocellular carcinoma (HCC) exhibit consistency and correlate with objective intraprocedural reductions in tumor perfusion as determined by quantitative four dimensional (4D) transcatheter intraarterial perfusion (TRIP) magnetic resonance (MR) imaging. MATERIALS AND METHODS This prospective study was approved by the institutional review board. Eighteen consecutive patients underwent TACE in a combined MR/interventional radiology (MR-IR) suite. Three board-certified interventional radiologists independently graded the angiographic endpoint of each procedure based on a previously described subjective angiographic chemoembolization endpoint (SACE) scale. A consensus SACE rating was established for each patient. Patients underwent quantitative 4D TRIP-MR imaging immediately before and after TACE, from which mean whole tumor perfusion (Fρ) was calculated. Consistency of SACE ratings between observers was evaluated using the intraclass correlation coefficient (ICC). The relationship between SACE ratings and intraprocedural TRIP-MR imaging perfusion changes was evaluated using Spearman’s rank correlation coefficient. RESULTS The SACE rating scale demonstrated very good consistency among all observers (ICC = 0.80). The consensus SACE rating was significantly correlated with both absolute (r = 0.54, P = 0.022) and percent (r = 0.85, P < 0.001) intraprocedural perfusion reduction. CONCLUSION The SACE rating scale demonstrates very good consistency between raters, and significantly correlates with objectively measured intraprocedural perfusion reductions during TACE. These results support the use of the SACE scale as a standardized alternative method to quantitative 4D TRIP-MR imaging to classify patients based on embolic endpoints of TACE. PMID:22021520

Tomographic diffractive microscopy with a wavefront sensor.

PubMed

Ruan, Y; Bon, P; Mudry, E; Maire, G; Chaumet, P C; Giovannini, H; Belkebir, K; Talneau, A; Wattellier, B; Monneret, S; Sentenac, A

2012-05-15

Tomographic diffractive microscopy is a recent imaging technique that reconstructs quantitatively the three-dimensional permittivity map of a sample with a resolution better than that of conventional wide-field microscopy. Its main drawbacks lie in the complexity of the setup and in the slowness of the image recording as both the amplitude and the phase of the field scattered by the sample need to be measured for hundreds of successive illumination angles. In this Letter, we show that, using a wavefront sensor, tomographic diffractive microscopy can be implemented easily on a conventional microscope. Moreover, the number of illuminations can be dramatically decreased if a constrained reconstruction algorithm is used to recover the sample map of permittivity.

Coherent three-dimensional X-ray cryo-imaging.

PubMed

Robinson, Ian

2015-09-01

The combination of cryogenic sample temperatures with three-dimensional coherent diffractive imaging for the case of whole frozen-hydrated cells is discussed in the light of theoretical predictions of the achievable resolution.

A four-dimensional motion field atlas of the tongue from tagged and cine magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Xing, Fangxu; Prince, Jerry L.; Stone, Maureen; Wedeen, Van J.; El Fakhri, Georges; Woo, Jonghye

2017-02-01

Representation of human tongue motion using three-dimensional vector fields over time can be used to better understand tongue function during speech, swallowing, and other lingual behaviors. To characterize the inter-subject variability of the tongue's shape and motion of a population carrying out one of these functions it is desirable to build a statistical model of the four-dimensional (4D) tongue. In this paper, we propose a method to construct a spatio-temporal atlas of tongue motion using magnetic resonance (MR) images acquired from fourteen healthy human subjects. First, cine MR images revealing the anatomical features of the tongue are used to construct a 4D intensity image atlas. Second, tagged MR images acquired to capture internal motion are used to compute a dense motion field at each time frame using a phase-based motion tracking method. Third, motion fields from each subject are pulled back to the cine atlas space using the deformation fields computed during the cine atlas construction. Finally, a spatio-temporal motion field atlas is created to show a sequence of mean motion fields and their inter-subject variation. The quality of the atlas was evaluated by deforming cine images in the atlas space. Comparison between deformed and original cine images showed high correspondence. The proposed method provides a quantitative representation to observe the commonality and variability of the tongue motion field for the first time, and shows potential in evaluation of common properties such as strains and other tensors based on motion fields.

A Four-dimensional Motion Field Atlas of the Tongue from Tagged and Cine Magnetic Resonance Imaging.

PubMed

Xing, Fangxu; Prince, Jerry L; Stone, Maureen; Wedeen, Van J; Fakhri, Georges El; Woo, Jonghye

2017-01-01

Representation of human tongue motion using three-dimensional vector fields over time can be used to better understand tongue function during speech, swallowing, and other lingual behaviors. To characterize the inter-subject variability of the tongue's shape and motion of a population carrying out one of these functions it is desirable to build a statistical model of the four-dimensional (4D) tongue. In this paper, we propose a method to construct a spatio-temporal atlas of tongue motion using magnetic resonance (MR) images acquired from fourteen healthy human subjects. First, cine MR images revealing the anatomical features of the tongue are used to construct a 4D intensity image atlas. Second, tagged MR images acquired to capture internal motion are used to compute a dense motion field at each time frame using a phase-based motion tracking method. Third, motion fields from each subject are pulled back to the cine atlas space using the deformation fields computed during the cine atlas construction. Finally, a spatio-temporal motion field atlas is created to show a sequence of mean motion fields and their inter-subject variation. The quality of the atlas was evaluated by deforming cine images in the atlas space. Comparison between deformed and original cine images showed high correspondence. The proposed method provides a quantitative representation to observe the commonality and variability of the tongue motion field for the first time, and shows potential in evaluation of common properties such as strains and other tensors based on motion fields.

Application of a Two Camera Video Imaging System to Three-Dimensional Vortex Tracking in the 80- by 120-Foot Wind Tunnel

NASA Technical Reports Server (NTRS)

Meyn, Larry A.; Bennett, Mark S.

1993-01-01

A description is presented of two enhancements for a two-camera, video imaging system that increase the accuracy and efficiency of the system when applied to the determination of three-dimensional locations of points along a continuous line. These enhancements increase the utility of the system when extracting quantitative data from surface and off-body flow visualizations. The first enhancement utilizes epipolar geometry to resolve the stereo "correspondence" problem. This is the problem of determining, unambiguously, corresponding points in the stereo images of objects that do not have visible reference points. The second enhancement, is a method to automatically identify and trace the core of a vortex in a digital image. This is accomplished by means of an adaptive template matching algorithm. The system was used to determine the trajectory of a vortex generated by the Leading-Edge eXtension (LEX) of a full-scale F/A-18 aircraft tested in the NASA Ames 80- by 120-Foot Wind Tunnel. The system accuracy for resolving the vortex trajectories is estimated to be +/-2 inches over distance of 60 feet. Stereo images of some of the vortex trajectories are presented. The system was also used to determine the point where the LEX vortex "bursts". The vortex burst point locations are compared with those measured in small-scale tests and in flight and found to be in good agreement.

Three-Dimensional Optical Mapping of Nanoparticle Distribution in Intact Tissues.

PubMed

Sindhwani, Shrey; Syed, Abdullah Muhammad; Wilhelm, Stefan; Glancy, Dylan R; Chen, Yih Yang; Dobosz, Michael; Chan, Warren C W

2016-05-24

The role of tissue architecture in mediating nanoparticle transport, targeting, and biological effects is unknown due to the lack of tools for imaging nanomaterials in whole organs. Here, we developed a rapid optical mapping technique to image nanomaterials in intact organs ex vivo and in three-dimensions (3D). We engineered a high-throughput electrophoretic flow device to simultaneously transform up to 48 tissues into optically transparent structures, allowing subcellular imaging of nanomaterials more than 1 mm deep into tissues which is 25-fold greater than current techniques. A key finding is that nanomaterials can be retained in the processed tissue by chemical cross-linking of surface adsorbed serum proteins to the tissue matrix, which enables nanomaterials to be imaged with respect to cells, blood vessels, and other structures. We developed a computational algorithm to analyze and quantitatively map nanomaterial distribution. This method can be universally applied to visualize the distribution and interactions of materials in whole tissues and animals including such applications as the imaging of nanomaterials, tissue engineered constructs, and biosensors within their intact biological environment.

Performance analysis of three-dimensional ridge acquisition from live finger and palm surface scans

NASA Astrophysics Data System (ADS)

Fatehpuria, Abhishika; Lau, Daniel L.; Yalla, Veeraganesh; Hassebrook, Laurence G.

2007-04-01

Fingerprints are one of the most commonly used and relied-upon biometric technology. But often the captured fingerprint image is far from ideal due to imperfect acquisition techniques that can be slow and cumbersome to use without providing complete fingerprint information. Most of the diffculties arise due to the contact of the fingerprint surface with the sensor platen. To overcome these diffculties we have been developing a noncontact scanning system for acquiring a 3-D scan of a finger with suffciently high resolution which is then converted into a 2-D rolled equivalent image. In this paper, we describe certain quantitative measures evaluating scanner performance. Specifically, we use some image software components developed by the National Institute of Standards and Technology, to derive our performance metrics. Out of the eleven identified metrics, three were found to be most suitable for evaluating scanner performance. A comparison is also made between 2D fingerprint images obtained by the traditional means and the 2D images obtained after unrolling the 3D scans and the quality of the acquired scans is quantified using the metrics.

Quantitative assessment of oral mucosa and labial minor salivary glands in patients with Sjögren’s syndrome using swept source OCT

PubMed Central

Grulkowski, Ireneusz; Nowak, Jan K.; Karnowski, Karol; Zebryk, Paweł; Puszczewicz, Mariusz; Walkowiak, Jaroslaw; Wojtkowski, Maciej

2013-01-01

Three-dimensional imaging of the mucosa of the lower lip and labial minor salivary glands is demonstrated in vivo using swept source optical coherence tomography (OCT) system at 1310 nm with modified interface. Volumetric data sets of the inner surface of the lower lip covering ~230 mm2 field are obtained from patients with Sjögren’s syndrome and a control group. OCT enables high-resolution visualization of mucosal architecture using cross-sectional images as well as en-face projection images. Comprehensive morphometry of the labial minor salivary glands is performed, and statistical significance is assessed. Statistically significant differences in morphometric parameters are found when subgroups of patients with Sjögren’s syndrome are analyzed. PMID:24466492

Quantitative assessment of oral mucosa and labial minor salivary glands in patients with Sjögren's syndrome using swept source OCT.

PubMed

Grulkowski, Ireneusz; Nowak, Jan K; Karnowski, Karol; Zebryk, Paweł; Puszczewicz, Mariusz; Walkowiak, Jaroslaw; Wojtkowski, Maciej

2013-12-16

Three-dimensional imaging of the mucosa of the lower lip and labial minor salivary glands is demonstrated in vivo using swept source optical coherence tomography (OCT) system at 1310 nm with modified interface. Volumetric data sets of the inner surface of the lower lip covering ~230 mm(2) field are obtained from patients with Sjögren's syndrome and a control group. OCT enables high-resolution visualization of mucosal architecture using cross-sectional images as well as en-face projection images. Comprehensive morphometry of the labial minor salivary glands is performed, and statistical significance is assessed. Statistically significant differences in morphometric parameters are found when subgroups of patients with Sjögren's syndrome are analyzed.

Instantaneous three-dimensional visualization of concentration distributions in turbulent flows with crossed-plane laser-induced fluorescence imaging

NASA Astrophysics Data System (ADS)

Hoffmann, A.; Zimmermann, F.; Scharr, H.; Krömker, S.; Schulz, C.

2005-01-01

A laser-based technique for measuring instantaneous three-dimensional species concentration distributions in turbulent flows is presented. The laser beam from a single laser is formed into two crossed light sheets that illuminate the area of interest. The laser-induced fluorescence (LIF) signal emitted from excited species within both planes is detected with a single camera via a mirror arrangement. Image processing enables the reconstruction of the three-dimensional data set in close proximity to the cutting line of the two light sheets. Three-dimensional intensity gradients are computed and compared to the two-dimensional projections obtained from the two directly observed planes. Volume visualization by digital image processing gives unique insight into the three-dimensional structures within the turbulent processes. We apply this technique to measurements of toluene-LIF in a turbulent, non-reactive mixing process of toluene and air and to hydroxyl (OH) LIF in a turbulent methane-air flame upon excitation at 248 nm with a tunable KrF excimer laser.

Segmentation of fluorescence microscopy images for quantitative analysis of cell nuclear architecture.

PubMed

Russell, Richard A; Adams, Niall M; Stephens, David A; Batty, Elizabeth; Jensen, Kirsten; Freemont, Paul S

2009-04-22

Considerable advances in microscopy, biophysics, and cell biology have provided a wealth of imaging data describing the functional organization of the cell nucleus. Until recently, cell nuclear architecture has largely been assessed by subjective visual inspection of fluorescently labeled components imaged by the optical microscope. This approach is inadequate to fully quantify spatial associations, especially when the patterns are indistinct, irregular, or highly punctate. Accurate image processing techniques as well as statistical and computational tools are thus necessary to interpret this data if meaningful spatial-function relationships are to be established. Here, we have developed a thresholding algorithm, stable count thresholding (SCT), to segment nuclear compartments in confocal laser scanning microscopy image stacks to facilitate objective and quantitative analysis of the three-dimensional organization of these objects using formal statistical methods. We validate the efficacy and performance of the SCT algorithm using real images of immunofluorescently stained nuclear compartments and fluorescent beads as well as simulated images. In all three cases, the SCT algorithm delivers a segmentation that is far better than standard thresholding methods, and more importantly, is comparable to manual thresholding results. By applying the SCT algorithm and statistical analysis, we quantify the spatial configuration of promyelocytic leukemia nuclear bodies with respect to irregular-shaped SC35 domains. We show that the compartments are closer than expected under a null model for their spatial point distribution, and furthermore that their spatial association varies according to cell state. The methods reported are general and can readily be applied to quantify the spatial interactions of other nuclear compartments.

Segmentation of Fluorescence Microscopy Images for Quantitative Analysis of Cell Nuclear Architecture

PubMed Central

Russell, Richard A.; Adams, Niall M.; Stephens, David A.; Batty, Elizabeth; Jensen, Kirsten; Freemont, Paul S.

2009-01-01

Abstract Considerable advances in microscopy, biophysics, and cell biology have provided a wealth of imaging data describing the functional organization of the cell nucleus. Until recently, cell nuclear architecture has largely been assessed by subjective visual inspection of fluorescently labeled components imaged by the optical microscope. This approach is inadequate to fully quantify spatial associations, especially when the patterns are indistinct, irregular, or highly punctate. Accurate image processing techniques as well as statistical and computational tools are thus necessary to interpret this data if meaningful spatial-function relationships are to be established. Here, we have developed a thresholding algorithm, stable count thresholding (SCT), to segment nuclear compartments in confocal laser scanning microscopy image stacks to facilitate objective and quantitative analysis of the three-dimensional organization of these objects using formal statistical methods. We validate the efficacy and performance of the SCT algorithm using real images of immunofluorescently stained nuclear compartments and fluorescent beads as well as simulated images. In all three cases, the SCT algorithm delivers a segmentation that is far better than standard thresholding methods, and more importantly, is comparable to manual thresholding results. By applying the SCT algorithm and statistical analysis, we quantify the spatial configuration of promyelocytic leukemia nuclear bodies with respect to irregular-shaped SC35 domains. We show that the compartments are closer than expected under a null model for their spatial point distribution, and furthermore that their spatial association varies according to cell state. The methods reported are general and can readily be applied to quantify the spatial interactions of other nuclear compartments. PMID:19383481

Quantitative evaluation of 3D images produced from computer-generated holograms

NASA Astrophysics Data System (ADS)

Sheerin, David T.; Mason, Ian R.; Cameron, Colin D.; Payne, Douglas A.; Slinger, Christopher W.

1999-08-01

Advances in computing and optical modulation techniques now make it possible to anticipate the generation of near real- time, reconfigurable, high quality, three-dimensional images using holographic methods. Computer generated holography (CGH) is the only technique which holds promise of producing synthetic images having the full range of visual depth cues. These realistic images will be viewable by several users simultaneously, without the need for headtracking or special glasses. Such a data visualization tool will be key to speeding up the manufacture of new commercial and military equipment by negating the need for the production of physical 3D models in the design phase. DERA Malvern has been involved in designing and testing fixed CGH in order to understand the connection between the complexity of the CGH, the algorithms used to design them, the processes employed in their implementation and the quality of the images produced. This poster describes results from CGH containing up to 108 pixels. The methods used to evaluate the reconstructed images are discussed and quantitative measures of image fidelity made. An understanding of the effect of the various system parameters upon final image quality enables a study of the possible system trade-offs to be carried out. Such an understanding of CGH production and resulting image quality is key to effective implementation of a reconfigurable CGH system currently under development at DERA.

The effect of in situ/in vitro three-dimensional quantitative computed tomography image voxel size on the finite element model of human vertebral cancellous bone.

PubMed

Lu, Yongtao; Engelke, Klaus; Glueer, Claus-C; Morlock, Michael M; Huber, Gerd

2014-11-01

Quantitative computed tomography-based finite element modeling technique is a promising clinical tool for the prediction of bone strength. However, quantitative computed tomography-based finite element models were created from image datasets with different image voxel sizes. The aim of this study was to investigate whether there is an influence of image voxel size on the finite element models. In all 12 thoracolumbar vertebrae were scanned prior to autopsy (in situ) using two different quantitative computed tomography scan protocols, which resulted in image datasets with two different voxel sizes (0.29 × 0.29 × 1.3 mm(3) vs 0.18 × 0.18 × 0.6 mm(3)). Eight of them were scanned after autopsy (in vitro) and the datasets were reconstructed with two voxel sizes (0.32 × 0.32 × 0.6 mm(3) vs. 0.18 × 0.18 × 0.3 mm(3)). Finite element models with cuboid volume of interest extracted from the vertebral cancellous part were created and inhomogeneous bilinear bone properties were defined. Axial compression was simulated. No effect of voxel size was detected on the apparent bone mineral density for both the in situ and in vitro cases. However, the apparent modulus and yield strength showed significant differences in the two voxel size group pairs (in situ and in vitro). In conclusion, the image voxel size may have to be considered when the finite element voxel modeling technique is used in clinical applications. © IMechE 2014.

Multiparallel Three-Dimensional Optical Microscopy

NASA Technical Reports Server (NTRS)

Nguyen, Lam K.; Price, Jeffrey H.; Kellner, Albert L.; Bravo-Zanoquera, Miguel

2010-01-01

Multiparallel three-dimensional optical microscopy is a method of forming an approximate three-dimensional image of a microscope sample as a collection of images from different depths through the sample. The imaging apparatus includes a single microscope plus an assembly of beam splitters and mirrors that divide the output of the microscope into multiple channels. An imaging array of photodetectors in each channel is located at a different distance along the optical path from the microscope, corresponding to a focal plane at a different depth within the sample. The optical path leading to each photodetector array also includes lenses to compensate for the variation of magnification with distance so that the images ultimately formed on all the photodetector arrays are of the same magnification. The use of optical components common to multiple channels in a simple geometry makes it possible to obtain high light-transmission efficiency with an optically and mechanically simple assembly. In addition, because images can be read out simultaneously from all the photodetector arrays, the apparatus can support three-dimensional imaging at a high scanning rate.

The study of integration about measurable image and 4D production

NASA Astrophysics Data System (ADS)

Zhang, Chunsen; Hu, Pingbo; Niu, Weiyun

2008-12-01

In this paper, we create the geospatial data of three-dimensional (3D) modeling by the combination of digital photogrammetry and digital close-range photogrammetry. For large-scale geographical background, we make the establishment of DEM and DOM combination of three-dimensional landscape model based on the digital photogrammetry which uses aerial image data to make "4D" (DOM: Digital Orthophoto Map, DEM: Digital Elevation Model, DLG: Digital Line Graphic and DRG: Digital Raster Graphic) production. For the range of building and other artificial features which the users are interested in, we realize that the real features of the three-dimensional reconstruction adopting the method of the digital close-range photogrammetry can come true on the basis of following steps : non-metric cameras for data collection, the camera calibration, feature extraction, image matching, and other steps. At last, we combine three-dimensional background and local measurements real images of these large geographic data and realize the integration of measurable real image and the 4D production.The article discussed the way of the whole flow and technology, achieved the three-dimensional reconstruction and the integration of the large-scale threedimensional landscape and the metric building.

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.

Diagnostic value of three-dimensional magnetic resonance imaging of inner ear after intratympanic gadolinium injection, and clinical application of magnetic resonance imaging scoring system in patients with delayed endolymphatic hydrops.

PubMed

Gu, X; Fang, Z-M; Liu, Y; Lin, S-L; Han, B; Zhang, R; Chen, X

2014-01-01

Three-dimensional fluid-attenuated inversion recovery magnetic resonance imaging of the inner ear after intratympanic injection of gadolinium, together with magnetic resonance imaging scoring of the perilymphatic space, were used to investigate the positive identification rate of hydrops and determine the technique's diagnostic value for delayed endolymphatic hydrops. Twenty-five patients with delayed endolymphatic hydrops underwent pure tone audiometry, bithermal caloric testing, vestibular-evoked myogenic potential testing and three-dimensional magnetic resonance imaging of the inner ear after bilateral intratympanic injection of gadolinium. The perilymphatic space of the scanned images was analysed to investigate the positive identification rate of endolymphatic hydrops. According to the magnetic resonance imaging scoring of the perilymphatic space and the diagnostic standard, 84 per cent of the patients examined had endolymphatic hydrops. In comparison, the positive identification rates for vestibular-evoked myogenic potential and bithermal caloric testing were 52 per cent and 72 per cent respectively. Three-dimensional magnetic resonance imaging after intratympanic injection of gadolinium is valuable in the diagnosis of delayed endolymphatic hydrops and its classification. The perilymphatic space scoring system improved the diagnostic accuracy of magnetic resonance imaging.

Image formation of thick three-dimensional objects in differential-interference-contrast microscopy.

