Lensless Tomographic Imaging of Near Surface Structures of Frozen Hydrated Malaria-Infected Human Erythrocytes by Coherent X-Ray Diffraction Microscopy.

PubMed

Frank, Viktoria; Chushkin, Yuriy; Fröhlich, Benjamin; Abuillan, Wasim; Rieger, Harden; Becker, Alexandra S; Yamamoto, Akihisa; Rossetti, Fernanda F; Kaufmann, Stefan; Lanzer, Michael; Zontone, Federico; Tanaka, Motomu

2017-10-26

Lensless, coherent X-ray diffraction microscopy has been drawing considerable attentions for tomographic imaging of whole human cells. In this study, we performed cryogenic coherent X-ray diffraction imaging of human erythrocytes with and without malaria infection. To shed light on structural features near the surface, "ghost cells" were prepared by the removal of cytoplasm. From two-dimensional images, we found that the surface of erythrocytes after 32 h of infection became much rougher compared to that of healthy, uninfected erythrocytes. The Gaussian roughness of an infected erythrocyte surface (69 nm) is about two times larger than that of an uninfected one (31 nm), reflecting the formation of protein knobs on infected erythrocyte surfaces. Three-dimensional tomography further enables to obtain images of the whole cells with no remarkable radiation damage, whose accuracy was estimated using phase retrieval transfer functions to be as good as 64 nm for uninfected and 80 nm for infected erythrocytes, respectively. Future improvements in phase retrieval algorithm, increase in degree of coherence, and higher flux in combination with complementary X-ray fluorescence are necessary to gain both structural and chemical details of mesoscopic architectures, such as cytoskeletons, membraneous structures, and protein complexes, in frozen hydrated human cells, especially under diseased states.

Quantitative Cryo-Scanning Transmission Electron Microscopy of Biological Materials.

PubMed

Elbaum, Michael

2018-05-11

Electron tomography provides a detailed view into the 3D structure of biological cells and tissues. Physical fixation by vitrification of the aqueous medium provides the most faithful preservation of biological specimens in the native, fully hydrated state. Cryo-microscopy is challenging, however, because of the sensitivity to electron irradiation and due to the weak electron scattering of organic material. Tomography is even more challenging because of the dependence on multiple exposures of the same area. Tomographic imaging is typically performed in wide-field transmission electron microscopy (TEM) mode with phase contrast generated by defocus. Scanning transmission electron microscopy (STEM) is an alternative mode based on detection of scattering from a focused probe beam, without imaging optics following the specimen. While careful configuration of the illumination and detectors is required to generate useful contrast, STEM circumvents the major restrictions of phase contrast TEM to very thin specimens and provides a signal that is more simply interpreted in terms of local composition and density. STEM has gained popularity in recent years for materials science. The extension of STEM to cryomicroscopy and tomography of cells and macromolecules is summarized herein. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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%.

Microinterferometric optical phase tomography for measuring small, asymmetric refractive-index differences in the profiles of optical fibers and fiber devices.

PubMed

Bachim, Brent L; Gaylord, Thomas K

2005-01-20

A new technique, microinterferometric optical phase tomography, is introduced for use in measuring small, asymmetric refractive-index differences in the profiles of optical fibers and fiber devices. The method combines microscopy-based fringe-field interferometry with parallel projection-based computed tomography to characterize fiber index profiles. The theory relating interference measurements to the projection set required for tomographic reconstruction is given, and discrete numerical simulations are presented for three test index profiles that establish the technique's ability to characterize fiber with small, asymmetric index differences. An experimental measurement configuration and specific interferometry and tomography practices employed in the technique are discussed.

Experimental and theoretical analysis for improved microscope design of optical projection tomographic microscopy.

PubMed

Coe, Ryan L; Seibel, Eric J

2013-09-01

We present theoretical and experimental results of axial displacement of objects relative to a fixed condenser focal plane (FP) in optical projection tomographic microscopy (OPTM). OPTM produces three-dimensional, reconstructed images of single cells from two-dimensional projections. The cell rotates in a microcapillary to acquire projections from different perspectives where the objective FP is scanned through the cell while the condenser FP remains fixed at the center of the microcapillary. This work uses a combination of experimental and theoretical methods to improve the OPTM instrument design.

Combining operando synchrotron X-ray tomographic microscopy and scanning X-ray diffraction to study lithium ion batteries

PubMed Central

Pietsch, Patrick; Hess, Michael; Ludwig, Wolfgang; Eller, Jens; Wood, Vanessa

2016-01-01

We present an operando study of a lithium ion battery combining scanning X-ray diffraction (SXRD) and synchrotron radiation X-ray tomographic microscopy (SRXTM) simultaneously for the first time. This combination of techniques facilitates the investigation of dynamic processes in lithium ion batteries containing amorphous and/or weakly attenuating active materials. While amorphous materials pose a challenge for diffraction techniques, weakly attenuating material systems pose a challenge for attenuation-contrast tomography. Furthermore, combining SXRD and SRXTM can be used to correlate processes occurring at the atomic level in the crystal lattices of the active materials with those at the scale of electrode microstructure. To demonstrate the benefits of this approach, we investigate a silicon powder electrode in lithium metal half-cell configuration. Combining SXRD and SRXTM, we are able to (i) quantify the dissolution of the metallic lithium electrode and the expansion of the silicon electrode, (ii) better understand the formation of the Li15Si4 phase, and (iii) non-invasively probe kinetic limitations within the silicon electrode. A simple model based on the 1D diffusion equation allows us to qualitatively understand the observed kinetics and demonstrates why high-capacity electrodes are more prone to inhomogeneous lithiation reactions. PMID:27324109

Combining operando synchrotron X-ray tomographic microscopy and scanning X-ray diffraction to study lithium ion batteries

NASA Astrophysics Data System (ADS)

Pietsch, Patrick; Hess, Michael; Ludwig, Wolfgang; Eller, Jens; Wood, Vanessa

2016-06-01

We present an operando study of a lithium ion battery combining scanning X-ray diffraction (SXRD) and synchrotron radiation X-ray tomographic microscopy (SRXTM) simultaneously for the first time. This combination of techniques facilitates the investigation of dynamic processes in lithium ion batteries containing amorphous and/or weakly attenuating active materials. While amorphous materials pose a challenge for diffraction techniques, weakly attenuating material systems pose a challenge for attenuation-contrast tomography. Furthermore, combining SXRD and SRXTM can be used to correlate processes occurring at the atomic level in the crystal lattices of the active materials with those at the scale of electrode microstructure. To demonstrate the benefits of this approach, we investigate a silicon powder electrode in lithium metal half-cell configuration. Combining SXRD and SRXTM, we are able to (i) quantify the dissolution of the metallic lithium electrode and the expansion of the silicon electrode, (ii) better understand the formation of the Li15Si4 phase, and (iii) non-invasively probe kinetic limitations within the silicon electrode. A simple model based on the 1D diffusion equation allows us to qualitatively understand the observed kinetics and demonstrates why high-capacity electrodes are more prone to inhomogeneous lithiation reactions.

3D "spectracoustic" system: a modular, tomographic, spectroscopic mapping imaging, non-invasive, diagnostic system for detection of small starting developing tumors like melanoma

NASA Astrophysics Data System (ADS)

Karagiannis, Georgios

2017-03-01

This work led to a new method named 3D spectracoustic tomographic mapping imaging. The current and the future work is related to the fabrication of a combined acoustic microscopy transducer and infrared illumination probe permitting the simultaneous acquisition of the spectroscopic and the tomographic information. This probe provides with the capability of high fidelity and precision registered information from the combined modalities named spectracoustic information.

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy

PubMed Central

Otón, J.; Vilas, J. L.; Kazemi, M.; Melero, R.; del Caño, L.; Cuenca, J.; Conesa, P.; Gómez-Blanco, J.; Marabini, R.; Carazo, J. M.

2017-01-01

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET). PMID:29312997

Tomographic phase analysis to detect the site of accessory conduction pathway in Wolff-Parkinson-White syndrome

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

Nakajima, K.; Bunko, H.; Tada, A.

1984-01-01

Phase analysis has been applied to Wolff-Parkinson-White syndrome (WPW) to detect the site of accessory conduction pathway (ACP); however, there was a limitation to estimate the precise location of ACP by planar phase analysis. In this study, the authors applied phase analysis to gated blood pool tomography. Twelve patients with WPW who underwent epicardial mapping and surgical division of ACP were studied by both of gated emission computed tomography (GECT) and routine gated blood pool study (GBPS). The GBPS was performed with Tc-99m red blood cells in multiple projections; modified left anterior oblique, right anterior oblique and/or left lateral views.more » In GECT, short axial, horizontal and vertical long axial blood pool images were reconstructed. Phase analysis was performed using fundamental frequency of the Fourier transform in both GECT and GBPS images, and abnormal initial contractions on both the planar and tomographic phase analysis were compared with the location of surgically confirmed ACPs. In planar phase analysis, abnormal initial phase was identified in 7 out of 12 (58%) patients, while in tomographic phase analysis, the localization of ACP was predicted in 11 out of 12 (92%) patients. Tomographic phase analysis is superior to planar phase images in 8 out of 12 patients to estimate the location of ACP. Phase analysis by GECT can avoid overlap of blood pool in cardiac chambers and has advantage to identify the propagation of phase three-dimensionally. Tomographic phase analysis is a good adjunctive method for patients with WPW to estimate the site of ACP.« less

Microscopy illumination engineering using a low-cost liquid crystal display.

PubMed

Guo, Kaikai; Bian, Zichao; Dong, Siyuan; Nanda, Pariksheet; Wang, Ying Min; Zheng, Guoan

2015-02-01

Illumination engineering is critical for obtaining high-resolution, high-quality images in microscope settings. In a typical microscope, the condenser lens provides sample illumination that is uniform and free from glare. The associated condenser diaphragm can be manually adjusted to obtain the optimal illumination numerical aperture. In this paper, we report a programmable condenser lens for active illumination control. In our prototype setup, we used a $15 liquid crystal display as a transparent spatial light modulator and placed it at the back focal plane of the condenser lens. By setting different binary patterns on the display, we can actively control the illumination and the spatial coherence of the microscope platform. We demonstrated the use of such a simple scheme for multimodal imaging, including bright-field microscopy, darkfield microscopy, phase-contrast microscopy, polarization microscopy, 3D tomographic imaging, and super-resolution Fourier ptychographic imaging. The reported illumination engineering scheme is cost-effective and compatible with most existing platforms. It enables a turnkey solution with high flexibility for researchers in various communities. From the engineering point-of-view, the reported illumination scheme may also provide new insights for the development of multimodal microscopy and Fourier ptychographic imaging.

Solid Solution Characterization in Metal by Original Tomographic Scanning Microwave Microscopy Technique

NASA Astrophysics Data System (ADS)

Bourillot, Eric; Vitry, Pauline; Optasanu, Virgil; Plassard, Cédric; Lacroute, Yvon; Montessin, Tony; Lesniewska, Eric

A general challenge in metallic components is the need for materials research to improve the service lifetime of the structural tanks or tubes subjected to harsh environments or the storage medium for the products. One major problem is the formation of lightest chemical elements bubbles or different chemical association, which can have a significant impact on the mechanical properties and structural stability of materials. The high migration mobility of these light chemical elements in solids presents a challenge for experimental characterization. Here, we present work relating to an original non-destructive, with high spatial resolution, tomographic technique based on Scanning Microwave Microscopy (SMM), which is used to visualize in-depth chemical composition of solid solution of a light chemical element in a metal. The experiments showed the capacity of SMM to detect volume. Measurements realized at different frequencies give access to a tomographic study of the sample.

X-ray tomographic microscopy analysis of the dendrite orientation transition in Al-Zn

NASA Astrophysics Data System (ADS)

Friedli, Jonathan; Fife, Julie L.; Di Napoli, Paolo; Rappaz, Michel

2012-07-01

Recently, Gonzales and Rappaz [Met. Mat. Trans. A37:2797, 2006] showed the influence of an increasing zinc content on the growth directions of aluminum dendrites. langle100rangle and langle110rangle dendrites were observed below 25wt.% and above 55wt.% zinc, respectively, whereas textured seaweeds and langle320rangle dendrites were observed at intermediate compositions. Considering the complexity of these structures, it is necessary to first characterize them in further details and second, to model them using the phase field method. The so-called Dendrite Orientation Transition (DOT) was thus reinvestigated in quenched Bridgman solidification samples. The combination of X-ray tomographic microscopy and electron backscattered diffraction (EBSD) analysis on a whole range of compositions, from 5 to 90wt.% Zn, allowed insights with unprecedented details about texture, growth directions and mechanisms of the aforementioned structures. We show that seaweeds rather than dendrites are found at all intermediate compositions. Their growth was confirmed to be constrained within a (100) symmetry plane. However, new findings indicate that the observed macroscopic texture does not necessarily correspond to the actual growth directions of the microstructure. Further, it seems to operate by an alternating growth direction mechanism and could be linked to the competition between the langle100rangle and langle110rangle characters of regular dendrites observed at the limits of the DOT. These characters, as well as 3D seaweeds, are observed in phase-field simulations of equiaxed growth and directional solidification, respectively. This study emphasizes the importance of accurate experimental data to validate numerical models and details the progress that such combinations provide for the understanding of growth mechanisms.

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

Dendritic Growth Morphologies in Al-Zn Alloys—Part I: X-ray Tomographic Microscopy

NASA Astrophysics Data System (ADS)

Friedli, Jonathan; Fife, J. L.; di Napoli, P.; Rappaz, M.

2013-12-01

Upon solidification, most metallic alloys form dendritic structures that grow along directions corresponding to low index crystal axes, e.g., directions in fcc aluminum. However, recent findings[1,2] have shown that an increase in the zinc content in Al-Zn alloys continuously changes the dendrite growth direction from to in {100} planes. At intermediate compositions, between 25 wt pct and 55 wt pct Zn, dendrites and textured seaweeds were reported. The reason for this dendrite orientation transition is that this system exhibits a large solubility of zinc, a hexagonal metal, in the primary fcc aluminum phase, thus modifying its weak solid-liquid interfacial energy anisotropy. Owing to the complexity of the phenomenology, there is still no satisfactory theory that predicts all the observed microstructures. The current study is thus aimed at better understanding the formation of these structures. This is provided by the access to their 3D morphologies via synchrotron-based X-ray tomographic microscopy of quenched Bridgman solidified specimens in combination with the determination of the crystal orientation of the dendrites by electron-backscattered diffraction. Most interestingly, all alloys with intermediate compositions were shown to grow as seaweeds, constrained to grow mostly in a (001) symmetry plane, by an alternating growth direction mechanism. Thus, these structures are far from random and are considered less hierarchically ordered than common dendrites.

Computational diffraction tomographic microscopy with transport of intensity equation using a light-emitting diode array

NASA Astrophysics Data System (ADS)

Li, Jiaji; Chen, Qian; Zhang, Jialin; Zuo, Chao

2017-10-01

Optical diffraction tomography (ODT) is an effective label-free technique for quantitatively refractive index imaging, which enables long-term monitoring of the internal three-dimensional (3D) structures and molecular composition of biological cells with minimal perturbation. However, existing optical tomographic methods generally rely on interferometric configuration for phase measurement and sophisticated mechanical systems for sample rotation or beam scanning. Thereby, the measurement is suspect to phase error coming from the coherent speckle, environmental vibrations, and mechanical error during data acquisition process. To overcome these limitations, we present a new ODT technique based on non-interferometric phase retrieval and programmable illumination emitting from a light-emitting diode (LED) array. The experimental system is built based on a traditional bright field microscope, with the light source replaced by a programmable LED array, which provides angle-variable quasi-monochromatic illumination with an angular coverage of +/-37 degrees in both x and y directions (corresponding to an illumination numerical aperture of ˜ 0.6). Transport of intensity equation (TIE) is utilized to recover the phase at different illumination angles, and the refractive index distribution is reconstructed based on the ODT framework under first Rytov approximation. The missing-cone problem in ODT is addressed by using the iterative non-negative constraint algorithm, and the misalignment of the LED array is further numerically corrected to improve the accuracy of refractive index quantification. Experiments on polystyrene beads and thick biological specimens show that the proposed approach allows accurate refractive index reconstruction while greatly reduced the system complexity and environmental sensitivity compared to conventional interferometric ODT approaches.

Hard X-ray Microscopy with sub 30 nm Spatial Resolution

NASA Astrophysics Data System (ADS)

Tang, Mau-Tsu; Song, Yen-Fang; Yin, Gung-Chian; Chen, Fu-Rong; Chen, Jian-Hua; Chen, Yi-Ming; Liang, Keng S.; Duewer, F.; Yun, Wenbing

2007-01-01

A transmission X-ray microscope (TXM) has been installed at the BL01B beamline at National Synchrotron Radiation Research Center in Taiwan. This state-of-the-art TXM operational in a range 8-11 keV provides 2D images and 3D tomography with spatial resolution 60 nm, and with the Zernike-phase contrast mode for imaging light materials such as biological specimens. A spatial resolution of the TXM better than 30 nm, apparently the best result in hard X-ray microscopy, has been achieved by employing the third diffraction order of the objective zone plate. The TXM has been applied in diverse research fields, including analysis of failure mechanisms in microelectronic devices, tomographic structures of naturally grown photonic specimens, and the internal structure of fault zone gouges from an earthquake core. Here we discuss the scope and prospects of the project, and the progress of the TXM in NSRRC.

The study of documentary photographs of the early 20th century by the optical coherence microscopy method

NASA Astrophysics Data System (ADS)

Ryseva, Ekaterina; Zhukova, Ekaterina

2013-05-01

The wide field and spectral methods of optical coherence microscopy were used for extensive studying the photographs printed in the early 20th century. Tomographic images (B-scans) of photo and paper materials are presented and discussed.

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

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

Kulawik, K., E-mail: kulawik@agh.edu.pl; Buffat, P.A., E-mail: philippe.buffat@epfl.ch; Ecole Polytechnique Fédérale de Lausanne, CIME, Station 12, CH-1015 Lausanne Switzerland

Microstructural characterization of Inconel 718 superalloy after three different heat treatment variants was performed by electron microscopy and electron tomography techniques, taking advantage of recent development in quantitative electron microscopy. Distribution maps of the chemical elements, collected by ChemiSTEM™ EDX system, offer a clear contrast between γ′, γ″, and the γ matrix. It was found that the γ′ phase contains mainly Ni, Al, and Ti, while the γ″ phase contains Ni, Nb, and Ti. Thus application of the Al and Nb STEM–EDX elemental maps enables identification and size measurements of γ′ and γ″ nanoparticles. 3D morphology of γ′ and γ″more » precipitates was examined by electron microscopy and FIB–SEM tomography. Employed methods revealed that in all three heat treatment variants the γ′ particles are almost spheroidal while the γ″ precipitates are mainly elongated-disc shaped. However, the precipitate sizes differed for each variant contributing to differences in the yield strength. Tomographic images were used for estimation of the volume fraction of the both strengthening phases. - Highlights: • ChemiSTEM™ EDX elemental maps bring a fast mean to differentiate γ′ and γ″ particles. • Such maps enable for the explicit size measurements of γ′ and γ″ nanoparticles. • Explicit γ′ and γ″ phases total volume fraction was measured employing FIB–SEM. • γ′/γ″ co-precipitates and sandwich-like γ′/γ″/γ′ particles were present. • HRSTEM-HAADF imaging revealed atomic columns of the γ′/γ″ co-precipitates.« less

Rapid, low dose X-ray diffractive imaging of the malaria parasite Plasmodium falciparum.

PubMed

Jones, Michael W M; Dearnley, Megan K; van Riessen, Grant A; Abbey, Brian; Putkunz, Corey T; Junker, Mark D; Vine, David J; McNulty, Ian; Nugent, Keith A; Peele, Andrew G; Tilley, Leann

2014-08-01

Phase-diverse X-ray coherent diffractive imaging (CDI) provides a route to high sensitivity and spatial resolution with moderate radiation dose. It also provides a robust solution to the well-known phase-problem, making on-line image reconstruction feasible. Here we apply phase-diverse CDI to a cellular sample, obtaining images of an erythrocyte infected by the sexual stage of the malaria parasite, Plasmodium falciparum, with a radiation dose significantly lower than the lowest dose previously reported for cellular imaging using CDI. The high sensitivity and resolution allow key biological features to be identified within intact cells, providing complementary information to optical and electron microscopy. This high throughput method could be used for fast tomographic imaging, or to generate multiple replicates in two-dimensions of hydrated biological systems without freezing or fixing. This work demonstrates that phase-diverse CDI is a valuable complementary imaging method for the biological sciences and ready for immediate application. © 2013 Elsevier B.V. All rights reserved.

Solving the inverse scattering problem in reflection-mode dynamic speckle-field phase microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhou, Renjie; So, Peter T. C.; Yaqoob, Zahid; Jin, Di; Hosseini, Poorya; Kuang, Cuifang; Singh, Vijay Raj; Kim, Yang-Hyo; Dasari, Ramachandra R.

2017-02-01

Most of the quantitative phase microscopy systems are unable to provide depth-resolved information for measuring complex biological structures. Optical diffraction tomography provides a non-trivial solution to it by 3D reconstructing the object with multiple measurements through different ways of realization. Previously, our lab developed a reflection-mode dynamic speckle-field phase microscopy (DSPM) technique, which can be used to perform depth resolved measurements in a single shot. Thus, this system is suitable for measuring dynamics in a layer of interest in the sample. DSPM can be also used for tomographic imaging, which promises to solve the long-existing "missing cone" problem in 3D imaging. However, the 3D imaging theory for this type of system has not been developed in the literature. Recently, we have developed an inverse scattering model to rigorously describe the imaging physics in DSPM. Our model is based on the diffraction tomography theory and the speckle statistics. Using our model, we first precisely calculated the defocus response and the depth resolution in our system. Then, we further calculated the 3D coherence transfer function to link the 3D object structural information with the axially scanned imaging data. From this transfer function, we found that in the reflection mode excellent sectioning effect exists in the low lateral spatial frequency region, thus allowing us to solve the "missing cone" problem. Currently, we are working on using this coherence transfer function to reconstruct layered structures and complex cells.

Tomographic imaging of transparent biological samples using the pyramid phase microscope

PubMed Central

Iglesias, Ignacio

2016-01-01

We show how a pyramid phase microscope can be used to obtain tomographic information of the spatial variation of refractive index in biological samples using the Radon transform. A method that uses the information provided by the phase microscope for axial and lateral repositioning of the sample when it rotates is also described. Its application to the reconstruction of mouse embryos in the blastocyst stage is demonstrated. PMID:27570696

Hard x-ray phase contrastmicroscopy - techniques and applications

NASA Astrophysics Data System (ADS)

Holzner, Christian

In 1918, Einstein provided the first description of the nature of the refractive index for X-rays, showing that phase contrast effects are significant. A century later, most x-ray microscopy and nearly all medical imaging remains based on absorption contrast, even though phase contrast offers orders of magnitude improvements in contrast and reduced radiation exposure at multi-keV x-ray energies. The work presented is concerned with developing practical and quantitative methods of phase contrast for x-ray microscopy. A theoretical framework for imaging in phase contrast is put forward; this is used to obtain quantitative images in a scanning microscope using a segmented detector, and to correct for artifacts in a commercial phase contrast x-ray nano-tomography system. The principle of reciprocity between scanning and full-field microscopes is then used to arrive at a novel solution: Zernike contrast in a scanning microscope. These approaches are compared on a theoretical and experimental basis in direct connection with applications using multi-keV x-ray microscopes at the Advanced Photon Source at Argonne National Laboratory. Phase contrast provides the best means to image mass and ultrastructure of light elements that mainly constitute biological matter, while stimulated x-ray fluorescence provides high sensitivity for studies of the distribution of heavier trace elements, such as metals. These approaches are combined in a complementary way to yield quantitative maps of elemental concentration from 2D images, with elements placed in their ultrastructural context. The combination of x-ray fluorescence and phase contrast poses an ideal match for routine, high resolution tomographic imaging of biological samples in the future. The presented techniques and demonstration experiments will help pave the way for this development.

Data-processing strategies for nano-tomography with elemental specification

NASA Astrophysics Data System (ADS)

Liu, Yijin; Cats, Korneel H.; Nelson Weker, Johanna; Andrews, Joy C.; Weckhuysen, Bert M.; Pianetta, Piero

2013-10-01

Combining the energy tunability provided by synchrotron X-ray sources with transmission X-ray microscopy, the morphology of materials can be resolved in 3D at spatial resolution down to 30 nm with elemental/chemical specification. In order to study the energy dependence of the absorption coefficient over the investigated volume, the tomographic reconstruction and image registration (before and/or after the tomographic reconstruction) are critical. We show in this paper the comparison of two different data processing strategies and conclude that the signal to noise ratio (S/N) in the final result can be improved via performing tomographic reconstruction prior to the evaluation of energy dependence. Our result echoes the dose fractionation theorem, and is particularly helpful when the element of interest has low concentration.

Imaging cells and sub-cellular structures with ultrahigh resolution full-field X-ray microscopy.

PubMed

Chien, C C; Tseng, P Y; Chen, H H; Hua, T E; Chen, S T; Chen, Y Y; Leng, W H; Wang, C H; Hwu, Y; Yin, G C; Liang, K S; Chen, F R; Chu, Y S; Yeh, H I; Yang, Y C; Yang, C S; Zhang, G L; Je, J H; Margaritondo, G

2013-01-01

Our experimental results demonstrate that full-field hard-X-ray microscopy is finally able to investigate the internal structure of cells in tissues. This result was made possible by three main factors: the use of a coherent (synchrotron) source of X-rays, the exploitation of contrast mechanisms based on the real part of the refractive index and the magnification provided by high-resolution Fresnel zone-plate objectives. We specifically obtained high-quality microradiographs of human and mouse cells with 29 nm Rayleigh spatial resolution and verified that tomographic reconstruction could be implemented with a final resolution level suitable for subcellular features. We also demonstrated that a phase retrieval method based on a wave propagation algorithm could yield good subcellular images starting from a series of defocused microradiographs. The concluding discussion compares cellular and subcellular hard-X-ray microradiology with other techniques and evaluates its potential impact on biomedical research. Copyright © 2012 Elsevier Inc. All rights reserved.

Partially coherent lensfree tomographic microscopy⋄

PubMed Central

Isikman, Serhan O.; Bishara, Waheb; Ozcan, Aydogan

2012-01-01

Optical sectioning of biological specimens provides detailed volumetric information regarding their internal structure. To provide a complementary approach to existing three-dimensional (3D) microscopy modalities, we have recently demonstrated lensfree optical tomography that offers high-throughput imaging within a compact and simple platform. In this approach, in-line holograms of objects at different angles of partially coherent illumination are recorded using a digital sensor-array, which enables computing pixel super-resolved tomographic images of the specimen. This imaging modality, which forms the focus of this review, offers micrometer-scale 3D resolution over large imaging volumes of, for example, 10–15 mm3, and can be assembled in light weight and compact architectures. Therefore, lensfree optical tomography might be particularly useful for lab-on-a-chip applications as well as for microscopy needs in resource-limited settings. PMID:22193016

Lensfree On-Chip Microscopy and Tomography for Bio-Medical Applications

PubMed Central

Isikman, Serhan O.; Bishara, Waheb; Mudanyali, Onur; Sencan, Ikbal; Su, Ting-Wei; Tseng, Derek; Yaglidere, Oguzhan; Sikora, Uzair; Ozcan, Aydogan

2012-01-01

Lensfree on-chip holographic microscopy is an emerging technique that offers imaging of biological specimens over a large field-of-view without using any lenses or bulky optical components. Lending itself to a compact, cost-effective and mechanically robust architecture, lensfree on-chip holographic microscopy can offer an alternative toolset addressing some of the emerging needs of microscopic analysis and diagnostics in low-resource settings, especially for telemedicine applications. In this review, we summarize the latest achievements in lensfree optical microscopy based on partially coherent on-chip holography, including portable telemedicine microscopy, cell-phone based microscopy and field-portable optical tomographic microscopy. We also discuss some of the future directions for telemedicine microscopy and its prospects to help combat various global health challenges. PMID:24478572

Advantages of phase retrieval for fast x-ray tomographic microscopy

NASA Astrophysics Data System (ADS)

Mokso, R.; Marone, F.; Irvine, S.; Nyvlt, M.; Schwyn, D.; Mader, K.; Taylor, G. K.; Krapp, H. G.; Skeren, M.; Stampanoni, M.