PubMed

Trattner, Sigal; Kashdan, Eugene; Feigin, Micha; Sochen, Nir

2014-05-01

The differential-interference-contrast (DIC) microscope is of widespread use in life sciences as it enables noninvasive visualization of transparent objects. The goal of this work is to model the image formation process of thick three-dimensional objects in DIC microscopy. The model is based on the principles of electromagnetic wave propagation and scattering. It simulates light propagation through the components of the DIC microscope to the image plane using a combined geometrical and physical optics approach and replicates the DIC image of the illuminated object. The model is evaluated by comparing simulated images of three-dimensional spherical objects with the recorded images of polystyrene microspheres. Our computer simulations confirm that the model captures the major DIC image characteristics of the simulated object, and it is sensitive to the defocusing effects.

Classification by Using Multispectral Point Cloud Data

NASA Astrophysics Data System (ADS)

Liao, C. T.; Huang, H. H.

2012-07-01

Remote sensing images are generally recorded in two-dimensional format containing multispectral information. Also, the semantic information is clearly visualized, which ground features can be better recognized and classified via supervised or unsupervised classification methods easily. Nevertheless, the shortcomings of multispectral images are highly depending on light conditions, and classification results lack of three-dimensional semantic information. On the other hand, LiDAR has become a main technology for acquiring high accuracy point cloud data. The advantages of LiDAR are high data acquisition rate, independent of light conditions and can directly produce three-dimensional coordinates. However, comparing with multispectral images, the disadvantage is multispectral information shortage, which remains a challenge in ground feature classification through massive point cloud data. Consequently, by combining the advantages of both LiDAR and multispectral images, point cloud data with three-dimensional coordinates and multispectral information can produce a integrate solution for point cloud classification. Therefore, this research acquires visible light and near infrared images, via close range photogrammetry, by matching images automatically through free online service for multispectral point cloud generation. Then, one can use three-dimensional affine coordinate transformation to compare the data increment. At last, the given threshold of height and color information is set as threshold in classification.

High-throughput 3D whole-brain quantitative histopathology in rodents

PubMed Central

Vandenberghe, Michel E.; Hérard, Anne-Sophie; Souedet, Nicolas; Sadouni, Elmahdi; Santin, Mathieu D.; Briet, Dominique; Carré, Denis; Schulz, Jocelyne; Hantraye, Philippe; Chabrier, Pierre-Etienne; Rooney, Thomas; Debeir, Thomas; Blanchard, Véronique; Pradier, Laurent; Dhenain, Marc; Delzescaux, Thierry

2016-01-01

Histology is the gold standard to unveil microscopic brain structures and pathological alterations in humans and animal models of disease. However, due to tedious manual interventions, quantification of histopathological markers is classically performed on a few tissue sections, thus restricting measurements to limited portions of the brain. Recently developed 3D microscopic imaging techniques have allowed in-depth study of neuroanatomy. However, quantitative methods are still lacking for whole-brain analysis of cellular and pathological markers. Here, we propose a ready-to-use, automated, and scalable method to thoroughly quantify histopathological markers in 3D in rodent whole brains. It relies on block-face photography, serial histology and 3D-HAPi (Three Dimensional Histology Analysis Pipeline), an open source image analysis software. We illustrate our method in studies involving mouse models of Alzheimer’s disease and show that it can be broadly applied to characterize animal models of brain diseases, to evaluate therapeutic interventions, to anatomically correlate cellular and pathological markers throughout the entire brain and to validate in vivo imaging techniques. PMID:26876372

Three-dimensional inversion recovery manganese-enhanced MRI of mouse brain using super-resolution reconstruction to visualize nuclei involved in higher brain function.

PubMed

Poole, Dana S; Plenge, Esben; Poot, Dirk H J; Lakke, Egbert A J F; Niessen, Wiro J; Meijering, Erik; van der Weerd, Louise

2014-07-01

The visualization of activity in mouse brain using inversion recovery spin echo (IR-SE) manganese-enhanced MRI (MEMRI) provides unique contrast, but suffers from poor resolution in the slice-encoding direction. Super-resolution reconstruction (SRR) is a resolution-enhancing post-processing technique in which multiple low-resolution slice stacks are combined into a single volume of high isotropic resolution using computational methods. In this study, we investigated, first, whether SRR can improve the three-dimensional resolution of IR-SE MEMRI in the slice selection direction, whilst maintaining or improving the contrast-to-noise ratio of the two-dimensional slice stacks. Second, the contrast-to-noise ratio of SRR IR-SE MEMRI was compared with a conventional three-dimensional gradient echo (GE) acquisition. Quantitative experiments were performed on a phantom containing compartments of various manganese concentrations. The results showed that, with comparable scan times, the signal-to-noise ratio of three-dimensional GE acquisition is higher than that of SRR IR-SE MEMRI. However, the contrast-to-noise ratio between different compartments can be superior with SRR IR-SE MEMRI, depending on the chosen inversion time. In vivo experiments were performed in mice receiving manganese using an implanted osmotic pump. The results showed that SRR works well as a resolution-enhancing technique in IR-SE MEMRI experiments. In addition, the SRR image also shows a number of brain structures that are more clearly discernible from the surrounding tissues than in three-dimensional GE acquisition, including a number of nuclei with specific higher brain functions, such as memory, stress, anxiety and reward behavior. Copyright © 2014 John Wiley & Sons, Ltd.

Quantitative analysis of eyes and other optical systems in linear optics.

PubMed

Harris, William F; Evans, Tanya; van Gool, Radboud D

2017-05-01

To show that 14-dimensional spaces of augmented point P and angle Q characteristics, matrices obtained from the ray transference, are suitable for quantitative analysis although only the latter define an inner-product space and only on it can one define distances and angles. The paper examines the nature of the spaces and their relationships to other spaces including symmetric dioptric power space. The paper makes use of linear optics, a three-dimensional generalization of Gaussian optics. Symmetric 2 × 2 dioptric power matrices F define a three-dimensional inner-product space which provides a sound basis for quantitative analysis (calculation of changes, arithmetic means, etc.) of refractive errors and thin systems. For general systems the optical character is defined by the dimensionally-heterogeneous 4 × 4 symplectic matrix S, the transference, or if explicit allowance is made for heterocentricity, the 5 × 5 augmented symplectic matrix T. Ordinary quantitative analysis cannot be performed on them because matrices of neither of these types constitute vector spaces. Suitable transformations have been proposed but because the transforms are dimensionally heterogeneous the spaces are not naturally inner-product spaces. The paper obtains 14-dimensional spaces of augmented point P and angle Q characteristics. The 14-dimensional space defined by the augmented angle characteristics Q is dimensionally homogenous and an inner-product space. A 10-dimensional subspace of the space of augmented point characteristics P is also an inner-product space. The spaces are suitable for quantitative analysis of the optical character of eyes and many other systems. Distances and angles can be defined in the inner-product spaces. The optical systems may have multiple separated astigmatic and decentred refracting elements. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

Highly conducting divalent Mg{sup 2+} cation solid electrolytes with well-ordered three-dimensional network structure

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

Tamura, Shinji; Yamane, Megumi; Hoshino, Yasunori

2016-03-15

A three-dimensionally well-ordered NASICON-type Mg{sup 2+} cation conductor, (Mg{sub x}Hf{sub 1−x}){sub 4/(4−2x)}Nb(PO{sub 4}){sub 3}, was firstly developed by partial substitution of lower valent Mg{sup 2+} cation onto the Hf{sup 4+} sites in a HfNb(PO{sub 4}){sub 3} solid to realize high Mg{sup 2+} cation conductivity even at moderate temperatures. Due to the formation of well-ordered NASICON-type structure, both the high Mg{sup 2+} cation conductivity below 450 °C and the low activation energy for Mg{sup 2+} cation migration was successfully realized for the (Mg{sub 0.1}Hf{sub 0.9}){sub 4/3.8}Nb(PO{sub 4}){sub 3} solid. Pure Mg{sup 2+} cation conduction in the NASICON-type (Mg{sub 0.1}Hf{sub 0.9}){sub 4/3.8}Nb(PO{submore » 4}){sub 3} solid was directly and quantitatively demonstrated by means of two kinds of dc electrolysis. - Graphical abstract: Image of the Mg{sup 2+} cation conduction in NASICON-type (Mg{sub 0.1}Hf{sub 0.9}){sub 4/3.8}Nb(PO{sub 4}){sub 3} and its Mg{sup 2+} conductivity. - Highlights: • We develop a three-dimensionally well-ordered NASICON-type Mg{sup 2+} cation conductor. • A high magnesium cation conductivity is realized even at moderate temperatures. • Divalent magnesium cation conduction is demonstrated directly and quantitatively.« less

Phenotypic Characterization of Toxic Compound Effects on Liver Spheroids Derived from iPSC Using Confocal Imaging and Three-Dimensional Image Analysis.

PubMed

Sirenko, Oksana; Hancock, Michael K; Hesley, Jayne; Hong, Dihui; Cohen, Avrum; Gentry, Jason; Carlson, Coby B; Mann, David A

2016-09-01

Cell models are becoming more complex to better mimic the in vivo environment and provide greater predictivity for compound efficacy and toxicity. There is an increasing interest in exploring the use of three-dimensional (3D) spheroids for modeling developmental and tissue biology with the goal of accelerating translational research in these areas. Accordingly, the development of high-throughput quantitative assays using 3D cultures is an active area of investigation. In this study, we have developed and optimized methods for the formation of 3D liver spheroids derived from human iPS cells and used those for toxicity assessment. We used confocal imaging and 3D image analysis to characterize cellular information from a 3D matrix to enable a multi-parametric comparison of different spheroid phenotypes. The assay enables characterization of compound toxicities by spheroid size (volume) and shape, cell number and spatial distribution, nuclear characterization, number and distribution of cells expressing viability, apoptosis, mitochondrial potential, and viability marker intensities. In addition, changes in the content of live, dead, and apoptotic cells as a consequence of compound exposure were characterized. We tested 48 compounds and compared induced pluripotent stem cell (iPSC)-derived hepatocytes and HepG2 cells in both two-dimensional (2D) and 3D cultures. We observed significant differences in the pharmacological effects of compounds across the two cell types and between the different culture conditions. Our results indicate that a phenotypic assay using 3D model systems formed with human iPSC-derived hepatocytes is suitable for high-throughput screening and can be used for hepatotoxicity assessment in vitro.

Comparison of sound speed measurements on two different ultrasound tomography devices

NASA Astrophysics Data System (ADS)

Sak, Mark; Duric, Neb; Littrup, Peter; Bey-Knight, Lisa; Sherman, Mark; Gierach, Gretchen; Malyarenko, Antonina

2014-03-01

Ultrasound tomography (UST) employs sound waves to produce three-dimensional images of breast tissue and precisely measures the attenuation of sound speed secondary to breast tissue composition. High breast density is a strong breast cancer risk factor and sound speed is directly proportional to breast density. UST provides a quantitative measure of breast density based on three-dimensional imaging without compression, thereby overcoming the shortcomings of many other imaging modalities. The quantitative nature of the UST breast density measures are tied to an external standard, so sound speed measurement in breast tissue should be independent of specific hardware. The work presented here compares breast sound speed measurement obtained with two different UST devices. The Computerized Ultrasound Risk Evaluation (CURE) system located at the Karmanos Cancer Institute in Detroit, Michigan was recently replaced with the SoftVue ultrasound tomographic device. Ongoing clinical trials have used images generated from both sets of hardware, so maintaining consistency in sound speed measurements is important. During an overlap period when both systems were in the same exam room, a total of 12 patients had one or both of their breasts imaged on both systems on the same day. There were 22 sound speed scans analyzed from each system and the average breast sound speeds were compared. Images were either reconstructed using saved raw data (for both CURE and SoftVue) or were created during the image acquisition (saved in DICOM format for SoftVue scans only). The sound speed measurements from each system were strongly and positively correlated with each other. The average difference in sound speed between the two sets of data was on the order of 1-2 m/s and this result was not statistically significant. The only sets of images that showed a statistical difference were the DICOM images created during the SoftVue scan compared to the SoftVue images reconstructed from the raw data. However, the discrepancy between the sound speed values could be easily handled by uniformly increasing the DICOM sound speed by approximately 0.5 m/s. These results suggest that there is no fundamental difference in sound speed measurement for the two systems and support combining data generated with these instruments in future studies.

System for forming a quadrified image comprising angularly related fields of view of a three dimensional object

NASA Technical Reports Server (NTRS)

Chamberlain, F. R. (Inventor)

1980-01-01

A system for generating, within a single frame of photographic film, a quadrified image including images of angularly (including orthogonally) related fields of view of a near field three dimensional object is described. It is characterized by three subsystems each of which includes a plurality of reflective surfaces for imaging a different field of view of the object at a different quadrant of the quadrified image. All of the subsystems have identical path lengths to the object photographed.

Microwave imaging by three-dimensional Born linearization of electromagnetic scattering

NASA Astrophysics Data System (ADS)

Caorsi, S.; Gragnani, G. L.; Pastorino, M.

1990-11-01

An approach to microwave imaging is proposed that uses a three-dimensional vectorial form of the Born approximation to linearize the equation of electromagnetic scattering. The inverse scattering problem is numerically solved for three-dimensional geometries by means of the moment method. A pseudoinversion algorithm is adopted to overcome ill conditioning. Results show that the method is well suited for qualitative imaging purposes, while its capability for exactly reconstructing the complex dielectric permittivity is affected by the limitations inherent in the Born approximation and in ill conditioning.

Three-dimensional ultrasound and image-directed surgery: implications for operating room personnel.

PubMed

Macedonia, C

1997-04-01

The proliferation of new imaging technologies is having a profound impact on all surgical specialties. New means of surgical visualization are allowing more surgeries to be performed less invasively. Three-dimensional ultrasound is a technology that has potential as a diagnostic tool, as a presurgical planning simulator, and as an adjunct to image-directed surgery. This article describes how three-dimensional ultrasound is being used by the United States Department of Defense and how it may change the role of the perioperative nurse in the near future.

Depth-enhanced three-dimensional-two-dimensional convertible display based on modified integral imaging.

PubMed

Park, Jae-Hyeung; Kim, Hak-Rin; Kim, Yunhee; Kim, Joohwan; Hong, Jisoo; Lee, Sin-Doo; Lee, Byoungho

2004-12-01

A depth-enhanced three-dimensional-two-dimensional convertible display that uses a polymer-dispersed liquid crystal based on the principle of integral imaging is proposed. In the proposed method, a lens array is located behind a transmission-type display panel to form an array of point-light sources, and a polymer-dispersed liquid crystal is electrically controlled to pass or to scatter light coming from these point-light sources. Therefore, three-dimensional-two-dimensional conversion is accomplished electrically without any mechanical movement. Moreover, the nonimaging structure of the proposed method increases the expressible depth range considerably. We explain the method of operation and present experimental results.

National Defense Center of Excellence for Industrial Metrology and 3D Imaging

DTIC Science & Technology

2012-10-18

validation rather than mundane data-reduction/analysis tasks. Indeed, the new financial and technical resources being brought to bear by integrating CT...of extremely fast axial scanners. By replacing the single-spot detector by a detector array, a three-dimensional image is acquired by one depth scan...the number of acquired voxels per complete two-dimensional or three-dimensional image, the axial and lateral resolution, the depth range, the

3D SAPIV particle field reconstruction method based on adaptive threshold.

PubMed

Qu, Xiangju; Song, Yang; Jin, Ying; Li, Zhenhua; Wang, Xuezhen; Guo, ZhenYan; Ji, Yunjing; He, Anzhi

2018-03-01

Particle image velocimetry (PIV) is a necessary flow field diagnostic technique that provides instantaneous velocimetry information non-intrusively. Three-dimensional (3D) PIV methods can supply the full understanding of a 3D structure, the complete stress tensor, and the vorticity vector in the complex flows. In synthetic aperture particle image velocimetry (SAPIV), the flow field can be measured with large particle intensities from the same direction by different cameras. During SAPIV particle reconstruction, particles are commonly reconstructed by manually setting a threshold to filter out unfocused particles in the refocused images. In this paper, the particle intensity distribution in refocused images is analyzed, and a SAPIV particle field reconstruction method based on an adaptive threshold is presented. By using the adaptive threshold to filter the 3D measurement volume integrally, the three-dimensional location information of the focused particles can be reconstructed. The cross correlations between images captured from cameras and images projected by the reconstructed particle field are calculated for different threshold values. The optimal threshold is determined by cubic curve fitting and is defined as the threshold value that causes the correlation coefficient to reach its maximum. The numerical simulation of a 16-camera array and a particle field at two adjacent time events quantitatively evaluates the performance of the proposed method. An experimental system consisting of a camera array of 16 cameras was used to reconstruct the four adjacent frames in a vortex flow field. The results show that the proposed reconstruction method can effectively reconstruct the 3D particle fields.

On the importance of FIB-SEM specific segmentation algorithms for porous media

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

Salzer, Martin, E-mail: martin.salzer@uni-ulm.de; Thiele, Simon, E-mail: simon.thiele@imtek.uni-freiburg.de; Zengerle, Roland, E-mail: zengerle@imtek.uni-freiburg.de

2014-09-15

A new algorithmic approach to segmentation of highly porous three dimensional image data gained by focused ion beam tomography is described which extends the key-principle of local threshold backpropagation described in Salzer et al. (2012). The technique of focused ion beam tomography has shown to be capable of imaging the microstructure of functional materials. In order to perform a quantitative analysis on the corresponding microstructure a segmentation task needs to be performed. However, algorithmic segmentation of images obtained with focused ion beam tomography is a challenging problem for highly porous materials if filling the pore phase, e.g. with epoxy resin,more » is difficult. The gray intensities of individual voxels are not sufficient to determine the phase represented by them and usual thresholding methods are not applicable. We thus propose a new approach to segmentation that pays respect to the specifics of the imaging process of focused ion beam tomography. As an application of our approach, the segmentation of three dimensional images for a cathode material used in polymer electrolyte membrane fuel cells is discussed. We show that our approach preserves significantly more of the original nanostructure than a thresholding approach. - Highlights: • We describe a new approach to the segmentation of FIB-SEM images of porous media. • The first and last occurrences of structures are detected by analysing the z-profiles. • The algorithm is validated by comparing it to a manual segmentation. • The new approach shows significantly less artifacts than a thresholding approach. • A structural analysis also shows improved results for the obtained microstructure.« less

Study of the structure of 3-D composites based on carbon nanotubes in bovine serum albumin matrix by X-ray microtomography

NASA Astrophysics Data System (ADS)

Ignatov, D.; Zhurbina, N.; Gerasimenko, A.

2017-01-01

3-D composites are widely used in tissue engineering. A comprehensive analysis by X-ray microtomography was conducted to study the structure of the 3-D composites. Comprehensive analysis of the structure of the 3-D composites consisted of scanning, image reconstruction of shadow projections, two-dimensional and three-dimensional visualization of the reconstructed images and quantitative analysis of the samples. Experimental samples of composites were formed by laser vaporization of the aqueous dispersion BSA and single-walled (SWCNTs) and multi-layer (MWCNTs) carbon nanotubes. The samples have a homogeneous structure over the entire volume, the percentage of porosity of 3-D composites based on SWCNTs and MWCNTs - 16.44%, 28.31%, respectively. An average pore diameter of 3-D composites based on SWCNTs and MWCNTs - 45 μm 93 μm. 3-D composites based on carbon nanotubes in bovine serum albumin matrix can be used in tissue engineering of bone and cartilage, providing cell proliferation and blood vessel sprouting.

Cardiac dimensional analysis by use of biplane cineradiography: description and validation of method.

PubMed

Lipscomb, K

1980-01-01

Biplane cineradiography is a potentially powerful tool for precise measurement of intracardiac dimensions. The most systematic approach to these measurements is the creation of a three-dimensional coordinate system within the x-ray field. Using this system, interpoint distances, such as between radiopaque clips or coronary artery bifurcations, can be calculated by use of the Pythagoras theorem. Alternatively, calibration factors can be calculated in order to determine the absolute dimensions of a structure, such as a ventricle or coronary artery. However, cineradiography has two problems that have precluded widespread use of the system. These problems are pincushion distortion and variable image magnification. In this paper, methodology to quantitate and compensate for these variables is presented. The method uses radiopaque beads permanently mounted in the x-ray field. The position of the bead images on the x-ray film determine the compensation factors. Using this system, measurements are made with a standard deviation of approximately 1% of the true value.

Phenotype classification of single cells using SRS microscopy, RNA sequencing, and microfluidics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Streets, Aaron M.; Cao, Chen; Zhang, Xiannian; Huang, Yanyi

2016-03-01

Phenotype classification of single cells reveals biological variation that is masked in ensemble measurement. This heterogeneity is found in gene and protein expression as well as in cell morphology. Many techniques are available to probe phenotypic heterogeneity at the single cell level, for example quantitative imaging and single-cell RNA sequencing, but it is difficult to perform multiple assays on the same single cell. In order to directly track correlation between morphology and gene expression at the single cell level, we developed a microfluidic platform for quantitative coherent Raman imaging and immediate RNA sequencing (RNA-Seq) of single cells. With this device we actively sort and trap cells for analysis with stimulated Raman scattering microscopy (SRS). The cells are then processed in parallel pipelines for lysis, and preparation of cDNA for high-throughput transcriptome sequencing. SRS microscopy offers three-dimensional imaging with chemical specificity for quantitative analysis of protein and lipid distribution in single cells. Meanwhile, the microfluidic platform facilitates single-cell manipulation, minimizes contamination, and furthermore, provides improved RNA-Seq detection sensitivity and measurement precision, which is necessary for differentiating biological variability from technical noise. By combining coherent Raman microscopy with RNA sequencing, we can better understand the relationship between cellular morphology and gene expression at the single-cell level.

Quantitative three-dimensional analysis of root canal curvature in maxillary first molars using micro-computed tomography.

PubMed

Lee, Jong-Ki; Ha, Byung-Hyun; Choi, Jeong-Ho; Heo, Seok-Mo; Perinpanayagam, Hiran

2006-10-01

In endodontic therapy, access and instrumentation are strongly affected by root canal curvature. However, the few studies that have actually measured curvature are mostly from two-dimensional radiographs. The purpose of this study was to measure the three-dimensional (3D) canal curvature in maxillary first molars using micro-computed tomography (microCT) and mathematical modeling. Extracted maxillary first molars (46) were scanned by microCT (502 image slices/tooth, 1024 X 1024 pixels, voxel size of 19.5 x 19.5 x 39.0 microm) and their canals reconstructed by 3D modeling software. The intersection of major and minor axes in the canal space of each image slice were connected to create an imaginary central axis for each canal. The radius of curvature of the tangential circle was measured and inverted as a measure of curvature using custom-made mathematical modeling software. Root canal curvature was greatest in the apical third and least in the middle third for all canals. The greatest curvatures were in the mesiobuccal (MB) canal (0.76 +/- 0.48 mm(-1)) with abrupt curves, and the least curvatures were in the palatal (P) canal (0.38 +/- 0.34 mm(-1)) with a gradual curve. This study has measured the 3D curvature of root canals in maxillary first molars and reinforced the value of microCT with mathematical modeling.

3D Surface Reconstruction for Lower Limb Prosthetic Model using Radon Transform

NASA Astrophysics Data System (ADS)

Sobani, S. S. Mohd; Mahmood, N. H.; Zakaria, N. A.; Razak, M. A. Abdul

2018-03-01

This paper describes the idea to realize three-dimensional surfaces of objects with cylinder-based shapes where the techniques adopted and the strategy developed for a non-rigid three-dimensional surface reconstruction of an object from uncalibrated two-dimensional image sequences using multiple-view digital camera and turntable setup. The surface of an object is reconstructed based on the concept of tomography with the aid of performing several digital image processing algorithms on the two-dimensional images captured by a digital camera in thirty-six different projections and the three-dimensional structure of the surface is analysed. Four different objects are used as experimental models in the reconstructions and each object is placed on a manually rotated turntable. The results shown that the proposed method has successfully reconstruct the three-dimensional surface of the objects and practicable. The shape and size of the reconstructed three-dimensional objects are recognizable and distinguishable. The reconstructions of objects involved in the test are strengthened with the analysis where the maximum percent error obtained from the computation is approximately 1.4 % for the height whilst 4.0%, 4.79% and 4.7% for the diameters at three specific heights of the objects.

Nanoscopic imaging of thick heterogeneous soft-matter structures in aqueous solution

PubMed Central

Bartsch, Tobias F.; Kochanczyk, Martin D.; Lissek, Emanuel N.; Lange, Janina R.; Florin, Ernst-Ludwig

2016-01-01

Precise nanometre-scale imaging of soft structures at room temperature poses a major challenge to any type of microscopy because fast thermal fluctuations lead to significant motion blur if the position of the structure is measured with insufficient bandwidth. Moreover, precise localization is also affected by optical heterogeneities, which lead to deformations in the imaged local geometry, the severity depending on the sample and its thickness. Here we introduce quantitative thermal noise imaging, a three-dimensional scanning probe technique, as a method for imaging soft, optically heterogeneous and porous matter with submicroscopic spatial resolution in aqueous solution. By imaging both individual microtubules and collagen fibrils in a network, we demonstrate that structures can be localized with a precision of ∼10 nm and that their local dynamics can be quantified with 50 kHz bandwidth and subnanometre amplitudes. Furthermore, we show how image distortions caused by optically dense structures can be corrected for. PMID:27596919

Quantitative fluorescence microscopy and image deconvolution.

PubMed

Swedlow, Jason R

2013-01-01

Quantitative imaging and image deconvolution have become standard techniques for the modern cell biologist because they can form the basis of an increasing number of assays for molecular function in a cellular context. There are two major types of deconvolution approaches--deblurring and restoration algorithms. Deblurring algorithms remove blur but treat a series of optical sections as individual two-dimensional entities and therefore sometimes mishandle blurred light. Restoration algorithms determine an object that, when convolved with the point-spread function of the microscope, could produce the image data. The advantages and disadvantages of these methods are discussed in this chapter. Image deconvolution in fluorescence microscopy has usually been applied to high-resolution imaging to improve contrast and thus detect small, dim objects that might otherwise be obscured. Their proper use demands some consideration of the imaging hardware, the acquisition process, fundamental aspects of photon detection, and image processing. This can prove daunting for some cell biologists, but the power of these techniques has been proven many times in the works cited in the chapter and elsewhere. Their usage is now well defined, so they can be incorporated into the capabilities of most laboratories. A major application of fluorescence microscopy is the quantitative measurement of the localization, dynamics, and interactions of cellular factors. The introduction of green fluorescent protein and its spectral variants has led to a significant increase in the use of fluorescence microscopy as a quantitative assay system. For quantitative imaging assays, it is critical to consider the nature of the image-acquisition system and to validate its response to known standards. Any image-processing algorithms used before quantitative analysis should preserve the relative signal levels in different parts of the image. A very common image-processing algorithm, image deconvolution, is used to remove blurred signal from an image. There are two major types of deconvolution approaches, deblurring and restoration algorithms. Deblurring algorithms remove blur, but treat a series of optical sections as individual two-dimensional entities, and therefore sometimes mishandle blurred light. Restoration algorithms determine an object that, when convolved with the point-spread function of the microscope, could produce the image data. The advantages and disadvantages of these methods are discussed. Copyright © 1998 Elsevier Inc. All rights reserved.

Coherent imaging with incoherent light in digital holographic microscopy

NASA Astrophysics Data System (ADS)

Chmelik, Radim

2012-01-01

Digital holographic microscope (DHM) allows for imaging with a quantitative phase contrast. In this way it becomes an important instrument, a completely non-invasive tool for a contrast intravital observation of living cells and a cell drymass density distribution measurement. A serious drawback of current DHMs is highly coherent illumination which makes the lateral resolution worse and impairs the image quality by a coherence noise and a parasitic interference. An uncompromising solution to this problem can be found in the Leith concept of incoherent holography. An off-axis hologram can be formed with arbitrary degree of light coherence in systems equipped with an achromatic interferometer and thus the resolution and the image quality typical for an incoherent-light wide-field microscopy can be achieved. In addition, advanced imaging modes based on limited coherence can be utilized. The typical example is a coherence-gating effect which provides a finite axial resolution and makes DHM image similar to that of a confocal microscope. These possibilities were described theoretically using the formalism of three-dimensional coherent transfer functions and proved experimentally by the coherence-controlled holographic microscope which is DHM based on the Leith achromatic interferometer. Quantitative-phase-contrast imaging is demonstrated with incoherent light by the living cancer cells observation and their motility evaluation. The coherence-gating effect was proved by imaging of model samples through a scattering layer and living cells inside an opalescent medium.

Comprehensive Cardiovascular magnetic resonance of myocardial mechanics in mice using three-dimensional cine DENSE

PubMed Central

2011-01-01

Background Quantitative noninvasive imaging of myocardial mechanics in mice enables studies of the roles of individual genes in cardiac function. We sought to develop comprehensive three-dimensional methods for imaging myocardial mechanics in mice. Methods A 3D cine DENSE pulse sequence was implemented on a 7T small-bore scanner. The sequence used three-point phase cycling for artifact suppression and a stack-of-spirals k-space trajectory for efficient data acquisition. A semi-automatic 2D method was adapted for 3D image segmentation, and automated 3D methods to calculate strain, twist, and torsion were employed. A scan protocol that covered the majority of the left ventricle in a scan time of less than 25 minutes was developed, and seven healthy C57Bl/6 mice were studied. Results Using these methods, multiphase normal and shear strains were measured, as were myocardial twist and torsion. Peak end-systolic values for the normal strains at the mid-ventricular level were 0.29 ± 0.17, -0.13 ± 0.03, and -0.18 ± 0.14 for Err, Ecc, and Ell, respectively. Peak end-systolic values for the shear strains were 0.00 ± 0.08, 0.04 ± 0.12, and 0.03 ± 0.07 for Erc, Erl, and Ecl, respectively. The peak end-systolic normalized torsion was 5.6 ± 0.9°. Conclusions Using a 3D cine DENSE sequence tailored for cardiac imaging in mice at 7 T, a comprehensive assessment of 3D myocardial mechanics can be achieved with a scan time of less than 25 minutes and an image analysis time of approximately 1 hour. PMID:22208954

An iterative three-dimensional electron density imaging algorithm using uncollimated compton scattered x rays from a polyenergetic primary pencil beam.

PubMed

Van Uytven, Eric; Pistorius, Stephen; Gordon, Richard

2007-01-01

X-ray film-screen mammography is currently the gold standard for detecting breast cancer. However, one disadvantage is that it projects a three-dimensional (3D) object onto a two-dimensional (2D) image, reducing contrast between small lesions and layers of normal tissue. Another limitation is its reduced sensitivity in women with mammographically dense breasts. Computed tomography (CT) produces a 3D image yet has had a limited role in mammography due to its relatively high dose, low resolution, and low contrast. As a first step towards implementing quantitative 3D mammography, which may improve the ability to detect and specify breast tumors, we have developed an analytical technique that can use Compton scatter to obtain 3D information of an object from a single projection. Imaging material with a pencil beam of polychromatic x rays produces a characteristic scattered photon spectrum at each point on the detector plane. A comparable distribution may be calculated using a known incident x-ray energy spectrum, beam shape, and an initial estimate of the object's 3D mass attenuation and electron density. Our iterative minimization algorithm changes the initially arbitrary electron density voxel matrix to reduce regular differences between the analytically predicted and experimentally measured spectra at each point on the detector plane. The simulated electron density converges to that of the object as the differences are minimized. The reconstruction algorithm has been validated using simulated data produced by the EGSnrc Monte Carlo code system. We applied the imaging algorithm to a cylindrically symmetric breast tissue phantom containing multiple inhomogeneities. A preliminary ROC analysis scores greater than 0.96, which indicate that under the described simplifying conditions, this approach shows promise in identifying and localizing inhomogeneities which simulate 0.5 mm calcifications with an image voxel resolution of 0.25 cm and at a dose comparable to mammography.

Analysis of autostereoscopic three-dimensional images using multiview wavelets.

PubMed

Saveljev, Vladimir; Palchikova, Irina

2016-08-10

We propose that multiview wavelets can be used in processing multiview images. The reference functions for the synthesis/analysis of multiview images are described. The synthesized binary images were observed experimentally as three-dimensional visual images. The symmetric multiview B-spline wavelets are proposed. The locations recognized in the continuous wavelet transform correspond to the layout of the test objects. The proposed wavelets can be applied to the multiview, integral, and plenoptic images.

Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

PubMed

Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

2017-08-01

Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

A three-dimensional quality-guided phase unwrapping method for MR elastography

NASA Astrophysics Data System (ADS)

Wang, Huifang; Weaver, John B.; Perreard, Irina I.; Doyley, Marvin M.; Paulsen, Keith D.

2011-07-01

Magnetic resonance elastography (MRE) uses accumulated phases that are acquired at multiple, uniformly spaced relative phase offsets, to estimate harmonic motion information. Heavily wrapped phase occurs when the motion is large and unwrapping procedures are necessary to estimate the displacements required by MRE. Two unwrapping methods were developed and compared in this paper. The first method is a sequentially applied approach. The three-dimensional MRE phase image block for each slice was processed by two-dimensional unwrapping followed by a one-dimensional phase unwrapping approach along the phase-offset direction. This unwrapping approach generally works well for low noise data. However, there are still cases where the two-dimensional unwrapping method fails when noise is high. In this case, the baseline of the corrupted regions within an unwrapped image will not be consistent. Instead of separating the two-dimensional and one-dimensional unwrapping in a sequential approach, an interleaved three-dimensional quality-guided unwrapping method was developed to combine both the two-dimensional phase image continuity and one-dimensional harmonic motion information. The quality of one-dimensional harmonic motion unwrapping was used to guide the three-dimensional unwrapping procedures and it resulted in stronger guidance than in the sequential method. In this work, in vivo results generated by the two methods were compared.

Determination of Three-Dimensional Left Ventricle Motion to Analyze Ventricular Dyssyncrony in SPECT Images

NASA Astrophysics Data System (ADS)

Rebelo, Marina de Sá; Aarre, Ann Kirstine Hummelgaard; Clemmesen, Karen-Louise; Brandão, Simone Cristina Soares; Giorgi, Maria Clementina; Meneghetti, José Cláudio; Gutierrez, Marco Antonio

2009-12-01

A method to compute three-dimension (3D) left ventricle (LV) motion and its color coded visualization scheme for the qualitative analysis in SPECT images is proposed. It is used to investigate some aspects of Cardiac Resynchronization Therapy (CRT). The method was applied to 3D gated-SPECT images sets from normal subjects and patients with severe Idiopathic Heart Failure, before and after CRT. Color coded visualization maps representing the LV regional motion showed significant difference between patients and normal subjects. Moreover, they indicated a difference between the two groups. Numerical results of regional mean values representing the intensity and direction of movement in radial direction are presented. A difference of one order of magnitude in the intensity of the movement on patients in relation to the normal subjects was observed. Quantitative and qualitative parameters gave good indications of potential application of the technique to diagnosis and follow up of patients submitted to CRT.

Fractal Dimensionality of Pore and Grain Volume of a Siliciclastic Marine Sand

NASA Astrophysics Data System (ADS)

Reed, A. H.; Pandey, R. B.; Lavoie, D. L.

Three-dimensional (3D) spatial distributions of pore and grain volumes were determined from high-resolution computer tomography (CT) images of resin-impregnated marine sands. Using a linear gradient extrapolation method, cubic three-dimensional samples were constructed from two-dimensional CT images. Image porosity (0.37) was found to be consistent with the estimate of porosity by water weight loss technique (0.36). Scaling of the pore volume (Vp) with the linear size (L), V~LD provides the fractal dimensionalities of the pore volume (D=2.74+/-0.02) and grain volume (D=2.90+/-0.02) typical for sedimentary materials.

A 3D-printed anatomical pancreas and kidney phantom for optimizing SPECT/CT reconstruction settings in beta cell imaging using 111In-exendin.

PubMed

Woliner-van der Weg, Wietske; Deden, Laura N; Meeuwis, Antoi P W; Koenrades, Maaike; Peeters, Laura H C; Kuipers, Henny; Laanstra, Geert Jan; Gotthardt, Martin; Slump, Cornelis H; Visser, Eric P

2016-12-01

Quantitative single photon emission computed tomography (SPECT) is challenging, especially for pancreatic beta cell imaging with 111 In-exendin due to high uptake in the kidneys versus much lower uptake in the nearby pancreas. Therefore, we designed a three-dimensionally (3D) printed phantom representing the pancreas and kidneys to mimic the human situation in beta cell imaging. The phantom was used to assess the effect of different reconstruction settings on the quantification of the pancreas uptake for two different, commercially available software packages. 3D-printed, hollow pancreas and kidney compartments were inserted into the National Electrical Manufacturers Association (NEMA) NU2 image quality phantom casing. These organs and the background compartment were filled with activities simulating relatively high and low pancreatic 111 In-exendin uptake for, respectively, healthy humans and type 1 diabetes patients. Images were reconstructed using Siemens Flash 3D and Hermes Hybrid Recon, with varying numbers of iterations and subsets and corrections. Images were visually assessed on homogeneity and artefacts, and quantitatively by the pancreas-to-kidney activity concentration ratio. Phantom images were similar to clinical images and showed comparable artefacts. All corrections were required to clearly visualize the pancreas. Increased numbers of subsets and iterations improved the quantitative performance but decreased homogeneity both in the pancreas and the background. Based on the phantom analyses, the Hybrid Recon reconstruction with 6 iterations and 16 subsets was found to be most suitable for clinical use. This work strongly contributed to quantification of pancreatic 111 In-exendin uptake. It showed how clinical images of 111 In-exendin can be interpreted and enabled selection of the most appropriate protocol for clinical use.

Hematopoiesis in 3 dimensions: human and murine bone marrow architecture visualized by confocal microscopy.

PubMed

Takaku, Tomoiku; Malide, Daniela; Chen, Jichun; Calado, Rodrigo T; Kajigaya, Sachiko; Young, Neal S

2010-10-14

In many animals, blood cell production occurs in the bone marrow. Hematopoiesis is complex, requiring self-renewing and pluripotent stem cells, differentiated progenitor and precursor cells, and supportive stroma, adipose tissue, vascular structures, and extracellular matrix. Although imaging is a vital tool in hematology research, the 3-dimensional architecture of the bone marrow tissue in situ remains largely uncharacterized. The major hindrance to imaging the intact marrow is the surrounding bone structures are almost impossible to cut/image through. We have overcome these obstacles and describe a method whereby whole-mounts of bone marrow tissue were immunostained and imaged in 3 dimensions by confocal fluorescence and reflection microscopy. We have successfully mapped by multicolor immunofluorescence the localization pattern of as many as 4 cell features simultaneously over large tiled views and to depths of approximately 150 μm. Three-dimensional images can be assessed qualitatively and quantitatively to appreciate the distribution of cell types and their interrelationships, with minimal perturbations of the tissue. We demonstrate its application to normal mouse and human marrow, to murine models of marrow failure, and to patients with aplastic anemia, myeloid, and lymphoid cell malignancies. The technique should be generally adaptable for basic laboratory investigation and for clinical diagnosis of hematologic diseases.

Development of a system for acquiring, reconstructing, and visualizing three-dimensional ultrasonic angiograms

NASA Astrophysics Data System (ADS)

Edwards, Warren S.; Ritchie, Cameron J.; Kim, Yongmin; Mack, Laurence A.

1995-04-01

We have developed a three-dimensional (3D) imaging system using power Doppler (PD) ultrasound (US). This system can be used for visualizing and analyzing the vascular anatomy of parenchymal organs. To create the 3D PD images, we acquired a series of two-dimensional PD images from a commercial US scanner and recorded the position and orientation of each image using a 3D magnetic position sensor. Three-dimensional volumes were reconstructed using specially designed software and then volume rendered for display. We assessed the feasibility and geometric accuracy of our system with various flow phantoms. The system was then tested on a volunteer by scanning a transplanted kidney. The reconstructed volumes of the flow phantom contained less than 1 mm of geometric distortion and the 3D images of the transplanted kidney depicted the segmental, arcuate, and interlobar vessels.

The Performance Evaluation of Multi-Image 3d Reconstruction Software with Different Sensors

NASA Astrophysics Data System (ADS)

Mousavi, V.; Khosravi, M.; Ahmadi, M.; Noori, N.; Naveh, A. Hosseini; Varshosaz, M.

2015-12-01

Today, multi-image 3D reconstruction is an active research field and generating three dimensional model of the objects is one the most discussed issues in Photogrammetry and Computer Vision that can be accomplished using range-based or image-based methods. Very accurate and dense point clouds generated by range-based methods such as structured light systems and laser scanners has introduced them as reliable tools in the industry. Image-based 3D digitization methodologies offer the option of reconstructing an object by a set of unordered images that depict it from different viewpoints. As their hardware requirements are narrowed down to a digital camera and a computer system, they compose an attractive 3D digitization approach, consequently, although range-based methods are generally very accurate, image-based methods are low-cost and can be easily used by non-professional users. One of the factors affecting the accuracy of the obtained model in image-based methods is the software and algorithm used to generate three dimensional model. These algorithms are provided in the form of commercial software, open source and web-based services. Another important factor in the accuracy of the obtained model is the type of sensor used. Due to availability of mobile sensors to the public, popularity of professional sensors and the advent of stereo sensors, a comparison of these three sensors plays an effective role in evaluating and finding the optimized method to generate three-dimensional models. Lots of research has been accomplished to identify a suitable software and algorithm to achieve an accurate and complete model, however little attention is paid to the type of sensors used and its effects on the quality of the final model. The purpose of this paper is deliberation and the introduction of an appropriate combination of a sensor and software to provide a complete model with the highest accuracy. To do this, different software, used in previous studies, were compared and the most popular ones in each category were selected (Arc 3D, Visual SfM, Sure, Agisoft). Also four small objects with distinct geometric properties and especial complexities were chosen and their accurate models as reliable true data was created using ATOS Compact Scan 2M 3D scanner. Images were taken using Fujifilm Real 3D stereo camera, Apple iPhone 5 and Nikon D3200 professional camera and three dimensional models of the objects were obtained using each of the software. Finally, a comprehensive comparison between the detailed reviews of the results on the data set showed that the best combination of software and sensors for generating three-dimensional models is directly related to the object shape as well as the expected accuracy of the final model. Generally better quantitative and qualitative results were obtained by using the Nikon D3200 professional camera, while Fujifilm Real 3D stereo camera and Apple iPhone 5 were the second and third respectively in this comparison. On the other hand, three software of Visual SfM, Sure and Agisoft had a hard competition to achieve the most accurate and complete model of the objects and the best software was different according to the geometric properties of the object.

High-speed, two-dimensional synchrotron white-beam x-ray radiography of spray breakup and atomization

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

Halls, Benjamin R.; Radke, Christopher D.; Reuter, Benjamin J.