2013-12-01

In near-field imaging with partially coherent x-rays, the phase shifting properties of the sample are encoded in the diffraction fringes that appear as an additional intensity modulation in the x-ray projection images. These Fresnel fringes are often regarded as purely an enhancement of the visibility at the interfaces. We show that retrieving the phase information contained in these patterns significantly advances the developments in fast micro-tomography. Improving temporal resolution without intensifying radiation damage implies a shortening of the exposure time rather than increasing the photon flux on the sample. Phase retrieval, to a large extent, compensates the consequent photon count moderation in the images, by fully exploiting the stronger refraction effect as compared with absorption. Two single-distance phase retrieval methods are evaluated for the case of an in situ 3 Hz micro-tomography of a rapidly evolving liquid foam, and an in vivo 6 Hz micro-tomography of a blowfly. A new dual-detector setup is introduced for simultaneous acquisition of two near-field diffraction patterns. Our goal is to couple high temporal, spatial and density resolution in a single imaging system in a dose-efficient manner, opening further options for dynamic four-dimensional studies.

Linear information retrieval method in X-ray grating-based phase contrast imaging and its interchangeability with tomographic reconstruction

NASA Astrophysics Data System (ADS)

Wu, Z.; Gao, K.; Wang, Z. L.; Shao, Q. G.; Hu, R. F.; Wei, C. X.; Zan, G. B.; Wali, F.; Luo, R. H.; Zhu, P. P.; Tian, Y. C.

2017-06-01

In X-ray grating-based phase contrast imaging, information retrieval is necessary for quantitative research, especially for phase tomography. However, numerous and repetitive processes have to be performed for tomographic reconstruction. In this paper, we report a novel information retrieval method, which enables retrieving phase and absorption information by means of a linear combination of two mutually conjugate images. Thanks to the distributive law of the multiplication as well as the commutative law and associative law of the addition, the information retrieval can be performed after tomographic reconstruction, thus simplifying the information retrieval procedure dramatically. The theoretical model of this method is established in both parallel beam geometry for Talbot interferometer and fan beam geometry for Talbot-Lau interferometer. Numerical experiments are also performed to confirm the feasibility and validity of the proposed method. In addition, we discuss its possibility in cone beam geometry and its advantages compared with other methods. Moreover, this method can also be employed in other differential phase contrast imaging methods, such as diffraction enhanced imaging, non-interferometric imaging, and edge illumination.

Measurement of ciliary beat frequency using Doppler optical coherence tomography.

PubMed

Lemieux, Bryan T; Chen, Jason J; Jing, Joseph; Chen, Zhongping; Wong, Brian J F

2015-11-01

Measuring ciliary beat frequency (CBF) is a technical challenge and difficult to perform in vivo. Doppler optical coherence tomography (D-OCT) is a mesoscopic noncontact imaging modality that provides high-resolution tomographic images and detects micromotion simultaneously in living tissues. In this work we used D-OCT to measure CBF in ex vivo tissue as the first step toward translating this technology to clinical use. Fresh ex vivo samples of rabbit tracheal mucosa were imaged using both D-OCT and phase-contrast microscopy (n = 5). The D-OCT system was designed and built to specification in our lab (1310-nm swept source vertical-cavity surface-emitting laser [VCSEL], 6-μm axial resolution). The samples were placed in culture and incubated at 37°C. A fast Fourier transform was performed on the D-OCT signal recorded on the surface of the samples to gauge CBF. High-speed digital video of the epithelium recorded via phase-contrast microscopy was analyzed to confirm the CBF measurements. The D-OCT system detected Doppler signal at the epithelial layer of ex vivo rabbit tracheal samples suggestive of ciliary motion. CBF was measured at 9.36 ± 1.22 Hz using D-OCT and 9.08 ± 0.48 Hz using phase-contrast microscopy. No significant differences were found between the 2 methods (p > 0.05). D-OCT allows for the quantitative measurement of CBF without the need to resolve individual cilia. Furthermore, D-OCT technology can be incorporated into endoscopic platforms that allow clinicians to readily measure CBF in the office and provide a direct measurement of mucosal health. © 2015 ARS-AAOA, LLC.

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

PubMed

Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

2016-10-14

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.

Tomographic imaging of subducted lithosphere below northwest Pacific island arcs

USGS Publications Warehouse

Van Der Hilst, R.; Engdahl, R.; Spakman, W.; Nolet, G.

1991-01-01

The seismic tomography problem does not have a unique solution, and published tomographic images have been equivocal with regard to the deep structure of subducting slabs. An improved tomographic method, using a more realistic background Earth model and surf ace-reflected as well as direct seismic phases, shows that slabs beneath the Japan and Izu Bonin island arcs are deflected at the boundary between upper and lower mantle, whereas those beneath the northern Kuril and Mariana arcs sink into the lower mantle.

Phase contrast imaging of cochlear soft tissue.

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

Smith, S.; Hwang, M.; Rau, C.

A noninvasive technique to image soft tissue could expedite diagnosis and disease management in the auditory system. We propose inline phase contrast imaging with hard X-rays as a novel method that overcomes the limitations of conventional absorption radiography for imaging soft tissue. In this study, phase contrast imaging of mouse cochleae was performed at the Argonne National Laboratory Advanced Photon Source. The phase contrast tomographic reconstructions show soft tissue structures of the cochlea, including the inner pillar cells, the inner spiral sulcus, the tectorial membrane, the basilar membrane, and the Reissner's membrane. The results suggest that phase contrast X-ray imagingmore » and tomographic techniques hold promise to noninvasively image cochlear structures at an unprecedented cellular level.« less

Multi-color phase imaging and sickle cell anemia (Conference Presentation)

NASA Astrophysics Data System (ADS)

Hosseini, Poorya; Zhou, Renjie; Yaqoob, Zahid; So, Peter T. C.

2016-03-01

Quantitative phase measurements at multiple wavelengths has created an opportunity for exploring new avenues in phase microscopy such as enhancing imaging-depth (1), measuring hemoglobin concentrations in erythrocytes (2), and more recently in tomographic mapping of the refractive index of live cells (3). To this end, quantitative phase imaging has been demonstrated both at few selected spectral points as well as with high spectral resolution (4,5). However, most of these developed techniques compromise imaging speed, field of view, or the spectral resolution to perform interferometric measurements at multiple colors. In the specific application of quantitative phase in studying blood diseases and red blood cells, current techniques lack the required sensitivity to quantify biological properties of interest at individual cell level. Recently, we have set out to develop a stable quantitative interferometric microscope allowing for measurements of such properties for red cells without compromising field of view or speed of the measurements. The feasibility of the approach will be initially demonstrated in measuring dispersion curves of known solutions, followed by measuring biological properties of red cells in sickle cell anemia. References: 1. Mann CJ, Bingham PR, Paquit VC, Tobin KW. Quantitative phase imaging by three-wavelength digital holography. Opt Express. 2008;16(13):9753-64. 2. Park Y, Yamauchi T, Choi W, Dasari R, Feld MS. Spectroscopic phase microscopy for quantifying hemoglobin concentrations in intact red blood cells. Opt Lett. 2009;34(23):3668-70. 3. Hosseini P, Sung Y, Choi Y, Lue N, Yaqoob Z, So P. Scanning color optical tomography (SCOT). Opt Express. 2015;23(15):19752-62. 4. Jung J-H, Jang J, Park Y. Spectro-refractometry of individual microscopic objects using swept-source quantitative phase imaging. Anal Chem. 2013;85(21):10519-25. 5. Rinehart M, Zhu Y, Wax A. Quantitative phase spectroscopy. Biomed Opt Express. 2012;3(5):958-65.

Tomographic brain imaging with nucleolar detail and automatic cell counting

NASA Astrophysics Data System (ADS)

Hieber, Simone E.; Bikis, Christos; Khimchenko, Anna; Schweighauser, Gabriel; Hench, Jürgen; Chicherova, Natalia; Schulz, Georg; Müller, Bert

2016-09-01

Brain tissue evaluation is essential for gaining in-depth insight into its diseases and disorders. Imaging the human brain in three dimensions has always been a challenge on the cell level. In vivo methods lack spatial resolution, and optical microscopy has a limited penetration depth. Herein, we show that hard X-ray phase tomography can visualise a volume of up to 43 mm3 of human post mortem or biopsy brain samples, by demonstrating the method on the cerebellum. We automatically identified 5,000 Purkinje cells with an error of less than 5% at their layer and determined the local surface density to 165 cells per mm2 on average. Moreover, we highlight that three-dimensional data allows for the segmentation of sub-cellular structures, including dendritic tree and Purkinje cell nucleoli, without dedicated staining. The method suggests that automatic cell feature quantification of human tissues is feasible in phase tomograms obtained with isotropic resolution in a label-free manner.

Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM

PubMed Central

Kishchenko, Gregory P.; Danev, Radostin; Fisher, Rebecca; He, Jie; Hsieh, Chyongere; Marko, Michael; Sui, Haixin

2015-01-01

Zernike phase-plate (ZPP) imaging greatly increases contrast in cryo-electron microscopy, however fringe artifacts appear in the images. A computational de-fringing method has been proposed, but it has not been widely employed, perhaps because the importance of de-fringing has not been clearly demonstrated. For testing purposes, we employed Zernike phase-plate imaging in a cryo-electron tomographic study of radial-spoke complexes attached to microtubule doublets. We found that the contrast enhancement by ZPP imaging made nonlinear denoising insensitive to the filtering parameters, such that simple low-frequency band-pass filtering made the same improvement in map quality. We employed sub-tomogram averaging, which compensates for the effect of the “missing wedge” and considerably improves map quality. We found that fringes (caused by the abrupt cut-on of the central hole in the phase plate) can lead to incorrect representation of a structure that is well-known from the literature. The expected structure was restored by amplitude scaling, as proposed in the literature. Our results show that de-fringing is an important part of image-processing for cryo-electron tomography of macromolecular complexes with ZPP imaging. PMID:26210582

Cryotomography x-ray microscopy state

DOEpatents

Le Gros, Mark; Larabell, Carolyn A.

2010-10-26

An x-ray microscope stage enables alignment of a sample about a rotation axis to enable three dimensional tomographic imaging of the sample using an x-ray microscope. A heat exchanger assembly provides cooled gas to a sample during x-ray microscopic imaging.

Current developments in clinical multiphoton tomography

NASA Astrophysics Data System (ADS)

König, Karsten; Weinigel, Martin; Breunig, Hans Georg; Gregory, Axel; Fischer, Peter; Kellner-Höfer, Marcel; Bückle, Rainer

2010-02-01

Two-photon microscopy has been introduced in 1990 [1]. 13 years later, CE-marked clinical multiphoton systems for 3D imaging of human skin with subcellular resolution have been launched by the JenLab company with the tomograph DermaInspectTM. In 2010, the second generation of clinical multiphoton tomographs was introduced. The novel mobile multiphoton tomograph MPTflexTM, equipped with a flexible articulated optical arm, provides an increased flexibility and accessibility especially for clinical and cosmetical examinations. The multiphoton excitation of fluorescent biomolecules like NAD(P)H, flavins, porphyrins, elastin, and melanin as well as the second harmonic generation of collagen is induced by picojoule femtosecond laser pulses from an tunable turn-key near infrared laser system. The ability for rapid highquality image acquisition, the user-friendly operation of the system, and the compact and flexible design qualifies this system to be used for melanoma detection, diagnostics of dermatological disorders, cosmetic research, and skin aging measurements as well as in situ drug monitoring and animal research. So far, more than 1,000 patients and volunteers have been investigated with the multiphoton tomographs in Europe, Asia, and Australia.

Computational modeling of optical projection tomographic microscopy using the finite difference time domain method.

PubMed

Coe, Ryan L; Seibel, Eric J

2012-12-01

We present a method for modeling image formation in optical projection tomographic microscopy (OPTM) using high numerical aperture (NA) condensers and objectives. Similar to techniques used in computed tomography, OPTM produces three-dimensional, reconstructed images of single cells from two-dimensional projections. The model is capable of simulating axial scanning of a microscope objective to produce projections, which are reconstructed using filtered backprojection. Simulation of optical scattering in transmission optical microscopy is designed to analyze all aspects of OPTM image formation, such as degree of specimen staining, refractive-index matching, and objective scanning. In this preliminary work, a set of simulations is performed to examine the effect of changing the condenser NA, objective scan range, and complex refractive index on the final reconstruction of a microshell with an outer radius of 1.5 μm and an inner radius of 0.9 μm. The model lays the groundwork for optimizing OPTM imaging parameters and triaging efforts to further improve the overall system design. As the model is expanded in the future, it will be used to simulate a more realistic cell, which could lead to even greater impact.

Longitudinal phase space tomography using a booster cavity at PITZ

NASA Astrophysics Data System (ADS)

Malyutin, D.; Gross, M.; Isaev, I.; Khojoyan, M.; Kourkafas, G.; Krasilnikov, M.; Marchetti, B.; Otevrel, M.; Stephan, F.; Vashchenko, G.

2017-11-01

The knowledge of the longitudinal phase space (LPS) of electron beams is of great importance for optimizing the performance of high brightness photo injectors. To get the longitudinal phase space of an electron bunch in a linear accelerator a tomographic technique can be used. The method is based on measurements of the bunch momentum spectra while varying the bunch energy chirp. The energy chirp can be varied by one of the RF accelerating structures in the accelerator and the resulting momentum distribution can be measured with a dipole spectrometer further downstream. As a result, the longitudinal phase space can be reconstructed. Application of the tomographic technique for reconstruction of the longitudinal phase space is introduced in detail in this paper. Measurement results from the PITZ facility are shown and analyzed.

Electron Microscopy Imaging of Zinc Soaps Nucleation in Oil Paint.

PubMed

Hermans, Joen; Osmond, Gillian; van Loon, Annelies; Iedema, Piet; Chapman, Robyn; Drennan, John; Jack, Kevin; Rasch, Ronald; Morgan, Garry; Zhang, Zhi; Monteiro, Michael; Keune, Katrien

2018-06-04

Using the recently developed techniques of electron tomography, we have explored the first stages of disfiguring formation of zinc soaps in modern oil paintings. The formation of complexes of zinc ions with fatty acids in paint layers is a major threat to the stability and appearance of many late 19th and early 20th century oil paintings. Moreover, the occurrence of zinc soaps in oil paintings leading to defects is disturbingly common, but the chemical reactions and migration mechanisms leading to large zinc soap aggregates or zones remain poorly understood. State-of-the-art scanning (SEM) and transmission (TEM) electron microscopy techniques, primarily developed for biological specimens, have enabled us to visualize the earliest stages of crystalline zinc soap growth in a reconstructed zinc white (ZnO) oil paint sample. In situ sectioning techniques and sequential imaging within the SEM allowed three-dimensional tomographic reconstruction of sample morphology. Improvements in the detection and discrimination of backscattered electrons enabled us to identify local precipitation processes with small atomic number contrast. The SEM images were correlated to low-dose and high-sensitivity TEM images, with high-resolution tomography providing unprecedented insight into the structure of nucleating zinc soaps at the molecular level. The correlative approach applied here to study phase separation, and crystallization processes specific to a problem in art conservation creates possibilities for visualization of phase formation in a wide range of soft materials.

Influence of the limited detector size on spatial variations of the reconstruction accuracy in holographic tomography

NASA Astrophysics Data System (ADS)

Kostencka, Julianna; Kozacki, Tomasz; Hennelly, Bryan; Sheridan, John T.

2017-06-01

Holographic tomography (HT) allows noninvasive, quantitative, 3D imaging of transparent microobjects, such as living biological cells and fiber optics elements. The technique is based on acquisition of multiple scattered fields for various sample perspectives using digital holographic microscopy. Then, the captured data is processed with one of the tomographic reconstruction algorithms, which enables 3D reconstruction of refractive index distribution. In our recent works we addressed the issue of spatially variant accuracy of the HT reconstructions, which results from the insufficient model of diffraction that is applied in the widely-used tomographic reconstruction algorithms basing on the Rytov approximation. In the present study, we continue investigating the spatially variant properties of the HT imaging, however, we are now focusing on the limited spatial size of holograms as a source of this problem. Using the Wigner distribution representation and the Ewald sphere approach, we show that the limited size of the holograms results in a decreased quality of tomographic imaging in off-center regions of the HT reconstructions. This is because the finite detector extent becomes a limiting aperture that prohibits acquisition of full information about diffracted fields coming from the out-of-focus structures of a sample. The incompleteness of the data results in an effective truncation of the tomographic transfer function for the out-of-center regions of the tomographic image. In this paper, the described effect is quantitatively characterized for three types of the tomographic systems: the configuration with 1) object rotation, 2) scanning of the illumination direction, 3) the hybrid HT solution combing both previous approaches.

The role of upper mantle mineral phase transitions on the current structure of large-scale Earth's mantle convection.

NASA Astrophysics Data System (ADS)

Thoraval, C.

2017-12-01

Describing the large-scale structures of mantle convection and quantifying the mass transfer between upper and lower mantle request to account for the role played by mineral phase transitions in the transition zone. We build a density distribution within the Earth mantle from velocity anomalies described by global seismic tomographic models. The density distribution includes thermal anomalies and topographies of the phase transitions at depths of 410 and 660 km. We compute the flow driven by this density distribution using a 3D spherical circulation model, which account for depth-dependent viscosity. The dynamic topographies at the surface and at the CMB and the geoid are calculated as well. Within the range of viscosity profiles allowing for a satisfying restitution of the long wavelength geoid, we perform a parametric study to decipher the role of the characteristics of phase diagrams - mainly the Clapeyron's slopes - and of the kinetics of phase transitions, which may modify phase transition topographies. Indeed, when a phase transition is delayed, the boundary between two mineral phases is both dragged by the flow and interfere with it. The results are compared to recent estimations of surface dynamic topography and to the phase transition topographies as revealed by seismic studies. The consequences are then discussed in terms of structure of mantle flow. Comparisons between various tomographic models allow us to enlighten the most robust features. At last, the role played by the phase transitions on the lateral variations of mass transfer between upper and lower mantle are quantified by comparison to cases with no phase transitions and confronted to regional tomographic models, which reflect the variability of the behaviors of the descending slabs in the transition zone.

Tomographic flow cytometry assisted by intelligent wavefronts analysis

NASA Astrophysics Data System (ADS)

Merola, F.; Memmolo, P.; Miccio, L.; Mugnano, M.; Ferraro, P.

2017-06-01

High-throughput single-cell analysis is a challenging target for implementing advanced biomedical applications. An excellent candidate for this aim is label-free tomographic phase microscopy. However, in-line tomography is very difficult to be implemented in practice, as it requires complex setup for rotating the sample and/or illuminate the cell along numerous directions [1]. We exploit random rolling of cells while they are flowing along a microfluidic channel demonstrating that it is possible to obtain in-line phase-contrast tomography by adopting strategies for intelligent wavefronts analysis thus obtaining complete retrieval of both 3D-position and orientation of rotating cells [2]. Thus, by numerical wavefront analysis a-priori knowledge of such information is no longer needed. This approach makes continuos-flow cyto-tomography suitable for practical operation in real-world, single-cell analysis and with substantial simplification of the optical system avoiding any mechanical/optical scanning of light source. Demonstration is given for different classes of biosamples, red-blood-cells (RBCs), diatom algae and fibroblast cells [3]. Accurate characterization of each type of cells is reported despite their very different nature and materials content, thus showing the proposed method can be extended, by adopting two alternate strategies of wavefront-analysis, to many classes of cells. In particular, for RBCs we furnish important parameters as 3D morphology, Corpuscular Hemoglobin (CH), Volume (V), and refractive index (RI) for each single cell in the total population [3]. This could open a new route in blood disease diagnosis, for example for the isolation and characterization of "foreign" cells in the blood stream, the so called Circulating Tumor Cells (CTC), early manifestation of metastasis.

High-Resolution Phase-Contrast Imaging of Submicron Particles in Unstained Lung Tissue

NASA Astrophysics Data System (ADS)

Schittny, J. C.; Barré, S. F.; Mokso, R.; Haberthür, D.; Semmler-Behnke, M.; Kreyling, W. G.; Tsuda, A.; Stampanoni, M.

2011-09-01

To access the risks and chances of deposition of submicron particles in the gas-exchange area of the lung, a precise three-dimensional (3D)-localization of the sites of deposition is essential—especially because local peaks of deposition are expected in the acinar tree and in individual alveoli. In this study we developed the workflow for such an investigation. We administered 200-nm gold particles to young adult rats by intratracheal instillation. After fixation and paraffin embedding, their lungs were imaged unstained using synchrotron radiation x-ray tomographic microscopy (SRXTM) at the beamline TOMCAT (Swiss Light Source, Villigen, Switzerland) at sample detector distances of 2.5 mm (absorption contrast) and of 52.5 mm (phase contrast). A segmentation based on a global threshold of grey levels was successfully done on absorption-contrast images for the gold and on the phase-contrast images for the tissue. The smallest spots containing gold possessed a size of 1-2 voxels of 370-nm side length. We conclude that a combination of phase and absorption contrast SRXTM imaging is necessary to obtain the correct segmentation of both tissue and gold particles. This method will be used for the 3D localization of deposited particles in the gas-exchange area of the lung.

Preparation of nanowire specimens for laser-assisted atom probe tomography

NASA Astrophysics Data System (ADS)

Blumtritt, H.; Isheim, D.; Senz, S.; Seidman, D. N.; Moutanabbir, O.

2014-10-01

The availability of reliable and well-engineered commercial instruments and data analysis software has led to development in recent years of robust and ergonomic atom-probe tomographs. Indeed, atom-probe tomography (APT) is now being applied to a broader range of materials classes that involve highly important scientific and technological problems in materials science and engineering. Dual-beam focused-ion beam microscopy and its application to the fabrication of APT microtip specimens have dramatically improved the ability to probe a variety of systems. However, the sample preparation is still challenging especially for emerging nanomaterials such as epitaxial nanowires which typically grow vertically on a substrate through metal-catalyzed vapor phase epitaxy. The size, morphology, density, and sensitivity to radiation damage are the most influential parameters in the preparation of nanowire specimens for APT. In this paper, we describe a step-by-step process methodology to allow a precisely controlled, damage-free transfer of individual, short silicon nanowires onto atom probe microposts. Starting with a dense array of tiny nanowires and using focused ion beam, we employed a sequence of protective layers and markers to identify the nanowire to be transferred and probed while protecting it against Ga ions during lift-off processing and tip sharpening. Based on this approach, high-quality three-dimensional atom-by-atom maps of single aluminum-catalyzed silicon nanowires are obtained using a highly focused ultraviolet laser-assisted local electrode atom probe tomograph.

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.

X-ray tomographic image magnification process, system and apparatus therefor

DOEpatents

Kinney, J.H.; Bonse, U.K.; Johnson, Q.C.; Nichols, M.C.; Saroyan, R.A.; Massey, W.N.; Nusshardt, R.

1993-09-14

A computerized three-dimensional x-ray tomographic microscopy system is disclosed, comprising: (a) source means for providing a source of parallel x-ray beams, (b) staging means for staging and sequentially rotating a sample to be positioned in the path of the (c) x-ray image magnifier means positioned in the path of the beams downstream from the sample, (d) detecting means for detecting the beams after being passed through and magnified by the image magnifier means, and (e) computing means for analyzing values received from the detecting means, and converting the values into three-dimensional representations. Also disclosed is a process for magnifying an x-ray image, and apparatus therefor. 25 figures.

X-ray tomographic image magnification process, system and apparatus therefor

DOEpatents

Kinney, John H.; Bonse, Ulrich K.; Johnson, Quintin C.; Nichols, Monte C.; Saroyan, Ralph A.; Massey, Warren N.; Nusshardt, Rudolph

1993-01-01

A computerized three-dimensional x-ray tomographic microscopy system is disclosed, comprising: a) source means for providing a source of parallel x-ray beams, b) staging means for staging and sequentially rotating a sample to be positioned in the path of the c) x-ray image magnifier means positioned in the path of the beams downstream from the sample, d) detecting means for detecting the beams after being passed through and magnified by the image magnifier means, and e) computing means for analyzing values received from the detecting means, and converting the values into three-dimensional representations. Also disclosed is a process for magnifying an x-ray image, and apparatus therefor.

3D Printing of Plant Golgi Stacks from Their Electron Tomographic Models.

PubMed

Mai, Keith Ka Ki; Kang, Madison J; Kang, Byung-Ho

2017-01-01

Three-dimensional (3D) printing is an effective tool for preparing tangible 3D models from computer visualizations to assist in scientific research and education. With the recent popularization of 3D printing processes, it is now possible for individual laboratories to convert their scientific data into a physical form suitable for presentation or teaching purposes. Electron tomography is an electron microscopy method by which 3D structures of subcellular organelles or macromolecular complexes are determined at nanometer-level resolutions. Electron tomography analyses have revealed the convoluted membrane architectures of Golgi stacks, chloroplasts, and mitochondria. But the intricacy of their 3D organizations is difficult to grasp from tomographic models illustrated on computer screens. Despite the rapid development of 3D printing technologies, production of organelle models based on experimental data with 3D printing has rarely been documented. In this chapter, we present a simple guide to creating 3D prints of electron tomographic models of plant Golgi stacks using the two most accessible 3D printing technologies.

Developing a denoising filter for electron microscopy and tomography data in the cloud.

PubMed

Starosolski, Zbigniew; Szczepanski, Marek; Wahle, Manuel; Rusu, Mirabela; Wriggers, Willy

2012-09-01

The low radiation conditions and the predominantly phase-object image formation of cryo-electron microscopy (cryo-EM) result in extremely high noise levels and low contrast in the recorded micrographs. The process of single particle or tomographic 3D reconstruction does not completely eliminate this noise and is even capable of introducing new sources of noise during alignment or when correcting for instrument parameters. The recently developed Digital Paths Supervised Variance (DPSV) denoising filter uses local variance information to control regional noise in a robust and adaptive manner. The performance of the DPSV filter was evaluated in this review qualitatively and quantitatively using simulated and experimental data from cryo-EM and tomography in two and three dimensions. We also assessed the benefit of filtering experimental reconstructions for visualization purposes and for enhancing the accuracy of feature detection. The DPSV filter eliminates high-frequency noise artifacts (density gaps), which would normally preclude the accurate segmentation of tomography reconstructions or the detection of alpha-helices in single-particle reconstructions. This collaborative software development project was carried out entirely by virtual interactions among the authors using publicly available development and file sharing tools.

Visualization of neuritic plaques in Alzheimer’s disease by polarization-sensitive optical coherence microscopy

NASA Astrophysics Data System (ADS)

Baumann, Bernhard; Woehrer, Adelheid; Ricken, Gerda; Augustin, Marco; Mitter, Christian; Pircher, Michael; Kovacs, Gabor G.; Hitzenberger, Christoph K.

2017-03-01

One major hallmark of Alzheimer’s disease (AD) and cerebral amyloid angiopathy (CAA) is the deposition of extracellular senile plaques and vessel wall deposits composed of amyloid-beta (Aβ). In AD, degeneration of neurons is preceded by the formation of Aβ plaques, which show different morphological forms. Most of them are birefringent owing to the parallel arrangement of amyloid fibrils. Here, we present polarization sensitive optical coherence microscopy (PS-OCM) for imaging mature neuritic Aβ plaques based on their birefringent properties. Formalin-fixed, post-mortem brain samples of advanced stage AD patients were investigated. In several cortical brain regions, neuritic Aβ plaques were successfully visualized in tomographic and three-dimensional (3D) images. Cortical grey matter appeared polarization preserving, whereas neuritic plaques caused increased phase retardation. Consistent with the results from PS-OCM imaging, the 3D structure of senile Aβ plaques was computationally modelled for different illumination settings and plaque sizes. Furthermore, the birefringent properties of cortical and meningeal vessel walls in CAA were investigated in selected samples. Significantly increased birefringence was found in smaller vessels. Overall, these results provide evidence that PS-OCM is able to assess amyloidosis based on intrinsic birefringent properties.

High-speed and high-resolution quantitative phase imaging with digital-micromirror device-based illumination (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhou, Renjie; Jin, Di; Yaqoob, Zahid; So, Peter T. C.