High-speed, two-dimensional synchrotron x-ray radiography and phase-contrast imaging are demonstrated in propulsion sprays. Measurements are performed at the 7-BM beamline at the Advanced Photon Source user facility at Argonne National Laboratory using a recently developed broadband x-ray white beam. This novel enhancement allows for high speed, high fidelity x-ray imaging for the community at large. Quantitative path-integrated liquid distributions and spatio-temporal dynamics of the sprays were imaged with a LuAG:Ce scintillator optically coupled to a high-speed CMOS camera. Images are collected with a microscope objective at frame rates of 20 kHz and with a macro lens at 120 kHz, achievingmore » spatial resolutions of 12 μm and 65 μm, respectively. Imaging with and without potassium iodide (KI) as a contrast-enhancing agent is compared, and the effects of broadband attenuation and spatial beam characteristics are determined through modeling and experimental calibration. In addition, phase contrast is used to differentiate liquid streams with varying concentrations of KI. The experimental approach is applied to different spray conditions, including quantitative measurements of mass distribution during primary atomization and qualitative visualization of turbulent binary fluid mixing. High-speed, two-dimensional synchrotron white-beam x-ray radiography of spray breakup and atomization. Available from: https://www.researchgate.net/publication/312567827_High-speed_two-dimensional_synchrotron_white-beam_x-ray_radiography_of_spray_breakup_and_atomization [accessed Aug 31, 2017].« less

Three-dimensional head anthropometric analysis

NASA Astrophysics Data System (ADS)

Enciso, Reyes; Shaw, Alex M.; Neumann, Ulrich; Mah, James

2003-05-01

Currently, two-dimensional photographs are most commonly used to facilitate visualization, assessment and treatment of facial abnormalities in craniofacial care but are subject to errors because of perspective, projection, lack metric and 3-dimensional information. One can find in the literature a variety of methods to generate 3-dimensional facial images such as laser scans, stereo-photogrammetry, infrared imaging and even CT however each of these methods contain inherent limitations and as such no systems are in common clinical use. In this paper we will focus on development of indirect 3-dimensional landmark location and measurement of facial soft-tissue with light-based techniques. In this paper we will statistically evaluate and validate a current three-dimensional image-based face modeling technique using a plaster head model. We will also develop computer graphics tools for indirect anthropometric measurements in a three-dimensional head model (or polygonal mesh) including linear distances currently used in anthropometry. The measurements will be tested against a validated 3-dimensional digitizer (MicroScribe 3DX).

Development and Translation of Hybrid Optoacoustic/Ultrasonic Tomography for Early Breast Cancer Detection

DTIC Science & Technology

2014-09-01

to develop an optimized system design and associated image reconstruction algorithms for a hybrid three-dimensional (3D) breast imaging system that...research is to develop an optimized system design and associated image reconstruction algorithms for a hybrid three-dimensional (3D) breast imaging ...i) developed time-of- flight extraction algorithms to perform USCT, (ii) developing image reconstruction algorithms for USCT, (iii) developed

Pathophysiology of Degenerative Mitral Regurgitation: New 3-Dimensional Imaging Insights.

PubMed

Antoine, Clemence; Mantovani, Francesca; Benfari, Giovanni; Mankad, Sunil V; Maalouf, Joseph F; Michelena, Hector I; Enriquez-Sarano, Maurice

2018-01-01

Despite its high prevalence, little is known about mechanisms of mitral regurgitation in degenerative mitral valve disease apart from the leaflet prolapse itself. Mitral valve is a complex structure, including mitral annulus, mitral leaflets, papillary muscles, chords, and left ventricular walls. All these structures are involved in physiological and pathological functioning of this valvuloventricular complex but up to now were difficult to analyze because of inherent limitations of 2-dimensional imaging. The advent of 3-dimensional echocardiography, computed tomography, and cardiac magnetic resonance imaging overcoming these limitations provides new insights into mechanistic analysis of degenerative mitral regurgitation. This review will detail the contribution of quantitative and qualitative dynamic analysis of mitral annulus and mitral leaflets by new imaging methods in the understanding of degenerative mitral regurgitation pathophysiology. © 2018 American Heart Association, Inc.

Three-dimensional marginal separation

NASA Technical Reports Server (NTRS)

Duck, Peter W.

1988-01-01

The three dimensional marginal separation of a boundary layer along a line of symmetry is considered. The key equation governing the displacement function is derived, and found to be a nonlinear integral equation in two space variables. This is solved iteratively using a pseudo-spectral approach, based partly in double Fourier space, and partly in physical space. Qualitatively, the results are similar to previously reported two dimensional results (which are also computed to test the accuracy of the numerical scheme); however quantitatively the three dimensional results are much different.

Preliminary study of rib articulated model based on dynamic fluoroscopy images

NASA Astrophysics Data System (ADS)

Villard, Pierre-Frederic; Escamilla, Pierre; Kerrien, Erwan; Gorges, Sebastien; Trousset, Yves; Berger, Marie-Odile

2014-03-01

We present in this paper a preliminary study of rib motion tracking during Interventional Radiology (IR) fluoroscopy guided procedures. It consists in providing a physician with moving rib three-dimensional (3D) models projected in the fluoroscopy plane during a treatment. The strategy is to help to quickly recognize the target and the no-go areas i.e. the tumor and the organs to avoid. The method consists in i) elaborating a kinematic model of each rib from a preoperative computerized tomography (CT) scan, ii) processing the on-line fluoroscopy image and iii) optimizing the parameters of the kinematic law such as the transformed 3D rib projected on the medical image plane fit well with the previously processed image. The results show a visually good rib tracking that has been quantitatively validated by showing a periodic motion as well as a good synchronism between ribs.

Lesson learned and dispelled myths: three-dimensional imaging of the human vagina.

PubMed

Barnhart, Kurt T; Pretorius, E Scott; Malamud, Daniel

2004-05-01

Three-dimensional imaging of the human vagina demonstrates that the cross section can be a "W," rather than an "H," and that intravaginal gel can ascend into the endocervix and presumably into the endometrium.

A Low-Cost PC-Based Image Workstation for Dynamic Interactive Display of Three-Dimensional Anatomy

NASA Astrophysics Data System (ADS)

Barrett, William A.; Raya, Sai P.; Udupa, Jayaram K.

1989-05-01

A system for interactive definition, automated extraction, and dynamic interactive display of three-dimensional anatomy has been developed and implemented on a low-cost PC-based image workstation. An iconic display is used for staging predefined image sequences through specified increments of tilt and rotation over a solid viewing angle. Use of a fast processor facilitates rapid extraction and rendering of the anatomy into predefined image views. These views are formatted into a display matrix in a large image memory for rapid interactive selection and display of arbitrary spatially adjacent images within the viewing angle, thereby providing motion parallax depth cueing for efficient and accurate perception of true three-dimensional shape, size, structure, and spatial interrelationships of the imaged anatomy. The visual effect is that of holding and rotating the anatomy in the hand.

Breast MRI radiomics: comparison of computer- and human-extracted imaging phenotypes.

PubMed

Sutton, Elizabeth J; Huang, Erich P; Drukker, Karen; Burnside, Elizabeth S; Li, Hui; Net, Jose M; Rao, Arvind; Whitman, Gary J; Zuley, Margarita; Ganott, Marie; Bonaccio, Ermelinda; Giger, Maryellen L; Morris, Elizabeth A

2017-01-01

In this study, we sought to investigate if computer-extracted magnetic resonance imaging (MRI) phenotypes of breast cancer could replicate human-extracted size and Breast Imaging-Reporting and Data System (BI-RADS) imaging phenotypes using MRI data from The Cancer Genome Atlas (TCGA) project of the National Cancer Institute. Our retrospective interpretation study involved analysis of Health Insurance Portability and Accountability Act-compliant breast MRI data from The Cancer Imaging Archive, an open-source database from the TCGA project. This study was exempt from institutional review board approval at Memorial Sloan Kettering Cancer Center and the need for informed consent was waived. Ninety-one pre-operative breast MRIs with verified invasive breast cancers were analysed. Three fellowship-trained breast radiologists evaluated the index cancer in each case according to size and the BI-RADS lexicon for shape, margin, and enhancement (human-extracted image phenotypes [HEIP]). Human inter-observer agreement was analysed by the intra-class correlation coefficient (ICC) for size and Krippendorff's α for other measurements. Quantitative MRI radiomics of computerised three-dimensional segmentations of each cancer generated computer-extracted image phenotypes (CEIP). Spearman's rank correlation coefficients were used to compare HEIP and CEIP. Inter-observer agreement for HEIP varied, with the highest agreement seen for size (ICC 0.679) and shape (ICC 0.527). The computer-extracted maximum linear size replicated the human measurement with p  < 10 -12 . CEIP of shape, specifically sphericity and irregularity, replicated HEIP with both p values < 0.001. CEIP did not demonstrate agreement with HEIP of tumour margin or internal enhancement. Quantitative radiomics of breast cancer may replicate human-extracted tumour size and BI-RADS imaging phenotypes, thus enabling precision medicine.

Three-dimensional propagation in near-field tomographic X-ray phase retrieval

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

Ruhlandt, Aike, E-mail: aruhlan@gwdg.de; Salditt, Tim

An extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions is presented, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resultingmore » in superior reconstruction quality.« less

Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform1[C][W][OA

PubMed Central

Clark, Randy T.; MacCurdy, Robert B.; Jung, Janelle K.; Shaff, Jon E.; McCouch, Susan R.; Aneshansley, Daniel J.; Kochian, Leon V.

2011-01-01

A novel imaging and software platform was developed for the high-throughput phenotyping of three-dimensional root traits during seedling development. To demonstrate the platform’s capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and imaged daily for 10 d. Rotational image sequences consisting of 40 two-dimensional images were captured using an optically corrected digital imaging system. Three-dimensional root reconstructions were generated and analyzed using a custom-designed software, RootReader3D. Using the automated and interactive capabilities of RootReader3D, five rice root types were classified and 27 phenotypic root traits were measured to characterize these two genotypes. Where possible, measurements from the three-dimensional platform were validated and were highly correlated with conventional two-dimensional measurements. When comparing gellan gum-grown plants with those grown under hydroponic and sand culture, significant differences were detected in morphological root traits (P < 0.05). This highly flexible platform provides the capacity to measure root traits with a high degree of spatial and temporal resolution and will facilitate novel investigations into the development of entire root systems or selected components of root systems. In combination with the extensive genetic resources that are now available, this platform will be a powerful resource to further explore the molecular and genetic determinants of root system architecture. PMID:21454799

Quantitative evaluation of software packages for single-molecule localization microscopy.

PubMed

Sage, Daniel; Kirshner, Hagai; Pengo, Thomas; Stuurman, Nico; Min, Junhong; Manley, Suliana; Unser, Michael

2015-08-01

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.

Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction.

PubMed

Zhao, Yao; Schreiner, Sarah M; Koo, Peter K; Colombi, Paolo; King, Megan C; Mochrie, Simon G J

2016-07-12

Many aspects of chromatin biology are influenced by the nuclear compartment in which a locus resides, from transcriptional regulation to DNA repair. Further, the dynamic and variable localization of a particular locus across cell populations and over time makes analysis of a large number of cells critical. As a consequence, robust and automatable methods to measure the position of individual loci within the nuclear volume in populations of cells are necessary to support quantitative analysis of nuclear position. Here, we describe a three-dimensional membrane reconstruction approach that uses fluorescently tagged nuclear envelope or endoplasmic reticulum membrane marker proteins to precisely map the nuclear volume. This approach is robust to a variety of nuclear shapes, providing greater biological accuracy than alternative methods that enforce nuclear circularity, while also describing nuclear position in all three dimensions. By combining this method with established approaches to reconstruct the position of diffraction-limited chromatin markers-in this case, lac Operator arrays bound by lacI-GFP-the distribution of loci positions within the nuclear volume with respect to the nuclear periphery can be quantitatively obtained. This stand-alone image analysis pipeline should be of broad practical utility for individuals interested in various aspects of chromatin biology, while also providing, to our knowledge, a new conceptual framework for investigators who study organelle shape. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Two- and three-dimensional ultrasound imaging to facilitate detection and targeting of taut bands in myofascial pain syndrome.

PubMed

Shankar, Hariharan; Reddy, Sapna

2012-07-01

Ultrasound imaging has gained acceptance in pain management interventions. Features of myofascial pain syndrome have been explored using ultrasound imaging and elastography. There is a paucity of reports showing the benefit clinically. This report provides three-dimensional features of taut bands and highlights the advantages of using two-dimensional ultrasound imaging to improve targeting of taut bands in deeper locations. Fifty-eight-year-old man with pain and decreased range of motion of the right shoulder was referred for further management of pain above the scapula after having failed conservative management for myofascial pain syndrome. Three-dimensional ultrasound images provided evidence of aberrancy in the architecture of the muscle fascicles around the taut bands compared to the adjacent normal muscle tissue during serial sectioning of the accrued image. On two-dimensional ultrasound imaging over the palpated taut band, areas of hyperechogenicity were visualized in the trapezius and supraspinatus muscles. Subsequently, the patient received ultrasound-guided real-time lidocaine injections to the trigger points with successful resolution of symptoms. This is a successful demonstration of utility of ultrasound imaging of taut bands in the management of myofascial pain syndrome. Utility of this imaging modality in myofascial pain syndrome requires further clinical validation. Wiley Periodicals, Inc.

Integration of Computed Tomography and Three-Dimensional Echocardiography for Hybrid Three-Dimensional Printing in Congenital Heart Disease.

PubMed

Gosnell, Jordan; Pietila, Todd; Samuel, Bennett P; Kurup, Harikrishnan K N; Haw, Marcus P; Vettukattil, Joseph J

2016-12-01

Three-dimensional (3D) printing is an emerging technology aiding diagnostics, education, and interventional, and surgical planning in congenital heart disease (CHD). Three-dimensional printing has been derived from computed tomography, cardiac magnetic resonance, and 3D echocardiography. However, individually the imaging modalities may not provide adequate visualization of complex CHD. The integration of the strengths of two or more imaging modalities has the potential to enhance visualization of cardiac pathomorphology. We describe the feasibility of hybrid 3D printing from two imaging modalities in a patient with congenitally corrected transposition of the great arteries (L-TGA). Hybrid 3D printing may be useful as an additional tool for cardiologists and cardiothoracic surgeons in planning interventions in children and adults with CHD.

Adaptation of an articulated fetal skeleton model to three-dimensional fetal image data

NASA Astrophysics Data System (ADS)

Klinder, Tobias; Wendland, Hannes; Wachter-Stehle, Irina; Roundhill, David; Lorenz, Cristian

2015-03-01

The automatic interpretation of three-dimensional fetal images poses specific challenges compared to other three-dimensional diagnostic data, especially since the orientation of the fetus in the uterus and the position of the extremities is highly variable. In this paper, we present a comprehensive articulated model of the fetal skeleton and the adaptation of the articulation for pose estimation in three-dimensional fetal images. The model is composed out of rigid bodies where the articulations are represented as rigid body transformations. Given a set of target landmarks, the model constellation can be estimated by optimization of the pose parameters. Experiments are carried out on 3D fetal MRI data yielding an average error per case of 12.03+/-3.36 mm between target and estimated landmark positions.

Quantitative imaging of volcanic plumes — Results, needs, and future trends

USGS Publications Warehouse

Platt, Ulrich; Lübcke, Peter; Kuhn, Jonas; Bobrowski, Nicole; Prata, Fred; Burton, Mike; Kern, Christoph

2015-01-01

Recent technology allows two-dimensional “imaging” of trace gas distributions in plumes. In contrast to older, one-dimensional remote sensing techniques, that are only capable of measuring total column densities, the new imaging methods give insight into details of transport and mixing processes as well as chemical transformation within plumes. We give an overview of gas imaging techniques already being applied at volcanoes (SO2cameras, imaging DOAS, FT-IR imaging), present techniques where first field experiments were conducted (LED-LIDAR, tomographic mapping), and describe some techniques where only theoretical studies with application to volcanology exist (e.g. Fabry–Pérot Imaging, Gas Correlation Spectroscopy, bi-static LIDAR). Finally, we discuss current needs and future trends in imaging technology.

Laboratory-size three-dimensional water-window x-ray microscope with Wolter type I mirror optics

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

Ohsuka, Shinji; The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu-cho, Nishi-ku, Hamamatsu-City, 431-1202; Ohba, Akira

2016-01-28

We constructed a laboratory-size three-dimensional water-window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques. It consists of an electron-impact x-ray source emitting oxygen Kα x-rays, Wolter type I grazing incidence mirror optics, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit better than 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm-scale three-dimensional fine structures were resolved.

Measuring Symmetry in Children With Unrepaired Cleft Lip: Defining a Standard for the Three-Dimensional Midfacial Reference Plane.

PubMed

Wu, Jia; Heike, Carrie; Birgfeld, Craig; Evans, Kelly; Maga, Murat; Morrison, Clinton; Saltzman, Babette; Shapiro, Linda; Tse, Raymond

2016-11-01

  Quantitative measures of facial form to evaluate treatment outcomes for cleft lip (CL) are currently limited. Computer-based analysis of three-dimensional (3D) images provides an opportunity for efficient and objective analysis. The purpose of this study was to define a computer-based standard of identifying the 3D midfacial reference plane of the face in children with unrepaired cleft lip for measurement of facial symmetry.   The 3D images of 50 subjects (35 with unilateral CL, 10 with bilateral CL, five controls) were included in this study.   Five methods of defining a midfacial plane were applied to each image, including two human-based (Direct Placement, Manual Landmark) and three computer-based (Mirror, Deformation, Learning) methods.   Six blinded raters (three cleft surgeons, two craniofacial pediatricians, and one craniofacial researcher) independently ranked and rated the accuracy of the defined planes.   Among computer-based methods, the Deformation method performed significantly better than the others. Although human-based methods performed best, there was no significant difference compared with the Deformation method. The average correlation coefficient among raters was .4; however, it was .7 and .9 when the angular difference between planes was greater than 6° and 8°, respectively.   Raters can agree on the 3D midfacial reference plane in children with unrepaired CL using digital surface mesh. The Deformation method performed best among computer-based methods evaluated and can be considered a useful tool to carry out automated measurements of facial symmetry in children with unrepaired cleft lip.

Development of technique for three-dimensional visualization of grain boundaries by white X-ray microbeam

NASA Astrophysics Data System (ADS)

Kajiwara, K.; Shobu, T.; Toyokawa, H.; Sato, M.

2014-04-01

A technique for three-dimensional visualization of grain boundaries was developed at BL28B2 at SPring-8. The technique uses white X-ray microbeam diffraction and a rotating slit. Three-dimensional images of small silicon single crystals filled in a plastic tube were successfully obtained using this technique for demonstration purposes. The images were consistent with those obtained by X-ray computed tomography.

Right ventricular volumes assessed by echocardiographic three-dimensional knowledge-based reconstruction compared with magnetic resonance imaging in a clinical setting.

PubMed

Neukamm, Christian; Try, Kirsti; Norgård, Gunnar; Brun, Henrik

2014-01-01

A technique that uses two-dimensional images to create a knowledge-based, three-dimensional model was tested and compared to magnetic resonance imaging. Measurement of right ventricular volumes and function is important in the follow-up of patients after pulmonary valve replacement. Magnetic resonance imaging is the gold standard for volumetric assessment. Echocardiographic methods have been validated and are attractive alternatives. Thirty patients with tetralogy of Fallot (25 ± 14 years) after pulmonary valve replacement were examined. Magnetic resonance imaging volumetric measurements and echocardiography-based three-dimensional reconstruction were performed. End-diastolic volume, end-systolic volume, and ejection fraction were measured, and the results were compared. Magnetic resonance imaging measurements gave coefficient of variation in the intraobserver study of 3.5, 4.6, and 5.3 and in the interobserver study of 3.6, 5.9, and 6.7 for end-diastolic volume, end-systolic volume, and ejection fraction, respectively. Echocardiographic three-dimensional reconstruction was highly feasible (97%). In the intraobserver study, the corresponding values were 6.0, 7.0, and 8.9 and in the interobserver study 7.4, 10.8, and 13.4. In comparison of the methods, correlations with magnetic resonance imaging were r = 0.91, 0.91, and 0.38, and the corresponding coefficient of variations were 9.4, 10.8, and 14.7. Echocardiography derived volumes (mL/m(2)) were significantly higher than magnetic resonance imaging volumes in end-diastolic volume 13.7 ± 25.6 and in end-systolic volume 9.1 ± 17.0 (both P < .05). The knowledge-based three-dimensional right ventricular volume method was highly feasible. Intra and interobserver variabilities were satisfactory. Agreement with magnetic resonance imaging measurements for volumes was reasonable but unsatisfactory for ejection fraction. Knowledge-based reconstruction may replace magnetic resonance imaging measurements for serial follow-up, whereas magnetic resonance imaging should be used for surgical decision making.

3D fluorescence anisotropy imaging using selective plane illumination microscopy.

PubMed

Hedde, Per Niklas; Ranjit, Suman; Gratton, Enrico

2015-08-24

Fluorescence anisotropy imaging is a popular method to visualize changes in organization and conformation of biomolecules within cells and tissues. In such an experiment, depolarization effects resulting from differences in orientation, proximity and rotational mobility of fluorescently labeled molecules are probed with high spatial resolution. Fluorescence anisotropy is typically imaged using laser scanning and epifluorescence-based approaches. Unfortunately, those techniques are limited in either axial resolution, image acquisition speed, or by photobleaching. In the last decade, however, selective plane illumination microscopy has emerged as the preferred choice for three-dimensional time lapse imaging combining axial sectioning capability with fast, camera-based image acquisition, and minimal light exposure. We demonstrate how selective plane illumination microscopy can be utilized for three-dimensional fluorescence anisotropy imaging of live cells. We further examined the formation of focal adhesions by three-dimensional time lapse anisotropy imaging of CHO-K1 cells expressing an EGFP-paxillin fusion protein.

Ultrasound-aided Multi-parametric Photoacoustic Microscopy of the Mouse Brain.

PubMed

Ning, Bo; Sun, Naidi; Cao, Rui; Chen, Ruimin; Kirk Shung, K; Hossack, John A; Lee, Jin-Moo; Zhou, Qifa; Hu, Song

2015-12-21

High-resolution quantitative imaging of cerebral oxygen metabolism in mice is crucial for understanding brain functions and formulating new strategies to treat neurological disorders, but remains a challenge. Here, we report on our newly developed ultrasound-aided multi-parametric photoacoustic microscopy (PAM), which enables simultaneous quantification of the total concentration of hemoglobin (CHb), the oxygen saturation of hemoglobin (sO2), and cerebral blood flow (CBF) at the microscopic level and through the intact mouse skull. The three-dimensional skull and vascular anatomies delineated by the dual-contrast (i.e., ultrasonic and photoacoustic) system provide important guidance for dynamically focused contour scan and vessel orientation-dependent correction of CBF, respectively. Moreover, bi-directional raster scan allows determining the direction of blood flow in individual vessels. Capable of imaging all three hemodynamic parameters at the same spatiotemporal scale, our ultrasound-aided PAM fills a critical gap in preclinical neuroimaging and lays the foundation for high-resolution mapping of the cerebral metabolic rate of oxygen (CMRO2)-a quantitative index of cerebral oxygen metabolism. This technical innovation is expected to shed new light on the mechanism and treatment of a broad spectrum of neurological disorders, including Alzheimer's disease and ischemic stroke.

Mouse fetal whole intestine culture system for ex vivo manipulation of signaling pathways and three-dimensional live imaging of villus development.

PubMed

Walton, Katherine D; Kolterud, Asa

2014-09-04

Most morphogenetic processes in the fetal intestine have been inferred from thin sections of fixed tissues, providing snapshots of changes over developmental stages. Three-dimensional information from thin serial sections can be challenging to interpret because of the difficulty of reconstructing serial sections perfectly and maintaining proper orientation of the tissue over serial sections. Recent findings by Grosse et al., 2011 highlight the importance of three- dimensional information in understanding morphogenesis of the developing villi of the intestine(1). Three-dimensional reconstruction of singly labeled intestinal cells demonstrated that the majority of the intestinal epithelial cells contact both the apical and basal surfaces. Furthermore, three-dimensional reconstruction of the actin cytoskeleton at the apical surface of the epithelium demonstrated that the intestinal lumen is continuous and that secondary lumens are an artifact of sectioning. Those two points, along with the demonstration of interkinetic nuclear migration in the intestinal epithelium, defined the developing intestinal epithelium as a pseudostratified epithelium and not stratified as previously thought(1). The ability to observe the epithelium three-dimensionally was seminal to demonstrating this point and redefining epithelial morphogenesis in the fetal intestine. With the evolution of multi-photon imaging technology and three-dimensional reconstruction software, the ability to visualize intact, developing organs is rapidly improving. Two-photon excitation allows less damaging penetration deeper into tissues with high resolution. Two-photon imaging and 3D reconstruction of the whole fetal mouse intestines in Walton et al., 2012 helped to define the pattern of villus outgrowth(2). Here we describe a whole organ culture system that allows ex vivo development of villi and extensions of that culture system to allow the intestines to be three-dimensionally imaged during their development.

The role of three-dimensional imaging in optimizing diagnosis, classification and surgical treatment of hepatocellular carcinoma with portal vein tumor thrombus.

PubMed

Wei, Xu-Biao; Xu, Jie; Li, Nan; Yu, Ying; Shi, Jie; Guo, Wei-Xing; Cheng, Hong-Yan; Wu, Meng-Chao; Lau, Wan-Yee; Cheng, Shu-Qun

2016-03-01

Accurate assessment of characteristics of tumor and portal vein tumor thrombus is crucial in the management of hepatocellular carcinoma. Comparison of the three-dimensional imaging with multiple-slice computed tomography in the diagnosis and treatment of hepatocellular carcinoma with portal vein tumor thrombus. Patients eligible for surgical resection were divided into the three-dimensional imaging group or the multiple-slice computed tomography group according to the type of preoperative assessment. The clinical data were collected and compared. 74 patients were enrolled into this study. The weighted κ values for comparison between the thrombus type based on preoperative evaluation and intraoperative findings were 0.87 for the three-dimensional reconstruction group (n = 31) and 0.78 for the control group (n = 43). Three-dimensional reconstruction was significantly associated with a higher rate of en-bloc resection of tumor and thrombus (P = 0.025). Using three-dimensional reconstruction, significant correlation existed between the predicted and actual volumes of the resected specimens (r = 0.82, P < 0.01), as well as the predicted and actual resection margins (r = 0.97, P < 0.01). Preoperative three-dimensional reconstruction significantly decreased tumor recurrence and tumor-related death, with hazard ratios of 0.49 (95% confidential interval, 0.27-0.90) and 0.41 (95% confidential interval, 0.21-0.78), respectively. For hepatocellular carcinoma with portal vein tumor thrombus, three-dimensional imaging was efficient in facilitating surgical treatment and benefiting postoperative survivals. Copyright © 2015 International Hepato-Pancreato-Biliary Association Inc. Published by Elsevier Ltd. All rights reserved.

An improved three-dimensional non-scanning laser imaging system based on digital micromirror device

NASA Astrophysics Data System (ADS)

Xia, Wenze; Han, Shaokun; Lei, Jieyu; Zhai, Yu; Timofeev, Alexander N.

2018-01-01

Nowadays, there are two main methods to realize three-dimensional non-scanning laser imaging detection, which are detection method based on APD and detection method based on Streak Tube. However, the detection method based on APD possesses some disadvantages, such as small number of pixels, big pixel interval and complex supporting circuit. The detection method based on Streak Tube possesses some disadvantages, such as big volume, bad reliability and high cost. In order to resolve the above questions, this paper proposes an improved three-dimensional non-scanning laser imaging system based on Digital Micromirror Device. In this imaging system, accurate control of laser beams and compact design of imaging structure are realized by several quarter-wave plates and a polarizing beam splitter. The remapping fiber optics is used to sample the image plane of receiving optical lens, and transform the image into line light resource, which can realize the non-scanning imaging principle. The Digital Micromirror Device is used to convert laser pulses from temporal domain to spatial domain. The CCD with strong sensitivity is used to detect the final reflected laser pulses. In this paper, we also use an algorithm which is used to simulate this improved laser imaging system. In the last, the simulated imaging experiment demonstrates that this improved laser imaging system can realize three-dimensional non-scanning laser imaging detection.

Second-harmonic patterned polarization-analyzed reflection confocal microscope

NASA Astrophysics Data System (ADS)

Okoro, Chukwuemeka; Toussaint, Kimani C.

2017-08-01

We introduce the second-harmonic patterned polarization-analyzed reflection confocal (SPPARC) microscope-a multimodal imaging platform that integrates Mueller matrix polarimetry with reflection confocal and second-harmonic generation (SHG) microscopy. SPPARC microscopy provides label-free three-dimensional (3-D), SHG-patterned confocal images that lend themselves to spatially dependent, linear polarimetric analysis for extraction of rich polarization information based on the Mueller calculus. To demonstrate its capabilities, we use SPPARC microscopy to analyze both porcine tendon and ligament samples and find differences in both circular degree-of-polarization and depolarization parameters. Moreover, using the collagen-generated SHG signal as an endogenous counterstain, we show that the technique can be used to provide 3-D polarimetric information of the surrounding extrafibrillar matrix plus cells or EFMC region. The unique characteristics of SPPARC microscopy holds strong potential for it to more accurately and quantitatively describe microstructural changes in collagen-rich samples in three spatial dimensions.

A new software for dimensional measurements in 3D endodontic root canal instrumentation.

PubMed

Sinibaldi, Raffaele; Pecci, Raffaella; Somma, Francesco; Della Penna, Stefania; Bedini, Rossella

2012-01-01

The main issue to be faced to get size estimates of 3D modification of the dental canal after endodontic treatment is the co-registration of the image stacks obtained through micro computed tomography (micro-CT) scans before and after treatment. Here quantitative analysis of micro-CT images have been performed by means of new dedicated software targeted to the analysis of root canal after endodontic instrumentation. This software analytically calculates the best superposition between the pre and post structures using the inertia tensor of the tooth. This strategy avoid minimization procedures, which can be user dependent, and time consuming. Once the co-registration have been achieved dimensional measurements have then been performed by contemporary evaluation of quantitative parameters over the two superimposed stacks of micro-CT images. The software automatically calculated the changes of volume, surface and symmetry axes in 3D occurring after the instrumentation. The calculation is based on direct comparison of the canal and canal branches selected by the user on the pre treatment image stack.

Design and Implementation of a Self-Directed Stereochemistry Lesson Using Embedded Virtual Three-Dimensional Images in a Portable Document Format

ERIC Educational Resources Information Center

Cody, Jeremy A.; Craig, Paul A.; Loudermilk, Adam D.; Yacci, Paul M.; Frisco, Sarah L.; Milillo, Jennifer R.

2012-01-01

A novel stereochemistry lesson was prepared that incorporated both handheld molecular models and embedded virtual three-dimensional (3D) images. The images are fully interactive and eye-catching for the students; methods for preparing 3D molecular images in Adobe Acrobat are included. The lesson was designed and implemented to showcase the 3D…

Image gathering, coding, and processing: End-to-end optimization for efficient and robust acquisition of visual information

NASA Technical Reports Server (NTRS)

Huck, Friedrich O.; Fales, Carl L.

1990-01-01

Researchers are concerned with the end-to-end performance of image gathering, coding, and processing. The applications range from high-resolution television to vision-based robotics, wherever the resolution, efficiency and robustness of visual information acquisition and processing are critical. For the presentation at this workshop, it is convenient to divide research activities into the following two overlapping areas: The first is the development of focal-plane processing techniques and technology to effectively combine image gathering with coding, with an emphasis on low-level vision processing akin to the retinal processing in human vision. The approach includes the familiar Laplacian pyramid, the new intensity-dependent spatial summation, and parallel sensing/processing networks. Three-dimensional image gathering is attained by combining laser ranging with sensor-array imaging. The second is the rigorous extension of information theory and optimal filtering to visual information acquisition and processing. The goal is to provide a comprehensive methodology for quantitatively assessing the end-to-end performance of image gathering, coding, and processing.

Image fusion-guided portal vein puncture during transjugular intrahepatic portosystemic shunt placement.

PubMed

Rouabah, K; Varoquaux, A; Caporossi, J M; Louis, G; Jacquier, A; Bartoli, J M; Moulin, G; Vidal, V

2016-11-01

The purpose of this study was to assess the feasibility and utility of image fusion (Easy-TIPS) obtained from pre-procedure CT angiography and per-procedure real-time fluoroscopy for portal vein puncture during transjugular intrahepatic portosystemic shunt (TIPS) placement. Eighteen patients (15 men, 3 women) with a mean age of 63 years (range: 48-81 years; median age, 65 years) were included in the study. All patients underwent TIPS placement by two groups of radiologists (one group with radiologists of an experience<3 years and one with an experience≥3 years) using fusion imaging obtained from three-dimensional computed tomography angiography of the portal vein and real-time fluoroscopic images of the portal vein. Image fusion was used to guide the portal vein puncture during TIPS placement. At the end of the procedure, the interventional radiologists evaluated the utility of fusion imaging for portal vein puncture during TIPS placement. Mismatch between three-dimensional computed tomography angiography and real-time fluoroscopic images of the portal vein on image fusion was quantitatively analyzed. Posttreatment CT time, number of the puncture attempts, total radiation exposure and radiation from the retrograde portography were also recorded. Image fusion was considered useful for portal vein puncture in 13/18 TIPS procedures (72%). The mean posttreatment time to obtain fusion images was 16.4minutes. 3D volume rendered CT angiography images was strictly superimposed on direct portography in 10/18 procedures (56%). The mismatch mean value was 0.69cm in height and 0.28cm laterally. A mean number of 4.6 portal vein puncture attempts was made. Eight patients required less than three attempts. The mean radiation dose from retrograde portography was 421.2dGy.cm 2 , corresponding to a mean additional exposure of 19%. Fusion imaging resulting from image fusion from pre-procedural CT angiography is feasible, safe and makes portal puncture easier during TIPS placement. Copyright © 2016 Editions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

Real time three dimensional sensing system

DOEpatents

Gordon, S.J.

1996-12-31

The invention is a three dimensional sensing system which utilizes two flexibly located cameras for receiving and recording visual information with respect to a sensed object illuminated by a series of light planes. Each pixel of each image is converted to a digital word and the words are grouped into stripes, each stripe comprising contiguous pixels. One pixel of each stripe in one image is selected and an epi-polar line of that point is drawn in the other image. The three dimensional coordinate of each selected point is determined by determining the point on said epi-polar line which also lies on a stripe in the second image and which is closest to a known light plane. 7 figs.

Real time three dimensional sensing system

DOEpatents

Gordon, Steven J.

1996-01-01

The invention is a three dimensional sensing system which utilizes two flexibly located cameras for receiving and recording visual information with respect to a sensed object illuminated by a series of light planes. Each pixel of each image is converted to a digital word and the words are grouped into stripes, each stripe comprising contiguous pixels. One pixel of each stripe in one image is selected and an epi-polar line of that point is drawn in the other image. The three dimensional coordinate of each selected point is determined by determining the point on said epi-polar line which also lies on a stripe in the second image and which is closest to a known light plane.

Three-dimensional quantitative evaluation of midfacial skeletal changes after trans-sutural distraction osteogenesis for midfacial hypoplasia in growing patients with cleft lip and palate.

PubMed

Tong, Haizhou; Gao, Feng; Yin, Jiapeng; Shi, Zehong; Song, Tao; Li, Haidong; Sun, Xiaomei; Wang, Yongqian; Yin, Ningbei; Zhao, Zhenmin

2015-11-01

Trans-sutural distraction osteogenesis (TSDO) is an alternative method for the early treatment of midfacial hypoplasia in growing patients with cleft lip and palate (CLP). The purpose of this study was to analyze three-dimensional (3D) midfacial skeletal changes after TSDO and to explore the mechanism in this process. All patients with nonsyndromic CLP who underwent bone-borne TSDO for midfacial hypoplasia from 2005 to 2014 were reviewed in this retrospective study. 3D morphological and quantitative measurement analyses were performed to evaluate midfacial skeletal changes by superimposition of preoperative and postoperative computed tomographic images. Twenty-six patients with mean age of 11.5 years met the inclusion criteria. The 3D morphological findings exhibited the most significant suture stress changes at the pterygomaxillary suture area, with obvious bone generation in all patients. The whole midfacial skeleton had progressively increased advancement in a craniocaudal direction along the midface segment, associated with morphological changes in skeleton itself. The 3D quantitative measurement findings showed differential advancement of each landmark at the maxillary alveolar, zygomatic bone, orbital rim, and nasal bone, which was consistent with morphological findings. TSDO allows rotation advancement of the midfacial skeleton to achieve occlusal correction and facial harmony through the mechanism of both suture remodeling and bone remodeling. Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Evaluation of training nurses to perform semi-automated three-dimensional left ventricular ejection fraction using a customised workstation-based training protocol.

PubMed

Guppy-Coles, Kristyan B; Prasad, Sandhir B; Smith, Kym C; Hillier, Samuel; Lo, Ada; Atherton, John J

2015-06-01

We aimed to determine the feasibility of training cardiac nurses to evaluate left ventricular function utilising a semi-automated, workstation-based protocol on three dimensional echocardiography images. Assessment of left ventricular function by nurses is an attractive concept. Recent developments in three dimensional echocardiography coupled with border detection assistance have reduced inter- and intra-observer variability and analysis time. This could allow abbreviated training of nurses to assess cardiac function. A comparative, diagnostic accuracy study evaluating left ventricular ejection fraction assessment utilising a semi-automated, workstation-based protocol performed by echocardiography-naïve nurses on previously acquired three dimensional echocardiography images. Nine cardiac nurses underwent two brief lectures about cardiac anatomy, physiology and three dimensional left ventricular ejection fraction assessment, before a hands-on demonstration in 20 cases. We then selected 50 cases from our three dimensional echocardiography library based on optimal image quality with a broad range of left ventricular ejection fractions, which was quantified by two experienced sonographers and the average used as the comparator for the nurses. Nurses independently measured three dimensional left ventricular ejection fraction using the Auto lvq package with semi-automated border detection. The left ventricular ejection fraction range was 25-72% (70% with a left ventricular ejection fraction <55%). All nurses showed excellent agreement with the sonographers. Minimal intra-observer variability was noted on both short-term (same day) and long-term (>2 weeks later) retest. It is feasible to train nurses to measure left ventricular ejection fraction utilising a semi-automated, workstation-based protocol on previously acquired three dimensional echocardiography images. Further study is needed to determine the feasibility of training nurses to acquire three dimensional echocardiography images on real-world patients to measure left ventricular ejection fraction. Nurse-performed evaluation of left ventricular function could facilitate the broader application of echocardiography to allow cost-effective screening and monitoring for left ventricular dysfunction in high-risk populations. © 2014 John Wiley & Sons Ltd.

Investigation of the relative orientation of the system of optical sensors to monitor the technosphere objects

NASA Astrophysics Data System (ADS)

Petrochenko, Andrey; Konyakhin, Igor

2017-06-01

In connection with the development of robotics have become increasingly popular variety of three-dimensional reconstruction of the system mapping and image-set received from the optical sensors. The main objective of technical and robot vision is the detection, tracking and classification of objects of the space in which these systems and robots operate [15,16,18]. Two-dimensional images sometimes don't contain sufficient information to address those or other problems: the construction of the map of the surrounding area for a route; object identification, tracking their relative position and movement; selection of objects and their attributes to complement the knowledge base. Three-dimensional reconstruction of the surrounding space allows you to obtain information on the relative positions of objects, their shape, surface texture. Systems, providing training on the basis of three-dimensional reconstruction of the results of the comparison can produce two-dimensional images of three-dimensional model that allows for the recognition of volume objects on flat images. The problem of the relative orientation of industrial robots with the ability to build threedimensional scenes of controlled surfaces is becoming actual nowadays.

3D light scanning macrography.

PubMed

Huber, D; Keller, M; Robert, D

2001-08-01

The technique of 3D light scanning macrography permits the non-invasive surface scanning of small specimens at magnifications up to 200x. Obviating both the problem of limited depth of field inherent to conventional close-up macrophotography and the metallic coating required by scanning electron microscopy, 3D light scanning macrography provides three-dimensional digital images of intact specimens without the loss of colour, texture and transparency information. This newly developed technique offers a versatile, portable and cost-efficient method for the non-invasive digital and photographic documentation of small objects. Computer controlled device operation and digital image acquisition facilitate fast and accurate quantitative morphometric investigations, and the technique offers a broad field of research and educational applications in biological, medical and materials sciences.

Computed Tomography Studies of Lung Mechanics

PubMed Central

Simon, Brett A.; Christensen, Gary E.; Low, Daniel A.; Reinhardt, Joseph M.

2005-01-01

The study of lung mechanics has progressed from global descriptions of lung pressure and volume relationships to the high-resolution, three-dimensional, quantitative measurement of dynamic regional mechanical properties and displacements. X-ray computed tomography (CT) imaging is ideally suited to the study of regional lung mechanics in intact subjects because of its high spatial and temporal resolution, correlation of functional data with anatomic detail, increasing volumetric data acquisition, and the unique relationship between CT density and lung air content. This review presents an overview of CT measurement principles and limitations for the study of regional mechanics, reviews some of the early work that set the stage for modern imaging approaches and impacted the understanding and management of patients with acute lung injury, and presents evolving novel approaches for the analysis and application of dynamic volumetric lung image data. PMID:16352757

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.

Processing And Display Of Medical Three Dimensional Arrays Of Numerical Data Using Octree Encoding

NASA Astrophysics Data System (ADS)

Amans, Jean-Louis; Darier, Pierre

1986-05-01

imaging modalities such as X-Ray computerized Tomography (CT), Nuclear Medecine and Nuclear Magnetic Resonance can produce three-dimensional (3-D) arrays of numerical data of medical object internal structures. The analysis of 3-D data by synthetic generation of realistic images is an important area of computer graphics and imaging.

Magnetic Resonance Imaging of Three-Dimensional Cervical Anatomy in the Second and Third Trimester

PubMed Central

HOUSE, Michael; BHADELIA, Rafeeque A.; MYERS, Kristin; SOCRATE, Simona

2009-01-01

OBJECTIVE Although a short cervix is known to be associated with preterm birth, the patterns of three-dimensional, anatomic changes leading to a short cervix are unknown. Our objective was to 1) construct three-dimensional anatomic models during normal pregnancy and 2) use the models to compare cervical anatomy in the second and third trimester. STUDY DESIGN A cross sectional study was performed in a population of patients referred to magnetic resonance imaging (MRI) for a fetal indication. Using magnetic resonance images for guidance, three-dimensional solid models of the following anatomic structures were constructed: amniotic cavity, uterine wall, cervical stroma, cervical mucosa and anterior vaginal wall. To compare cervical anatomy in the second and third trimester, models were matched according the size of the bony pelvis. RESULTS Fourteen patients were imaged and divided into two groups according to gestational age: 20 – 24 weeks (n=7)) and 31 – 36 weeks (n=7). Compared to the second trimester, the third trimester was associated with significant descent of the amniotic sac. (p=.02). Descent of the amniotic sac was associated with modified anatomy of the uterocervical junction. These 3-dimensional changes were associated with a cervix that appeared shorter in the third trimester. CONCLUSION We report a technique for constructing MRI-based, three-dimensional anatomic models during pregnancy. Compared to the second trimester, the third trimester is associated with three-dimensional changes in the cervix and lower uterine segment. PMID:19297070

[Localization of perforators in the lower leg by digital antomy imaging methods].