2017-02-01

Due to the large number of available mirrors, the patterning speed, low-cost, and compactness, digital-micromirror devices (DMDs) have been extensively used in biomedical imaging system. Recently, DMDs have been brought to the quantitative phase microscopy (QPM) field to achieve synthetic-aperture imaging and tomographic imaging. Last year, our group demonstrated using DMD for QPM, where the phase-retrieval is based on a recently developed Fourier ptychography algorithm. In our previous system, the illumination angle was varied through coding the aperture plane of the illumination system, which has a low efficiency on utilizing the laser power. In our new DMD-based QPM system, we use the Lee-holograms, which is conjugated to the sample plane, to change the illumination angles for much higher power efficiency. Multiple-angle illumination can also be achieved with this method. With this versatile system, we can achieve FPM-based high-resolution phase imaging with 250 nm lateral resolution using the Rayleigh criteria. Due to the use of a powerful laser, the imaging speed would only be limited by the camera acquisition speed. With a fast camera, we expect to achieve close to 100 fps phase imaging speed that has not been achieved in current FPM imaging systems. By adding reference beam, we also expect to achieve synthetic-aperture imaging while directly measuring the phase of the sample fields. This would reduce the phase-retrieval processing time to allow for real-time imaging applications in the future.

Morphometric analysis of erythrocytes from patients with thalassemia using tomographic diffractive microscopy

NASA Astrophysics Data System (ADS)

Lin, Yang-Hsien; Huang, Shin-Shyang; Wu, Shang-Ju; Sung, Kung-Bin

2017-11-01

Complete blood count is the most common test to detect anemia, but it is unable to obtain the abnormal shape of erythrocytes, which highly correlates with the hematologic function. Tomographic diffractive microscopy (TDM) is an emerging technique capable of quantifying three-dimensional (3-D) refractive index (RI) distributions of erythrocytes without labeling. TDM was used to characterize optical and morphological properties of 172 erythrocytes from healthy volunteers and 419 erythrocytes from thalassemic patients. To efficiently extract and analyze the properties of erythrocytes, we developed an adaptive region-growing method for automatically delineating erythrocytes from 3-D RI maps. The thalassemic erythrocytes not only contained lower hemoglobin content but also showed doughnut shape and significantly lower volume, surface area, effective radius, and average thickness. A multi-indices prediction model achieved perfect accuracy of diagnosing thalassemia using four features, including the optical volume, surface-area-to-volume ratio, sphericity index, and surface area. The results demonstrate the ability of TDM to provide quantitative, hematologic measurements and to assess morphological features of erythrocytes to distinguish healthy and thalassemic erythrocytes.

2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance.

PubMed

Beltran, M A; Paganin, D M; Uesugi, K; Kitchen, M J

2010-03-29

A method of tomographic phase retrieval is developed for multi-material objects whose components each has a distinct complex refractive index. The phase-retrieval algorithm, based on the Transport-of-Intensity equation, utilizes propagation-based X-ray phase contrast images acquired at a single defocus distance for each tomographic projection. The method requires a priori knowledge of the complex refractive index for each material present in the sample, together with the total projected thickness of the object at each orientation. The requirement of only a single defocus distance per projection simplifies the experimental setup and imposes no additional dose compared to conventional tomography. The algorithm was implemented using phase contrast data acquired at the SPring-8 Synchrotron facility in Japan. The three-dimensional (3D) complex refractive index distribution of a multi-material test object was quantitatively reconstructed using a single X-ray phase-contrast image per projection. The technique is robust in the presence of noise, compared to conventional absorption based tomography.

Experimentally enhanced model-based deconvolution of propagation-based phase-contrast data

NASA Astrophysics Data System (ADS)

Pichotka, M.; Palma, K.; Hasn, S.; Jakubek, J.; Vavrik, D.

2016-12-01

In recent years phase-contrast has become a much investigated modality in radiographic imaging. The radiographic setups employed in phase-contrast imaging are typically rather costly and complex, e.g. high performance Talbot-Laue interferometers operated at synchrotron light sources. In-line phase-contrast imaging states the most pedestrian approach towards phase-contrast enhancement. Utilizing small angle deflection within the imaged sample and the entailed interference of the deflected and un-deflected beam during spatial propagation, in-line phase-contrast imaging only requires a well collimated X-ray source with a high contrast & high resolution detector. Employing high magnification the above conditions are intrinsically fulfilled in cone-beam micro-tomography. As opposed of 2D imaging, where contrast enhancement is generally considered beneficial, in tomographic modalities the in-line phase-contrast effect can be quite a nuisance since it renders the inverse problem posed by tomographic reconstruction inconsistent, thus causing reconstruction artifacts. We present an experimentally enhanced model-based approach to disentangle absorption and in-line phase-contrast. The approach employs comparison of transmission data to a system model computed iteratively on-line. By comparison of the forward model to absorption data acquired in continuous rotation strong local deviations of the data residual are successively identified as likely candidates for in-line phase-contrast. By inducing minimal vibrations (few mrad) to the sample around the peaks of such deviations the transmission signal can be decomposed into a constant absorptive fraction and an oscillating signal caused by phase-contrast which again allows to generate separate maps for absorption and phase-contrast. The contributions of phase-contrast and the corresponding artifacts are subsequently removed from the tomographic dataset. In principle, if a 3D handling of the sample is available, this method also allows to track discontinuities throughout the volume and therefore states a powerful tool in 3D defectoscopy.

Phase contrast: the frontier of x-ray and electron imaging

NASA Astrophysics Data System (ADS)

Hwu, Y.; Margaritondo, G.

2013-12-01

Phase contrast has been a fundamental component of microscopy since the early 1940s. In broad terms, it refers to the formation of images using not the combination of wave intensities but their amplitudes with the corresponding phase factors. The impact on visible microscopy of biological specimens has been major. This contrast mechanism is now playing an increasingly important role in other kinds of microscopy, notably those based on electrons or x-rays. It notably solves the background problem of weak absorption contrast. New breakthroughs and new techniques are continuously produced, unfortunately unknown to most of the scientists that could exploit them. The present special cluster issue of reviews was inspired by this situation. The case of x-rays is very interesting. Phase contrast requires a high degree of longitudinal and lateral coherence. But conventional x-ray sources are not coherent. The progress of synchrotron sources yielded high coherence as a key byproduct—and started a rapid expansion of phase contrast radiology. No review—or cluster of reviews—can possibly cover all the facets of the recent progress. Without trying to be absolutely comprehensive, the present special cluster issue touches a variety of issues, giving a very broad picture. Liu et al review in general terms the different phase-based hard-x-ray techniques, with an interesting variety of examples. Then, Suortti et al and Wang et al present more specialized overviews of crystal and grating based x-ray imaging techniques, very powerful in the analysis of biological specimens. Mokso et al discuss the many facets of tomography using phase effects, expanding the picture of tomographic reconstruction of the three previous reviews. Wu et al treat the rapid progress in hard-x-ray focusing and its impact on radiology and tomography for materials science and biomedical research. The next two reviews deal with special and very interesting classes of applications. Specifically, Lee et al discuss the use of the new radiology techniques in the study of liquids, and Coan et al present the progress in phase-contrast radiology analysis of real patients. Although x-ray imaging is the main focus of the special cluster issue, the picture would not be complete without a view on the parallel and very exciting developments in electron microscopy. The last review, by Wu et al , is dedicated indeed to this broader picture, presenting recent progress in Zernike-related electron phase contrast. We trust that the special cluster issue will not only update readers on the evolution of a very important class of experimental techniques, but also prepare them for the forthcoming developments. We are indeed at the threshold of another revolution. The recently inaugurated first x-ray free electron lasers bring, together with many other record performances, full lateral coherence and excellent longitudinal coherence. The first imaging experiments show in practice their impact, and indicate that this field, far from saturating its progress, is ready for new major breakthroughs.

Microscale reconstruction of biogeochemical substrates using multimode X-ray tomography and scanning electron microscopy

NASA Astrophysics Data System (ADS)

Miller, M.; Miller, E.; Liu, J.; Lund, R. M.; McKinley, J. P.

2012-12-01

X-ray computed tomography (CT), scanning electron microscopy (SEM), electron microprobe analysis (EMP), and computational image analysis are mature technologies used in many disciplines. Cross-discipline combination of these imaging and image-analysis technologies is the focus of this research, which uses laboratory and light-source resources in an iterative approach. The objective is to produce images across length scales, taking advantage of instrumentation that is optimized for each scale, and to unify them into a single compositional reconstruction. Initially, CT images will be collected using both x-ray absorption and differential phase contrast modes. The imaged sample will then be physically sectioned and the exposed surfaces imaged and characterized via SEM/EMP. The voxel slice corresponding to the physical sample surface will be isolated computationally, and the volumetric data will be combined with two-dimensional SEM images along CT image planes. This registration step will take advantage of the similarity between the X-ray absorption (CT) and backscattered electron (SEM) coefficients (both proportional to average atomic number in the interrogated volume) as well as the images' mutual information. Elemental and solid-phase distributions on the exposed surfaces, co-registered with SEM images, will be mapped using EMP. The solid-phase distribution will be propagated into three-dimensional space using computational methods relying on the estimation of compositional distributions derived from the CT data. If necessary, solid-phase and pore-space boundaries will be resolved using X-ray differential phase contrast tomography, x-ray fluorescence tomography, and absorption-edge microtomography at a light-source facility. Computational methods will be developed to register and model images collected over varying scales and data types. Image resolution, physically and dynamically, is qualitatively different for the electron microscopy and CT methodologies. Routine CT images are resolved at 10-20 μm, while SEM images are resolved at 10-20 nm; grayscale values vary according to collection time and instrument sensitivity; and compositional sensitivities via EMP vary in interrogation volume and scale. We have so far successfully registered SEM imagery within a multimode tomographic volume and have used standard methods to isolate pore space within the volume. We are developing a three-dimensional solid-phase identification and registration method that is constrained by bulk-sample X-ray diffraction Rietveld refinements. The results of this project will prove useful in fields that require the fine-scale definition of solid-phase distributions and relationships, and could replace more inefficient methods for making these estimations.

Regridding reconstruction algorithm for real-time tomographic imaging

PubMed Central

Marone, F.; Stampanoni, M.

2012-01-01

Sub-second temporal-resolution tomographic microscopy is becoming a reality at third-generation synchrotron sources. Efficient data handling and post-processing is, however, difficult when the data rates are close to 10 GB s−1. This bottleneck still hinders exploitation of the full potential inherent in the ultrafast acquisition speed. In this paper the fast reconstruction algorithm gridrec, highly optimized for conventional CPU technology, is presented. It is shown that gridrec is a valuable alternative to standard filtered back-projection routines, despite being based on the Fourier transform method. In fact, the regridding procedure used for resampling the Fourier space from polar to Cartesian coordinates couples excellent performance with negligible accuracy degradation. The stronger dependence of the observed signal-to-noise ratio for gridrec reconstructions on the number of angular views makes the presented algorithm even superior to filtered back-projection when the tomographic problem is well sampled. Gridrec not only guarantees high-quality results but it provides up to 20-fold performance increase, making real-time monitoring of the sub-second acquisition process a reality. PMID:23093766

High resolution imaging and lithography with hard x rays using parabolic compound refractive lenses

NASA Astrophysics Data System (ADS)

Schroer, C. G.; Benner, B.; Günzler, T. F.; Kuhlmann, M.; Zimprich, C.; Lengeler, B.; Rau, C.; Weitkamp, T.; Snigirev, A.; Snigireva, I.; Appenzeller, J.

2002-03-01

Parabolic compound refractive lenses are high quality optical components for hard x rays. They are particularly suited for full field imaging, with applications in microscopy and x-ray lithography. Taking advantage of the large penetration depth of hard x rays, the interior of opaque samples can be imaged with submicrometer resolution. To obtain the three-dimensional structure of a sample, microscopy is combined with tomographic techniques. In a first hard x-ray lithography experiment, parabolic compound refractive lenses have been used to project the reduced image of a lithography mask onto a resist. Future developments are discussed.

Chemical imaging analysis of the brain with X-ray methods

NASA Astrophysics Data System (ADS)

Collingwood, Joanna F.; Adams, Freddy

2017-04-01

Cells employ various metal and metalloid ions to augment the structure and the function of proteins and to assist with vital biological processes. In the brain they mediate biochemical processes, and disrupted metabolism of metals may be a contributing factor in neurodegenerative disorders. In this tutorial review we will discuss the particular role of X-ray methods for elemental imaging analysis of accumulated metal species and metal-containing compounds in biological materials, in the context of post-mortem brain tissue. X-rays have the advantage that they have a short wavelength and can penetrate through a thick biological sample. Many of the X-ray microscopy techniques that provide the greatest sensitivity and specificity for trace metal concentrations in biological materials are emerging at synchrotron X-ray facilities. Here, the extremely high flux available across a wide range of soft and hard X-rays, combined with state-of-the-art focusing techniques and ultra-sensitive detectors, makes it viable to undertake direct imaging of a number of elements in brain tissue. The different methods for synchrotron imaging of metals in brain tissues at regional, cellular, and sub-cellular spatial resolution are discussed. Methods covered include X-ray fluorescence for elemental imaging, X-ray absorption spectrometry for speciation imaging, X-ray diffraction for structural imaging, phase contrast for enhanced contrast imaging and scanning transmission X-ray microscopy for spectromicroscopy. Two- and three-dimensional (confocal and tomographic) imaging methods are considered as well as the correlation of X-ray microscopy with other imaging tools.

Scanning transmission electron microscopy through-focal tilt-series on biological specimens.

PubMed

Trepout, Sylvain; Messaoudi, Cédric; Perrot, Sylvie; Bastin, Philippe; Marco, Sergio

2015-10-01

Since scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (≥500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (≥500 nm) biological samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exceptionally Preserved Cambrian Trilobite Digestive System Revealed in 3D by Synchrotron-Radiation X-Ray Tomographic Microscopy

PubMed Central

Eriksson, Mats E.; Terfelt, Fredrik

2012-01-01

The Cambrian ‘Orsten’ fauna comprises exceptionally preserved and phosphatised microscopic arthropods. The external morphology of these fossils is well known, but their internal soft-tissue anatomy has remained virtually unknown. Here, we report the first non-biomineralised tissues from a juvenile polymerid trilobite, represented by digestive structures, glands, and connective strands harboured in a hypostome from the Swedish ‘Orsten’ fauna. Synchrotron-radiation X-ray tomographic microscopy enabled three-dimensional internal recordings at sub-micrometre resolution. The specimen provides the first unambiguous evidence for a J-shaped anterior gut and the presence of a crop with a constricted alimentary tract in the Trilobita. Moreover, the gut is Y-shaped in cross section, probably due to a collapsed lumen of that shape, another feature which has not previously been observed in trilobites. The combination of anatomical features suggests that the trilobite hypostome is functionally analogous to the labrum of euarthropods and that it was a sophisticated element closely integrated with the digestive system. This study also briefly addresses the preservational bias of the ‘Orsten’ fauna, particularly the near-absence of polymerid trilobites, and the taphonomy of the soft-tissue-harbouring hypostome. PMID:22558180

Exceptionally preserved Cambrian trilobite digestive system revealed in 3D by synchrotron-radiation X-ray tomographic microscopy.

PubMed

Eriksson, Mats E; Terfelt, Fredrik

2012-01-01

The Cambrian 'Orsten' fauna comprises exceptionally preserved and phosphatised microscopic arthropods. The external morphology of these fossils is well known, but their internal soft-tissue anatomy has remained virtually unknown. Here, we report the first non-biomineralised tissues from a juvenile polymerid trilobite, represented by digestive structures, glands, and connective strands harboured in a hypostome from the Swedish 'Orsten' fauna. Synchrotron-radiation X-ray tomographic microscopy enabled three-dimensional internal recordings at sub-micrometre resolution. The specimen provides the first unambiguous evidence for a J-shaped anterior gut and the presence of a crop with a constricted alimentary tract in the Trilobita. Moreover, the gut is Y-shaped in cross section, probably due to a collapsed lumen of that shape, another feature which has not previously been observed in trilobites. The combination of anatomical features suggests that the trilobite hypostome is functionally analogous to the labrum of euarthropods and that it was a sophisticated element closely integrated with the digestive system. This study also briefly addresses the preservational bias of the 'Orsten' fauna, particularly the near-absence of polymerid trilobites, and the taphonomy of the soft-tissue-harbouring hypostome.

Virtual taphonomy using synchrotron tomographic microscopy reveals cryptic features and internal structure of modern and fossil plants

PubMed Central

Smith, Selena Y.; Collinson, Margaret E.; Rudall, Paula J.; Simpson, David A.; Marone, Federica; Stampanoni, Marco

2009-01-01

While more commonly applied in zoology, synchrotron radiation X-ray tomographic microscopy (SRXTM) is well-suited to nondestructive study of the morphology and anatomy of both fossil and modern plants. SRXTM uses hard X-rays and a monochromatic light source to provide high-resolution data with little beam-hardening, resulting in slice data with clear boundaries between materials. Anatomy is readily visualized, including various planes of section from a single specimen, as clear as in traditional histological sectioning at low magnifications. Thus, digital sectioning of rare or difficult material is possible. Differential X-ray attenuation allows visualization of different layers or chemistries to enable virtual 3-dimensional (3D) dissections of material. Virtual potential fossils can be visualized and digital tissue removal reveals cryptic underlying morphology. This is essential for fossil identification and for comparisons between assemblages where fossils are preserved by different means. SRXTM is a powerful approach for botanical studies using morphology and anatomy. The ability to gain search images in both 2D and 3D for potential fossils gives paleobotanists a tool—virtual taphonomy—to improve our understanding of plant evolution and paleobiogeography. PMID:19574457

Digital holography applications in ophthalmology, biometry, and optical trapping characterization

NASA Astrophysics Data System (ADS)

Potcoava, Mariana Camelia

This dissertation combines various holographic techniques with application on the two- and three-dimensional imaging of ophthalmic tissue, fingerprints, and microsphere samples with micrometer resolution. Digital interference holography (DIH) uses scanned wavelengths to synthesize short-coherence interference tomographic images. We used DIH for in vitro imaging of human optic nerve head and retina. Tomographic images were produced by superposition of holograms. Holograms were obtained with a signal-to-noise ratio of approximately 50 dB. Optic nerve head characteristics (shape, diameter, cup depth, and cup width) were quantified with a few micron resolution (4.06--4.8mum). Multiple layers were distinguishable in cross-sectional images of the macula. To our knowledge, this is the first report of DIH use to image human macular and optic nerve tissue. Holographic phase microscopy is used to produce images of thin film patterns left by latent fingerprints. Two or more holographic phase images with different wavelengths are combined for optical phase unwrapping of images of patent prints. We demonstrated digital interference holography images of a plastic print, and latent prints. These demonstrations point to significant contributions to biometry by using digital interference holography to identify and quantify Level 1 (pattern), Level 2 (minutia points), and Level 3 (pores and ridge contours). Quantitative studies of physical and biological processes and precise non-contact manipulation of nanometer/micrometer trapped objects can be effectuated with nanometer accuracy due to the development of optical tweezers. A three-dimensional gradient trap is produced at the focus position of a high NA microscope objective. Particles are trapped axially and laterally due to the gradient force. The particle is confined in a potential well and the trap acts as a harmonic spring. The elastic constant or the stiffness along any axis is determined from the particle displacements in time along each specific axis. Thus, we report the sensing of small particles using optical trapping in combination with the digital Gabor holography to calibrate the optical force and the position and of the copolymer microsphere in the x, y, z direction with nm precision.

Tomographic wavefront retrieval by combined use of geometric and plenoptic sensors

NASA Astrophysics Data System (ADS)

Trujillo-Sevilla, J. M.; Rodríguez-Ramos, L. F.; Fernández-Valdivia, Juan J.; Marichal-Hernández, José G.; Rodríguez-Ramos, J. M.

2014-05-01

Modern astronomic telescopes take advantage of multi-conjugate adaptive optics, in which wavefront sensors play a key role. A single sensor capable of measuring wavefront phases at any angle of observation would be helpful when improving atmospheric tomographic reconstruction. A new sensor combining both geometric and plenoptic arrangements is proposed, and a simulation demonstrating its working principle is also shown. Results show that this sensor is feasible, and also that single extended objects can be used to perform tomography of atmospheric turbulence.

3D+time acquisitions of 3D cell culture by means of lens-free tomographic microscopy

NASA Astrophysics Data System (ADS)

Berdeu, Anthony; Laperrousaz, Bastien; Bordy, Thomas; Morales, S.; Gidrol, Xavier; Picollet-D'hahan, Nathalie; Allier, Cédric

2018-02-01

We propose a three-dimensional (3D) imaging platform based on lens-free microscopy to perform multi-angle acquisitions on 3D cell cultures embedded in extracellular matrix (ECM). We developed algorithms based on the Fourier diffraction theorem to perform fully 3D reconstructions of biological samples and we adapted the lens-free microscope to incubator conditions. Here we demonstrate for the first time, 3D+time lens-free acquisitions of 3D cell culture over 8 days directly into the incubator. The 3D reconstructed volume is as large as 5 mm3 and provides a unique way to observe in the same 3D cell culture experiment multiple cell migration strategies. Namely, in a 3D cell culture of prostate epithelial cells embedded within a Matrigel® matrix, we are able to distinguish single cell 'leaders', migration of cell clusters, migration of large aggregates of cells, and also close-gap and large-scale branching. In addition, we observe long-scale 3D deformations of the ECM that modify the geometry of the 3D cell culture. Interestingly, we also observed the opposite, i.e. we found that large aggregates of cells may deform the ECM by generating traction forces over very long distances. In sum we put forward a novel 3D lens-free microscopy tomographic technique to study the single and collective cell migrations, the cell-to-cell interactions and the cell-to-matrix interactions.

Exploring Chondrule and CAI Rims Using Micro- and Nano-Scale Petrological and Compositional Analysis

NASA Astrophysics Data System (ADS)

Cartwright, J. A.; Perez-Huerta, A.; Leitner, J.; Vollmer, C.

2017-12-01

As the major components within chondrites, chondrules (mm-sized droplets of quenched silicate melt) and calcium-aluminum-rich inclusions (CAI, refractory) represent the most abundant and the earliest materials that solidified from the solar nebula. However, the exact formation mechanisms of these clasts, and whether these processes are related, remains unconstrained, despite extensive petrological and compositional study. By taking advantage of recent advances in nano-scale tomographical techniques, we have undertaken a combined micro- and nano-scale study of CAI and chondrule rim morphologies, to investigate their formation mechanisms. The target lithologies for this research are Wark-Lovering rims (WLR), and fine-grained rims (FGR) around CAIs and chondrules respectively, present within many chondrites. The FGRs, which are up to 100 µm thick, are of particular interest as recent studies have identified presolar grains within them. These grains predate the formation of our Solar System, suggesting FGR formation under nebular conditions. By contrast, WLRs are 10-20 µm thick, made of different compositional layers, and likely formed by flash-heating shortly after CAI formation, thus recording nebular conditions. A detailed multi-scale study of these respective rims will enable us to better understand their formation histories and determine the potential for commonality between these two phases, despite reports of an observed formation age difference of up to 2-3 Myr. We are using a combination of complimentary techniques on our selected target areas: 1) Micro-scale characterization using standard microscopic and compositional techniques (SEM-EBSD, EMPA); 2) Nano-scale characterization of structures using transmission electron microscopy (TEM) and elemental, isotopic and tomographic analysis with NanoSIMS and atom probe tomography (APT). Preliminary nano-scale APT analysis of FGR morphologies within the Allende carbonaceous chondrite has successfully discerned complex chondritic mineralogies and compositional differences across boundaries, which is one of the first applications of in-situ APT techniques to chondrites. Further data reduction will allow us to characterize the exact phases present, and further chondrite analyses are in progress.

Using artificial neural networks (ANN) for open-loop tomography

NASA Astrophysics Data System (ADS)

Osborn, James; De Cos Juez, Francisco Javier; Guzman, Dani; Butterley, Timothy; Myers, Richard; Guesalaga, Andres; Laine, Jesus

2011-09-01

The next generation of adaptive optics (AO) systems require tomographic techniques in order to correct for atmospheric turbulence along lines of sight separated from the guide stars. Multi-object adaptive optics (MOAO) is one such technique. Here, we present a method which uses an artificial neural network (ANN) to reconstruct the target phase given off-axis references sources. This method does not require any input of the turbulence profile and is therefore less susceptible to changing conditions than some existing methods. We compare our ANN method with a standard least squares type matrix multiplication method (MVM) in simulation and find that the tomographic error is similar to the MVM method. In changing conditions the tomographic error increases for MVM but remains constant with the ANN model and no large matrix inversions are required.

Correlative Fluorescence and Electron Microscopy in 3D-Scanning Electron Microscope Perspective.

PubMed

Franks, Jonathan; Wallace, Callen T; Shibata, Masateru; Suga, Mitsuo; Erdman, Natasha; Stolz, Donna B; Watkins, Simon C

2017-04-03

The ability to correlate fluorescence microscopy (FM) and electron microscopy (EM) data obtained on biological (cell and tissue) specimens is essential to bridge the resolution gap between the data obtained by these different imaging techniques. In the past such correlations were limited to either EM navigation in two dimensions to the locations previously highlighted by fluorescence markers, or subsequent high-resolution acquisition of tomographic information using a TEM. We present a novel approach whereby a sample previously investigated by FM is embedded and subjected to sequential mechanical polishing and backscatter imaging by scanning electron microscope. The resulting three dimensional EM tomogram of the sample can be directly correlated to the FM data. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

PtyNAMi: ptychographic nano-analytical microscope at PETRA III: interferometrically tracking positions for 3D x-ray scanning microscopy using a ball-lens retroreflector

NASA Astrophysics Data System (ADS)

Schroer, Christian G.; Seyrich, Martin; Kahnt, Maik; Botta, Stephan; Döhrmann, Ralph; Falkenberg, Gerald; Garrevoet, Jan; Lyubomirskiy, Mikhail; Scholz, Maria; Schropp, Andreas; Wittwer, Felix

2017-09-01

In recent years, ptychography has revolutionized x-ray microscopy in that it is able to overcome the diffraction limit of x-ray optics, pushing the spatial resolution limit down to a few nanometers. However, due to the weak interaction of x rays with matter, the detection of small features inside a sample requires a high coherent fluence on the sample, a high degree of mechanical stability, and a low background signal from the x-ray microscope. The x-ray scanning microscope PtyNAMi at PETRA III is designed for high-spatial-resolution 3D imaging with high sensitivity. The design concept is presented with a special focus on real-time metrology of the sample position during tomographic scanning microscopy.

Recent progress of hard x-ray imaging microscopy and microtomography at BL37XU of SPring-8

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

Suzuki, Yoshio, E-mail: yoshio@spring8.or.jp; Takeuchi, Akihisa; Terada, Yasuko

2016-01-28

A hard x-ray imaging microscopy and microtomography system is now being developed at the beamline 37XU of SPring-8. In the latest improvement, a spatial resolution of about 50 nm is achieved in two-dimensional imaging at 6 keV x-ray energy using a Fresnel zone plate objective with an outermost zone width of 35 nm. In the tomographic measurement, a spatial resolution of about 100 nm is achieved at 8 keV using an x-ray guide tube condenser optic and a Fresnel zone plate objective with an outermost zone width of 50 nm.

Interlaced X-ray diffraction computed tomography

PubMed Central

Vamvakeros, Antonios; Jacques, Simon D. M.; Di Michiel, Marco; Senecal, Pierre; Middelkoop, Vesna; Cernik, Robert J.; Beale, Andrew M.