PubMed

Wei, Peng; Ma, Liang-Liang; Fang, Ye-Dong; Xia, Wei-Zhi; Ding, Mao-Chao; Mei, Jin

2012-03-01

To offer both the accurate three-dimensional anatomical information and algorithmic morphology of perforators in the lower leg for perforator flaps design. The cadaver was injected with a modified lead oxide-gelatin mixture. Radiography was first performed and the images were analyzed using the software Photoshop and Scion Image. Then spiral CT scan was also performed and 3-dimensional images were reconstructed with MIMICS 10.01 software. There are (27 +/- 4) perforators whose outer diameter > or = 0.5 mm ( average, 0.8 +/- 0.2 mm). The average pedicle length within the superficial fascia is (37.3 +/- 18.6) mm. The average supplied area of each perforator is (49.5 +/- 25.5) cm2. The three-dimensional model displayed accurate morphology structure and three-dimensional distribution of the perforator-to- perforator and perforator-to-source artery. The 3D reconstruction model can clearly show the geometric, local details and three-dimensional distribution. It is a considerable method for the study of morphological characteristics of the individual perforators in human calf and preoperative planning of the perforator flap.

Laser electro-optic system for rapid three-dimensional /3-D/ topographic mapping of surfaces

NASA Technical Reports Server (NTRS)

Altschuler, M. D.; Altschuler, B. R.; Taboada, J.

1981-01-01

It is pointed out that the generic utility of a robot in a factory/assembly environment could be substantially enhanced by providing a vision capability to the robot. A standard videocamera for robot vision provides a two-dimensional image which contains insufficient information for a detailed three-dimensional reconstruction of an object. Approaches which supply the additional information needed for the three-dimensional mapping of objects with complex surface shapes are briefly considered and a description is presented of a laser-based system which can provide three-dimensional vision to a robot. The system consists of a laser beam array generator, an optical image recorder, and software for controlling the required operations. The projection of a laser beam array onto a surface produces a dot pattern image which is viewed from one or more suitable perspectives. Attention is given to the mathematical method employed, the space coding technique, the approaches used for obtaining the transformation parameters, the optics for laser beam array generation, the hardware for beam array coding, and aspects of image acquisition.

Three-dimensional Echocardiography of Right Ventricular Function Correlates with Severity of Pediatric Pulmonary Hypertension.

PubMed

Jone, Pei-Ni; Patel, Sonali S; Cassidy, Courtney; Ivy, David Dunbar

2016-12-01

Right ventricular function and biomarkers of B-type natriuretic peptide (BNP) and N-Terminal pro-BNP (NT pro-BNP) are used to determine the severity of right ventricular failure and outcomes from pulmonary hypertension. Real-time three-dimensional echocardiography (3DE) is a novel quantitative measure of the right ventricle and decreases the geometric assumptions from conventional two-dimensional echocardiography (2DE). We correlated right ventricular functional measures using 2DE and single-beat 3DE with biomarkers and hemodynamics to determine the severity of pediatric pulmonary hypertension. We retrospectively evaluated 35 patients (mean age 12.67 ± 5.78 years) with established pulmonary hypertension who had echocardiograms and biomarkers on the same day. Ten out of 35 patients had hemodynamic evaluation within 3 days. 2DE evaluation included tricuspid annular plane systolic excursion (TAPSE), right ventricular myocardial performance index from tissue Doppler imaging (RV TDI MPI), and right ventricular fractional area change (FAC). Three-dimensional echocardiography evaluation included right ventricular ejection fraction (EF), end-systolic volume, and end-diastolic volume. The quality of the 3DE was graded as good, fair, or poor. Pearson correlation coefficients were utilized to evaluate between biomarkers and echocardiographic parameters and between hemodynamics and echocardiography. Three-dimensional echocardiography and FAC correlated significantly with BNP and NT pro-BNP. TAPSE and RV TDI MPI did not correlate significantly with biomarkers. 3D right ventricular EF correlated significantly with hemodynamics. Two-dimensional echocardiography did not correlate with hemodynamics. Single-beat 3DE is a noninvasive, feasible tool in the quantification of right ventricular function and maybe more accurate than conventional 2DE in evaluating severity of pulmonary hypertension. © 2016 Wiley Periodicals, Inc.

Numerical simulation of soft palate movement and airflow in human upper airway by fluid-structure interaction method

NASA Astrophysics Data System (ADS)

Sun, Xiuzhen; Yu, Chi; Wang, Yuefang; Liu, Yingxi

2007-08-01

In this paper, the authors present airflow field characteristics of human upper airway and soft palate movement attitude during breathing. On the basis of the data taken from the spiral computerized tomography images of a healthy person and a patient with Obstructive Sleep Apnea-Hypopnea Syndrome (OSAHS), three-dimensional models of upper airway cavity and soft palate are reconstructed by the method of surface rendering. Numerical simulation is performed for airflow in the upper airway and displacement of soft palate by fluid-structure interaction analysis. The reconstructed three-dimensional models precisely preserve the original configuration of upper airways and soft palate. The results of the pressure and velocity distributions in the airflow field are quantitatively determined, and the displacement of soft palate is presented. Pressure gradients of airway are lower for the healthy person and the airflow distribution is quite uniform in the case of free breathing. However, the OSAHS patient remarkably escalates both the pressure and velocity in the upper airway, and causes higher displacement of the soft palate. The present study is useful in revealing pathogenesis and quantitative mutual relationship between configuration and function of the upper airway as well as in diagnosing diseases related to anatomical structure and function of the upper airway.

Space-Based Three-Dimensional Imaging of Equatorial Plasma Bubbles: Advancing the Understanding of Ionospheric Density Depletions and Scintillation

DTIC Science & Technology

2012-03-28

Scintillation 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Comberiate, Joseph M. 5e. TASK NUMBER 5f. WORK...bubble climatology. A tomographic reconstruction technique was modified and applied to SSUSI data to reconstruct three-dimensional cubes of ionospheric... modified and applied to SSUSI data to reconstruct three-dimensional cubes of ionospheric electron density. These data cubes allowed for 3-D imaging of

Real-time Three-dimensional Echocardiography: From Diagnosis to Intervention.

PubMed

Orvalho, João S

2017-09-01

Echocardiography is one of the most important diagnostic tools in veterinary cardiology, and one of the greatest recent developments is real-time three-dimensional imaging. Real-time three-dimensional echocardiography is a new ultrasonography modality that provides comprehensive views of the cardiac valves and congenital heart defects. The main advantages of this technique, particularly real-time three-dimensional transesophageal echocardiography, are the ability to visualize the catheters, and balloons or other devices, and the ability to image the structure that is undergoing intervention with unprecedented quality. This technique may become one of the main choices for the guidance of interventional cardiology procedures. Copyright © 2017 Elsevier Inc. All rights reserved.

Multifunctional, three-dimensional tomography for analysis of eletrectrohydrodynamic jetting

NASA Astrophysics Data System (ADS)

Nguyen, Xuan Hung; Gim, Yeonghyeon; Ko, Han Seo

2015-05-01

A three-dimensional optical tomography technique was developed to reconstruct three-dimensional objects using a set of two-dimensional shadowgraphic images and normal gray images. From three high-speed cameras, which were positioned at an offset angle of 45° between each other, number, size, and location of electrohydrodynamic jets with respect to the nozzle position were analyzed using shadowgraphic tomography employing multiplicative algebraic reconstruction technique (MART). Additionally, a flow field inside a cone-shaped liquid (Taylor cone) induced under an electric field was observed using a simultaneous multiplicative algebraic reconstruction technique (SMART), a tomographic method for reconstructing light intensities of particles, combined with three-dimensional cross-correlation. Various velocity fields of circulating flows inside the cone-shaped liquid caused by various physico-chemical properties of liquid were also investigated.

Fine Metal Mask 3-Dimensional Measurement by using Scanning Digital Holographic Microscope

NASA Astrophysics Data System (ADS)

Shin, Sanghoon; Yu, Younghun

2018-04-01

For three-dimensional microscopy, fast and high axial resolution are very important. Extending the depth of field for digital holographic is necessary for three-dimensional measurements of thick samples. We propose an optical sectioning method for optical scanning digital holography that is performed in the frequency domain by spatial filtering of a reconstructed amplitude image. We established a scanning dual-wavelength off-axis digital holographic microscope to measure samples that exhibit a large amount of coherent noise and a thickness larger than the depth of focus of the objective lens. As a demonstration, we performed a three-dimensional measurement of a fine metal mask with a reconstructed sectional phase image and filtering with a reconstructed amplitude image.

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT)

PubMed Central

Faulwetter, Sarah; Chatzinikolaou, Eva; Michalakis, Nikitas; Filiopoulou, Irene; Minadakis, Nikos; Panteri, Emmanouela; Perantinos, George; Gougousis, Alexandros; Arvanitidis, Christos

2016-01-01

Abstract Background During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet. New information The Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices. PMID:27956848

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT).

PubMed

Keklikoglou, Kleoniki; Faulwetter, Sarah; Chatzinikolaou, Eva; Michalakis, Nikitas; Filiopoulou, Irene; Minadakis, Nikos; Panteri, Emmanouela; Perantinos, George; Gougousis, Alexandros; Arvanitidis, Christos

2016-01-01

During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CT vlab ) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet. The Micro-CT vlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CT vlab can be accessed either on a normal computer or through a dedicated version for mobile devices.

A study to evaluate the reliability of using two-dimensional photographs, three-dimensional images, and stereoscopic projected three-dimensional images for patient assessment.

PubMed

Zhu, S; Yang, Y; Khambay, B

2017-03-01

Clinicians are accustomed to viewing conventional two-dimensional (2D) photographs and assume that viewing three-dimensional (3D) images is similar. Facial images captured in 3D are not viewed in true 3D; this may alter clinical judgement. The aim of this study was to evaluate the reliability of using conventional photographs, 3D images, and stereoscopic projected 3D images to rate the severity of the deformity in pre-surgical class III patients. Forty adult patients were recruited. Eight raters assessed facial height, symmetry, and profile using the three different viewing media and a 100-mm visual analogue scale (VAS), and appraised the most informative viewing medium. Inter-rater consistency was above good for all three media. Intra-rater reliability was not significantly different for rating facial height using 2D (P=0.704), symmetry using 3D (P=0.056), and profile using projected 3D (P=0.749). Using projected 3D for rating profile and symmetry resulted in significantly lower median VAS scores than either 3D or 2D images (all P<0.05). For 75% of the raters, stereoscopic 3D projection was the preferred method for rating. The reliability of assessing specific characteristics was dependent on the viewing medium. Clinicians should be aware that the visual information provided when viewing 3D images is not the same as when viewing 2D photographs, especially for facial depth, and this may change the clinical impression. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Terahertz Imaging of Three-Dimensional Dehydrated Breast Cancer Tumors

NASA Astrophysics Data System (ADS)

Bowman, Tyler; Wu, Yuhao; Gauch, John; Campbell, Lucas K.; El-Shenawee, Magda

2017-06-01

This work presents the application of terahertz imaging to three-dimensional formalin-fixed, paraffin-embedded human breast cancer tumors. The results demonstrate the capability of terahertz for in-depth scanning to produce cross section images without the need to slice the tumor. Samples of tumors excised from women diagnosed with infiltrating ductal carcinoma and lobular carcinoma are investigated using a pulsed terahertz time domain imaging system. A time of flight estimation is used to obtain vertical and horizontal cross section images of tumor tissues embedded in paraffin block. Strong agreement is shown comparing the terahertz images obtained by electronically scanning the tumor in-depth in comparison with histopathology images. The detection of cancer tissue inside the block is found to be accurate to depths over 1 mm. Image processing techniques are applied to provide improved contrast and automation of the obtained terahertz images. In particular, unsharp masking and edge detection methods are found to be most effective for three-dimensional block imaging.

Echocardiographic strain and strain-rate imaging: a new tool to study regional myocardial function.

PubMed

D'hooge, Jan; Bijnens, Bart; Thoen, Jan; Van de Werf, Frans; Sutherland, George R; Suetens, Paul

2002-09-01

Ultrasonic imaging is the noninvasive clinical imaging modality of choice for diagnosing heart disease. At present, two-dimensional ultrasonic grayscale images provide a relatively cheap, fast, bedside method to study the morphology of the heart. Several methods have been proposed to assess myocardial function. These have been based on either grayscale or motion (velocity) information measured in real-time. However, the quantitative assessment of regional myocardial function remains an important goal in clinical cardiology. To do this, ultrasonic strain and strain-rate imaging have been introduced. In the clinical setting, these techniques currently only allow one component of the true three-dimensional deformation to be measured. Clinical, multidimensional strain (rate) information can currently thus only be obtained by combining data acquired using different transducer positions. Nevertheless, given the appropriate postprocessing, the clinical value of these techniques has already been shown. Moreover, multidimensional strain and strain-rate estimation of the heart in vivo by means of a single ultrasound acquisition has been shown to be feasible. In this paper, the new techniques of ultrasonic strain rate and strain imaging of the heart are reviewed in terms of definitions, data acquisition, strain-rate estimation, postprocessing, and parameter extraction. Their clinical validation and relevance will be discussed using clinical examples on relevant cardiac pathology. Based on these examples, suggestions are made for future developments of these techniques.

Comparison of image features calculated in different dimensions for computer-aided diagnosis of lung nodules

NASA Astrophysics Data System (ADS)

Xu, Ye; Lee, Michael C.; Boroczky, Lilla; Cann, Aaron D.; Borczuk, Alain C.; Kawut, Steven M.; Powell, Charles A.

2009-02-01

Features calculated from different dimensions of images capture quantitative information of the lung nodules through one or multiple image slices. Previously published computer-aided diagnosis (CADx) systems have used either twodimensional (2D) or three-dimensional (3D) features, though there has been little systematic analysis of the relevance of the different dimensions and of the impact of combining different dimensions. The aim of this study is to determine the importance of combining features calculated in different dimensions. We have performed CADx experiments on 125 pulmonary nodules imaged using multi-detector row CT (MDCT). The CADx system computed 192 2D, 2.5D, and 3D image features of the lesions. Leave-one-out experiments were performed using five different combinations of features from different dimensions: 2D, 3D, 2.5D, 2D+3D, and 2D+3D+2.5D. The experiments were performed ten times for each group. Accuracy, sensitivity and specificity were used to evaluate the performance. Wilcoxon signed-rank tests were applied to compare the classification results from these five different combinations of features. Our results showed that 3D image features generate the best result compared with other combinations of features. This suggests one approach to potentially reducing the dimensionality of the CADx data space and the computational complexity of the system while maintaining diagnostic accuracy.

Trends in fluorescence imaging and related techniques to unravel biological information.

PubMed

Haustein, Elke; Schwille, Petra

2007-09-01

Optical microscopy is among the most powerful tools that the physical sciences have ever provided biology. It is indispensable for basic lab work, as well as for cutting edge research, as the visual monitoring of life processes still belongs to the most compelling evidences for a multitude of biomedical applications. Along with the rapid development of new probes and methods for the analysis of laser induced fluorescence, optical microscopy over past years experienced a vast increase of both new techniques and novel combinations of established methods to study biological processes with unprecedented spatial and temporal precision. On the one hand, major technical advances have significantly improved spatial resolution. On the other hand, life scientists are moving toward three- and even four-dimensional cell biology and biophysics involving time as a crucial coordinate to quantitatively understand living specimen. Monitoring the whole cell or tissue in real time, rather than producing snap-shot-like two-dimensional projections, will enable more physiological and, thus, more clinically relevant experiments, whereas an increase in temporal resolution facilitates monitoring fast nonperiodic processes as well as the quantitative analysis of characteristic dynamics.

Trends in fluorescence imaging and related techniques to unravel biological information

PubMed Central

Haustein, Elke; Schwille, Petra

2007-01-01

Optical microscopy is among the most powerful tools that the physical sciences have ever provided biology. It is indispensable for basic lab work, as well as for cutting edge research, as the visual monitoring of life processes still belongs to the most compelling evidences for a multitude of biomedical applications. Along with the rapid development of new probes and methods for the analysis of laser induced fluorescence, optical microscopy over past years experienced a vast increase of both new techniques and novel combinations of established methods to study biological processes with unprecedented spatial and temporal precision. On the one hand, major technical advances have significantly improved spatial resolution. On the other hand, life scientists are moving toward three- and even four-dimensional cell biology and biophysics involving time as a crucial coordinate to quantitatively understand living specimen. Monitoring the whole cell or tissue in real time, rather than producing snap-shot-like two-dimensional projections, will enable more physiological and, thus, more clinically relevant experiments, whereas an increase in temporal resolution facilitates monitoring fast nonperiodic processes as well as the quantitative analysis of characteristic dynamics. PMID:19404444

Three-Dimensional Anisotropic Acoustic and Elastic Full-Waveform Seismic Inversion

NASA Astrophysics Data System (ADS)

Warner, M.; Morgan, J. V.

2013-12-01

Three-dimensional full-waveform inversion is a high-resolution, high-fidelity, quantitative, seismic imaging technique that has advanced rapidly within the oil and gas industry. The method involves the iterative improvement of a starting model using a series of local linearized updates to solve the full non-linear inversion problem. During the inversion, forward modeling employs the full two-way three-dimensional heterogeneous anisotropic acoustic or elastic wave equation to predict the observed raw field data, wiggle-for-wiggle, trace-by-trace. The method is computationally demanding; it is highly parallelized, and runs on large multi-core multi-node clusters. Here, we demonstrate what can be achieved by applying this newly practical technique to several high-density 3D seismic datasets that were acquired to image four contrasting sedimentary targets: a gas cloud above an oil reservoir, a radially faulted dome, buried fluvial channels, and collapse structures overlying an evaporate sequence. We show that the resulting anisotropic p-wave velocity models match in situ measurements in deep boreholes, reproduce detailed structure observed independently on high-resolution seismic reflection sections, accurately predict the raw seismic data, simplify and sharpen reverse-time-migrated reflection images of deeper horizons, and flatten Kirchhoff-migrated common-image gathers. We also show that full-elastic 3D full-waveform inversion of pure pressure data can generate a reasonable shear-wave velocity model for one of these datasets. For two of the four datasets, the inclusion of significant transversely isotropic anisotropy with a vertical axis of symmetry was necessary in order to fit the kinematics of the field data properly. For the faulted dome, the full-waveform-inversion p-wave velocity model recovers the detailed structure of every fault that can be seen on coincident seismic reflection data. Some of the individual faults represent high-velocity zones, some represent low-velocity zones, some have more-complex internal structure, and some are visible merely as offsets between two regions with contrasting velocity. Although this has not yet been demonstrated quantitatively for this dataset, it seems likely that at least some of this fine structure in the recovered velocity model is related to the detailed lithology, strain history and fluid properties within the individual faults. We have here applied this technique to seismic data that were acquired by the extractive industries, however this inversion scheme is immediately scalable and applicable to a much wider range of problems given sufficient quality and density of observed data. Potential targets range from shallow magma chambers beneath active volcanoes, through whole-crustal sections across plate boundaries, to regional and whole-Earth models.

Quantitative investigation of red blood cell three-dimensional geometric and chemical changes in the storage lesion using digital holographic microscopy.

PubMed

Jaferzadeh, Keyvan; Moon, Inkyu

2015-11-01

Quantitative phase information obtained by digital holographic microscopy (DHM) can provide new insight into the functions and morphology of single red blood cells (RBCs). Since the functionality of a RBC is related to its three-dimensional (3-D) shape, quantitative 3-D geometric changes induced by storage time can help hematologists realize its optimal functionality period. We quantitatively investigate RBC 3-D geometric changes in the storage lesion using DHM. Our experimental results show that the substantial geometric transformation of the biconcave-shaped RBCs to the spherocyte occurs due to RBC storage lesion. This transformation leads to progressive loss of cell surface area, surface-to-volume ratio, and functionality of RBCs. Furthermore, our quantitative analysis shows that there are significant correlations between chemical and morphological properties of RBCs.

MO-FG-CAMPUS-JeP1-03: Luminescence Imaging of Water During Proton Beam Irradiation for Range Estimation

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

Yamamoto, S; Komori, M; Toshito, T

Purpose: Since proton therapy has the ability to selectively deliver a dose to a target tumor, the dose distribution should be accurately measured. A precise and efficient method to evaluate the dose distribution is desired. We found that luminescence was emitted from water during proton irradiation and thought this phenomenon could be used for estimating the dose distribution. Methods: For this purpose, we placed water phantoms set on a table with a spot-scanning proton-therapy system, and luminescence images of these phantoms were measured with a high-sensitivity cooled charge coupled device (CCD) camera during proton-beam irradiation. We also conducted the imagingmore » of phantoms of pure-water, fluorescein solution and acrylic block. We made three dimensional images from the projection data. Results: The luminescence images of water phantoms during the proton-beam irradiations showed clear Bragg peaks, and the measured proton ranges from the images were almost the same as those obtained with an ionization chamber. The image of the pure-water phantom also showed almost the same distribution as the tap-water phantom, indicating that the luminescence image was not related to impurities in the water. The luminescence image of fluorescein solution had ∼3 times higher intensity than water, with the same proton range as that of water. The luminescence image of the acrylic phantom had 14.5% shorter proton range than that of water; the proton range in the acrylic phantom was relatively matched with the calculated value. The luminescence images of the tap-water phantom during proton irradiation could be obtained in less than 2 sec. Three dimensional images were successfully obtained which have more quantitative information. Conclusion: Luminescence imaging during proton-beam irradiation has the potential to be a new method for range estimations in proton therapy.« less

Three-dimensional rendering of segmented object using matlab - biomed 2010.

PubMed

Anderson, Jeffrey R; Barrett, Steven F

2010-01-01

The three-dimensional rendering of microscopic objects is a difficult and challenging task that often requires specialized image processing techniques. Previous work has been described of a semi-automatic segmentation process of fluorescently stained neurons collected as a sequence of slice images with a confocal laser scanning microscope. Once properly segmented, each individual object can be rendered and studied as a three-dimensional virtual object. This paper describes the work associated with the design and development of Matlab files to create three-dimensional images from the segmented object data previously mentioned. Part of the motivation for this work is to integrate both the segmentation and rendering processes into one software application, providing a seamless transition from the segmentation tasks to the rendering and visualization tasks. Previously these tasks were accomplished on two different computer systems, windows and Linux. This transition basically limits the usefulness of the segmentation and rendering applications to those who have both computer systems readily available. The focus of this work is to create custom Matlab image processing algorithms for object rendering and visualization, and merge these capabilities to the Matlab files that were developed especially for the image segmentation task. The completed Matlab application will contain both the segmentation and rendering processes in a single graphical user interface, or GUI. This process for rendering three-dimensional images in Matlab requires that a sequence of two-dimensional binary images, representing a cross-sectional slice of the object, be reassembled in a 3D space, and covered with a surface. Additional segmented objects can be rendered in the same 3D space. The surface properties of each object can be varied by the user to aid in the study and analysis of the objects. This inter-active process becomes a powerful visual tool to study and understand microscopic objects.