2016-01-01

An X-ray diffraction computed tomography data-collection strategy that allows, post experiment, a choice between temporal and spatial resolution is reported. This strategy enables time-resolved studies on comparatively short timescales, or alternatively allows for improved spatial resolution if the system under study, or components within it, appear to be unchanging. The application of the method for studying an Mn–Na–W/SiO2 fixed-bed reactor in situ is demonstrated. Additionally, the opportunities to improve the data-collection strategy further, enabling post-collection tuning between statistical, temporal and spatial resolutions, are discussed. In principle, the interlaced scanning approach can also be applied to other pencil-beam tomographic techniques, like X-ray fluorescence computed tomography, X-ray absorption fine structure computed tomography, pair distribution function computed tomography and tomographic scanning transmission X-ray microscopy. PMID:27047305

4D x-ray phase contrast tomography for repeatable motion of biological samples

NASA Astrophysics Data System (ADS)

Hoshino, Masato; Uesugi, Kentaro; Yagi, Naoto

2016-09-01

X-ray phase contrast tomography based on a grating interferometer was applied to fast and dynamic measurements of biological samples. To achieve this, the scanning procedure in the tomographic scan was improved. A triangle-shaped voltage signal from a waveform generator to a Piezo stage was used for the fast phase stepping in the grating interferometer. In addition, an optical fiber coupled x-ray scientific CMOS camera was used to achieve fast and highly efficient image acquisitions. These optimizations made it possible to perform an x-ray phase contrast tomographic measurement within an 8 min scan with density resolution of 2.4 mg/cm3. A maximum volume size of 13 × 13 × 6 mm3 was obtained with a single tomographic measurement with a voxel size of 6.5 μm. The scanning procedure using the triangle wave was applied to four-dimensional measurements in which highly sensitive three-dimensional x-ray imaging and a time-resolved dynamic measurement of biological samples were combined. A fresh tendon in the tail of a rat was measured under a uniaxial stretching and releasing condition. To maintain the freshness of the sample during four-dimensional phase contrast tomography, the temperature of the bathing liquid of the sample was kept below 10° using a simple cooling system. The time-resolved deformation of the tendon and each fascicle was measured with a temporal resolution of 5.7 Hz. Evaluations of cross-sectional area size, length of the axis, and mass density in the fascicle during a stretching process provided a basis for quantitative analysis of the deformation of tendon fascicle.

4D x-ray phase contrast tomography for repeatable motion of biological samples.

PubMed

Hoshino, Masato; Uesugi, Kentaro; Yagi, Naoto

2016-09-01

X-ray phase contrast tomography based on a grating interferometer was applied to fast and dynamic measurements of biological samples. To achieve this, the scanning procedure in the tomographic scan was improved. A triangle-shaped voltage signal from a waveform generator to a Piezo stage was used for the fast phase stepping in the grating interferometer. In addition, an optical fiber coupled x-ray scientific CMOS camera was used to achieve fast and highly efficient image acquisitions. These optimizations made it possible to perform an x-ray phase contrast tomographic measurement within an 8 min scan with density resolution of 2.4 mg/cm 3 . A maximum volume size of 13 × 13 × 6 mm 3 was obtained with a single tomographic measurement with a voxel size of 6.5 μm. The scanning procedure using the triangle wave was applied to four-dimensional measurements in which highly sensitive three-dimensional x-ray imaging and a time-resolved dynamic measurement of biological samples were combined. A fresh tendon in the tail of a rat was measured under a uniaxial stretching and releasing condition. To maintain the freshness of the sample during four-dimensional phase contrast tomography, the temperature of the bathing liquid of the sample was kept below 10° using a simple cooling system. The time-resolved deformation of the tendon and each fascicle was measured with a temporal resolution of 5.7 Hz. Evaluations of cross-sectional area size, length of the axis, and mass density in the fascicle during a stretching process provided a basis for quantitative analysis of the deformation of tendon fascicle.

Sodankylä ionospheric tomography dataset 2003-2014

NASA Astrophysics Data System (ADS)

Norberg, J.; Roininen, L.; Kero, A.; Raita, T.; Ulich, T.; Markkanen, M.; Juusola, L.; Kauristie, K.

2015-12-01

Sodankylä Geophysical Observatory has been operating a tomographic receiver network and collecting the produced data since 2003. The collected dataset consists of phase difference curves measured from Russian COSMOS dual-frequency (150/400 MHz) low-Earth-orbit satellite signals, and tomographic electron density reconstructions obtained from these measurements. In this study vertical total electron content (VTEC) values are integrated from the reconstructed electron densities to make a qualitative and quantitative analysis to validate the long-term performance of the tomographic system. During the observation period, 2003-2014, there were three-to-five operational stations at the Fenno-Scandinavian sector. Altogether the analysis consists of around 66 000 overflights, but to ensure the quality of the reconstructions, the examination is limited to cases with descending (north to south) overflights and maximum elevation over 60°. These constraints limit the number of overflights to around 10 000. Based on this dataset, one solar cycle of ionospheric vertical total electron content estimates is constructed. The measurements are compared against International Reference Ionosphere IRI-2012 model, F10.7 solar flux index and sunspot number data. Qualitatively the tomographic VTEC estimate corresponds to reference data very well, but the IRI-2012 model are on average 40 % higher of that of the tomographic results.

Complex deformation in the Caucasus region revealed by ambient noise seismic tomography

NASA Astrophysics Data System (ADS)

Legendre, Cédric P.; Tseng, Tai-Lin; Chen, Ying-Nien; Huang, Tzu-Ying; Gung, Yuan-Cheng; Karakhanyan, Arkadiy; Huang, Bor-Shouh

2017-08-01

Cross-correlation of 3years of ambient seismic noise recorded at 35 seismic stations deployed in Caucasus region yields hundreds of short-period surface-wave phase-speed dispersion curves on inter-station paths. We inverted these measurements using two techniques to construct tomographic images of the principal geological units of Caucasus. High-resolution isotropic and azimuthally anisotropic phase-velocity maps (at periods between 5 and 20s) and shear-velocity tomographic maps between 5 and 30km are generated. The resulting maps show a velocity dichotomy between the Caucasus region and the surrounding that is interpreted in term of changes in crustal thickness. There is also a strong dichotomy in the anisotropic pattern between the eastern part and the western part of the Caucasus. This difference in both amplitudes and directions of the 2ψ anisotropy is linked to the tectonic regime changes in the region. These observations suggest a good correlation between the tomographic models and the geology of the region. It was also possible to identify the early stage of the indentation of the Arabian Plate into the Eurasian plate, as well as to detect the possible magma chamber responsible for the Javakheti highland.

3D homogeneity study in PMMA layers using a Fourier domain OCT system

NASA Astrophysics Data System (ADS)

Briones-R., Manuel de J.; Torre-Ibarra, Manuel H. De La; Tavera, Cesar G.; Luna H., Juan M.; Mendoza-Santoyo, Fernando

2016-11-01

Micro-metallic particles embedded in polymers are now widely used in several industrial applications in order to modify the mechanical properties of the bulk. A uniform distribution of these particles inside the polymers is highly desired for instance, when a biological backscattering is simulated or a bio-framework is designed. A 3D Fourier domain optical coherence tomography system to detect the polymer's internal homogeneity is proposed. This optical system has a 2D camera sensor array that records a fringe pattern used to reconstruct with a single shot the tomographic image of the sample. The system gathers the full 3D tomographic and optical phase information during a controlled deformation by means of a motion linear stage. This stage avoids the use of expensive tilting stages, which in addition are commonly controlled by piezo drivers. As proof of principle, a series of different deformations were proposed to detect the uniform or non-uniform internal deposition of copper micro particles. The results are presented as images coming from the 3D tomographic micro reconstruction of the samples, and the 3D optical phase information that identifies the in-homogeneity regions within the Poly methyl methacrylate (PMMA) volume.

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

Segal-Peretz, Tamar; Zhou, Chun; Ren, Jiaxing

The three-dimensional assembly of poly (styrene-b-methyl methacrylate) (PS-b-PMMA) in chemoepitaxy and graphoepitaxy directed self-assembly (DSA) was investigated using scanning transmission electron microscopy (STEM) tomography. The tomographic characterization revealed hidden morphologies and defects at the BCP- chemical pattern interface in lamellar DSA, and probed the formation of cylinders at the bottom of cylindrical DSA for contact hole shrink. Lastly, future work will include control over 3D assembly in sub-10 nm processes.

Computational adaptive optics for broadband optical interferometric tomography of biological tissue.

PubMed

Adie, Steven G; Graf, Benedikt W; Ahmad, Adeel; Carney, P Scott; Boppart, Stephen A

2012-05-08

Aberrations in optical microscopy reduce image resolution and contrast, and can limit imaging depth when focusing into biological samples. Static correction of aberrations may be achieved through appropriate lens design, but this approach does not offer the flexibility of simultaneously correcting aberrations for all imaging depths, nor the adaptability to correct for sample-specific aberrations for high-quality tomographic optical imaging. Incorporation of adaptive optics (AO) methods have demonstrated considerable improvement in optical image contrast and resolution in noninterferometric microscopy techniques, as well as in optical coherence tomography. Here we present a method to correct aberrations in a tomogram rather than the beam of a broadband optical interferometry system. Based on Fourier optics principles, we correct aberrations of a virtual pupil using Zernike polynomials. When used in conjunction with the computed imaging method interferometric synthetic aperture microscopy, this computational AO enables object reconstruction (within the single scattering limit) with ideal focal-plane resolution at all depths. Tomographic reconstructions of tissue phantoms containing subresolution titanium-dioxide particles and of ex vivo rat lung tissue demonstrate aberration correction in datasets acquired with a highly astigmatic illumination beam. These results also demonstrate that imaging with an aberrated astigmatic beam provides the advantage of a more uniform depth-dependent signal compared to imaging with a standard gaussian beam. With further work, computational AO could enable the replacement of complicated and expensive optical hardware components with algorithms implemented on a standard desktop computer, making high-resolution 3D interferometric tomography accessible to a wider group of users and nonspecialists.

Phase decomposition and ordering in Ni-11.3 at.% Ti studied with atom probe tomography.

PubMed

Al-Kassab, T; Kompatscher, M; Kirchheim, R; Kostorz, G; Schönfeld, B

2014-09-01

The decomposition behavior of Ni-rich Ni-Ti was reassessed using Tomographic Atom Probe (TAP) and Laser Assisted Wide Angle Tomographic Atom Probe. Single crystalline specimens of Ni-11.3 at.% Ti were investigated, the states selected from the decomposition path were the metastable γ″ and γ' states introduced on the basis of small-angle neutron scattering (SANS) and the two-phase model for evaluation. The composition values of the precipitates in these states could not be confirmed by APT data as the interface of the ordered precipitates may not be neglected. The present results rather suggest to apply a three-phase model for the interpretation of SANS measurements, in which the width of the interface remains nearly unchanged and the L12 structure close to 3:1 stoichiometry is maintained in the core of the precipitates from the γ″ to the γ' state. Copyright © 2014 Elsevier Ltd. All rights reserved.

Surface Wave Tomography with Spatially Varying Smoothing Based on Continuous Model Regionalization

NASA Astrophysics Data System (ADS)

Liu, Chuanming; Yao, Huajian

2017-03-01

Surface wave tomography based on continuous regionalization of model parameters is widely used to invert for 2-D phase or group velocity maps. An inevitable problem is that the distribution of ray paths is far from homogeneous due to the spatially uneven distribution of stations and seismic events, which often affects the spatial resolution of the tomographic model. We present an improved tomographic method with a spatially varying smoothing scheme that is based on the continuous regionalization approach. The smoothness of the inverted model is constrained by the Gaussian a priori model covariance function with spatially varying correlation lengths based on ray path density. In addition, a two-step inversion procedure is used to suppress the effects of data outliers on tomographic models. Both synthetic and real data are used to evaluate this newly developed tomographic algorithm. In the synthetic tests, when the contrived model has different scales of anomalies but with uneven ray path distribution, we compare the performance of our spatially varying smoothing method with the traditional inversion method, and show that the new method is capable of improving the recovery in regions of dense ray sampling. For real data applications, the resulting phase velocity maps of Rayleigh waves in SE Tibet produced using the spatially varying smoothing method show similar features to the results with the traditional method. However, the new results contain more detailed structures and appears to better resolve the amplitude of anomalies. From both synthetic and real data tests we demonstrate that our new approach is useful to achieve spatially varying resolution when used in regions with heterogeneous ray path distribution.

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography

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

Li, Qiong; Gluch, Jürgen; Krüger, Peter

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have amore » direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. - Highlights: • The unstained whole pine pollen was visualized by high-resolution laboratory-based HXRM for the first time. • The comparison study of pollen grains by LM, SEM and high-resolution laboratory-based HXRM. • Phase contrast imaging provides significantly higher contrast of the raw images compared to absorption contrast imaging. • Surface and internal structure of the pine pollen including exine, intine and cellular structures are clearly visualized. • 3D volume data of unstained whole pollen grains are acquired and the specific volumes of the different layer are calculated.« less

Gold Nanoparticle Quantitation by Whole Cell Tomography.

PubMed

Sanders, Aric W; Jeerage, Kavita M; Schwartz, Cindi L; Curtin, Alexandra E; Chiaramonti, Ann N

2015-12-22

Many proposed biomedical applications for engineered gold nanoparticles require their incorporation by mammalian cells in specific numbers and locations. Here, the number of gold nanoparticles inside of individual mammalian stem cells was characterized using fast focused ion beam-scanning electron microscopy based tomography. Enhanced optical microscopy was used to provide a multiscale map of the in vitro sample, which allows cells of interest to be identified within their local environment. Cells were then serially sectioned using a gallium ion beam and imaged using a scanning electron beam. To confirm the accuracy of single cross sections, nanoparticles in similar cross sections were imaged using transmission electron microscopy and scanning helium ion microscopy. Complete tomographic series were then used to count the nanoparticles inside of each cell and measure their spatial distribution. We investigated the influence of slice thickness on counting single particles and clusters as well as nanoparticle packing within clusters. For 60 nm citrate stabilized particles, the nanoparticle cluster packing volume is 2.15 ± 0.20 times the volume of the bare gold nanoparticles.

Two-dimensional tomographic terahertz imaging by homodyne self-mixing.

PubMed

Mohr, Till; Breuer, Stefan; Giuliani, G; Elsäßer, Wolfgang

2015-10-19

We realize a compact two-dimensional tomographic terahertz imaging experiment involving only one photoconductive antenna (PCA) simultaneously serving as a transmitter and receiver of the terahertz radiation. A hollow-core Teflon cylinder filled with α-Lactose monohydrate powder is studied at two terahertz frequencies, far away and at a specific absorption line of the powder. This sample is placed between the antenna and a chopper wheel, which serves as back reflector of the terahertz radiation into the PCA. Amplitude and phase information of the continuous-wave (CW) terahertz radiation are extracted from the measured homodyne self-mixing (HSM) signal after interaction with the cylinder. The influence of refraction is studied by modeling the set-up utilizing ZEMAX and is discussed by means of the measured 1D projections. The tomographic reconstruction by using the Simultaneous Algebraic Reconstruction Technique (SART) allows to identify both object geometry and α-Lactose filling.

Three-dimensional study of the vector potential of magnetic structures.

PubMed

Phatak, Charudatta; Petford-Long, Amanda K; De Graef, Marc

2010-06-25

The vector potential is central to a number of areas of condensed matter physics, such as superconductivity and magnetism. We have used a combination of electron wave phase reconstruction and electron tomographic reconstruction to experimentally measure and visualize the three-dimensional vector potential in and around a magnetic Permalloy structure. The method can probe the vector potential of the patterned structures with a resolution of about 13 nm. A transmission electron microscope operated in the Lorentz mode is used to record four tomographic tilt series. Measurements for a square Permalloy structure with an internal closure domain configuration are presented.

Optical diffraction tomography microscopy with transport of intensity equation using a light-emitting diode array

NASA Astrophysics Data System (ADS)

Li, Jiaji; Chen, Qian; Zhang, Jialin; Zhang, Zhao; Zhang, Yan; Zuo, Chao

2017-08-01

Optical diffraction tomography (ODT) is an effective label-free technique for quantitatively refractive index imaging, which enables long-term monitoring of the internal three-dimensional (3D) structures and molecular composition of biological cells with minimal perturbation. However, existing optical tomographic methods generally rely on interferometric configuration for phase measurement and sophisticated mechanical systems for sample rotation or beam scanning. Thereby, the measurement is suspect to phase error coming from the coherent speckle, environmental vibrations, and mechanical error during data acquisition process. To overcome these limitations, we present a new ODT technique based on non-interferometric phase retrieval and programmable illumination emitting from a light-emitting diode (LED) array. The experimental system is built based on a traditional bright field microscope, with the light source replaced by a programmable LED array, which provides angle-variable quasi-monochromatic illumination with an angular coverage of ±37 degrees in both x and y directions (corresponding to an illumination numerical aperture of ∼0.6). Transport of intensity equation (TIE) is utilized to recover the phase at different illumination angles, and the refractive index distribution is reconstructed based on the ODT framework under first Rytov approximation. The missing-cone problem in ODT is addressed by using the iterative non-negative constraint algorithm, and the misalignment of the LED array is further numerically corrected to improve the accuracy of refractive index quantification. Experiments on polystyrene beads and thick biological specimens show that the proposed approach allows accurate refractive index reconstruction while greatly reduced the system complexity and environmental sensitivity compared to conventional interferometric ODT approaches.

Portable Ultrasound Imaging of the Brain for Use in Forward Battlefield Areas

DTIC Science & Technology

2011-03-01

ultrasound measurement of skull thickness and sound speed, phase correction of beam distortion, the tomographic reconstruction algorithm, and the final...produce a coherent imaging source. We propose a corrective technique that will use ultrasound-based phased -array beam correction [3], optimized...not expected to be a significant factor in the ability to phase -correct the imaging beam . In addition to planning (2.2.1), the data is also be used

A resolution-enhancing image reconstruction method for few-view differential phase-contrast tomography

NASA Astrophysics Data System (ADS)

Guan, Huifeng; Anastasio, Mark A.

2017-03-01

It is well-known that properly designed image reconstruction methods can facilitate reductions in imaging doses and data-acquisition times in tomographic imaging. The ability to do so is particularly important for emerging modalities such as differential X-ray phase-contrast tomography (D-XPCT), which are currently limited by these factors. An important application of D-XPCT is high-resolution imaging of biomedical samples. However, reconstructing high-resolution images from few-view tomographic measurements remains a challenging task. In this work, a two-step sub-space reconstruction strategy is proposed and investigated for use in few-view D-XPCT image reconstruction. It is demonstrated that the resulting iterative algorithm can mitigate the high-frequency information loss caused by data incompleteness and produce images that have better preserved high spatial frequency content than those produced by use of a conventional penalized least squares (PLS) estimator.

Validation of pore network simulations of ex-situ water distributions in a gas diffusion layer of proton exchange membrane fuel cells with X-ray tomographic images

NASA Astrophysics Data System (ADS)

Agaesse, Tristan; Lamibrac, Adrien; Büchi, Felix N.; Pauchet, Joel; Prat, Marc

2016-11-01

Understanding and modeling two-phase flows in the gas diffusion layer (GDL) of proton exchange membrane fuel cells are important in order to improve fuel cells performance. They are scientifically challenging because of the peculiarities of GDLs microstructures. In the present work, simulations on a pore network model are compared to X-ray tomographic images of water distributions during an ex-situ water invasion experiment. A method based on watershed segmentation was developed to extract a pore network from the 3D segmented image of the dry GDL. Pore network modeling and a full morphology model were then used to perform two-phase simulations and compared to the experimental data. The results show good agreement between experimental and simulated microscopic water distributions. Pore network extraction parameters were also benchmarked using the experimental data and results from full morphology simulations.

Methods to mitigate data truncation artifacts in multi-contrast tomosynthesis image reconstructions

NASA Astrophysics Data System (ADS)

Garrett, John; Ge, Yongshuai; Li, Ke; Chen, Guang-Hong

2015-03-01

Differential phase contrast imaging is a promising new image modality that utilizes the refraction rather than the absorption of x-rays to image an object. A Talbot-Lau interferometer may be used to permit differential phase contrast imaging with a conventional medical x-ray source and detector. However, the current size of the gratings fabricated for these interferometers are often relatively small. As a result, data truncation image artifacts are often observed in a tomographic acquisition and reconstruction. When data are truncated in x-ray absorption imaging, the methods have been introduced to mitigate the truncation artifacts. However, the same strategy to mitigate absorption truncation artifacts may not be appropriate for differential phase contrast or dark field tomographic imaging. In this work, several new methods to mitigate data truncation artifacts in a multi-contrast imaging system have been proposed and evaluated for tomosynthesis data acquisitions. The proposed methods were validated using experimental data acquired for a bovine udder as well as several cadaver breast specimens using a benchtop system at our facility.

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.

Lithographed spectrometers for tomographic line mapping of the Epoch of Reionization

NASA Astrophysics Data System (ADS)

O'Brient, R.; Bock, J. J.; Bradford, C. M.; Crites, A.; Duan, R.; Hailey-Dunsheath, S.; Hunacek, J.; LeDuc, R.; Shirokoff, E.; Staniszewski, Z.; Turner, A.; Zemcov, M.

2014-08-01

The Tomographic Ionized carbon Mapping Experiment (TIME) is a multi-phased experiment that will topographically map [CII] emission from the Epoch of Reionization. We are developing lithographed spectrometers that couple to TES bolometers in anticipation of the second generation instrument. Our design intentionally mirrors many features of the parallel SuperSpec project, inductively coupling power from a trunk-line microstrip onto half-wave resonators. The resonators couple to a rat-race hybrids that feeds TES bolometers. Our 25 channel prototype shows spectrally positioned lines roughly matching design with a receiver optical efficiency of 15-20%, a level that is dominated by loss in components outside the spectrometer.

Charge transport in CdTe solar cells revealed by conductive tomographic atomic force microscopy

DOE PAGES

Luria, Justin; Kutes, Yasemin; Moore, Andrew; ...

2016-09-26

Polycrystalline photovoltaics comprising cadmium telluride (CdTe) represent a growing portion of the solar cell market, yet the physical picture of charge transport through the meso-scale grain morphology remains a topic of debate. It is unknown how thin film morphology affects the transport of electron-hole pairs. Accordingly this study is the first to generate three dimensional images of photocurrent throughout a thin-film solar cell, revealing the profound influence of grain boundaries and stacking faults on device efficiency.

Three Dimensional Assembly in Directed Self-assembly of Block Copolymers

DOE PAGES

Segal-Peretz, Tamar; Zhou, Chun; Ren, Jiaxing; ...

2016-09-02

The three-dimensional assembly of poly (styrene-b-methyl methacrylate) (PS-b-PMMA) in chemoepitaxy and graphoepitaxy directed self-assembly (DSA) was investigated using scanning transmission electron microscopy (STEM) tomography. The tomographic characterization revealed hidden morphologies and defects at the BCP- chemical pattern interface in lamellar DSA, and probed the formation of cylinders at the bottom of cylindrical DSA for contact hole shrink. Lastly, future work will include control over 3D assembly in sub-10 nm processes.

Degeneration and Regeneration of Subbasal Corneal Nerves after Infectious Keratitis: A Longitudinal In Vivo Confocal Microscopy Study.

PubMed

Müller, Rodrigo T; Abedi, Farshad; Cruzat, Andrea; Witkin, Deborah; Baniasadi, Neda; Cavalcanti, Bernardo M; Jamali, Arsia; Chodosh, James; Dana, Reza; Pavan-Langston, Deborah; Hamrah, Pedram

2015-11-01

To investigate the longitudinal alterations of subbasal corneal nerves in patients with infectious keratitis (IK) during the acute phase, cessation of treatment, and the recovery phase by in vivo confocal microscopy (IVCM). Prospective, longitudinal, case-control, single-center study. Fifty-six eyes of 56 patients with the diagnosis of bacterial (n=28), fungal (n=15), or Acanthamoeba (n=13) keratitis were included in the study. Thirty eyes of 30 normal volunteers constituted the control group. Corneal sensation and serial IVCM of the central cornea were performed prospectively using the Heidelberg Retina Tomograph 3/Rostock Cornea Module (Heidelberg Engineering, Heidelberg, Germany). The IVCM images were assessed at 3 time points: at the acute phase (first visit to the cornea service), at cessation of antimicrobial treatment, and up to 6 months after the resolution of infection. Total nerve number and length, main nerve trunks, branching, and corneal sensation were assessed during the follow-up period. Corneal nerves were reduced significantly during the acute phase in eyes with IK compared with controls across all subgroups, with total nerve length of 5.47±0.69 mm/mm2 versus 20.59±1.06 mm/mm2 (P<0.0001). At the cessation of treatment, corneal nerves in patients with IK had regenerated, including total nerve length (8.49±0.94 mm/mm2; P=0.02) and nerve branch length (4.80±0.37 mm/mm2; P=0.005). During the recovery phase, after resolution of infection, corneal nerves regenerated further, including total nerve length (12.13±1.97 mm/mm2; P=0.005), main nerve trunk length (5.80±1.00 mm/mm2; P=0.01), and nerve branch length (6.33±0.76 mm/mm2; P=0.003) as compared with the acute phase, but were still significantly lower when compared with controls (P<0.05 for all parameters). Corneal degeneration and regeneration correlated with corneal sensation (r=0.47; P=0.0009). Patients with IK who sustain profound loss of corneal nerves during the acute phase of infection demonstrate increased corneal nerve density during the first 6 months after the resolution of infection. However, despite significant nerve regeneration, corneal nerve density does not recover fully and remains low compared to controls. By providing an objective methodology to monitor corneal re-innervation, IVCM adds potentially important findings that may have implications for clinical management and surgical planning. Copyright © 2015 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

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

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

3D reconstruction of the magnetic vector potential using model based iterative reconstruction.

PubMed

Prabhat, K C; Aditya Mohan, K; Phatak, Charudatta; Bouman, Charles; De Graef, Marc

2017-11-01

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. A comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2012-12-05

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

3D reconstruction of the magnetic vector potential using model based iterative reconstruction

DOE PAGES

Prabhat, K. C.; Aditya Mohan, K.; Phatak, Charudatta; ...

2017-07-03

Lorentz transmission electron microscopy (TEM) observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials. Vector field electron tomography (VFET) can be used to reconstruct electromagnetic potentials of the nanoparticles from their corresponding LTEM images. The VFET approach is based on the conventional filtered back projection approach to tomographic reconstructions and the availability of an incomplete set of measurements due to experimental limitations means that the reconstructed vector fields exhibit significant artifacts. In this paper, we outline a model-based iterative reconstruction (MBIR) algorithm to reconstruct the magnetic vector potential of magnetic nanoparticles. We combine a forward model formore » image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a-posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to determine the vector potential. Here, a comparative reconstruction study of simulated as well as experimental data sets show that the MBIR approach yields quantifiably better reconstructions than the VFET approach.« less

Correlative Microscopy of Vitreous Sections Provides Insights into BAR-Domain Organization In Situ.

PubMed

Bharat, Tanmay A M; Hoffmann, Patrick C; Kukulski, Wanda

2018-04-10

Electron microscopy imaging of macromolecular complexes in their native cellular context is limited by the inherent difficulty to acquire high-resolution tomographic data from thick cells and to specifically identify elusive structures within crowded cellular environments. Here, we combined cryo-fluorescence microscopy with electron cryo-tomography of vitreous sections into a coherent correlative microscopy workflow, ideal for detection and structural analysis of elusive protein assemblies in situ. We used this workflow to address an open question on BAR-domain coating of yeast plasma membrane compartments known as eisosomes. BAR domains can sense or induce membrane curvature, and form scaffold-like membrane coats in vitro. Our results demonstrate that in cells, the BAR protein Pil1 localizes to eisosomes of varying membrane curvature. Sub-tomogram analysis revealed a dense protein coat on curved eisosomes, which was not present on shallow eisosomes, indicating that while BAR domains can assemble at shallow membranes in vivo, scaffold formation is tightly coupled to curvature generation. Copyright © 2018 MRC Laboratory of Molecular Biology. Published by Elsevier Ltd.. All rights reserved.

Sodankylä ionospheric tomography data set 2003-2014

NASA Astrophysics Data System (ADS)

Norberg, Johannes; Roininen, Lassi; Kero, Antti; Raita, Tero; Ulich, Thomas; Markkanen, Markku; Juusola, Liisa; Kauristie, Kirsti

2016-07-01

Sodankylä Geophysical Observatory has been operating a receiver network for ionospheric tomography and collecting the produced data since 2003. The collected data set consists of phase difference curves measured from COSMOS navigation satellites from the Russian Parus network (Wood and Perry, 1980) and tomographic electron density reconstructions obtained from these measurements. In this study vertical total electron content (VTEC) values are integrated from the reconstructed electron densities to make a qualitative and quantitative analysis to validate the long-term performance of the tomographic system. During the observation period, 2003-2014, there were three to five operational stations at the Fennoscandia sector. Altogether the analysis consists of around 66 000 overflights, but to ensure the quality of the reconstructions, the examination is limited to cases with descending (north to south) overflights and maximum elevation over 60°. These constraints limit the number of overflights to around 10 000. Based on this data set, one solar cycle of ionospheric VTEC estimates is constructed. The measurements are compared against the International Reference Ionosphere (IRI)-2012 model, F10.7 solar flux index and sunspot number data. Qualitatively the tomographic VTEC estimate corresponds to reference data very well, but the IRI-2012 model results are on average 40 % higher than that of the tomographic results.