CT liver volumetry using three-dimensional image data in living donor liver transplantation: Effects of slice thickness on volume calculation

PubMed Central

Hori, Masatoshi; Suzuki, Kenji; Epstein, Mark L.; Baron, Richard L.

2011-01-01

The purpose was to evaluate a relationship between slice thickness and calculated volume on CT liver volumetry by comparing the results for images with various slice thicknesses including three-dimensional images. Twenty adult potential liver donors (12 men, 8 women; mean age, 39 years; range, 24–64) underwent CT with a 64-section multi-detector row CT scanner after intra-venous injection of contrast material. Four image sets with slice thicknesses of 0.625 mm, 2.5 mm, 5 mm, and 10 mm were used. First, a program developed in our laboratory for automated liver extraction was applied to CT images, and the liver boundary was obtained automatically. Then, an abdominal radiologist reviewed all images on which automatically extracted boundaries were superimposed, and edited the boundary on each slice to enhance the accuracy. Liver volumes were determined by counting of the voxels within the liver boundary. Mean whole liver volumes estimated with CT were 1322.5 cm3 on 0.625-mm, 1313.3 cm3 on 2.5-mm, 1310.3 cm3 on 5-mm, and 1268.2 cm3 on 10-mm images. Volumes calculated for three-dimensional (0.625-mm-thick) images were significantly larger than those for thicker images (P<.0001). Partial liver volumes of right lobe, left lobe, and lateral segment were also evaluated in a similar manner. Estimated maximum differences in calculated volumes of lateral segment was −10.9 cm3 (−4.6%) between 0.625-mm and 5-mm images. In conclusion, liver volumes calculated on 2.5-mm or thicker images were significantly smaller than volumes calculated on three-dimensional images. If a maximum error of 5% in the calculated graft volume is within the range of having an insignificant clinical impact, 5-mm thick images are acceptable for CT volumetry. If not, three-dimensional images could be essential. PMID:21850689

3D-quantitative structure-activity relationship study for the design of novel enterovirus A71 3C protease inhibitors.

PubMed

Nie, Quandeng; Xu, Xiaoyi; Zhang, Qi; Ma, Yuying; Yin, Zheng; Shang, Luqing

2018-06-07

A three-dimensional quantitative structure-activity relationships model of enterovirus A71 3C protease inhibitors was constructed in this study. The protein-ligand interaction fingerprint was analyzed to generate a pharmacophore model. A predictive and reliable three-dimensional quantitative structure-activity relationships model was built based on the Flexible Alignment of AutoGPA. Moreover, three novel compounds (I-III) were designed and evaluated for their biochemical activity against 3C protease and anti-enterovirus A71 activity in vitro. III exhibited excellent inhibitory activity (IC 50 =0.031 ± 0.005 μM, EC 50 =0.036 ± 0.007 μM). Thus, this study provides a useful quantitative structure-activity relationships model to develop potent inhibitors for enterovirus A71 3C protease. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Analysis of the three-dimensional structure of a bubble wake using PIV and Galilean decomposition

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

Hassan, Y.A.; Schmidl, W.D.; Ortiz-Villafuerte, J.

1999-07-01

Bubbly flow plays a key role in a variety of natural and industrial processes. An accurate and complete description of the phase interactions in two-phase bubbly flow is not available at this time. These phase interactions are, in general, always three-dimensional and unsteady. Therefore, measurement techniques utilized to obtain qualitative and quantitative data from two-phase flow should be able to acquire transient and three-dimensional data, in order to provide information to test theoretical models and numerical simulations. Even for dilute bubble flows, in which bubble interaction is at a minimum, the turbulent motion of the liquid generated by the bubblemore » is yet to be completely understood. For many years, the design of systems with bubbly flows was based primarily on empiricism. Dilute bubbly flows are an extension of single bubble dynamics, and therefore improvements in the description and modeling of single bubble motion, the flow field around the bubble, and the dynamical interactions between the bubble and the flow will consequently improve bubbly flow modeling. The improved understanding of the physical phenomena will have far-reaching benefits in upgrading the operation and efficiency of current processes and in supporting the development of new and innovative approaches. A stereoscopic particle image velocimetry measurement of the flow generated by the passage of a single air-bubble rising in stagnant water, in a circular pipe is presented. Three-dimensional velocity fields within the measurement zone were obtained. Ensemble-averaged instantaneous velocities for a specific bubble path were calculated and interpolated to obtain mean three-dimensional velocity fields. A Galilean velocity decomposition is used to study the vorticity generated in the flow.« less

Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data

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

McKinney, Adriana L.; Varga, Tamas

Branching structures such as lungs, blood vessels and plant roots play a critical role in life. Growth, structure, and function of these branching structures have an immense effect on our lives. Therefore, quantitative size information on such structures in their native environment is invaluable for studying their growth and the effect of the environment on them. X-ray computed tomography (XCT) has been an effective tool for in situ imaging and analysis of branching structures. We developed a costless tool that approximates the surface and volume of branching structures. Our methodology of noninvasive imaging, segmentation and extraction of quantitative information ismore » demonstrated through the analysis of a plant root in its soil medium from 3D tomography data. XCT data collected on a grass specimen was used to visualize its root structure. A suite of open-source software was employed to segment the root from the soil and determine its isosurface, which was used to calculate its volume and surface. This methodology of processing 3D data is applicable to other branching structures even when the structure of interest is of similar x-ray attenuation to its environment and difficulties arise with sample segmentation.« less

On aerodynamic wake analysis and its relation to total aerodynamic drag in a wind tunnel environment

NASA Astrophysics Data System (ADS)

Guterres, Rui M.

The present work was developed with the goal of advancing the state of the art in the application of three-dimensional wake data analysis to the quantification of aerodynamic drag on a body in a low speed wind tunnel environment. Analysis of the existing tools, their strengths and limitations is presented. Improvements to the existing analysis approaches were made. Software tools were developed to integrate the analysis into a practical tool. A comprehensive derivation of the equations needed for drag computations based on three dimensional separated wake data is developed. A set of complete steps ranging from the basic mathematical concept to the applicable engineering equations is presented. An extensive experimental study was conducted. Three representative body types were studied in varying ground effect conditions. A detailed qualitative wake analysis using wake imaging and two and three dimensional flow visualization was performed. Several significant features of the flow were identified and their relation to the total aerodynamic drag established. A comprehensive wake study of this type is shown to be in itself a powerful tool for the analysis of the wake aerodynamics and its relation to body drag. Quantitative wake analysis techniques were developed. Significant post processing and data conditioning tools and precision analysis were developed. The quality of the data is shown to be in direct correlation with the accuracy of the computed aerodynamic drag. Steps are taken to identify the sources of uncertainty. These are quantified when possible and the accuracy of the computed results is seen to significantly improve. When post processing alone does not resolve issues related to precision and accuracy, solutions are proposed. The improved quantitative wake analysis is applied to the wake data obtained. Guidelines are established that will lead to more successful implementation of these tools in future research programs. Close attention is paid to implementation of issues that are of crucial importance for the accuracy of the results and that are not detailed in the literature. The impact of ground effect on the flows in hand is qualitatively and quantitatively studied. Its impact on the accuracy of the computations as well as the wall drag incompatibility with the theoretical model followed are discussed. The newly developed quantitative analysis provides significantly increased accuracy. The aerodynamic drag coefficient is computed within one percent of balance measured value for the best cases.

Three-dimensional displacement measurement of image point by point-diffraction interferometry

NASA Astrophysics Data System (ADS)

He, Xiao; Chen, Lingfeng; Meng, Xiaojie; Yu, Lei

2018-01-01

This paper presents a method for measuring the three-dimensional (3-D) displacement of an image point based on point-diffraction interferometry. An object Point-light-source (PLS) interferes with a fixed PLS and its interferograms are captured by an exit pupil. When the image point of the object PLS is slightly shifted to a new position, the wavefront of the image PLS changes. And its interferograms also change. Processing these figures (captured before and after the movement), the wavefront difference of the image PLS can be obtained and it contains the information of three-dimensional (3-D) displacement of the image PLS. However, the information of its three-dimensional (3-D) displacement cannot be calculated until the distance between the image PLS and the exit pupil is calibrated. Therefore, we use a plane-parallel-plate with a known refractive index and thickness to determine this distance, which is based on the Snell's law for small angle of incidence. Thus, since the distance between the exit pupil and the image PLS is a known quantity, the 3-D displacement of the image PLS can be simultaneously calculated through two interference measurements. Preliminary experimental results indicate that its relative error is below 0.3%. With the ability to accurately locate an image point (whatever it is real or virtual), a fiber point-light-source can act as the reticle by itself in optical measurement.

Technique of semiautomatic surface reconstruction of the visible Korean human data using commercial software.

PubMed

Park, Jin Seo; Shin, Dong Sun; Chung, Min Suk; Hwang, Sung Bae; Chung, Jinoh

2007-11-01

This article describes the technique of semiautomatic surface reconstruction of anatomic structures using widely available commercial software. This technique would enable researchers to promptly and objectively perform surface reconstruction, creating three-dimensional anatomic images without any assistance from computer engineers. To develop the technique, we used data from the Visible Korean Human project, which produced digitalized photographic serial images of an entire cadaver. We selected 114 anatomic structures (skin [1], bones [32], knee joint structures [7], muscles [60], arteries [7], and nerves [7]) from the 976 anatomic images which were generated from the left lower limb of the cadaver. Using Adobe Photoshop, the selected anatomic structures in each serial image were outlined, creating a segmented image. The Photoshop files were then converted into Adobe Illustrator files to prepare isolated segmented images, so that the contours of the structure could be viewed independent of the surrounding anatomy. Using Alias Maya, these isolated segmented images were then stacked to construct a contour image. Gaps between the contour lines were filled with surfaces, and three-dimensional surface reconstruction could be visualized with Rhinoceros. Surface imperfections were then corrected to complete the three-dimensional images in Alias Maya. We believe that the three-dimensional anatomic images created by these methods will have widespread application in both medical education and research. 2007 Wiley-Liss, Inc

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives.

PubMed

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q (2) values of 0.753 and 0.770, and r (2) values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2'-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure-property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature.

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives

PubMed Central

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure–activity relationship (3D-QSAR) and three-dimensional quantitative structure–selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q2 values of 0.753 and 0.770, and r2 values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2′-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure–property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature. PMID:25848211

Mapping morphological shape as a high-dimensional functional curve

PubMed Central

Fu, Guifang; Huang, Mian; Bo, Wenhao; Hao, Han; Wu, Rongling

2018-01-01

Abstract Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ. Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica. This population, distributed at altitudes 2000–4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of ‘function’ instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do. PMID:28062411

Quantitative Analysis of Cotton Canopy Size in Field Conditions Using a Consumer-Grade RGB-D Camera.

PubMed

Jiang, Yu; Li, Changying; Paterson, Andrew H; Sun, Shangpeng; Xu, Rui; Robertson, Jon

2017-01-01

Plant canopy structure can strongly affect crop functions such as yield and stress tolerance, and canopy size is an important aspect of canopy structure. Manual assessment of canopy size is laborious and imprecise, and cannot measure multi-dimensional traits such as projected leaf area and canopy volume. Field-based high throughput phenotyping systems with imaging capabilities can rapidly acquire data about plants in field conditions, making it possible to quantify and monitor plant canopy development. The goal of this study was to develop a 3D imaging approach to quantitatively analyze cotton canopy development in field conditions. A cotton field was planted with 128 plots, including four genotypes of 32 plots each. The field was scanned by GPhenoVision (a customized field-based high throughput phenotyping system) to acquire color and depth images with GPS information in 2016 covering two growth stages: canopy development, and flowering and boll development. A data processing pipeline was developed, consisting of three steps: plot point cloud reconstruction, plant canopy segmentation, and trait extraction. Plot point clouds were reconstructed using color and depth images with GPS information. In colorized point clouds, vegetation was segmented from the background using an excess-green (ExG) color filter, and cotton canopies were further separated from weeds based on height, size, and position information. Static morphological traits were extracted on each day, including univariate traits (maximum and mean canopy height and width, projected canopy area, and concave and convex volumes) and a multivariate trait (cumulative height profile). Growth rates were calculated for univariate static traits, quantifying canopy growth and development. Linear regressions were performed between the traits and fiber yield to identify the best traits and measurement time for yield prediction. The results showed that fiber yield was correlated with static traits after the canopy development stage ( R 2 = 0.35-0.71) and growth rates in early canopy development stages ( R 2 = 0.29-0.52). Multi-dimensional traits (e.g., projected canopy area and volume) outperformed one-dimensional traits, and the multivariate trait (cumulative height profile) outperformed univariate traits. The proposed approach would be useful for identification of quantitative trait loci (QTLs) controlling canopy size in genetics/genomics studies or for fiber yield prediction in breeding programs and production environments.

Mammalian Cardiovascular Patterning as Determined by Hemodynamic Forces and Blood Vessel Genetics

NASA Astrophysics Data System (ADS)

Anderson, Gregory Arthur

Cardiovascular development is a process that involves the timing of multiple molecular events, and numerous subtle three-dimensional conformational changes. Traditional developmental biology techniques have provided large quantities of information as to how these complex organ systems develop. However, the major drawback of the majority of current developmental biological imaging is that they are two-dimensional in nature. It is now well recognized that circulation of blood is required for normal patterning and remodeling of blood vessels. Normal blood vessel formation is dependent upon a complex network of signaling pathways, and genetic mutations in these pathways leads to impaired vascular development, heart failure, and lethality. As such, it is not surprising that mutant mice with aberrant cardiovascular patterning are so common, since normal development requires proper coordination between three systems: the heart, the blood, and the vasculature. This thesis describes the implementation of a three-dimensional imaging technique, optical projection tomography (OPT), in conjunction with a computer-based registration algorithm to statistically analyze developmental differences in groups of wild-type mouse embryos. Embryos that differ by only a few hours' gestational time are shown to have developmental differences in blood vessel formation and heart development progression that can be discerned. This thesis describes how we analyzed mouse models of cardiovascular perturbation by OPT to detect morphological differences in embryonic development in both qualitative and quantitative ways. Both a blood vessel specific mutation and a cardiac specific mutation were analyzed, providing evidence that developmental defects of these types can be quantified. Finally, we describe the implementation of OPT imaging to identify statistically significant phenotypes from three different mouse models of cardiovascular perturbation across a range of developmental time points. Image registration methods, combined with intensity- and deformation-based analyses are described and utilized to fully characterize myosin light chain 2a (Mlc2a), delta-like ligand 4 (Dll4), and Endoglin (Eng) mutant mouse embryos. We show that Eng mutant embryos are statistically similar to the Mlc2a phenotype, confirming that these mouse mutants suffer from a primary cardiac developmental defect. Thus, a loss of hemodynamic force caused by defective pumping of the heart is the primary developmental defect affecting these mice.

Three-dimensional and thermal surface imaging produces reliable measures of joint shape and temperature: a potential tool for quantifying arthritis

PubMed Central

Spalding, Steven J; Kwoh, C Kent; Boudreau, Robert; Enama, Joseph; Lunich, Julie; Huber, Daniel; Denes, Louis; Hirsch, Raphael

2008-01-01

Introduction The assessment of joints with active arthritis is a core component of widely used outcome measures. However, substantial variability exists within and across examiners in assessment of these active joint counts. Swelling and temperature changes, two qualities estimated during active joint counts, are amenable to quantification using noncontact digital imaging technologies. We sought to explore the ability of three dimensional (3D) and thermal imaging to reliably measure joint shape and temperature. Methods A Minolta 910 Vivid non-contact 3D laser scanner and a Meditherm med2000 Pro Infrared camera were used to create digital representations of wrist and metacarpalphalangeal (MCP) joints. Specialized software generated 3 quantitative measures for each joint region: 1) Volume; 2) Surface Distribution Index (SDI), a marker of joint shape representing the standard deviation of vertical distances from points on the skin surface to a fixed reference plane; 3) Heat Distribution Index (HDI), representing the standard error of temperatures. Seven wrists and 6 MCP regions from 5 subjects with arthritis were used to develop and validate 3D image acquisition and processing techniques. HDI values from 18 wrist and 9 MCP regions were obtained from 17 patients with active arthritis and compared to data from 10 wrist and MCP regions from 5 controls. Standard deviation (SD), coefficient of variation (CV), and intraclass correlation coefficients (ICC) were calculated for each quantitative measure to establish their reliability. CVs for volume and SDI were <1.3% and ICCs were greater than 0.99. Results Thermal measures were less reliable than 3D measures. However, significant differences were observed between control and arthritis HDI values. Two case studies of arthritic joints demonstrated quantifiable changes in swelling and temperature corresponding with changes in symptoms and physical exam findings. Conclusion 3D and thermal imaging provide reliable measures of joint volume, shape, and thermal patterns. Further refinement may lead to the use of these technologies to improve the assessment of disease activity in arthritis. PMID:18215307

Images as embedding maps and minimal surfaces: Movies, color, and volumetric medical images

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

Kimmel, R.; Malladi, R.; Sochen, N.

A general geometrical framework for image processing is presented. The authors consider intensity images as surfaces in the (x,I) space. The image is thereby a two dimensional surface in three dimensional space for gray level images. The new formulation unifies many classical schemes, algorithms, and measures via choices of parameters in a {open_quote}master{close_quotes} geometrical measure. More important, it is a simple and efficient tool for the design of natural schemes for image enhancement, segmentation, and scale space. Here the authors give the basic motivation and apply the scheme to enhance images. They present the concept of an image as amore » surface in dimensions higher than the three dimensional intuitive space. This will help them handle movies, color, and volumetric medical images.« less

Importance of preoperative imaging with 64-row three-dimensional multidetector computed tomography for safer video-assisted thoracic surgery in lung cancer.

PubMed

Akiba, Tadashi; Marushima, Hideki; Harada, Junta; Kobayashi, Susumu; Morikawa, Toshiaki

2009-01-01

Video-assisted thoracic surgery (VATS) has recently been adopted for complicated anatomical lung resections. During these thoracoscopic procedures, surgeons view the operative field on a two-dimensional (2-D) video monitor and cannot palpate the organ directly, thus frequently encountering anatomical difficulties. This study aimed to estimate the usefulness of preoperative three-dimensional (3-D) imaging of thoracic organs. We compared the preoperative 64-row three-dimensional multidetector computed tomography (3DMDCT) findings of lung cancer-affected thoracic organs to the operative findings. In comparison to the operative findings, the branches of pulmonary arteries, veins, and bronchi were well defined in the 3D-MDCT images of 27 patients. 3D-MDCT imaging is useful for preoperatively understanding the individual thoracic anatomy in lung cancer surgery. This modality can therefore contribute to safer anatomical pulmonary operations, especially in VATS.

Trends in radiology and experimental research.

PubMed

Sardanelli, Francesco

2017-01-01

European Radiology Experimental , the new journal launched by the European Society of Radiology, is placed in the context of three general and seven radiology-specific trends. After describing the impact of population aging, personalized/precision medicine, and information technology development, the article considers the following trends: the tension between subspecialties and the unity of the discipline; attention to patient safety; the challenge of reproducibility for quantitative imaging; standardized and structured reporting; search for higher levels of evidence in radiology (from diagnostic performance to patient outcome); the increasing relevance of interventional radiology; and continuous technological evolution. The new journal will publish not only studies on phantoms, cells, or animal models but also those describing development steps of imaging biomarkers or those exploring secondary end-points of large clinical trials. Moreover, consideration will be given to studies regarding: computer modelling and computer aided detection and diagnosis; contrast materials, tracers, and theranostics; advanced image analysis; optical, molecular, hybrid and fusion imaging; radiomics and radiogenomics; three-dimensional printing, information technology, image reconstruction and post-processing, big data analysis, teleradiology, clinical decision support systems; radiobiology; radioprotection; and physics in radiology. The journal aims to establish a forum for basic science, computer and information technology, radiology, and other medical subspecialties.

Construction of an unmanned aerial vehicle remote sensing system for crop monitoring

NASA Astrophysics Data System (ADS)

Jeong, Seungtaek; Ko, Jonghan; Kim, Mijeong; Kim, Jongkwon

2016-04-01

We constructed a lightweight unmanned aerial vehicle (UAV) remote sensing system and determined the ideal method for equipment setup, image acquisition, and image processing. Fields of rice paddy (Oryza sativa cv. Unkwang) grown under three different nitrogen (N) treatments of 0, 50, or 115 kg/ha were monitored at Chonnam National University, Gwangju, Republic of Korea, in 2013. A multispectral camera was used to acquire UAV images from the study site. Atmospheric correction of these images was completed using the empirical line method, and three-point (black, gray, and white) calibration boards were used as pseudo references. Evaluation of our corrected UAV-based remote sensing data revealed that correction efficiency and root mean square errors ranged from 0.77 to 0.95 and 0.01 to 0.05, respectively. The time series maps of simulated normalized difference vegetation index (NDVI) produced using the UAV images reproduced field variations of NDVI reasonably well, both within and between the different N treatments. We concluded that the UAV-based remote sensing technology utilized in this study is potentially an easy and simple way to quantitatively obtain reliable two-dimensional remote sensing information on crop growth.

Morphometric analysis of acetabular dysplasia in cerebral palsy: three-dimensional CT study.