Markov random field based automatic image alignment for electron tomography.

PubMed

Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

2008-03-01

We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

Phase contrast X-ray microtomography of the Rhodnius prolixus head: Comparison of direct reconstruction and phase retrieval approach

NASA Astrophysics Data System (ADS)

Almeida, A. P.; Braz, D.; Nogueira, L. P.; Colaço, M. V.; Soares, J.; Cardoso, S. C.; Garcia, E. S.; Azambuja, P.; Gonzalez, M. S.; Mohammadi, S.; Tromba, G.; Barroso, R. C.

2014-02-01

We have used phase-contrast X-ray microtomography (PPC-μCT) to study the head of the blood-feeding bug, Rhodnius prolixus, which is one of the most important insect vector of Trypanosoma cruzi, ethiologic agent of Chagas disease in Latin America. Images reconstructed from phase-retrieved projections processed by ANKA phase are compared to those obtained through direct tomographic reconstruction of the flat-field-corrected transmission radiographs. It should be noted that the relative locations of the important morphological internal structures are observable with a precision that is difficult to obtain without the phase retrieval approach.

Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces.

PubMed

Koning, Roman I; Celler, Katherine; Willemse, Joost; Bos, Erik; van Wezel, Gilles P; Koster, Abraham J

2014-01-01

Light microscopy and electron microscopy are complementary techniques that in a correlative approach enable identification and targeting of fluorescently labeled structures in situ for three-dimensional imaging at nanometer resolution. Correlative imaging allows electron microscopic images to be positioned in a broader temporal and spatial context. We employed cryo-correlative light and electron microscopy (cryo-CLEM), combining cryo-fluorescence light microscopy and cryo-electron tomography, on vitrified Streptomyces bacteria to study cell division. Streptomycetes are mycelial bacteria that grow as long hyphae and reproduce via sporulation. On solid media, Streptomyces subsequently form distinct aerial mycelia where cell division leads to the formation of unigenomic spores which separate and disperse to form new colonies. In liquid media, only vegetative hyphae are present divided by noncell separating crosswalls. Their multicellular life style makes them exciting model systems for the study of bacterial development and cell division. Complex intracellular structures have been visualized with transmission electron microscopy. Here, we describe the methods for cryo-CLEM that we applied for studying Streptomyces. These methods include cell growth, fluorescent labeling, cryo-fixation by vitrification, cryo-light microscopy using a Linkam cryo-stage, image overlay and relocation, cryo-electron tomography using a Titan Krios, and tomographic reconstruction. Additionally, methods for segmentation, volume rendering, and visualization of the correlative data are described. © 2014 Elsevier Inc. All rights reserved.

Comparison of propagation-based phase-contrast tomography approaches for the evaluation of dentin microstructure

NASA Astrophysics Data System (ADS)

Deyhle, Hans; Weitkamp, Timm; Lang, Sabrina; Schulz, Georg; Rack, Alexander; Zanette, Irene; Müller, Bert

2012-10-01

The complex hierarchical structure of human tooth hard tissues, enamel and dentin, guarantees function for decades. On the micrometer level the dentin morphology is dominated by the tubules, micrometer-narrow channels extending from the dentin-enamel junction to the pulp chamber. Their structure has been extensively studied, mainly with two-dimensional approaches. Dentin tubules are formed during tooth growth and their orientation is linked to the morphology of the nanometer-sized components, which is of interest for example for the development of bio-inspired dental fillings. Therefore, a method has to be identified that can access the three-dimensional organization of the tubules, e.g. density and orientation. Tomographic setups with pixel sizes in the sub-micrometer range allow for the three-dimensional visualization of tooth dentin tubules both in phase and absorption contrast modes. We compare high-resolution tomographic scans reconstructed with propagation based phase retrieval algorithms as well as reconstructions without phase retrieval concerning spatial and density resolution as well as rendering of the dentin microstructure to determine the approach best suited for dentin tubule imaging. Reasonable results were obtained with a single-distance phase retrieval algorithm and a propagation distance of about 75% of the critical distance of d2/λ, where d is the size of the smallest objects identifiable in the specimen and λ is the X-ray wavelength.

'Big Bang' tomography as a new route to atomic-resolution electron tomography.

PubMed

Van Dyck, Dirk; Jinschek, Joerg R; Chen, Fu-Rong

2012-06-13

Until now it has not been possible to image at atomic resolution using classical electron tomographic methods, except when the target is a perfectly crystalline nano-object imaged along a few zone axes. The main reasons are that mechanical tilting in an electron microscope with sub-ångström precision over a very large angular range is difficult, that many real-life objects such as dielectric layers in microelectronic devices impose geometrical constraints and that many radiation-sensitive objects such as proteins limit the total electron dose. Hence, there is a need for a new tomographic scheme that is able to deduce three-dimensional information from only one or a few projections. Here we present an electron tomographic method that can be used to determine, from only one viewing direction and with sub-ångström precision, both the position of individual atoms in the plane of observation and their vertical position. The concept is based on the fact that an experimentally reconstructed exit wave consists of the superposition of the spherical waves that have been scattered by the individual atoms of the object. Furthermore, the phase of a Fourier component of a spherical wave increases with the distance of propagation at a known 'phase speed'. If we assume that an atom is a point-like object, the relationship between the phase and the phase speed of each Fourier component is linear, and the distance between the atom and the plane of observation can therefore be determined by linear fitting. This picture has similarities with Big Bang cosmology, in which the Universe expands from a point-like origin such that the distance of any galaxy from the origin is linearly proportional to the speed at which it moves away from the origin (Hubble expansion). The proof of concept of the method has been demonstrated experimentally for graphene with a two-layer structure and it will work optimally for similar layered materials, such as boron nitride and molybdenum disulphide.

High-resolution velocity measurements using dual-view tomographic digital holographic microscopy

NASA Astrophysics Data System (ADS)

Gao, Jian; Agarwal, Karuna; Katz, Joseph

2017-11-01

A recently developed two-view tomographic digital holographic microscopy (DHM) system is used for measuring the flow around a pair of cubes with height of 90 wall units immersed in the inner layer of a turbulent channel flow at Reτ = 2500. Matching of the two views at 1- μm precision is achieved by implementing a self-calibration procedure that determines the three-dimensional, three-component (3D3C) distortion function, which corrects the geometric mapping. The procedure has been tested using distorted synthetic particle fields, and then implemented on experimental data. The two views are used to overcome the reduced accuracy of DHM in the axial direction of the reference beam due to elongation of the reconstructed traces. Multiplying the two precisely-matched 3D intensity fields is used for truncating the elongated traces. The velocity distributions are obtained by 3D particle tracking guided by 3D cross-correlation of the truncated intensity fields along with other size/shape/smoothness constraints. As demonstrated by how divergence-free the data is, the resulting 3D3C velocity field is substantially more accurate than results obtained from single-view DHM. Results show that the cube is surrounded by a vorticity ``canopy'' that extends from upstream of its front surface to the separated region in its near wake. Nearly axial necklace vortices remain confined to the near wall region between the cubes, but expand rapidly behind them. Funded by NSF and ONR.

Water vapour tomography using GPS phase observations: Results from the ESCOMPTE experiment

NASA Astrophysics Data System (ADS)

Nilsson, T.; Gradinarsky, L.; Elgered, G.

2007-10-01

Global Positioning System (GPS) tomography is a technique for estimating the 3-D structure of the atmospheric water vapour using data from a dense local network of GPS receivers. Several current methods utilize estimates of slant wet delays between the GPS satellites and the receivers on the ground, which are difficult to obtain with millimetre accuracy from the GPS observations. We present results of applying a new tomographic method to GPS data from the Expériance sur site pour contraindre les modèles de pollution atmosphérique et de transport d'emissions (ESCOMPTE) experiment in southern France. This method does not rely on any slant wet delay estimates, instead it uses the GPS phase observations directly. We show that the estimated wet refractivity profiles estimated by this method is on the same accuracy level or better compared to other tomographic methods. The results are in agreement with earlier simulations, for example the profile information is limited above 4 km.

Laboratory MCAO Test-Bed for Developing Wavefront Sensing Concepts.

PubMed

Goncharov, A V; Dainty, J C; Esposito, S; Puglisi, A

2005-07-11

An experimental optical bench test-bed for developing new wavefront sensing concepts for Multi-Conjugate Adaptive Optics (MCAO) systems is described. The main objective is to resolve imaging problems associated with wavefront sensing of the atmospheric turbulence for future MCAO systems on Extremely Large Telescopes (ELTs). The test-bed incorporates five reference sources, two deformable mirrors (DMs) and atmospheric phase screens to simulate a scaled version of a 10-m adaptive telescope operating at the K band. A recently proposed compact tomographic wavefront sensor is employed for star-oriented DMs control in the MCAO system. The MCAO test-bed is used to verify the feasibility of the wavefront sensing concept utilizing a field lenslet array for multi-pupil imaging on a single detector. First experimental results of MCAO correction with the proposed tomographic wavefront sensor are presented and compared to the theoretical prediction based on the characteristics of the phase screens, actuator density of the DMs and the guide star configuration.

Limited-angle tomography for analyzer-based phase-contrast X-ray imaging

PubMed Central

Majidi, Keivan; Wernick, Miles N; Li, Jun; Muehleman, Carol; Brankov, Jovan G

2014-01-01

Multiple-Image Radiography (MIR) is an analyzer-based phase-contrast X-ray imaging method (ABI), which is emerging as a potential alternative to conventional radiography. MIR simultaneously generates three planar parametric images containing information about scattering, refraction and attenuation properties of the object. The MIR planar images are linear tomographic projections of the corresponding object properties, which allows reconstruction of volumetric images using computed tomography (CT) methods. However, when acquiring a full range of linear projections around the tissue of interest is not feasible or the scanning time is limited, limited-angle tomography techniques can be used to reconstruct these volumetric images near the central plane, which is the plane that contains the pivot point of the tomographic movement. In this work, we use computer simulations to explore the applicability of limited-angle tomography to MIR. We also investigate the accuracy of reconstructions as a function of number of tomographic angles for a fixed total radiation exposure. We use this function to find an optimal range of angles over which data should be acquired for limited-angle tomography MIR (LAT-MIR). Next, we apply the LAT-MIR technique to experimentally acquired MIR projections obtained in a cadaveric human thumb study. We compare the reconstructed slices near the central plane to the same slices reconstructed by CT-MIR using the full angular view around the object. Finally, we perform a task-based evaluation of LAT-MIR performance for different numbers of angular views, and use template matching to detect cartilage in the refraction image near the central plane. We use the signal-to-noise ratio of this test as the detectability metric to investigate an optimum range of tomographic angles for detecting soft tissues in LAT-MIR. Both results show that there is an optimum range of angular view for data acquisition where LAT-MIR yields the best performance, comparable to CT-MIR only if one considers volumetric images near the central plane and not the whole volume. PMID:24898008

Limited-angle tomography for analyzer-based phase-contrast x-ray imaging

NASA Astrophysics Data System (ADS)

Majidi, Keivan; Wernick, Miles N.; Li, Jun; Muehleman, Carol; Brankov, Jovan G.

2014-07-01

Multiple-image radiography (MIR) is an analyzer-based phase-contrast x-ray imaging method, which is emerging as a potential alternative to conventional radiography. MIR simultaneously generates three planar parametric images containing information about scattering, refraction and attenuation properties of the object. The MIR planar images are linear tomographic projections of the corresponding object properties, which allows reconstruction of volumetric images using computed tomography (CT) methods. However, when acquiring a full range of linear projections around the tissue of interest is not feasible or the scanning time is limited, limited-angle tomography techniques can be used to reconstruct these volumetric images near the central plane, which is the plane that contains the pivot point of the tomographic movement. In this work, we use computer simulations to explore the applicability of limited-angle tomography to MIR. We also investigate the accuracy of reconstructions as a function of number of tomographic angles for a fixed total radiation exposure. We use this function to find an optimal range of angles over which data should be acquired for limited-angle tomography MIR (LAT-MIR). Next, we apply the LAT-MIR technique to experimentally acquired MIR projections obtained in a cadaveric human thumb study. We compare the reconstructed slices near the central plane to the same slices reconstructed by CT-MIR using the full angular view around the object. Finally, we perform a task-based evaluation of LAT-MIR performance for different numbers of angular views, and use template matching to detect cartilage in the refraction image near the central plane. We use the signal-to-noise ratio of this test as the detectability metric to investigate an optimum range of tomographic angles for detecting soft tissues in LAT-MIR. Both results show that there is an optimum range of angular view for data acquisition where LAT-MIR yields the best performance, comparable to CT-MIR only if one considers volumetric images near the central plane and not the whole volume.

Cell segmentation in phase contrast microscopy images via semi-supervised classification over optics-related features.

PubMed

Su, Hang; Yin, Zhaozheng; Huh, Seungil; Kanade, Takeo

2013-10-01

Phase-contrast microscopy is one of the most common and convenient imaging modalities to observe long-term multi-cellular processes, which generates images by the interference of lights passing through transparent specimens and background medium with different retarded phases. Despite many years of study, computer-aided phase contrast microscopy analysis on cell behavior is challenged by image qualities and artifacts caused by phase contrast optics. Addressing the unsolved challenges, the authors propose (1) a phase contrast microscopy image restoration method that produces phase retardation features, which are intrinsic features of phase contrast microscopy, and (2) a semi-supervised learning based algorithm for cell segmentation, which is a fundamental task for various cell behavior analysis. Specifically, the image formation process of phase contrast microscopy images is first computationally modeled with a dictionary of diffraction patterns; as a result, each pixel of a phase contrast microscopy image is represented by a linear combination of the bases, which we call phase retardation features. Images are then partitioned into phase-homogeneous atoms by clustering neighboring pixels with similar phase retardation features. Consequently, cell segmentation is performed via a semi-supervised classification technique over the phase-homogeneous atoms. Experiments demonstrate that the proposed approach produces quality segmentation of individual cells and outperforms previous approaches. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Hard X-ray full field microscopy and magnifying microtomography using compound refractive lenses

NASA Astrophysics Data System (ADS)

Schroer, Christian G.; Günzler, Til Florian; Benner, Boris; Kuhlmann, Marion; Tümmler, Johannes; Lengeler, Bruno; Rau, Christoph; Weitkamp, Timm; Snigirev, Anatoly; Snigireva, Irina

2001-07-01

For hard X-rays, parabolic compound refractive lenses (PCRLs) are genuine imaging devices like glass lenses for visible light. Based on these new lenses, a hard X-ray full field microscope has been constructed that is ideally suited to image the interior of opaque samples with a minimum of sample preparation. As a result of a large depth of field, CRL micrographs are sharp projection images of most samples. To obtain 3D information about a sample, tomographic techniques are combined with magnified imaging.

Tomographic reconstruction of heat release rate perturbations induced by helical modes in turbulent swirl flames

NASA Astrophysics Data System (ADS)

Moeck, Jonas P.; Bourgouin, Jean-François; Durox, Daniel; Schuller, Thierry; Candel, Sébastien

2013-04-01

Swirl flows with vortex breakdown are widely used in industrial combustion systems for flame stabilization. This type of flow is known to sustain a hydrodynamic instability with a rotating helical structure, one common manifestation of it being the precessing vortex core. The role of this unsteady flow mode in combustion is not well understood, and its interaction with combustion instabilities and flame stabilization remains unclear. It is therefore important to assess the structure of the perturbation in the flame that is induced by this helical mode. Based on principles of tomographic reconstruction, a method is presented to determine the 3-D distribution of the heat release rate perturbation associated with the helical mode. Since this flow instability is rotating, a phase-resolved sequence of projection images of light emitted from the flame is identical to the Radon transform of the light intensity distribution in the combustor volume and thus can be used for tomographic reconstruction. This is achieved with one stationary camera only, a vast reduction in experimental and hardware requirements compared to a multi-camera setup or camera repositioning, which is typically required for tomographic reconstruction. Different approaches to extract the coherent part of the oscillation from the images are discussed. Two novel tomographic reconstruction algorithms specifically tailored to the structure of the heat release rate perturbations related to the helical mode are derived. The reconstruction techniques are first applied to an artificial field to illustrate the accuracy. High-speed imaging data acquired in a turbulent swirl-stabilized combustor setup with strong helical mode oscillations are then used to reconstruct the 3-D structure of the associated perturbation in the flame.

Transmission X-ray microscopy (TXM) reveals the nanostructure of a smectite gel.

PubMed

Zbik, Marek S; Martens, Wayde N; Frost, Ray L; Song, Yen-Fang; Chen, Yi-Ming; Chen, Jian-Hua

2008-08-19

The unusual behavior of smectites, the ability to change volume when wetted (swelling) or dried (shrinking), makes soil rich in smectites very unstable and dangerous for the building industry because of the movement of building foundations and poor slope stability. These macroscopic properties are dominated by the structural arrangement of the smectites' finest fraction. Here, we show in three dimensions how the swelling phenomenon in smectite, caused by a combination of hydratation and electrostatic forces, may expand the dry smectite volume not 10-fold, as previously thought, but to more than 1000-fold. A new technique, transmission X-ray microscopy, makes it possible to investigate the internal structure and 3-D tomographic reconstruction of clay aggregates. This reveals, for the first time, the smectite gel arrangement in the voluminous cellular tactoid structure within a natural aqueous environment.

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.

PubMed

Nakano, Miki; Miyashita, Osamu; Jonic, Slavica; Song, Changyong; Nam, Daewoong; Joti, Yasumasa; Tama, Florence

2017-07-01

The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

Multiscale tomographic analysis of heterogeneous cast Al-Si-X alloys.

PubMed

Asghar, Z; Requena, G; Sket, F

2015-07-01

The three-dimensional microstructure of cast AlSi12Ni and AlSi10Cu5Ni2 alloys is investigated by laboratory X-ray computed tomography, synchrotron X-ray computed microtomography, light optical tomography and synchrotron X-ray computed microtomography with submicrometre resolution. The results obtained with each technique are correlated with the size of the scanned volumes and resolved microstructural features. Laboratory X-ray computed tomography is sufficient to resolve highly absorbing aluminides but eutectic and primary Si remain unrevealed. Synchrotron X-ray computed microtomography at ID15/ESRF gives better spatial resolution and reveals primary Si in addition to aluminides. Synchrotron X-ray computed microtomography at ID19/ESRF reveals all the phases ≥ ∼1 μm in volumes about 80 times smaller than laboratory X-ray computed tomography. The volumes investigated by light optical tomography and submicrometre synchrotron X-ray computed microtomography are much smaller than laboratory X-ray computed tomography but both techniques provide local chemical information on the types of aluminides. The complementary techniques applied enable a full three-dimensional characterization of the microstructure of the alloys at length scales ranging over six orders of magnitude. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Tomographic sensing and localization of fluorescently labeled circulating cells in mice in vivo

NASA Astrophysics Data System (ADS)

Zettergren, Eric; Swamy, Tushar; Runnels, Judith; Lin, Charles P.; Niedre, Mark

2012-07-01

Sensing and enumeration of specific types of circulating cells in small animals is an important problem in many areas of biomedical research. Microscopy-based fluorescence in vivo flow cytometry methods have been developed previously, but these are typically limited to sampling of very small blood volumes, so that very rare circulating cells may escape detection. Recently, we described the development of a ‘diffuse fluorescence flow cytometer’ (DFFC) that allows sampling of much larger blood vessels and therefore circulating blood volumes in the hindlimb, forelimb or tail of a mouse. In this work, we extend this concept by developing and validating a method to tomographically localize circulating fluorescently labeled cells in the cross section of a tissue simulating optical flow phantom and mouse limb. This was achieved using two modulated light sources and an array of six fiber-coupled detectors that allowed rapid, high-sensitivity acquisition of full tomographic data sets at 10 Hz. These were reconstructed into two-dimensional cross-sectional images using Monte Carlo models of light propagation and the randomized algebraic reconstruction technique. We were able to obtain continuous images of moving cells in the sample cross section with 0.5 mm accuracy or better. We first demonstrated this concept in limb-mimicking optical flow photons with up to four flow channels, and then in the tails of mice with fluorescently labeled multiple myeloma cells. This approach increases the overall diagnostic utility of our DFFC instrument.

ImSyn: photonic image synthesis applied to synthetic aperture radar, microscopy, and ultrasound imaging

NASA Astrophysics Data System (ADS)

Turpin, Terry M.; Lafuse, James L.

1993-02-01

ImSynTM is an image synthesis technology, developed and patented by Essex Corporation. ImSynTM can provide compact, low cost, and low power solutions to some of the most difficult image synthesis problems existing today. The inherent simplicity of ImSynTM enables the manufacture of low cost and reliable photonic systems for imaging applications ranging from airborne reconnaissance to doctor's office ultrasound. The initial application of ImSynTM technology has been to SAR processing; however, it has a wide range of applications such as: image correlation, image compression, acoustic imaging, x-ray tomographic (CAT, PET, SPECT), magnetic resonance imaging (MRI), microscopy, range- doppler mapping (extended TDOA/FDOA). This paper describes ImSynTM in terms of synthetic aperture microscopy and then shows how the technology can be extended to ultrasound and synthetic aperture radar. The synthetic aperture microscope (SAM) enables high resolution three dimensional microscopy with greater dynamic range than real aperture microscopes. SAM produces complex image data, enabling the use of coherent image processing techniques. Most importantly SAM produces the image data in a form that is easily manipulated by a digital image processing workstation.

Quantitative tomographic imaging of intermolecular FRET in small animals

PubMed Central

Venugopal, Vivek; Chen, Jin; Barroso, Margarida; Intes, Xavier

2012-01-01

Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule. PMID:23243567

Correlation of Thermally Induced Pores with Microstructural Features Using High Energy X-rays

NASA Astrophysics Data System (ADS)

Menasche, David B.; Shade, Paul A.; Lind, Jonathan; Li, Shiu Fai; Bernier, Joel V.; Kenesei, Peter; Schuren, Jay C.; Suter, Robert M.

2016-11-01

Combined application of a near-field High Energy Diffraction Microscopy measurement of crystal lattice orientation fields and a tomographic measurement of pore distributions in a sintered nickel-based superalloy sample allows pore locations to be correlated with microstructural features. Measurements were carried out at the Advanced Photon Source beamline 1-ID using an X-ray energy of 65 keV for each of the measurement modes. The nickel superalloy sample was prepared in such a way as to generate significant thermally induced porosity. A three-dimensionally resolved orientation map is directly overlaid with the tomographically determined pore map through a careful registration procedure. The data are shown to reliably reproduce the expected correlations between specific microstructural features (triple lines and quadruple nodes) and pore positions. With the statistics afforded by the 3D data set, we conclude that within statistical limits, pore formation does not depend on the relative orientations of the grains. The experimental procedures and analysis tools illustrated are being applied to a variety of materials problems in which local heterogeneities can affect materials properties.

On the use of variable coherence in inverse scattering problems

NASA Astrophysics Data System (ADS)

Baleine, Erwan

Even though most of the properties of optical fields, such as wavelength, polarization, wavefront curvature or angular spectrum, have been commonly manipulated in a variety of remote sensing procedures, controlling the degree of coherence of light did not find wide applications until recently. Since the emergence of optical coherence tomography, a growing number of scattering techniques have relied on temporal coherence gating which provides efficient target selectivity in a way achieved only by bulky short pulse measurements. The spatial counterpart of temporal coherence, however, has barely been exploited in sensing applications. This dissertation examines, in different scattering regimes, a variety of inverse scattering problems based on variable spatial coherence gating. Within the framework of the radiative transfer theory, this dissertation demonstrates that the short range correlation properties of a medium under test can be recovered by varying the size of the coherence volume of an illuminating beam. Nonetheless, the radiative transfer formalism does not account for long range correlations and current methods for retrieving the correlation function of the complex susceptibility require cumbersome cross-spectral density measurements. Instead, a variable coherence tomographic procedure is proposed where spatial coherence gating is used to probe the structural properties of single scattering media over an extended volume and with a very simple detection system. Enhanced backscattering is a coherent phenomenon that survives strong multiple scattering. The variable coherence tomography approach is extended in this context to diffusive media and it is demonstrated that specific photon trajectories can be selected in order to achieve depth-resolved sensing. Probing the scattering properties of shallow and deeper layers is of considerable interest in biological applications such as diagnosis of skin related diseases. The spatial coherence properties of an illuminating field can be manipulated over dimensions much larger than the wavelength thus providing a large effective sensing area. This is a practical advantage over many near-field microscopic techniques, which offer a spatial resolution beyond the classical diffraction limit but, at the expense of scanning a probe over a large area of a sample which is time consuming, and, sometimes, practically impossible. Taking advantage of the large field of view accessible when using the spatial coherence gating, this dissertation introduces the principle of variable coherence scattering microscopy. In this approach, a subwavelength resolution is achieved from simple far-zone intensity measurements by shaping the degree of spatial coherence of an evanescent field. Furthermore, tomographic techniques based on spatial coherence gating are especially attractive because they rely on simple detection schemes which, in principle, do not require any optical elements such as lenses. To demonstrate this capability, a correlated lensless imaging method is proposed and implemented, where both amplitude and phase information of an object are obtained by varying the degree of spatial coherence of the incident beam. Finally, it should be noted that the idea of using the spatial coherence properties of fields in a tomographic procedure is applicable to any type of electromagnetic radiation. Operating on principles of statistical optics, these sensing procedures can become alternatives for various target detection schemes, cutting-edge microscopies or x-ray imaging methods.

Measurement of spatial refractive index distributions of fusion spliced optical fibers by digital holographic microtomography

NASA Astrophysics Data System (ADS)

Pan, Feng; Deng, Yating; Ma, Xichao; Xiao, Wen

2017-11-01

Digital holographic microtomography is improved and applied to the measurements of three-dimensional refractive index distributions of fusion spliced optical fibers. Tomographic images are reconstructed from full-angle phase projection images obtained with a setup-rotation approach, in which the laser source, the optical system and the image sensor are arranged on an optical breadboard and synchronously rotated around the fixed object. For retrieving high-quality tomographic images, a numerical method is proposed to compensate the unwanted movements of the object in the lateral, axial and vertical directions during rotation. The compensation is implemented on the two-dimensional phase images instead of the sinogram. The experimental results exhibit distinctly the internal structures of fusion splices between a single-mode fiber and other fibers, including a multi-mode fiber, a panda polarization maintaining fiber, a bow-tie polarization maintaining fiber and a photonic crystal fiber. In particular, the internal structure distortion in the fusion areas can be intuitively observed, such as the expansion of the stress zones of polarization maintaining fibers, the collapse of the air holes of photonic crystal fibers, etc.

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

PubMed

Lagerstedt, Ingvar; Moore, William J; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R; Kleywegt, Gerard J

2013-11-01

The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Multiphoton imaging microscopy at deeper layers with adaptive optics control of spherical aberration.

PubMed

Bueno, Juan M; Skorsetz, Martin; Palacios, Raquel; Gualda, Emilio J; Artal, Pablo

2014-01-01

Despite the inherent confocality and optical sectioning capabilities of multiphoton microscopy, three-dimensional (3-D) imaging of thick samples is limited by the specimen-induced aberrations. The combination of immersion objectives and sensorless adaptive optics (AO) techniques has been suggested to overcome this difficulty. However, a complex plane-by-plane correction of aberrations is required, and its performance depends on a set of image-based merit functions. We propose here an alternative approach to increase penetration depth in 3-D multiphoton microscopy imaging. It is based on the manipulation of the spherical aberration (SA) of the incident beam with an AO device while performing fast tomographic multiphoton imaging. When inducing SA, the image quality at best focus is reduced; however, better quality images are obtained from deeper planes within the sample. This is a compromise that enables registration of improved 3-D multiphoton images using nonimmersion objectives. Examples on ocular tissues and nonbiological samples providing different types of nonlinear signal are presented. The implementation of this technique in a future clinical instrument might provide a better visualization of corneal structures in living eyes.

Classification of cryo electron microscopy images, noisy tomographic images recorded with unknown projection directions, by simultaneously estimating reconstructions and application to an assembly mutant of Cowpea Chlorotic Mottle Virus and portals of the bacteriophage P22

NASA Astrophysics Data System (ADS)

Lee, Junghoon; Zheng, Yili; Yin, Zhye; Doerschuk, Peter C.; Johnson, John E.

2010-08-01

Cryo electron microscopy is frequently used on biological specimens that show a mixture of different types of object. Because the electron beam rapidly destroys the specimen, the beam current is minimized which leads to noisy images (SNR substantially less than 1) and only one projection image per object (with an unknown projection direction) is collected. For situations where the objects can reasonably be described as coming from a finite set of classes, an approach based on joint maximum likelihood estimation of the reconstruction of each class and then use of the reconstructions to label the class of each image is described and demonstrated on two challenging problems: an assembly mutant of Cowpea Chlorotic Mottle Virus and portals of the bacteriophage P22.

Mineralization of collagen may occur on fibril surfaces: evidence from conventional and high-voltage electron microscopy and three-dimensional imaging

NASA Technical Reports Server (NTRS)

Landis, W. J.; Hodgens, K. J.; Song, M. J.; Arena, J.; Kiyonaga, S.; Marko, M.; Owen, C.; McEwen, B. F.

1996-01-01

The interaction between collagen and mineral crystals in the normally calcifying leg tendons from the domestic turkey, Meleagris gallopavo, has been investigated at an ultrastructural level with conventional and high-voltage electron microscopy, computed tomography, and three-dimensional image reconstruction methods. Specimens treated by either aqueous or anhydrous techniques and resin-embedded were appropriately sectioned and regions of early tendon mineralization were photographed. On the basis of individual photomicrographs, stereoscopic pairs of images, and tomographic three-dimensional image reconstructions, platelet-shaped crystals may be demonstrated for the first time in association with the surface of collagen fibrils. Mineral is also observed in closely parallel arrays within collagen hole and overlap zones. The mineral deposition at these spatially distinct locations in the tendon provides insight into possible means by which calcification is mediated by collagen as a fundamental event in skeletal and dental formation among vertebrates.

The Ettention software package.

PubMed

Dahmen, Tim; Marsalek, Lukas; Marniok, Nico; Turoňová, Beata; Bogachev, Sviatoslav; Trampert, Patrick; Nickels, Stefan; Slusallek, Philipp

2016-02-01

We present a novel software package for the problem "reconstruction from projections" in electron microscopy. The Ettention framework consists of a set of modular building-blocks for tomographic reconstruction algorithms. The well-known block iterative reconstruction method based on Kaczmarz algorithm is implemented using these building-blocks, including adaptations specific to electron tomography. Ettention simultaneously features (1) a modular, object-oriented software design, (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU) or many-core architectures like Xeon Phi, and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface. We also provide developers with a clean and well-structured application programming interface (API) that allows for extending the software easily and thus makes it an ideal platform for algorithmic research while hiding most of the technical details of high-performance computing. Copyright © 2015 Elsevier B.V. All rights reserved.

Tomographic PIV behind a prosthetic heart valve

NASA Astrophysics Data System (ADS)

Hasler, D.; Landolt, A.; Obrist, D.

2016-05-01

The instantaneous three-dimensional velocity field past a bioprosthetic heart valve was measured using tomographic particle image velocimetry. Two digital cameras were used together with a mirror setup to record PIV images from four different angles. Measurements were conducted in a transparent silicone phantom with a simplified geometry of the aortic root. The refraction indices of the silicone phantom and the working fluid were matched to minimize optical distortion from the flow field to the cameras. The silicone phantom of the aorta was integrated in a flow loop driven by a piston pump. Measurements were conducted for steady and pulsatile flow conditions. Results of the instantaneous, ensemble and phase-averaged flow field are presented. The three-dimensional velocity field reveals a flow topology, which can be related to features of the aortic valve prosthesis.

Surface-Wave Tomographic Studies of the Hudson Bay Lithosphere: Implications for Paleoproterozoic Tectonic Processes and the Assembly of the Canadian Shield

NASA Astrophysics Data System (ADS)

Darbyshire, F. A.

2015-12-01

Hudson Bay is a shallow intracratonic basin that partially conceals the Trans-Hudson Orogen (THO) in northern Canada. The THO is thought to be a Himalayan-scale Paleoproterozoic orogenic event that was an important component of assembly of the Canadian Shield, marking the collision of the Archean Superior and Western Churchill plates. Until recently, only global and continental-scale seismic tomographic models had imaged the upper-mantle structure of the region, giving a broad but relatively low-resolution picture of the thick lithospheric keel. The Hudson Bay Lithospheric Experiment (HuBLE) investigated the present-day seismic structure beneath Hudson Bay and its surroundings, using a distributed broadband seismograph network installed around the periphery of the Bay and complemented by existing permanent and temporary seismographs further afield. This configuration, though not optimal for body-wave studies which use subvertical arrivals, is well-suited to surface wave tomographic techniques, with many paths crossing the Bay. As there is little seismicity in the region around the Canadian Shield, two-station measurements of teleseismic Rayleigh wave phase velocity formed the principal data set for lithospheric studies. The interstation measurements were combined in a linearized tomographic inversion for maps of phase velocity and azimuthal anisotropy at periods of 20-200 s; these maps were then used to calculate a pseudo-3D anisotropic upper-mantle shear-wavespeed model of the region. The model shows thick (~180-260 km), seismically fast lithosphere across the Hudson Bay region, with a near-vertical 'curtain' of lower wavespeeds trending NE-SW across the Bay, likely associated with more juvenile material trapped between the Archean Superior and Churchill continental cores during the THO. The lithosphere is layered, suggesting a 2-stage formation process. Seismic anisotropy patterns vary with depth; a circular pattern in the uppermost mantle wrapping around the Hudson Bay basin is superseded in the lower lithosphere by a pattern that mirrors THO-related structures within the crust; the lower layer thus likely formed when stress patterns related to the THO were still active.

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

Noise robustness of a combined phase retrieval and reconstruction method for phase-contrast tomography.

PubMed

Kongskov, Rasmus Dalgas; Jørgensen, Jakob Sauer; Poulsen, Henning Friis; Hansen, Per Christian

2016-04-01

Classical reconstruction methods for phase-contrast tomography consist of two stages: phase retrieval and tomographic reconstruction. A novel algebraic method combining the two was suggested by Kostenko et al. [Opt. Express21, 12185 (2013)OPEXFF1094-408710.1364/OE.21.012185], and preliminary results demonstrated improved reconstruction compared with a given two-stage method. Using simulated free-space propagation experiments with a single sample-detector distance, we thoroughly compare the novel method with the two-stage method to address limitations of the preliminary results. We demonstrate that the novel method is substantially more robust toward noise; our simulations point to a possible reduction in counting times by an order of magnitude.

Grating-based X-ray tomography of 3D food structures

NASA Astrophysics Data System (ADS)

Miklos, Rikke; Nielsen, Mikkel Schou; Einarsdottir, Hildur; Lametsch, René

2016-10-01

A novel grating based X-ray phase-contrast tomographic method has been used to study how partly substitution of meat proteins with two different types of soy proteins affect the structure of the formed protein gel in meat emulsions. The measurements were performed at the Swiss synchrotron radiation light source using a grating interferometric set-up.

Quantitative photothermal phase imaging of red blood cells using digital holographic photothermal microscope.

PubMed

Vasudevan, Srivathsan; Chen, George C K; Lin, Zhiping; Ng, Beng Koon

2015-05-10

Photothermal microscopy (PTM), a noninvasive pump-probe high-resolution microscopy, has been applied as a bioimaging tool in many biomedical studies. PTM utilizes a conventional phase contrast microscope to obtain highly resolved photothermal images. However, phase information cannot be extracted from these photothermal images, as they are not quantitative. Moreover, the problem of halos inherent in conventional phase contrast microscopy needs to be tackled. Hence, a digital holographic photothermal microscopy technique is proposed as a solution to obtain quantitative phase images. The proposed technique is demonstrated by extracting phase values of red blood cells from their photothermal images. These phase values can potentially be used to determine the temperature distribution of the photothermal images, which is an important study in live cell monitoring applications.

Cryo X-ray microscope with flat sample geometry for correlative fluorescence and nanoscale tomographic imaging.

PubMed

Schneider, Gerd; Guttmann, Peter; Rehbein, Stefan; Werner, Stephan; Follath, Rolf

2012-02-01

X-ray imaging offers a new 3-D view into cells. With its ability to penetrate whole hydrated cells it is ideally suited for pairing fluorescence light microscopy and nanoscale X-ray tomography. In this paper, we describe the X-ray optical set-up and the design of the cryo full-field transmission X-ray microscope (TXM) at the electron storage ring BESSY II. Compared to previous TXM set-ups with zone plate condenser monochromator, the new X-ray optical layout employs an undulator source, a spherical grating monochromator and an elliptically shaped glass capillary mirror as condenser. This set-up improves the spectral resolution by an order of magnitude. Furthermore, the partially coherent object illumination improves the contrast transfer of the microscope compared to incoherent conditions. With the new TXM, cells grown on flat support grids can be tilted perpendicular to the optical axis without any geometrical restrictions by the previously required pinhole for the zone plate monochromator close to the sample plane. We also developed an incorporated fluorescence light microscope which permits to record fluorescence, bright field and DIC images of cryogenic cells inside the TXM. For TXM tomography, imaging with multi-keV X-rays is a straightforward approach to increase the depth of focus. Under these conditions phase contrast imaging is necessary. For soft X-rays with shrinking depth of focus towards 10nm spatial resolution, thin optical sections through a thick specimen might be obtained by deconvolution X-ray microscopy. As alternative 3-D X-ray imaging techniques, the confocal cryo-STXM and the dual beam cryo-FIB/STXM with photoelectron detection are proposed. Copyright © 2012 Elsevier Inc. All rights reserved.

Residual Microstrain in Root Dentin after Canal Instrumentation Measured with Digital Moiré Interferometry.

PubMed

Lim, Helena; Li, Fang-Chi; Friedman, Shimon; Kishen, Anil

2016-09-01

Residual microstrain influences the resistance to crack propagation in a biomaterial. This study evaluated the residual microstrain and microdefects formed in dentin after canal instrumentation in teeth maintained in hydrated and nonhydrated environments. Canals of 18 extracted human premolars with single-root canals were instrumented in accordance with 3 groups: the ProTaper Universal (Dentsply Maillefer, Ballaigues, Switzerland) group: ProTaper Universal (S1, S2, F1, and F2) used in rotation, the WaveOne Primary (Dentsply Maillefer) group: the WaveOne (Primary) used in reciprocal motion, and the control group: hand files. Half the specimens (3/group) were maintained in deionized water (hydrated) and half in ambient relative humidity conditions (22°C, 55% RH) for 72 hours (nonhydrated). Customized high-sensitivity digital moiré interferometry was used to qualitatively evaluate pre- and postinstrumentation dentinal microstrain. Subsequently, specimens were examined for dentinal microdefects with micro-computed tomographic imaging and polarized light microscopy. Digital moiré interferometry showed only minor changes in postinstrumentation microstrain in hydrated dentin in all groups, suggestive of a stress relaxation behavior. Nonhydrated dentin in all groups showed localized concentration of postinstrumentation microstrain, which appeared higher in the WaveOne group than in the other groups. No dentinal microdefects were detected by micro-computed tomographic imaging and polarized light microscopy in hydrated and nonhydrated specimens in all groups. This study suggested that the biomechanical response of root dentin to instrumentation was influenced by hydration. Reciprocating, rotary, and hand instrumentation of well-hydrated roots did not cause an increase in residual microstrain or the formation of microdefects in root dentin. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Markov chain Monte Carlo estimation of quantum states

NASA Astrophysics Data System (ADS)

Diguglielmo, James; Messenger, Chris; Fiurášek, Jaromír; Hage, Boris; Samblowski, Aiko; Schmidt, Tabea; Schnabel, Roman

2009-03-01

We apply a Bayesian data analysis scheme known as the Markov chain Monte Carlo to the tomographic reconstruction of quantum states. This method yields a vector, known as the Markov chain, which contains the full statistical information concerning all reconstruction parameters including their statistical correlations with no a priori assumptions as to the form of the distribution from which it has been obtained. From this vector we can derive, e.g., the marginal distributions and uncertainties of all model parameters, and also of other quantities such as the purity of the reconstructed state. We demonstrate the utility of this scheme by reconstructing the Wigner function of phase-diffused squeezed states. These states possess non-Gaussian statistics and therefore represent a nontrivial case of tomographic reconstruction. We compare our results to those obtained through pure maximum-likelihood and Fisher information approaches.

Magnetic particle imaging: from proof of principle to preclinical applications

NASA Astrophysics Data System (ADS)

Knopp, T.; Gdaniec, N.; Möddel, M.

2017-07-01

Tomographic imaging has become a mandatory tool for the diagnosis of a majority of diseases in clinical routine. Since each method has its pros and cons, a variety of them is regularly used in clinics to satisfy all application needs. Magnetic particle imaging (MPI) is a relatively new tomographic imaging technique that images magnetic nanoparticles with a high spatiotemporal resolution in a quantitative way, and in turn is highly suited for vascular and targeted imaging. MPI was introduced in 2005 and now enters the preclinical research phase, where medical researchers get access to this new technology and exploit its potential under physiological conditions. Within this paper, we review the development of MPI since its introduction in 2005. Besides an in-depth description of the basic principles, we provide detailed discussions on imaging sequences, reconstruction algorithms, scanner instrumentation and potential medical applications.

A Simple Configuration for Quantitative Phase Contrast Microscopy of Transmissible Samples

NASA Astrophysics Data System (ADS)

Sengupta, Chandan; Dasgupta, Koustav; Bhattacharya, K.

Phase microscopy attempts to visualize and quantify the phase distribution of samples which are otherwise invisible under microscope without the use of stains. The two principal approaches to phase microscopy are essentially those of Fourier plane modulation and interferometric techniques. Although the former, first proposed by Zernike, had been the harbinger of phase microscopy, it was the latter that allowed for quantitative evaluation of phase samples. However interferometric techniques are fraught with associated problems such as complicated setup involving mirrors and beam-splitters, the need for a matched objective in the reference arm and also the need for vibration isolation. The present work proposes a single element cube beam-splitter (CBS) interferometer combined with a microscope objective (MO) for interference microscopy. Because of the monolithic nature of the interferometer, the system is almost insensitive to vibrations and relatively simple to align. It will be shown that phase shifting properties may also be introduced by suitable and proper use of polarizing devices. Initial results showing the quantitative three dimensional phase profiles of simulated and actual biological specimens are presented.

Proxies of oceanic Lithosphere/Asthenosphere Boundary from Global Seismic Anisotropy Tomography

NASA Astrophysics Data System (ADS)

Burgos, Gael; Montagner, Jean-Paul; Beucler, Eric; Trampert, Jeannot; Capdeville, Yann

2013-04-01

Surface waves provide essential information on the knowledge of the upper mantle global structure despite their low lateral resolution. This study, based on surface waves data, presents the development of a new anisotropic tomographic model of the upper mantle, a simplified isotropic model and the consequences of these results for the Lithosphere/Asthenosphere Boundary (LAB). As a first step, a large number of data is collected, these data are merged and regionalized in order to derive maps of phase and group velocity for the fundamental mode of Rayleigh and Love waves and their azimuthal dependence (maps of phase velocity are also obtained for the first six overtones). As a second step, a crustal a posteriori model is developped from the Monte-Carlo inversion of the shorter periods of the dataset, in order to take into account the effect of the shallow layers on the upper mantle. With the crustal model, a first Monte-Carlo inversion for the upper mantle structure is realized in a simplified isotropic parameterization to highlight the influence of the LAB properties on the surface waves data. Still using the crustal model, a first order perturbation theory inversion is performed in a fully anisotropic parameterization to build a 3-D tomographic model of the upper mantle (an extended model until the transition zone is also obtained by using the overtone data). Estimates of the LAB depth are derived from the upper mantle models and compared with the predictions of oceanic lithosphere cooling models. Seismic events are simulated using the Spectral Element Method in order to validate the ability of the anisotropic tomographic model of the upper mantle to re- produce observed seismograms.

Solving large tomographic linear systems: size reduction and error estimation

NASA Astrophysics Data System (ADS)

Voronin, Sergey; Mikesell, Dylan; Slezak, Inna; Nolet, Guust

2014-10-01

We present a new approach to reduce a sparse, linear system of equations associated with tomographic inverse problems. We begin by making a modification to the commonly used compressed sparse-row format, whereby our format is tailored to the sparse structure of finite-frequency (volume) sensitivity kernels in seismic tomography. Next, we cluster the sparse matrix rows to divide a large matrix into smaller subsets representing ray paths that are geographically close. Singular value decomposition of each subset allows us to project the data onto a subspace associated with the largest eigenvalues of the subset. After projection we reject those data that have a signal-to-noise ratio (SNR) below a chosen threshold. Clustering in this way assures that the sparse nature of the system is minimally affected by the projection. Moreover, our approach allows for a precise estimation of the noise affecting the data while also giving us the ability to identify outliers. We illustrate the method by reducing large matrices computed for global tomographic systems with cross-correlation body wave delays, as well as with surface wave phase velocity anomalies. For a massive matrix computed for 3.7 million Rayleigh wave phase velocity measurements, imposing a threshold of 1 for the SNR, we condensed the matrix size from 1103 to 63 Gbyte. For a global data set of multiple-frequency P wave delays from 60 well-distributed deep earthquakes we obtain a reduction to 5.9 per cent. This type of reduction allows one to avoid loss of information due to underparametrizing models. Alternatively, if data have to be rejected to fit the system into computer memory, it assures that the most important data are preserved.

Low-dose x-ray tomography through a deep convolutional neural network

DOE PAGES

Yang, Xiaogang; De Andrade, Vincent; Scullin, William; ...

2018-02-07

Synchrotron-based X-ray tomography offers the potential of rapid large-scale reconstructions of the interiors of materials and biological tissue at fine resolution. However, for radiation sensitive samples, there remain fundamental trade-offs between damaging samples during longer acquisition times and reducing signals with shorter acquisition times. We present a deep convolutional neural network (CNN) method that increases the acquired X-ray tomographic signal by at least a factor of 10 during low-dose fast acquisition by improving the quality of recorded projections. Short exposure time projections enhanced with CNN show similar signal to noise ratios as compared with long exposure time projections and muchmore » lower noise and more structural information than low-dose fats acquisition without CNN. We optimized this approach using simulated samples and further validated on experimental nano-computed tomography data of radiation sensitive mouse brains acquired with a transmission X-ray microscopy. We demonstrate that automated algorithms can reliably trace brain structures in datasets collected with low dose-CNN. As a result, this method can be applied to other tomographic or scanning based X-ray imaging techniques and has great potential for studying faster dynamics in specimens.« less

Low-dose x-ray tomography through a deep convolutional neural network

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

Yang, Xiaogang; De Andrade, Vincent; Scullin, William

Synchrotron-based X-ray tomography offers the potential of rapid large-scale reconstructions of the interiors of materials and biological tissue at fine resolution. However, for radiation sensitive samples, there remain fundamental trade-offs between damaging samples during longer acquisition times and reducing signals with shorter acquisition times. We present a deep convolutional neural network (CNN) method that increases the acquired X-ray tomographic signal by at least a factor of 10 during low-dose fast acquisition by improving the quality of recorded projections. Short exposure time projections enhanced with CNN show similar signal to noise ratios as compared with long exposure time projections and muchmore » lower noise and more structural information than low-dose fats acquisition without CNN. We optimized this approach using simulated samples and further validated on experimental nano-computed tomography data of radiation sensitive mouse brains acquired with a transmission X-ray microscopy. We demonstrate that automated algorithms can reliably trace brain structures in datasets collected with low dose-CNN. As a result, this method can be applied to other tomographic or scanning based X-ray imaging techniques and has great potential for studying faster dynamics in specimens.« less

In vivo tomographic imaging of deep seated cancer using fluorescence lifetime contrast

PubMed Central

Rice, William L.; Shcherbakova, Daria M; Verkusha, Vladislav V.; Kumar, Anand T.N.

2015-01-01

Preclinical cancer research would benefit from non-invasive imaging methods that allow tracking and visualization of early stage metastasis in vivo. While fluorescent proteins revolutionized intravital microscopy, two major challenges which still remain are tissue autofluorescence and hemoglobin absorption, which act to limit intravital optical techniques to large or subcutaneous tumors. Here we employ time-domain technology for the effective separation of tissue autofluorescence from extrinsic fluorophores, based on their distinct fluorescence lifetimes. Additionally, we employ cancer cells labelled with near infra-red fluorescent proteins (iRFP) to allow deep-tissue imaging. Our results demonstrate that time-domain imaging allows the detection of metastasis in deep-seated organs of living mice with a more than 20-fold increase in sensitivity compared to conventional continuous wave techniques. Furthermore, the distinct fluorescence lifetimes of each iRFP enables lifetime multiplexing of three different tumors, each expressing unique iRFP labels in the same animal. Fluorescence tomographic reconstructions reveal 3D distributions of iRFP720-expressing cancer cells in lungs and brain of live mice, allowing ready longitudinal monitoring of cancer cell fate with greater sensitivity than otherwise currently possible. PMID:25670171

Clinical studies of pigmented lesions in human skin by using a multiphoton tomograph

NASA Astrophysics Data System (ADS)

Balu, Mihaela; Kelly, Kristen M.; Zachary, Christopher B.; Harris, Ronald M.; Krasieva, Tatiana B.; König, Karsten; Tromberg, Bruce J.

2013-02-01

In vivo imaging of pigmented lesions in human skin was performed with a clinical multiphoton microscopy (MPM)-based tomograph (MPTflex, JenLab, Germany). Two-photon excited fluorescence was used for visualizing endogenous fluorophores such as NADH/FAD, keratin, melanin in the epidermal cells and elastin fibers in the dermis. Collagen fibers were imaged by second harmonic generation. Our study involved in vivo imaging of benign melanocytic nevi, atypical nevi and melanoma. The goal of this preliminary study was to identify in vivo the characteristic features and their frequency in pigmented lesions at different stages (benign, atypical and malignant) and to evaluate the ability of in vivo MPM to distinguish atypical nevi from melanoma. Comparison with histopathology was performed for the biopsied lesions. Benign melanocytic nevi were characterized by the presence of nevus cell nests at the epidermal-dermal junction. In atypical nevi, features such as lentiginous hyperplasia, acanthosis and architectural disorder were imaged. Cytological atypia was present in all the melanoma lesions imaged, showing the strongest correlation with malignancy. The MPM images demonstrated very good correlation with corresponding histological images, suggesting that MPM could be a promising tool for in vivo non-invasive pigmented lesion diagnosis, particularly distinguishing atypical nevi from melanoma.

Beam tracking phase tomography with laboratory sources

NASA Astrophysics Data System (ADS)

Vittoria, F. A.; Endrizzi, M.; Kallon, G. K. N.; Hagen, C. K.; Diemoz, P. C.; Zamir, A.; Olivo, A.

2018-04-01

An X-ray phase-contrast laboratory system is presented, based on the beam-tracking method. Beam-tracking relies on creating micro-beamlets of radiation by placing a structured mask before the sample, and analysing them by using a detector with sufficient resolution. The system is used in tomographic configuration to measure the three dimensional distribution of the linear attenuation coefficient, difference from unity of the real part of the refractive index, and of the local scattering power of specimens. The complementarity of the three signals is investigated, together with their potential use for material discrimination.

Predictive value of dual-energy spectral computed tomographic imaging on the histological origin of carcinomas in the ampullary region.

PubMed

Wei, Wei; Yu, Yongqiang; Lv, Weifu; Deng, Kexue; Yuan, Lei; Zhao, Yingming

2014-08-01

To investigate the value of dual-energy spectral computed tomographic imaging (DESCT) to predict the origin of carcinomas in the ampullary region. Fifty-seven patients with suspected ampullary region carcinomas underwent DESCT prior to biopsy or surgery. Among those patients, 30 were pancreatic adenocarcinomas, 11 were biliary adenocarcinomas, 16 were adenocarcinomas of the ampulla diagnosed by biopsy and/or pathological examination before or after surgical operation. We compared the CT spectral imaging features among the adenocarcinomas with the above-mentioned three different origins. Iodine concentration thresholds of 16.36, 21.86, and 21.86 mg/mL yielded a sensitivity and specificity of 100% for distinguishing between common bile duct adenocarcinomas and pancreatic adenocarcinomas in the arterial phase (AP), portal venous phase (PP), and delayed phase (DP), respectively. Thresholds of 16.70, 24.33, and 26.43 mg/mL yielded a sensitivity and specificity of 100% for distinguishing between common bile duct adenocarcinomas and ampullary adenocarcinomas in the AP, PP, and DP, respectively. Iodine concentration thresholds of 16.66 and 17.78 mg/mL yielded a sensitivity and specificity of 100% for distinguishing between ampullary adenocarcinomas and pancreatic adenocarcinomas in the PP and DP, respectively. DESCT with multiple parameters can provide useful diagnostic information and may be used to predict the histological origin of carcinomas in the ampullary region.

The finite body triangulation: algorithms, subgraphs, homogeneity estimation and application.

PubMed

Carson, Cantwell G; Levine, Jonathan S

2016-09-01

The concept of a finite body Dirichlet tessellation has been extended to that of a finite body Delaunay 'triangulation' to provide a more meaningful description of the spatial distribution of nonspherical secondary phase bodies in 2- and 3-dimensional images. A finite body triangulation (FBT) consists of a network of minimum edge-to-edge distances between adjacent objects in a microstructure. From this is also obtained the characteristic object chords formed by the intersection of the object boundary with the finite body tessellation. These two sets of distances form the basis of a parsimonious homogeneity estimation. The characteristics of the spatial distribution are then evaluated with respect to the distances between objects and the distances within them. Quantitative analysis shows that more physically representative distributions can be obtained by selecting subgraphs, such as the relative neighbourhood graph and the minimum spanning tree, from the finite body tessellation. To demonstrate their potential, we apply these methods to 3-dimensional X-ray computed tomographic images of foamed cement and their 2-dimensional cross sections. The Python computer code used to estimate the FBT is made available. Other applications for the algorithm - such as porous media transport and crack-tip propagation - are also discussed. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Biological applications of phase-contrast electron microscopy.

PubMed

Nagayama, Kuniaki

2014-01-01

Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.

Dendritic Growth Morphologies in Al-Zn Alloys—Part II: Phase-Field Computations

NASA Astrophysics Data System (ADS)

Dantzig, J. A.; Di Napoli, Paolo; Friedli, J.; Rappaz, M.

2013-12-01

In Part I of this article, the role of the Zn content in the development of solidification microstructures in Al-Zn alloys was investigated experimentally using X-ray tomographic microscopy. The transition region between dendrites found at low Zn content and dendrites found at high Zn content was characterized by textured seaweed-type structures. This Dendrite Orientation Transition (DOT) was explained by the effect of the Zn content on the weak anisotropy of the solid-liquid interfacial energy of Al. In order to further support this interpretation and to elucidate the growth mechanisms of the complex structures that form in the DOT region, a detailed phase-field study exploring anisotropy parameters' space is presented in this paper. For equiaxed growth, our results essentially recapitulate those of Haxhimali et al.[1] in simulations for pure materials. We find distinct regions of the parameter space associated with and dendrites, separated by a region where hyperbranched dendrites are observed. In simulations of directional solidification, we find similar behavior at the extrema, but in this case, the anisotropy parameters corresponding to the hyperbranched region produce textured seaweeds. As noted in the experimental work reported in Part I, these structures are actually dendrites that prefer to grow misaligned with respect to the thermal gradient direction. We also show that in this region, the dendrites grow with a blunted tip that oscillates and splits, resulting in an oriented trunk that continuously emits side branches in other directions. We conclude by making a correlation between the alloy composition and surface energy anisotropy parameters.

Microstructural evolution of gas hydrates in sedimentary matrices observed with synchrotron X-ray computed tomographic microscopy

NASA Astrophysics Data System (ADS)

Chaouachi, Marwen; Falenty, Andrzej; Sell, Kathleen; Enzmann, Frieder; Kersten, Michael; Haberthür, David; Kuhs, Werner F.