PubMed

Gose, Shinichi; Sakai, Takashi; Shibata, Toru; Murase, Tsuyoshi; Yoshikawa, Hideki; Sugamoto, Kazuomi

2009-12-01

Three-dimensional computed tomography (3D-CT) eliminates the positioning errors and allows the clinician to more accurately assess the radiographic parameters present. To elucidate the 3D geometry of the acetabulum and the extent of hip subluxation/dislocation in patients with cerebral palsy (CP), quantitative morphometric analysis was performed using 3D-CT data. We evaluated 150 hips in 75 patients with bilateral spastic CP. The mean age of the patients was 5.4 years (range: 2.7 to 6.9 y). The fitting plane of the ilium was projected onto the coronal plane and then onto the sagittal plane, and then the angle formed with a horizontal line was defined as CTalpha (the lateral opening angle) and CTbeta (the sagittal inclination angle), respectively. The center of the acetabulum and the femoral head were defined, and the distance between these centers was divided by the femoral head diameter, defined as CT migration percentage (CTMP, %). In 123 (82%) of the 150 hips, the femoral head center was located posteriorly, superiorly, and laterally relative to the acetabular center. Large CTalpha cases tended to show large CTMP. CTalpha and CTMP were significantly larger in the cases with Gross Motor Functional Classification System (GMFCS) level IV/V and spastic quadriplegia, than in the cases with GMFCS level II/III and spastic diplegia. CTbeta showed significant correlation with the acetabular defect on the lateral 3D reconstructed images. Three-dimensional acetabular geometry and migration percentage in CP patients can be analyzed quantitatively using 3D-CT regardless of the abnormal spastic posture. The extent of acetabular dysplasia and subluxation is more severe in patients with GMFCS level IV/V and spastic quadriplesia. Level 4.

3D sorghum reconstructions from depth images identify QTL regulating shoot architecture

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

Mccormick, Ryan F.; Truong, Sandra K.; Mullet, John E.

Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height,more » leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.« less

3D sorghum reconstructions from depth images identify QTL regulating shoot architecture

DOE PAGES

Mccormick, Ryan F.; Truong, Sandra K.; Mullet, John E.

2016-08-15

Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height,more » leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.« less

Quantification of HSV-1-mediated expression of the ferritin MRI reporter in the mouse brain

PubMed Central

Iordanova, B; Goins, WF; Clawson, DS; Hitchens, TK; Ahrens, ET

2017-01-01

The development of effective strategies for gene therapy has been hampered by difficulties verifying transgene delivery in vivo and quantifying gene expression non-invasively. Magnetic resonance imaging (MRI) offers high spatial resolution and three-dimensional views, without tissue depth limitations. The iron-storage protein ferritin is a prototype MRI gene reporter. Ferritin forms a paramagnetic ferrihydrite core that can be detected by MRI via its effect on the local magnetic field experienced by water protons. In an effort to better characterize the ferritin reporter for central nervous system applications, we expressed ferritin in the mouse brain in vivo using a neurotropic herpes simplex virus type 1 (HSV-1). We computed three-dimensional maps of MRI transverse relaxation rates in the mouse brain with ascending doses of ferritin-expressing HSV-1. We established that the transverse relaxation rates correlate significantly to the number of inoculated infectious particles. Our results are potentially useful for quantitatively assessing limitations of ferritin reporters for gene therapy applications. PMID:22996196

Extracellular oxygen concentration mapping with a confocal multiphoton laser scanning microscope and TCSPC card

NASA Astrophysics Data System (ADS)

Hosny, Neveen A.; Lee, David A.; Knight, Martin M.

2010-02-01

Extracellular oxygen concentrations influence cell metabolism and tissue function. Fluorescence Lifetime Imaging Microscopy (FLIM) offers a non-invasive method for quantifying local oxygen concentrations. However, existing methods show limited spatial resolution and/or require custom made systems. This study describes a new optimised approach for quantitative extracellular oxygen detection, providing an off-the-shelf system with high spatial resolution and an improved lifetime determination over previous techniques, while avoiding systematic photon pile-up. Fluorescence lifetime detection of an oxygen sensitive fluorescent dye, tris(2,2'-bipyridyl)ruthenium(II) chloride hexahydrate [Ru(bipy)3]2+, was measured using a Becker&Hickl time-correlated single photon counting (TCSPC) card with excitation provided by a multi-photon laser. This technique was able to identify a subpopulation of isolated chondrocyte cells, seeded in three-dimensional agarose gel, displaying a significant spatial oxygen gradient. Thus this technique provides a powerful tool for quantifying spatial oxygen gradients within three-dimensional cellular models.

Novel 16-channel receive coil array for accelerated upper airway MRI at 3 Tesla.

PubMed

Kim, Yoon-Chul; Hayes, Cecil E; Narayanan, Shrikanth S; Nayak, Krishna S

2011-06-01

Upper airway MRI can provide a noninvasive assessment of speech and swallowing disorders and sleep apnea. Recent work has demonstrated the value of high-resolution three-dimensional imaging and dynamic two-dimensional imaging and the importance of further improvements in spatio-temporal resolution. The purpose of the study was to describe a novel 16-channel 3 Tesla receive coil that is highly sensitive to the human upper airway and investigate the performance of accelerated upper airway MRI with the coil. In three-dimensional imaging of the upper airway during static posture, 6-fold acceleration is demonstrated using parallel imaging, potentially leading to capturing a whole three-dimensional vocal tract with 1.25 mm isotropic resolution within 9 sec of sustained sound production. Midsagittal spiral parallel imaging of vocal tract dynamics during natural speech production is demonstrated with 2 × 2 mm(2) in-plane spatial and 84 ms temporal resolution. Copyright © 2010 Wiley-Liss, Inc.

Athermally photoreduced graphene oxides for three-dimensional holographic images

PubMed Central

Li, Xiangping; Ren, Haoran; Chen, Xi; Liu, Juan; Li, Qin; Li, Chengmingyue; Xue, Gaolei; Jia, Jia; Cao, Liangcai; Sahu, Amit; Hu, Bin; Wang, Yongtian; Jin, Guofan; Gu, Min

2015-01-01

The emerging graphene-based material, an atomic layer of aromatic carbon atoms with exceptional electronic and optical properties, has offered unprecedented prospects for developing flat two-dimensional displaying systems. Here, we show that reduced graphene oxide enabled write-once holograms for wide-angle and full-colour three-dimensional images. This is achieved through the discovery of subwavelength-scale multilevel optical index modulation of athermally reduced graphene oxides by a single femtosecond pulsed beam. This new feature allows for static three-dimensional holographic images with a wide viewing angle up to 52 degrees. In addition, the spectrally flat optical index modulation in reduced graphene oxides enables wavelength-multiplexed holograms for full-colour images. The large and polarization-insensitive phase modulation over π in reduced graphene oxide composites enables to restore vectorial wavefronts of polarization discernible images through the vectorial diffraction of a reconstruction beam. Therefore, our technique can be leveraged to achieve compact and versatile holographic components for controlling light. PMID:25901676

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review.

PubMed

Goez, Manuel Mauricio; Torres-Madroñero, Maria Constanza; Röthlisberger, Sarah; Delgado-Trejos, Edilson

2018-02-01

Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images: Gaussian, Rayleigh, and exponential, with signal-to-noise ratios (SNRs) ranging 8-20 decibels (dB). We compared the performance of wavelet, contourlet, total variation (TV), and wavelet-total variation (WTTV) techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sensitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10-20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best performance with any level of Gaussian noise and low levels (20-14 dB) of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image. Copyright © 2018 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Production and hosting by Elsevier B.V. All rights reserved.

Hydrodynamic characteristics of the two-phase flow field at gas-evolving electrodes: numerical and experimental studies

NASA Astrophysics Data System (ADS)

Liu, Cheng-Lin; Sun, Ze; Lu, Gui-Min; Yu, Jian-Guo

2018-05-01

Gas-evolving vertical electrode system is a typical electrochemical industrial reactor. Gas bubbles are released from the surfaces of the anode and affect the electrolyte flow pattern and even the cell performance. In the current work, the hydrodynamics induced by the air bubbles in a cold model was experimentally and numerically investigated. Particle image velocimetry and volumetric three-component velocimetry techniques were applied to experimentally visualize the hydrodynamics characteristics and flow fields in a two-dimensional (2D) plane and a three-dimensional (3D) space, respectively. Measurements were performed at different gas rates. Furthermore, the corresponding mathematical model was developed under identical conditions for the qualitative and quantitative analyses. The experimental measurements were compared with the numerical results based on the mathematical model. The study of the time-averaged flow field, three velocity components, instantaneous velocity and turbulent intensity indicate that the numerical model qualitatively reproduces liquid motion. The 3D model predictions capture the flow behaviour more accurately than the 2D model in this study.

Hydrodynamic characteristics of the two-phase flow field at gas-evolving electrodes: numerical and experimental studies.

PubMed

Liu, Cheng-Lin; Sun, Ze; Lu, Gui-Min; Yu, Jian-Guo

2018-05-01

Gas-evolving vertical electrode system is a typical electrochemical industrial reactor. Gas bubbles are released from the surfaces of the anode and affect the electrolyte flow pattern and even the cell performance. In the current work, the hydrodynamics induced by the air bubbles in a cold model was experimentally and numerically investigated. Particle image velocimetry and volumetric three-component velocimetry techniques were applied to experimentally visualize the hydrodynamics characteristics and flow fields in a two-dimensional (2D) plane and a three-dimensional (3D) space, respectively. Measurements were performed at different gas rates. Furthermore, the corresponding mathematical model was developed under identical conditions for the qualitative and quantitative analyses. The experimental measurements were compared with the numerical results based on the mathematical model. The study of the time-averaged flow field, three velocity components, instantaneous velocity and turbulent intensity indicate that the numerical model qualitatively reproduces liquid motion. The 3D model predictions capture the flow behaviour more accurately than the 2D model in this study.

Hydrodynamic characteristics of the two-phase flow field at gas-evolving electrodes: numerical and experimental studies

PubMed Central

Lu, Gui-Min; Yu, Jian-Guo

2018-01-01

Gas-evolving vertical electrode system is a typical electrochemical industrial reactor. Gas bubbles are released from the surfaces of the anode and affect the electrolyte flow pattern and even the cell performance. In the current work, the hydrodynamics induced by the air bubbles in a cold model was experimentally and numerically investigated. Particle image velocimetry and volumetric three-component velocimetry techniques were applied to experimentally visualize the hydrodynamics characteristics and flow fields in a two-dimensional (2D) plane and a three-dimensional (3D) space, respectively. Measurements were performed at different gas rates. Furthermore, the corresponding mathematical model was developed under identical conditions for the qualitative and quantitative analyses. The experimental measurements were compared with the numerical results based on the mathematical model. The study of the time-averaged flow field, three velocity components, instantaneous velocity and turbulent intensity indicate that the numerical model qualitatively reproduces liquid motion. The 3D model predictions capture the flow behaviour more accurately than the 2D model in this study. PMID:29892347

Three-dimensional scene reconstruction from a two-dimensional image

NASA Astrophysics Data System (ADS)

Parkins, Franz; Jacobs, Eddie

2017-05-01

We propose and simulate a method of reconstructing a three-dimensional scene from a two-dimensional image for developing and augmenting world models for autonomous navigation. This is an extension of the Perspective-n-Point (PnP) method which uses a sampling of the 3D scene, 2D image point parings, and Random Sampling Consensus (RANSAC) to infer the pose of the object and produce a 3D mesh of the original scene. Using object recognition and segmentation, we simulate the implementation on a scene of 3D objects with an eye to implementation on embeddable hardware. The final solution will be deployed on the NVIDIA Tegra platform.

Ground Penetrating Radar Imaging of Ancient Clastic Deposits: A Tool for Three-Dimensional Outcrop Studies

NASA Astrophysics Data System (ADS)

Akinpelu, Oluwatosin Caleb

The growing need for better definition of flow units and depositional heterogeneities in petroleum reservoirs and aquifers has stimulated a renewed interest in outcrop studies as reservoir analogues in the last two decades. Despite this surge in interest, outcrop studies remain largely two-dimensional; a major limitation to direct application of outcrop knowledge to the three dimensional heterogeneous world of subsurface reservoirs. Behind-outcrop Ground Penetrating Radar (GPR) imaging provides high-resolution geophysical data, which when combined with two dimensional architectural outcrop observation, becomes a powerful interpretation tool. Due to the high resolution, non-destructive and non-invasive nature of the GPR signal, as well as its reflection-amplitude sensitivity to shaly lithologies, three-dimensional outcrop studies combining two dimensional architectural element data and behind-outcrop GPR imaging hold significant promise with the potential to revolutionize outcrop studies the way seismic imaging changed basin analysis. Earlier attempts at GPR imaging on ancient clastic deposits were fraught with difficulties resulting from inappropriate field techniques and subsequent poorly-informed data processing steps. This project documents advances in GPR field methodology, recommends appropriate data collection and processing procedures and validates the value of integrating outcrop-based architectural-element mapping with GPR imaging to obtain three dimensional architectural data from outcrops. Case studies from a variety of clastic deposits: Whirlpool Formation (Niagara Escarpment), Navajo Sandstone (Moab, Utah), Dunvegan Formation (Pink Mountain, British Columbia), Chinle Formation (Southern Utah) and St. Mary River Formation (Alberta) demonstrate the usefulness of this approach for better interpretation of outcrop scale ancient depositional processes and ultimately as a tool for refining existing facies models, as well as a predictive tool for subsurface reservoir modelling. While this approach is quite promising for detailed three-dimensional outcrop studies, it is not an all-purpose panacea; thick overburden, poor antenna-ground coupling in rough terrains typical of outcrops, low penetration and rapid signal attenuation in mudstone and diagenetic clay- rich deposits often limit the prospects of this novel technique.

X-ray fluorescence holography studies for a Cu3Au crystal

NASA Astrophysics Data System (ADS)

Dąbrowski, K. M.; Dul, D. T.; Jaworska-Gołąb, T.; Rysz, J.; Korecki, P.

2015-12-01

In this work we show that performing a numerical correction for beam attenuation and indirect excitation allows one to fully restore element sensitivity in the three-dimensional reconstruction of the atomic structure. This is exemplified by a comparison of atomic images reconstructed from holograms measured for ordered and disordered phases of a Cu3Au crystal that clearly show sensitivity to changes in occupancy of the atomic sites. Moreover, the numerical correction, which is based on quantitative methods of X-ray fluorescence spectroscopy, was extended to take into account the influence of a disturbed overlayer in the sample.

Three-dimensional hard and soft tissue imaging of the human cochlea by scanning laser optical tomography (SLOT)

PubMed Central

Mohebbi, Saleh; Andrade, José; Nolte, Lena; Meyer, Heiko; Heisterkamp, Alexander; Majdani, Omid

2017-01-01

The present study focuses on the application of scanning laser optical tomography (SLOT) for visualization of anatomical structures inside the human cochlea ex vivo. SLOT is a laser-based highly efficient microscopy technique which allows for tomographic imaging of the internal structure of transparent specimens. Thus, in the field of otology this technique is best convenient for an ex vivo study of the inner ear anatomy. For this purpose, the preparation before imaging comprises decalcification, dehydration as well as optical clearing of the cochlea samples in toto. Here, we demonstrate results of SLOT imaging visualizing hard and soft tissue structures with an optical resolution of down to 15 μm using extinction and autofluorescence as contrast mechanisms. Furthermore, the internal structure can be analyzed nondestructively and quantitatively in detail by sectioning of the three-dimensional datasets. The method of X-ray Micro Computed Tomography (μCT) has been previously applied to explanted cochlea and is solely based on absorption contrast. An advantage of SLOT is that it uses visible light for image formation and thus provides a variety of contrast mechanisms known from other light microscopy techniques, such as fluorescence or scattering. We show that SLOT data is consistent with μCT anatomical data and provides additional information by using fluorescence. We demonstrate that SLOT is applicable for cochlea with metallic cochlear implants (CI) that would lead to significant artifacts in μCT imaging. In conclusion, the present study demonstrates the capability of SLOT for resolution visualization of cleared human cochleae ex vivo using multiple contrast mechanisms and lays the foundation for a broad variety of additional studies. PMID:28873437

Temporally diffeomorphic cardiac motion estimation from three-dimensional echocardiography by minimization of intensity consistency error.

PubMed

Zhang, Zhijun; Ashraf, Muhammad; Sahn, David J; Song, Xubo

2014-05-01

Quantitative analysis of cardiac motion is important for evaluation of heart function. Three dimensional (3D) echocardiography is among the most frequently used imaging modalities for motion estimation because it is convenient, real-time, low-cost, and nonionizing. However, motion estimation from 3D echocardiographic sequences is still a challenging problem due to low image quality and image corruption by noise and artifacts. The authors have developed a temporally diffeomorphic motion estimation approach in which the velocity field instead of the displacement field was optimized. The optimal velocity field optimizes a novel similarity function, which we call the intensity consistency error, defined as multiple consecutive frames evolving to each time point. The optimization problem is solved by using the steepest descent method. Experiments with simulated datasets, images of anex vivo rabbit phantom, images of in vivo open-chest pig hearts, and healthy human images were used to validate the authors' method. Simulated and real cardiac sequences tests showed that results in the authors' method are more accurate than other competing temporal diffeomorphic methods. Tests with sonomicrometry showed that the tracked crystal positions have good agreement with ground truth and the authors' method has higher accuracy than the temporal diffeomorphic free-form deformation (TDFFD) method. Validation with an open-access human cardiac dataset showed that the authors' method has smaller feature tracking errors than both TDFFD and frame-to-frame methods. The authors proposed a diffeomorphic motion estimation method with temporal smoothness by constraining the velocity field to have maximum local intensity consistency within multiple consecutive frames. The estimated motion using the authors' method has good temporal consistency and is more accurate than other temporally diffeomorphic motion estimation methods.

Visidep (TM): A Three-Dimensional Imaging System For The Unaided Eye

NASA Astrophysics Data System (ADS)

McLaurin, A. Porter; Jones, Edwin R.; Cathey, LeConte

1984-05-01

The VISIDEP process for creating images in three dimensions on flat screens is suitable for photographic, electrographic and computer generated imaging systems. Procedures for generating these images vary from medium to medium due to the specific requirements of each technology. Imaging requirements for photographic and electrographic media are more directly tied to the hardware than are computer based systems. Applications of these technologies are not limited to entertainment, but have implications for training, interactive computer/video systems, medical imaging, and inspection equipment. Through minor modification the system can provide three-dimensional images with accurately measureable relationships for robotics and adds this factor for future developments in artificial intelligence. In almost any area requiring image analysis or critical review, VISIDEP provides the added advantage of three-dimensionality. All of this is readily accomplished without aids to the human eye. The system can be viewed in full color, false-color infra-red, and monochromatic modalities from any angle and is also viewable with a single eye. Thus, the potential of application for this developing system is extensive and covers the broad spectrum of human endeavor from entertainment to scientific study.

Visually estimated ejection fraction by two dimensional and triplane echocardiography is closely correlated with quantitative ejection fraction by real-time three dimensional echocardiography.

PubMed

Shahgaldi, Kambiz; Gudmundsson, Petri; Manouras, Aristomenis; Brodin, Lars-Ake; Winter, Reidar

2009-08-25

Visual assessment of left ventricular ejection fraction (LVEF) is often used in clinical routine despite general recommendations to use quantitative biplane Simpsons (BPS) measurements. Even thou quantitative methods are well validated and from many reasons preferable, the feasibility of visual assessment (eyeballing) is superior. There is to date only sparse data comparing visual EF assessment in comparison to quantitative methods available. The aim of this study was to compare visual EF assessment by two-dimensional echocardiography (2DE) and triplane echocardiography (TPE) using quantitative real-time three-dimensional echocardiography (RT3DE) as the reference method. Thirty patients were enrolled in the study. Eyeballing EF was assessed using apical 4-and 2 chamber views and TP mode by two experienced readers blinded to all clinical data. The measurements were compared to quantitative RT3DE. There were an excellent correlation between eyeballing EF by 2D and TP vs 3DE (r = 0.91 and 0.95 respectively) without any significant bias (-0.5 +/- 3.7% and -0.2 +/- 2.9% respectively). Intraobserver variability was 3.8% for eyeballing 2DE, 3.2% for eyeballing TP and 2.3% for quantitative 3D-EF. Interobserver variability was 7.5% for eyeballing 2D and 8.4% for eyeballing TP. Visual estimation of LVEF both using 2D and TP by an experienced reader correlates well with quantitative EF determined by RT3DE. There is an apparent trend towards a smaller variability using TP in comparison to 2D, this was however not statistically significant.

In search of Leonardo: computer-based facial image analysis of Renaissance artworks for identifying Leonardo as subject

NASA Astrophysics Data System (ADS)

Tyler, Christopher W.; Smith, William A. P.; Stork, David G.

2012-03-01

One of the enduring mysteries in the history of the Renaissance is the adult appearance of the archetypical "Renaissance Man," Leonardo da Vinci. His only acknowledged self-portrait is from an advanced age, and various candidate images of younger men are difficult to assess given the absence of documentary evidence. One clue about Leonardo's appearance comes from the remark of the contemporary historian, Vasari, that the sculpture of David by Leonardo's master, Andrea del Verrocchio, was based on the appearance of Leonardo when he was an apprentice. Taking a cue from this statement, we suggest that the more mature sculpture of St. Thomas, also by Verrocchio, might also have been a portrait of Leonardo. We tested the possibility Leonardo was the subject for Verrocchio's sculpture by a novel computational technique for the comparison of three-dimensional facial configurations. Based on quantitative measures of similarities, we also assess whether another pair of candidate two-dimensional images are plausibly attributable as being portraits of Leonardo as a young adult. Our results are consistent with the claim Leonardo is indeed the subject in these works, but we need comparisons with images in a larger corpora of candidate artworks before our results achieve statistical significance.