2015-06-01

The formation process of gas hydrates in sedimentary matrices is of crucial importance for the physical and transport properties of the resulting aggregates. This process has never been observed in situ at submicron resolution. Here we report on synchrotron-based microtomographic studies by which the nucleation and growth processes of gas hydrate were observed at 276 K in various sedimentary matrices such as natural quartz (with and without admixtures of montmorillonite type clay) or glass beads with different surface properties, at varying water saturation. Both juvenile water and metastably gas-enriched water obtained from gas hydrate decomposition was used. Xenon gas was employed to enhance the density contrast between gas hydrate and the fluid phases involved. The nucleation sites can be easily identified and the various growth patterns are clearly established. In sediments under-saturated with juvenile water, nucleation starts at the water-gas interface resulting in an initially several micrometer thick gas hydrate film; further growth proceeds to form isometric single crystals of 10-20 µm size. The growth of gas hydrate from gas-enriched water follows a different pattern, via the nucleation in the bulk of liquid producing polyhedral single crystals. A striking feature in both cases is the systematic appearance of a fluid phase film of up to several micron thickness between gas hydrates and the surface of the quartz grains. These microstructural findings are relevant for future efforts of quantitative rock physics modeling of gas hydrates in sedimentary matrices and explain the anomalous attenuation of seismic/sonic waves.

Early detection of melanoma with the combined use of acoustic microscopy, infrared reflectance and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Karagiannis, Georgios T.; Grivas, Ioannis; Tsingotjidou, Anastasia; Apostolidis, Georgios K.; Grigoriadou, Ifigeneia; Dori, I.; Poulatsidou, Kyriaki-Nefeli; Doumas, Argyrios; Wesarg, Stefan; Georgoulias, Panagiotis

2015-03-01

Malignant melanoma is a form of skin cancer, with increasing incidence worldwide. Early diagnosis is crucial for the prognosis and treatment of the disease. The objective of this study is to develop a novel animal model of melanoma and apply a combination of the non-invasive imaging techniques acoustic microscopy, infrared (IR) and Raman spectroscopies, for the detection of developing tumors. Acoustic microscopy provides information about the 3D structure of the tumor, whereas, both spectroscopic modalities give qualitative insight of biochemical changes during melanoma development. In order to efficiently set up the final devices, propagation of ultrasonic and electromagnetic waves in normal skin and melanoma simulated structures was performed. Synthetic and grape-extracted melanin (simulated tumors), endermally injected, were scanned and compared to normal skin. For both cases acoustic microscopy with central operating frequencies of 110MHz and 175MHz were used, resulting to the tomographic imaging of the simulated tumor, while with the spectroscopic modalities IR and Raman differences among spectra of normal and melanin- injected sites were identified in skin depth. Subsequently, growth of actual tumors in an animal melanoma model, with the use of human malignant melanoma cells was achieved. Acoustic microscopy and IR and Raman spectroscopies were also applied. The development of tumors at different time points was displayed using acoustic microscopy. Moreover, the changes of the IR and Raman spectra were studied between the melanoma tumors and adjacent healthy skin. The most significant changes between healthy skin and the melanoma area were observed in the range of 900-1800cm-1 and 350-2000cm-1, respectively.

Isotropic differential phase contrast microscopy for quantitative phase bio-imaging.

PubMed

Chen, Hsi-Hsun; Lin, Yu-Zi; Luo, Yuan

2018-05-16

Quantitative phase imaging (QPI) has been investigated to retrieve optical phase information of an object and applied to biological microscopy and related medical studies. In recent examples, differential phase contrast (DPC) microscopy can recover phase image of thin sample under multi-axis intensity measurements in wide-field scheme. Unlike conventional DPC, based on theoretical approach under partially coherent condition, we propose a new method to achieve isotropic differential phase contrast (iDPC) with high accuracy and stability for phase recovery in simple and high-speed fashion. The iDPC is simply implemented with a partially coherent microscopy and a programmable thin-film transistor (TFT) shield to digitally modulate structured illumination patterns for QPI. In this article, simulation results show consistency of our theoretical approach for iDPC under partial coherence. In addition, we further demonstrate experiments of quantitative phase images of a standard micro-lens array, as well as label-free live human cell samples. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Characterization of a High Strength, Refractory High Entropy Alloy, AlMo0.5NbTa0.5TiZr

NASA Astrophysics Data System (ADS)

Jensen, Jacob

High entropy alloys (HEAs) are a relatively new class of materials that have garnered significant interest over the last decade due to their intriguing balance of properties including high strength, toughness, and corrosion resistance. In contrast to conventional alloy systems, HEAs are based on four or more principal elements with near equimolar concentrations and tend to have simple microstructures due to the preferential formation of solid solution phases. HEAs appear to offer new pathways to lightweighting in structural applications, new alloys for elevated temperature components, and new magnetic materials, but more thorough characterization studies are needed to assess the viability of the recently developed multicomponent materials. One such HEA, AlMo0.5NbTa0.5TiZr, was selected to be the basis for this characterization study in part due to its strength at elevated temperatures (sigma0.2 = 1600 MPa at T = 800 °C) and low density compared with commercially available Ni-based superalloys. The refractory element containing HEA composition was developed in order to balance the high temperature strength of the refractory elements with the desirable properties achieved by the high entropy alloying design approach for potential use in aerospace thermal protection and structural applications. Ingots of AlMo0.5NbTa0.5TiZr were cast by vacuum arc melting followed by hot isostatic pressing (HIP) and homogenization at 1400 °C for 24 hrs with a furnace cool of 10 °C/min. The resulting microstructure was characterized at multiple length scales using x-ray diffraction (XRD), scanning transmission electron microscopy (SEM), conventional and scanning transmission electron microscopy (TEM and STEM), and x-ray energy dispersive spectroscopy (XEDS). The microstructure was found to consist of a periodic, coherent two phase mixture, where a disordered bcc phase is aligned orthogonally in an ordered B2 phase. Through microstructural evolution heat treatment studies, the nanoscale interpenetrating microstructure was discovered to form via a conditional spinodal reaction pathway involving a congruent ordering transformation preceding spinodal decomposition. In order to gain a comprehensive understanding of the true morphology of these phases and obtain a novel perspective of 3D elemental segregation in the HEA, STEM-high angle annular darkfield (HAADF) micrographs and XEDS spectral images were utilized in the tomographic reconstruction of the microstructure, which was inherently difficult to observe through conventional characterization techniques. The microstructure of the alloy was ultimately refined by incremental variations to the base alloy composition in an effort to remove deleterious intermetallic phases adversely affecting ductility. Despite the excellent compressive strength across a wide range of temperatures and the ability to tailor the microstructure by compositional modifications, microstructural and phase transformations in the desired operating temperature range indicate that the AlMo0.5NbTa0.5TiZr alloy may not be a suitable material for high temperature aerospace structural components.

A novel flexible clinical multiphoton tomograph for early melanoma detection, skin analysis, testing of anti-age products, and in situ nanoparticle tracking

NASA Astrophysics Data System (ADS)

Weinigel, Martin; Breunig, Hans Georg; Gregory, Axel; Fischer, Peter; Kellner-Höfer, Marcel; Bückle, Rainer; König, Karsten

2010-02-01

High-resolution 3D microscopy based on multiphoton induced autofluorescence and second harmonic generation have been introduced in 1990. 13 years later, CE-marked clinical multiphoton systems for 3D imaging of human skin with subcellular resolution have first been launched by JenLab company with the tomography DermaInspect®. This year, the second generation of clinical multiphoton tomographs was introduced. The novel multiphoton tomograph MPTflex, equipped with a flexible articulated optical arm, provides an increased flexibility and accessibility especially for clinical and cosmetical examinations. Improved image quality and signal to noise ratio (SNR) are achieved by a very short source-drain spacing, by larger active areas of the detectors and by single photon counting (SPC) technology. Shorter image acquisition time due to improved image quality reduces artifacts and simplifies the operation of the system. The compact folded optical design and the light-weight structure of the optical head eases the handling. Dual channel detectors enable to distinguish between intratissue elastic fibers and collagenous structures simultaneously. Through the use of piezo-driven optics a stack of optical cross-sections (optical sectioning) can be acquired and 3D imaging can be performed. The multiphoton excitation of biomolecules like NAD(P)H, flavins, porphyrins, elastin, and melanin is done by picojoule femtosecond laser pulses from an tunable turn-key femtosescond near infrared laser system. The ability for rapid high-quality image acquisition, the user-friendly operation of the system and the compact and flexible design qualifies this system to be used for melanoma detection, diagnostics of dermatological disorders, cosmetic research and skin aging measurements as well as in situ drug monitoring and animal research.

In vivo laser confocal microscopy findings in patients with map-dot-fingerprint (epithelial basement membrane) dystrophy.

PubMed

Kobayashi, Akira; Yokogawa, Hideaki; Sugiyama, Kazuhisa

2012-01-01

The purpose of this study was to investigate pathological changes of the corneal cell layer in patients with map-dot-fingerprint (epithelial basement membrane) dystrophy by in vivo laser corneal confocal microscopy. Two patients were evaluated using a cornea-specific in vivo laser scanning confocal microscope (Heidelberg Retina Tomograph 2 Rostock Cornea Module, HRT 2-RCM). The affected corneal areas of both patients were examined. Image analysis was performed to identify corneal epithelial and stromal deposits correlated with this dystrophy. Variously shaped (linear, multilaminar, curvilinear, ring-shape, geographic) highly reflective materials were observed in the "map" area, mainly in the basal epithelial cell layer. In "fingerprint" lesions, multiple linear and curvilinear hyporeflective lines were observed. Additionally, in the affected corneas, infiltration of possible Langerhans cells and other inflammatory cells was observed as highly reflective Langerhans cell-like or dot images. Finally, needle-shaped materials were observed in one patient. HRT 2-RCM laser confocal microscopy is capable of identifying corneal microstructural changes related to map-dot-fingerprint corneal dystrophy in vivo. The technique may be useful in elucidating the pathogenesis and natural course of map-dot-fingerprint corneal dystrophy and other similar basement membrane abnormalities.

Tomographic techniques for the study of exceptionally preserved fossils

PubMed Central

Sutton, Mark D

2008-01-01

Three-dimensional fossils, especially those preserving soft-part anatomy, are a rich source of palaeontological information; they can, however, be difficult to work with. Imaging of serial planes through an object (tomography) allows study of both the inside and outside of three-dimensional fossils. Tomography may be performed using physical grinding or sawing coupled with photography, through optical techniques of serial focusing, or using a variety of scanning technologies such as neutron tomography, magnetic resonance imaging and most usefully X-ray computed tomography. This latter technique is applicable at a variety of scales, and when combined with a synchrotron X-ray source can produce very high-quality data that may be augmented by phase-contrast information to enhance contrast. Tomographic data can be visualized in several ways, the most effective of which is the production of isosurface-based ‘virtual fossils’ that can be manipulated and dissected interactively. PMID:18426749

Tomography with energy dispersive diffraction

NASA Astrophysics Data System (ADS)

Stock, S. R.; Okasinski, J. S.; Woods, R.; Baldwin, J.; Madden, T.; Quaranta, O.; Rumaiz, A.; Kuczewski, T.; Mead, J.; Krings, T.; Siddons, P.; Miceli, A.; Almer, J. D.

2017-09-01

X-ray diffraction can be used as the signal for tomographic reconstruction and provides a cross-sectional map of the crystallographic phases and related quantities. Diffraction tomography has been developed over the last decade using monochromatic x-radiation and an area detector. This paper reports tomographic reconstruction with polychromatic radiation and an energy sensitive detector array. The energy dispersive diffraction (EDD) geometry, the instrumentation and the reconstruction process are described and related to the expected resolution. Results of EDD tomography are presented for two samples containing hydroxyapatite (hAp). The first is a 3D-printed sample with an elliptical crosssection and contains synthetic hAp. The second is a human second metacarpal bone from the Roman-era cemetery at Ancaster, UK and contains bio-hAp which may have been altered by diagenesis. Reconstructions with different diffraction peaks are compared. Prospects for future EDD tomography are also discussed.

Condenser-free contrast methods for transmitted-light microscopy

PubMed Central

WEBB, K F

2015-01-01

Phase contrast microscopy allows the study of highly transparent yet detail-rich specimens by producing intensity contrast from phase objects within the sample. Presented here is a generalized phase contrast illumination schema in which condenser optics are entirely abrogated, yielding a condenser-free yet highly effective method of obtaining phase contrast in transmitted-light microscopy. A ring of light emitting diodes (LEDs) is positioned within the light-path such that observation of the objective back focal plane places the illuminating ring in appropriate conjunction with the phase ring. It is demonstrated that true Zernike phase contrast is obtained, whose geometry can be flexibly manipulated to provide an arbitrary working distance between illuminator and sample. Condenser-free phase contrast is demonstrated across a range of magnifications (4–100×), numerical apertures (0.13–1.65NA) and conventional phase positions. Also demonstrated is condenser-free darkfield microscopy as well as combinatorial contrast including Rheinberg illumination and simultaneous, colour-contrasted, brightfield, darkfield and Zernike phase contrast. By providing enhanced and arbitrary working space above the preparation, a range of concurrent imaging and electrophysiological techniques will be technically facilitated. Condenser-free phase contrast is demonstrated in conjunction with scanning ion conductance microscopy (SICM), using a notched ring to admit the scanned probe. The compact, versatile LED illumination schema will further lend itself to novel next-generation transmitted-light microscopy designs. The condenser-free illumination method, using rings of independent or radially-scanned emitters, may be exploited in future in other electromagnetic wavebands, including X-rays or the infrared. PMID:25226859

Interferometric tomography of fuel cells for monitoring membrane water content.

PubMed

Waller, Laura; Kim, Jungik; Shao-Horn, Yang; Barbastathis, George

2009-08-17

We have developed a system that uses two 1D interferometric phase projections for reconstruction of 2D water content changes over time in situ in a proton exchange membrane (PEM) fuel cell system. By modifying the filtered backprojection tomographic algorithm, we are able to incorporate a priori information about the object distribution into a fast reconstruction algorithm which is suitable for real-time monitoring.

Cryo-transmission electron tomography of native casein micelles from bovine milk

PubMed Central

Trejo, R.; Dokland, T.; Jurat-Fuentes, J.; Harte, F.

2013-01-01

Caseins are the principal protein components in milk and an important ingredient in the food industry. In liquid milk, caseins are found as micelles of casein proteins and colloidal calcium nanoclusters. Casein micelles were isolated from raw skim milk by size exclusion chromatography and suspended in milk protein-free serum produced by ultrafiltration (molecular weight cut-off of 3 kDa) of raw skim milk. The micelles were imaged by cryo-electron microscopy and subjected to tomographic reconstruction methods to visualize the 3-dimensional and internal organization of native casein micelles. This provided new insights into the internal architecture of the casein micelle that had not been apparent from prior cryo-transmission electron microscopy studies. This analysis demonstrated the presence of water-filled cavities (~20 to 30 nm in diameter), channels (diameter greater than ~5 nm), and several hundred high-density nanoclusters (6 to 12 nm in diameter) within the interior of the micelles. No spherical protein submicellar structures were observed. PMID:22118067

Quantitative dispersion microscopy

PubMed Central

Fu, Dan; Choi, Wonshik; Sung, Yongjin; Yaqoob, Zahid; Dasari, Ramachandra R.; Feld, Michael

2010-01-01

Refractive index dispersion is an intrinsic optical property and a useful source of contrast in biological imaging studies. In this report, we present the first dispersion phase imaging of living eukaryotic cells. We have developed quantitative dispersion microscopy based on the principle of quantitative phase microscopy. The dual-wavelength quantitative phase microscope makes phase measurements at 310 nm and 400 nm wavelengths to quantify dispersion (refractive index increment ratio) of live cells. The measured dispersion of living HeLa cells is found to be around 1.088, which agrees well with that measured directly for protein solutions using total internal reflection. This technique, together with the dry mass and morphology measurements provided by quantitative phase microscopy, could prove to be a useful tool for distinguishing different types of biomaterials and studying spatial inhomogeneities of biological samples. PMID:21113234

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

PubMed

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S; Subramanian, Hariharan; Dravid, Vinayak P; Backman, Vadim

2017-06-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Volumetry of human taste buds using laser scanning microscopy.

PubMed

Just, T; Srur, E; Stachs, O; Pau, H W

2009-10-01

In vivo laser scanning confocal microscopy is a relatively new, non-invasive method for assessment of oral cavity epithelia. The penetration depth of approximately 200-400 microm allows visualisation of fungiform papillae and their taste buds. This paper describes the technique of in vivo volumetry of human taste buds. Confocal laser scanning microscopy used a diode laser at 670 nm for illumination. Digital laser scanning confocal microscopy equipment consisted of the Heidelberg Retina Tomograph HRTII and the Rostock Cornea Module. Volume scans of fungiform papillae were used for three-dimensional reconstruction of the taste bud. This technique supplied information on taste bud structure and enabled measurement and calculation of taste bud volume. Volumetric data from a 23-year-old man over a nine-day period showed only a small deviation in values. After three to four weeks, phenomenological changes in taste bud structures were found (i.e. a significant increase in volume, followed by disappearance of the taste bud and appearance of a new taste bud). The data obtained indicate the potential application of this non-invasive imaging modality: to evaluate variation of taste bud volume in human fungiform papillae with ageing; to study the effects of chorda tympani nerve transection on taste bud volume; and to demonstrate recovery of taste buds in patients with a severed chorda tympani nerve who show recovery of gustatory sensibility after surgery.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm

PubMed Central

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A.; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S.; Subramanian, Hariharan; Dravid, Vinayak P.; Backman, Vadim

2018-01-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass–density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass–density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass–density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass–density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass–density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes. PMID:28416035

Optofluidic time-stretch quantitative phase microscopy.

PubMed

Guo, Baoshan; Lei, Cheng; Wu, Yi; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Lee, Sangwook; Isozaki, Akihiro; Li, Ming; Jiang, Yiyue; Yasumoto, Atsushi; Di Carlo, Dino; Tanaka, Yo; Yatomi, Yutaka; Ozeki, Yasuyuki; Goda, Keisuke

2018-03-01

Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform. It achieves the continuous acquisition of both intensity and phase images with a high throughput of more than 10,000 particles or cells per second by overcoming speed limitations that exist in conventional quantitative phase imaging methods. Applications enabled by such capabilities are versatile and include characterization of cancer cells and microalgal cultures. In this paper, we review the principles and applications of optofluidic time-stretch quantitative phase microscopy and discuss its future perspective. Copyright © 2017 Elsevier Inc. All rights reserved.

Assessment of crustal velocity models using seismic refraction and reflection tomography

NASA Astrophysics Data System (ADS)

Zelt, Colin A.; Sain, Kalachand; Naumenko, Julia V.; Sawyer, Dale S.

2003-06-01

Two tomographic methods for assessing velocity models obtained from wide-angle seismic traveltime data are presented through four case studies. The modelling/inversion of wide-angle traveltimes usually involves some aspects that are quite subjective. For example: (1) identifying and including later phases that are often difficult to pick within the seismic coda, (2) assigning specific layers to arrivals, (3) incorporating pre-conceived structure not specifically required by the data and (4) selecting a model parametrization. These steps are applied to maximize model constraint and minimize model non-uniqueness. However, these steps may cause the overall approach to appear ad hoc, and thereby diminish the credibility of the final model. The effect of these subjective choices can largely be addressed by estimating the minimum model structure required by the least subjective portion of the wide-angle data set: the first-arrival times. For data sets with Moho reflections, the tomographic velocity model can be used to invert the PmP times for a minimum-structure Moho. In this way, crustal velocity and Moho models can be obtained that require the least amount of subjective input, and the model structure that is required by the wide-angle data with a high degree of certainty can be differentiated from structure that is merely consistent with the data. The tomographic models are not intended to supersede the preferred models, since the latter model is typically better resolved and more interpretable. This form of tomographic assessment is intended to lend credibility to model features common to the tomographic and preferred models. Four case studies are presented in which a preferred model was derived using one or more of the subjective steps described above. This was followed by conventional first-arrival and reflection traveltime tomography using a finely gridded model parametrization to derive smooth, minimum-structure models. The case studies are from the SE Canadian Cordillera across the Rocky Mountain Trench, central India across the Narmada-Son lineament, the Iberia margin across the Galicia Bank, and the central Chilean margin across the Valparaiso Basin and a subducting seamount. These case studies span the range of modern wide-angle experiments and data sets in terms of shot-receiver spacing, marine and land acquisition, lateral heterogeneity of the study area, and availability of wide-angle reflections and coincident near-vertical reflection data. The results are surprising given the amount of structure in the smooth, tomographically derived models that is consistent with the more subjectively derived models. The results show that exploiting the complementary nature of the subjective and tomographic approaches is an effective strategy for the analysis of wide-angle traveltime data.

Photoacoustic tomography using a Michelson interferometer with quadrature phase detection

NASA Astrophysics Data System (ADS)

Speirs, Rory W.; Bishop, Alexis I.

2013-07-01

We present a pressure sensor based on a Michelson interferometer, for use in photoacoustic tomography. Quadrature phase detection is employed allowing measurement at any point on the mirror surface without having to retune the interferometer, as is typically required by Fabry-Perot type detectors. This opens the door to rapid full surface detection, which is necessary for clinical applications. Theory relating acoustic pressure to detected acoustic particle displacements is used to calculate the detector sensitivity, which is validated with measurement. Proof-of-concept tomographic images of blood vessel phantoms have been taken with sub-millimeter resolution at depths of several millimeters.

Phase-contrast microtomography using an X-ray interferometer having a 40-μm analyzer

NASA Astrophysics Data System (ADS)

Momose, A.; Koyama, I.; Hamaishi, Y.; Yoshikawa, H.; Takeda, T.; Wu, J.; Itai, Y.; Takai, , K.; Uesugi, K.; Suzuki, Y.

2003-03-01

Phase-contrast X-ray tomographic experiment using a triple Laue-case (LLL) interferometer having a 40-μm lamella which was fabricated to improve spatial resolution, was carried out using undulator X-rays at SPring-8, Japan. Three-dimensional images mapping the refractive index were measured for various animal tissues. Comparing the images with those obtained in previous experiments using conventional LLL interferometers having a 1-mm lamella, improvement in the spatial resolution was demonstrated in that histological structures, such as hepatic lobules in liver and tubules in kidney, were revealed.

Imaging bacterial spores by soft-x-ray microscopy

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

Stead, A.D.; Ford, T.W.; Judge, J.

1997-04-01

Bacterial spores are able to survive dehydration, but neither the physiological nor structural basis of this have been fully elucidated. Furthermore, once hydrated, spores often require activation before they will germinate. Several treatments can be used to activate spores, but in the case of Bacillus subtlis the most effective is heat treatment. The physiological mechanism associated with activation is also not understood, but some workers suggest that the loss of calcium from the spores may be critical. However, just prior to germination, the spores change from being phase bright to phase dark when viewed by light microscopy. Imaging spores bymore » soft x-ray microscopy is possible without fixation. Thus, in contrast to electron microscopy, it is possible to compare the structure of dehydrated and hydrated spores in a manner not possible previously. A further advantage is that it is possible to monitor individual spores by phase contrast light microscopy immediately prior to imaging with soft x-rays; whereas, with both electron microscopy and biochemical studies, it is a population of spores being studied without knowledge of the phase characteristics of individual spores. This study has therefore tried to compare dehydrated and hydrated spores and to determine if there is a mass loss from individual spores as they pass the transition from being phase bright to phase dark.« less

Theory and preliminary experimental verification of quantitative edge illumination x-ray phase contrast tomography.

PubMed

Hagen, C K; Diemoz, P C; Endrizzi, M; Rigon, L; Dreossi, D; Arfelli, F; Lopez, F C M; Longo, R; Olivo, A

2014-04-07

X-ray phase contrast imaging (XPCi) methods are sensitive to phase in addition to attenuation effects and, therefore, can achieve improved image contrast for weakly attenuating materials, such as often encountered in biomedical applications. Several XPCi methods exist, most of which have already been implemented in computed tomographic (CT) modality, thus allowing volumetric imaging. The Edge Illumination (EI) XPCi method had, until now, not been implemented as a CT modality. This article provides indications that quantitative 3D maps of an object's phase and attenuation can be reconstructed from EI XPCi measurements. Moreover, a theory for the reconstruction of combined phase and attenuation maps is presented. Both reconstruction strategies find applications in tissue characterisation and the identification of faint, weakly attenuating details. Experimental results for wires of known materials and for a biological object validate the theory and confirm the superiority of the phase over conventional, attenuation-based image contrast.

Cardiac phase-synchronized myocardial thallium-201 single-photon emission tomography using list mode data acquisition and iterative tomographic reconstruction.

PubMed

Vemmer, T; Steinbüchel, C; Bertram, J; Eschner, W; Kögler, A; Luig, H

1997-03-01

The purpose of this study was to determine whether data acquisition in the list mode and iterative tomographic reconstruction would render feasible cardiac phase-synchronized thallium-201 single-photon emission tomography (SPET) of the myocardium under routine conditions without modifications in tracer dose, acquisition time, or number of steps of the a gamma camera. Seventy non-selected patients underwent 201T1 SPET imaging according to a routine protocol (74 MBq/2 mCi 201T1, 180 degrees rotation of the gamma camera, 32 steps, 30 min). Gamma camera data, ECG, and a time signal were recorded in list mode. The cardiac cycle was divided into eight phases, the end-diastolic phase encompassing the QRS complex, and the end-systolic phase the T wave. Both phase- and non-phase-synchronized tomograms based on the same list mode data were reconstructed iteratively. Phase-synchronized and non-synchronized images were compared. Patients were divided into two groups depending on whether or not coronary artery disease had been definitely diagnosed prior to SPET imaging. The numbers of patients in both groups demonstrating defects visible on the phase-synchronized but not on the non-synchronized images were compared. It was found that both postexercise and redistribution phase tomograms were suited for interpretation. The changes from end-diastolic to end-systolic images allowed a comparative assessment of regional wall motility and tracer uptake. End-diastolic tomograms provided the best definition of defects. Additional defects not apparent on non-synchronized images were visible in 40 patients, six of whom did not show any defect on the non-synchronized images. Of 42 patients in whom coronary artery disease had been definitely diagnosed, 19 had additional defects not visible on the non-synchronized images, in comparison to 21 of 28 in whom coronary artery disease was suspected (P < 0.02; chi 2). It is concluded that cardiac phase-synchronized 201T1 SPET of the myocardium was made feasible by list mode data acquisition and iterative reconstruction. The additional findings on the phase-synchronized tomograms, not visible on the non-synchronized ones, represented genuine defects. Cardiac phase-synchronized 201T1 SPET is advantageous in allowing simultaneous assessment of regional wall motion and tracer uptake, and in visualizing smaller defects.

Phase-contrast scanning transmission electron microscopy.

PubMed

Minoda, Hiroki; Tamai, Takayuki; Iijima, Hirofumi; Hosokawa, Fumio; Kondo, Yukihito

2015-06-01

This report introduces the first results obtained using phase-contrast scanning transmission electron microscopy (P-STEM). A carbon-film phase plate (PP) with a small center hole is placed in the condenser aperture plane so that a phase shift is introduced in the incident electron waves except those passing through the center hole. A cosine-type phase-contrast transfer function emerges when the phase-shifted scattered waves interfere with the non-phase-shifted unscattered waves, which passed through the center hole before incidence onto the specimen. The phase contrast resulting in P-STEM is optically identical to that in phase-contrast transmission electron microscopy that is used to provide high contrast for weak phase objects. Therefore, the use of PPs can enhance the phase contrast of the STEM images of specimens in principle. The phase shift resulting from the PP, whose thickness corresponds to a phase shift of π, has been confirmed using interference fringes displayed in the Ronchigram of a silicon single crystal specimen. The interference fringes were found to abruptly shift at the edge of the PP hole by π. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

HANFORD WASTE MINEROLOGY REFERENCE REPORT

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

DISSELKAMP RS

2010-06-18

This report lists the observed mineral phase phases present in the Hanford tanks. This task was accomplished by performing a review of numerous reports using experimental techniques including, but not limited to: x-ray diffraction, polarized light microscopy, scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, electron energy loss spectroscopy, and particle size distribution analyses. This report contains tables that can be used as a quick reference to identify the crystal phases present observed in Hanford waste.

Evaluation of laser ablation microtomy for correlative microscopy of hard tissues.

PubMed

Boyde, A

2018-02-27

Laser ablation machining or microtomy (LAM) is a relatively new approach to producing slide mounted sections of translucent materials. We evaluated the method with a variety of problems from the bone, joint and dental tissues fields where we require thin undecalcified and undistorted sections for correlative light microscopy (LM) and backscattered electron scanning electron microscopy (BSE SEM). All samples were embedded in poly-methylmethacrlate (PMMA) and flat block surfaces had been previously studied by BSE-SEM and confocal scanning light microscopy (CSLM). Most were also studied by X-yay microtomography (XMT). The block surface is stuck to a glass slide with cyanoacrylate adhesive. Setting the section thickness and levelling uses inbuilt optical coherence tomographic imaging. Tight focusing of near-infrared laser radiation in the sectioning plane gives extreme intensities causing photodisruption of material at the focal point. The laser beam is moved by a fast scanner to write a cutting line, which is simultaneously moved by an XY positioning unit to create a sectioning plane. The block is thereby released from the slide, leaving the section stuck to the slide. Light, wet polishing on the finest grade (4000 grit) silicon carbide polishing paper is used to remove a 1-2 μm thick damaged layer at the surface of the section. Sections produced by laser cutting are fine in quality and superior to those produced by mechanical cutting and can be thinner than the 'voxel' in most laboratory X-ray microtomography systems. The present extensive pilot studies have shown that it works to produce samples which we can study by both light and electron microscopy. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Nanometer resolution optical coherence tomography using broad bandwidth XUV and soft x-ray radiation

DOE PAGES

Fuchs, Silvio; Rödel, Christian; Blinne, Alexander; ...

2016-02-10

Optical coherence tomography (OCT) is a non-invasive technique for cross-sectional imaging. It is particularly advantageous for applications where conventional microscopy is not able to image deeper layers of samples in a reasonable time, e.g. in fast moving, deeper lying structures. However, at infrared and optical wavelengths, which are commonly used, the axial resolution of OCT is limited to about 1 μm, even if the bandwidth of the light covers a wide spectral range. Here, we present extreme ultraviolet coherence tomography (XCT) and thus introduce a new technique for non-invasive cross-sectional imaging of nanometer structures. XCT exploits the nanometerscale coherence lengthsmore » corresponding to the spectral transmission windows of, e.g., silicon samples. The axial resolution of coherence tomography is thus improved from micrometers to a few nanometers. Tomographic imaging with an axial resolution better than 18 nm is demonstrated for layer-type nanostructures buried in a silicon substrate. Using wavelengths in the water transmission window, nanometer-scale layers of platinum are retrieved with a resolution better than 8 nm. As a result, XCT as a nondestructive method for sub-surface tomographic imaging holds promise for several applications in semiconductor metrology and imaging in the water window.« less

Combining coherent hard X-ray tomographies with phase retrieval to generate three-dimensional models of forming bone

NASA Astrophysics Data System (ADS)

Bortel, Emely L.; Langer, Max; Rack, Alexander; Forien, Jean-Baptiste; Duda, Georg N.; Fratzl, Peter; Zaslansky, Paul

2017-11-01

Holotomography, a phase sensitive synchrotron-based μCT modality, is a quantitative 3D imaging method. By exploiting partial spatial X-ray coherence, bones can be imaged volumetrically with high resolution coupled with impressive density sensitivity. This tomographic method reveals the main characteristics of the important tissue compartments in forming bones, including the rapidly-changing soft tissue and the partially or fully mineralized bone regions, while revealing subtle density differences in 3D. Here we show typical results observed within the growing femur bone midshafts of healthy mice that are 1, 3, 7, 10 and 14 days old (postpartum). Our results make use of partially-coherent synchrotron radiation employing inline Fresnel-propagation in multiple tomographic datasets obtained in the imaging beamline ID19 of the ESRF. The exquisite detail creates maps of the juxtaposed soft, partially mineralized and highly mineralized bone revealing the environment in which bone cells create and shape the matrix. This high resolution 3D data is a step towards creating realistic computational models that may be used to study the dynamic processes involved in bone tissue formation and adaptation. Such data will enhance our understanding of the important biomechanical interactions directing maturation and shaping of the bone micro- and macro-geometries.

Confirmation of a change in the global shear velocity pattern at around 1000 km depth

NASA Astrophysics Data System (ADS)

Durand, S.; Debayle, E.; Ricard, Y.; Zaroli, C.; Lambotte, S.

2017-12-01

In this study, we confirm the existence of a change in the shear velocity spectrum around 1000 km depth based on a new shear velocity tomographic model of the Earth's mantle, SEISGLOB2. This model is based on Rayleigh surface wave phase velocities, self- and cross-coupling structure coefficients of spheroidal normal modes and body wave traveltimes which are, for the first time, combined in a tomographic inversion. SEISGLOB2 is developed up to spherical harmonic degree 40 and in 21 radial spline functions. The spectrum of SEISGLOB2 is the flattest (i.e. richest in 'short' wavelengths corresponding to spherical harmonic degrees greater than 10) around 1000 km depth and this flattening occurs between 670 and 1500 km depth. We also confirm various changes in the continuity of slabs and mantle plumes all around 1000 km depth where we also observed the upper boundary of Large Low Shear Velocity Provinces. The existence of a flatter spectrum, richer in short-wavelength heterogeneities, in a region of the mid-mantle can have great impacts on our understanding of the mantle dynamics and should thus be better understood in the future. Although a viscosity increase, a phase change or a compositional change can all concur to induce this change of pattern, its precise origin is still very uncertain.

Crustal Structure of Indonesia from Seismic Ambient Noise Tomography

NASA Astrophysics Data System (ADS)

Saygin, E.; Cummins, P. R.; Suhardjono, S.; Nishida, K.

2012-12-01

We image a region spanning from south Vietnam to north Australia using over 300 seismic stations by using ambient seismic noise cross-correlations. The backbone of the network is formed by using the broadband seismograph network of Indonesia with over 160 stations serving as mid-tie point in the region. The retrieved Green's functions from the cross-correlation of continuously recorded seismic ambient noise at the stations are used to perform surface wave dispersion analysis. We apply a multiple filter approach to measure the phase and group velocity dispersion of Rayleigh wave component of Green's functions. The traveltime information derived from the dispersion is then used in a nonlinear tomographic approach to map the velocity perturbation of the region. The forward problem for the tomographic imaging can accurately track the evolution of a wavefront in highly heterogeneous media. Therefore the highly complex velocity distribution of the region is accurately reflected into the forward calculations used in the inversion. In general, accretionary prisms in the region are marked with quite low group and phase velocities with perturbations up to 50%. Active volcanoes in Sumatra and Java islands are also marked with low velocities. Rajang delta in north-west Kalimantan and thick sediments in South China Sea are imaged with low velocities.

Three-dimensional visualization and display technologies; Proceedings of the Meeting, Los Angeles, CA, Jan. 18-20, 1989

NASA Technical Reports Server (NTRS)

Robbins, Woodrow E. (Editor); Fisher, Scott S. (Editor)

1989-01-01

Special attention was given to problems of stereoscopic display devices, such as CAD for enhancement of the design process in visual arts, stereo-TV improvement of remote manipulator performance, a voice-controlled stereographic video camera system, and head-mounted displays and their low-cost design alternatives. Also discussed was a novel approach to chromostereoscopic microscopy, computer-generated barrier-strip autostereography and lenticular stereograms, and parallax barrier three-dimensional TV. Additional topics include processing and user interface isssues and visualization applications, including automated analysis and fliud flow topology, optical tomographic measusrements of mixing fluids, visualization of complex data, visualization environments, and visualization management systems.

Laboratory-size three-dimensional x-ray microscope with Wolter type I mirror optics and an electron-impact water window x-ray source

NASA Astrophysics Data System (ADS)

Ohsuka, Shinji; Ohba, Akira; Onoda, Shinobu; Nakamoto, Katsuhiro; Nakano, Tomoyasu; Miyoshi, Motosuke; Soda, Keita; Hamakubo, Takao

2014-09-01

We constructed a laboratory-size three-dimensional water window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques, and observed bio-medical samples to evaluate its applicability to life science research fields. It consists of a condenser and an objective grazing incidence Wolter type I mirror, an electron-impact type oxygen Kα x-ray source, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit of around 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm scale three-dimensional fine structures were resolved.

Cryo-Electron Microscopy of Viruses Infecting Bacterium

NASA Astrophysics Data System (ADS)

Chiu, Wah

2010-03-01

Single particle cryo-EM can yield structures of infectious bacterial viruses with and without imposed icosahedral symmetry at subnanometer resolution. Reconstructions of infectious and empty phage particles show substantial differences in the portal vertex protein complex at one of the 12 pentameric vertices in the icosahedral virus particle through which the viral genomes are packaged or released. In addition, electron cryo-tomography of viruses during infecting its bacterial host cell displayed multiple conformations of the tail fiber of the virus. Our structural observations by single particle and tomographic reconstructions suggest a mechanism whereby the viral tail fibers, upon binding to the host cell, induce a cascade of structural alterations of the portal vertex protein complex that triggers DNA release.

Laboratory-size three-dimensional x-ray microscope with Wolter type I mirror optics and an electron-impact water window x-ray source.

PubMed

Ohsuka, Shinji; Ohba, Akira; Onoda, Shinobu; Nakamoto, Katsuhiro; Nakano, Tomoyasu; Miyoshi, Motosuke; Soda, Keita; Hamakubo, Takao

2014-09-01

We constructed a laboratory-size three-dimensional water window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques, and observed bio-medical samples to evaluate its applicability to life science research fields. It consists of a condenser and an objective grazing incidence Wolter type I mirror, an electron-impact type oxygen Kα x-ray source, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit of around 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm scale three-dimensional fine structures were resolved.

Microscopic Optical Projection Tomography In Vivo

PubMed Central

Meyer, Heiko; Ripoll, Jorge; Tavernarakis, Nektarios

2011-01-01

We describe a versatile optical projection tomography system for rapid three-dimensional imaging of microscopic specimens in vivo. Our tomographic setup eliminates the in xy and z strongly asymmetric resolution, resulting from optical sectioning in conventional confocal microscopy. It allows for robust, high resolution fluorescence as well as absorption imaging of live transparent invertebrate animals such as C. elegans. This system offers considerable advantages over currently available methods when imaging dynamic developmental processes and animal ageing; it permits monitoring of spatio-temporal gene expression and anatomical alterations with single-cell resolution, it utilizes both fluorescence and absorption as a source of contrast, and is easily adaptable for a range of small model organisms. PMID:21559481

Finite-frequency tomography using adjoint methods-Methodology and examples using membrane surface waves

NASA Astrophysics Data System (ADS)

Tape, Carl; Liu, Qinya; Tromp, Jeroen

2007-03-01

We employ adjoint methods in a series of synthetic seismic tomography experiments to recover surface wave phase-speed models of southern California. Our approach involves computing the Fréchet derivative for tomographic inversions via the interaction between a forward wavefield, propagating from the source to the receivers, and an `adjoint' wavefield, propagating from the receivers back to the source. The forward wavefield is computed using a 2-D spectral-element method (SEM) and a phase-speed model for southern California. A `target' phase-speed model is used to generate the `data' at the receivers. We specify an objective or misfit function that defines a measure of misfit between data and synthetics. For a given receiver, the remaining differences between data and synthetics are time-reversed and used as the source of the adjoint wavefield. For each earthquake, the interaction between the regular and adjoint wavefields is used to construct finite-frequency sensitivity kernels, which we call event kernels. An event kernel may be thought of as a weighted sum of phase-specific (e.g. P) banana-doughnut kernels, with weights determined by the measurements. The overall sensitivity is simply the sum of event kernels, which defines the misfit kernel. The misfit kernel is multiplied by convenient orthonormal basis functions that are embedded in the SEM code, resulting in the gradient of the misfit function, that is, the Fréchet derivative. A non-linear conjugate gradient algorithm is used to iteratively improve the model while reducing the misfit function. We illustrate the construction of the gradient and the minimization algorithm, and consider various tomographic experiments, including source inversions, structural inversions and joint source-structure inversions. Finally, we draw connections between classical Hessian-based tomography and gradient-based adjoint tomography.

The use of the multiwavelet transform for the estimation of surface wave group and phase velocities and their associated uncertainties

NASA Astrophysics Data System (ADS)

Poppeliers, C.; Preston, L. A.

2017-12-01

Measurements of seismic surface wave dispersion can be used to infer the structure of the Earth's subsurface. Typically, to identify group- and phase-velocity, a series of narrow-band filters are applied to surface wave seismograms. Frequency dependent arrival times of surface waves can then be identified from the resulting suite of narrow band seismograms. The frequency-dependent velocity estimates are then inverted for subsurface velocity structure. However, this technique has no method to estimate the uncertainty of the measured surface wave velocities, and subsequently there is no estimate of uncertainty on, for example, tomographic results. For the work here, we explore using the multiwavelet transform (MWT) as an alternate method to estimate surface wave speeds. The MWT decomposes a signal similarly to the conventional filter bank technique, but with two primary advantages: 1) the time-frequency localization is optimized in regard to the time-frequency tradeoff, and 2) we can use the MWT to estimate the uncertainty of the resulting surface wave group- and phase-velocities. The uncertainties of the surface wave speed measurements can then be propagated into tomographic inversions to provide uncertainties of resolved Earth structure. As proof-of-concept, we apply our technique to four seismic ambient noise correlograms that were collected from the University of Nevada Reno seismic network near the Nevada National Security Site. We invert the estimated group- and phase-velocities, as well the uncertainties, for 1-D Earth structure for each station pair. These preliminary results generally agree with 1-D velocities that are obtained from inverting dispersion curves estimated from a conventional Gaussian filter bank.

Enhanced x-ray imaging for a thin film cochlear implant with metal artefacts using phase retrieval tomography

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

Arhatari, B. D.; ARC Centre of Excellence for Coherent X-ray Science, Melbourne; Harris, A. R.

Phase retrieval tomography has been successfully used to enhance imaging in systems that exhibit poor absorption contrast. However, when highly absorbing regions are present in a sample, so-called metal artefacts can appear in the tomographic reconstruction. We demonstrate that straightforward approaches for metal artefact reconstruction, developed in absorption contrast tomography, can be applied when using phase retrieval. Using a prototype thin film cochlear implant that has high and low absorption components made from iridium (or platinum) and plastic, respectively, we show that segmentation of the various components is possible and hence measurement of the electrode geometry and relative location tomore » other regions of interest can be achieved.« less

Flow rate impacts on capillary pressure and interface curvature of connected and disconnected fluid phases during multiphase flow in sandstone

NASA Astrophysics Data System (ADS)

Herring, Anna L.; Middleton, Jill; Walsh, Rick; Kingston, Andrew; Sheppard, Adrian

2017-09-01

We investigate capillary pressure-saturation (PC-S) relationships for drainage-imbibition experiments conducted with air (nonwetting phase) and brine (wetting phase) in Bentheimer sandstone cores. Three different flow rate conditions, ranging over three orders of magnitude, are investigated. X-ray micro-computed tomographic imaging is used to characterize the distribution and amount of fluids and their interfacial characteristics. Capillary pressure is measured via (1) bulk-phase pressure transducer measurements, and (2) image-based curvature measurements, calculated using a novel 3D curvature algorithm. We distinguish between connected (percolating) and disconnected air clusters: curvatures measured on the connected phase interfaces are used to validate the curvature algorithm and provide an indication of the equilibrium condition of the data; curvature and volume distributions of disconnected clusters provide insight to the snap-off processes occurring during drainage and imbibition under different flow rate conditions.

New Insights on Mt. Etna's Crust and Relationship with the Regional Tectonic Framework from Joint Active and Passive P-Wave Seismic Tomography

NASA Astrophysics Data System (ADS)

Díaz-Moreno, A.; Barberi, G.; Cocina, O.; Koulakov, I.; Scarfì, L.; Zuccarello, L.; Prudencio, J.; García-Yeguas, A.; Álvarez, I.; García, L.; Ibáñez, J. M.

2018-01-01

In the Central Mediterranean region, the production of chemically diverse volcanic products (e.g., those from Mt. Etna and the Aeolian Islands archipelago) testifies to the complexity of the tectonic and geodynamic setting. Despite the large number of studies that have focused on this area, the relationships among volcanism, tectonics, magma ascent, and geodynamic processes remain poorly understood. We present a tomographic inversion of P-wave velocity using active and passive sources. Seismic signals were recorded using both temporary on-land and ocean bottom seismometers and data from a permanent local seismic network consisting of 267 seismic stations. Active seismic signals were generated using air gun shots mounted on the Spanish Oceanographic Vessel `Sarmiento de Gamboa'. Passive seismic sources were obtained from 452 local earthquakes recorded over a 4-month period. In total, 184,797 active P-phase and 11,802 passive P-phase first arrivals were inverted to provide three different velocity models. Our results include the first crustal seismic active tomography for the northern Sicily area, including the Peloritan-southern Calabria region and both the Mt. Etna and Aeolian volcanic environments. The tomographic images provide a detailed and complete regional seismotectonic framework and highlight a spatially heterogeneous tectonic regime, which is consistent with and extends the findings of previous models. One of our most significant results was a tomographic map extending to 14 km depth showing a discontinuity striking roughly NW-SE, extending from the Gulf of Patti to the Ionian Sea, south-east of Capo Taormina, corresponding to the Aeolian-Tindari-Letojanni fault system, a regional deformation belt. Moreover, for the first time, we observed a high-velocity anomaly located in the south-eastern sector of the Mt. Etna region, offshore of the Timpe area, which is compatible with the plumbing system of an ancient shield volcano located offshore of Mt. Etna.

Outcomes of the JNT 1955 Phase I Viability Study of Gamma Emission Tomography for Spent Fuel Verification

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

Jacobsson-Svard, Staffan; Smith, Leon E.; White, Timothy

The potential for gamma emission tomography (GET) to detect partial defects within a spent nuclear fuel assembly has been assessed within the IAEA Support Program project JNT 1955, phase I, which was completed and reported to the IAEA in October 2016. Two safeguards verification objectives were identified in the project; (1) independent determination of the number of active pins that are present in a measured assembly, in the absence of a priori information about the assembly; and (2) quantitative assessment of pin-by-pin properties, for example the activity of key isotopes or pin attributes such as cooling time and relative burnup,more » under the assumption that basic fuel parameters (e.g., assembly type and nominal fuel composition) are known. The efficacy of GET to meet these two verification objectives was evaluated across a range of fuel types, burnups and cooling times, while targeting a total interrogation time of less than 60 minutes. The evaluations were founded on a modelling and analysis framework applied to existing and emerging GET instrument designs. Monte Carlo models of different fuel types were used to produce simulated tomographer responses to large populations of “virtual” fuel assemblies. The simulated instrument response data were then processed using a variety of tomographic-reconstruction and image-processing methods, and scoring metrics were defined and used to evaluate the performance of the methods.This paper describes the analysis framework and metrics used to predict tomographer performance. It also presents the design of a “universal” GET (UGET) instrument intended to support the full range of verification scenarios envisioned by the IAEA. Finally, it gives examples of the expected partial-defect detection capabilities for some fuels and diversion scenarios, and it provides a comparison of predicted performance for the notional UGET design and an optimized variant of an existing IAEA instrument.« less

Real time quantitative phase microscopy based on single-shot transport of intensity equation (ssTIE) method

NASA Astrophysics Data System (ADS)

Yu, Wei; Tian, Xiaolin; He, Xiaoliang; Song, Xiaojun; Xue, Liang; Liu, Cheng; Wang, Shouyu

2016-08-01

Microscopy based on transport of intensity equation provides quantitative phase distributions which opens another perspective for cellular observations. However, it requires multi-focal image capturing while mechanical and electrical scanning limits its real time capacity in sample detections. Here, in order to break through this restriction, real time quantitative phase microscopy based on single-shot transport of the intensity equation method is proposed. A programmed phase mask is designed to realize simultaneous multi-focal image recording without any scanning; thus, phase distributions can be quantitatively retrieved in real time. It is believed the proposed method can be potentially applied in various biological and medical applications, especially for live cell imaging.

Carbon contamination in scanning transmission electron microscopy and its impact on phase-plate applications.

PubMed

Hettler, Simon; Dries, Manuel; Hermann, Peter; Obermair, Martin; Gerthsen, Dagmar; Malac, Marek

2017-05-01

We analyze electron-beam induced carbon contamination in a transmission electron microscope. The study is performed on thin films potentially suitable as phase plates for phase-contrast transmission electron microscopy. Electron energy-loss spectroscopy and phase-plate imaging is utilized to analyze the contamination. The deposited contamination layer is identified as a graphitic carbon layer which is not prone to electrostatic charging whereas a non-conductive underlying substrate charges. Several methods that inhibit contamination are evaluated and the impact of carbon contamination on phase-plate imaging is discussed. The findings are in general interesting for scanning transmission electron microscopy applications. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

In vivo laser confocal microscopy findings in patients with map-dot-fingerprint (epithelial basement membrane) dystrophy

PubMed Central

Kobayashi, Akira; Yokogawa, Hideaki; Sugiyama, Kazuhisa

2012-01-01

Background: The purpose of this study was to investigate pathological changes of the corneal cell layer in patients with map-dot-fingerprint (epithelial basement membrane) dystrophy by in vivo laser corneal confocal microscopy. Methods: Two patients were evaluated using a cornea-specific in vivo laser scanning confocal microscope (Heidelberg Retina Tomograph 2 Rostock Cornea Module, HRT 2-RCM). The affected corneal areas of both patients were examined. Image analysis was performed to identify corneal epithelial and stromal deposits correlated with this dystrophy. Results: Variously shaped (linear, multilaminar, curvilinear, ring-shape, geographic) highly reflective materials were observed in the “map” area, mainly in the basal epithelial cell layer. In “fingerprint” lesions, multiple linear and curvilinear hyporeflective lines were observed. Additionally, in the affected corneas, infiltration of possible Langerhans cells and other inflammatory cells was observed as highly reflective Langerhans cell-like or dot images. Finally, needle-shaped materials were observed in one patient. Conclusion: HRT 2-RCM laser confocal microscopy is capable of identifying corneal microstructural changes related to map-dot-fingerprint corneal dystrophy in vivo. The technique may be useful in elucidating the pathogenesis and natural course of map-dot-fingerprint corneal dystrophy and other similar basement membrane abnormalities. PMID:22888214

Nanoscale characterization of local structures and defects in photonic crystals using synchrotron-based transmission soft X-ray microscopy

PubMed Central

Nho, Hyun Woo; Kalegowda, Yogesh; Shin, Hyun-Joon; Yoon, Tae Hyun

2016-01-01

For the structural characterization of the polystyrene (PS)-based photonic crystals (PCs), fast and direct imaging capabilities of full field transmission X-ray microscopy (TXM) were demonstrated at soft X-ray energy. PS-based PCs were prepared on an O2-plasma treated Si3N4 window and their local structures and defects were investigated using this label-free TXM technique with an image acquisition speed of ~10 sec/frame and marginal radiation damage. Micro-domains of face-centered cubic (FCC (111)) and hexagonal close-packed (HCP (0001)) structures were dominantly found in PS-based PCs, while point and line defects, FCC (100), and 12-fold symmetry structures were also identified as minor components. Additionally, in situ observation capability for hydrated samples and 3D tomographic reconstruction of TXM images were also demonstrated. This soft X-ray full field TXM technique with faster image acquisition speed, in situ observation, and 3D tomography capability can be complementally used with the other X-ray microscopic techniques (i.e., scanning transmission X-ray microscopy, STXM) as well as conventional characterization methods (e.g., electron microscopic and optical/fluorescence microscopic techniques) for clearer structure identification of self-assembled PCs and better understanding of the relationship between their structures and resultant optical properties. PMID:27087141

Tomographic image reconstruction using x-ray phase information

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji; Hirano, Keiichi

1996-04-01

We have been developing phase-contrast x-ray computed tomography (CT) to make possible the observation of biological soft tissues without contrast enhancement. Phase-contrast x-ray CT requires for its input data the x-ray phase-shift distributions or phase-mapping images caused by an object. These were measured with newly developed fringe-scanning x-ray interferometry. Phase-mapping images at different projection directions were obtained by rotating the object in an x-ray interferometer, and were processed with a standard CT algorithm. A phase-contrast x-ray CT image of a nonstained cancerous tissue was obtained using 17.7 keV synchrotron x rays with 12 micrometer voxel size, although the size of the observation area was at most 5 mm. The cancerous lesions were readily distinguishable from normal tissues. Moreover, fine structures corresponding to cancerous degeneration and fibrous tissues were clearly depicted. It is estimated that the present system is sensitive down to a density deviation of 4 mg/cm3.

Measuring of temperatures of phase objects using a point-diffraction interferometer plate made with the thermocavitation process

NASA Astrophysics Data System (ADS)

Aguilar, Juan C.; Berriel-Valdos, L. R.; Aguilar, J. Felix; Mejia-Romero, S.

An optical system formed by four point-diffraction interferometers is used for measuring the refractive index distribution of a phase object. The phase of the object is assumed enough smooth to be computed in terms of the Radon Transform and it is processed with a tomographic iterative algorithm. Then, the associated refractive index distribution is calculated. To recovery the phase from the inteferograms we use the Kreis method, which is useful for interferograms having only few fringes. As an application of our technique, the temperature distribution of a candle flame is retrieved, this was made with the aid of the Gladstone-Dale equation. We also describe the process of manufacturing the point-diffraction interferometer (PDI) plates. These were made by means of the thermocavitation process. The obtained three dimensional distribution of temperature is presented.

In vivo confocal microscopy of the cornea: New developments in image acquisition, reconstruction and analysis using the HRT-Rostock Corneal Module

PubMed Central

Petroll, W. Matthew; Robertson, Danielle M.

2015-01-01

The optical sectioning ability of confocal microscopy allows high magnification images to be obtained from different depths within a thick tissue specimen, and is thus ideally suited to the study of intact tissue in living subjects. In vivo confocal microscopy has been used in a variety of corneal research and clinical applications since its development over 25 years ago. In this article we review the latest developments in quantitative corneal imaging with the Heidelberg Retinal Tomograph with Rostock Corneal Module (HRT-RCM). We provide an overview of the unique strengths and weaknesses of the HRT-RCM. We discuss techniques for performing 3-D imaging with the HRT-RCM, including hardware and software modifications that allow full thickness confocal microscopy through focusing (CMTF) of the cornea, which can provide quantitative measurements of corneal sublayer thicknesses, stromal cell and extracellular matrix backscatter, and depth dependent changes in corneal keratocyte density. We also review current approaches for quantitative imaging of the subbasal nerve plexus, which require a combination of advanced image acquisition and analysis procedures, including wide field mapping and 3-D reconstruction of nerve structures. The development of new hardware, software, and acquisition techniques continues to expand the number of applications of the HRT-RCM for quantitative in vivo corneal imaging at the cellular level. Knowledge of these rapidly evolving strategies should benefit corneal clinicians and basic scientists alike. PMID:25998608

Integral refractive index imaging of flowing cell nuclei using quantitative phase microscopy combined with fluorescence microscopy.

PubMed

Dardikman, Gili; Nygate, Yoav N; Barnea, Itay; Turko, Nir A; Singh, Gyanendra; Javidi, Barham; Shaked, Natan T

2018-03-01

We suggest a new multimodal imaging technique for quantitatively measuring the integral (thickness-average) refractive index of the nuclei of live biological cells in suspension. For this aim, we combined quantitative phase microscopy with simultaneous 2-D fluorescence microscopy. We used 2-D fluorescence microscopy to localize the nucleus inside the quantitative phase map of the cell, as well as for measuring the nucleus radii. As verified offline by both 3-D confocal fluorescence microscopy and 2-D fluorescence microscopy while rotating the cells during flow, the nucleus of cells in suspension that are not during division can be assumed to be an ellipsoid. The entire shape of a cell in suspension can be assumed to be a sphere. Then, the cell and nucleus 3-D shapes can be evaluated based on their in-plain radii available from the 2-D phase and fluorescent measurements, respectively. Finally, the nucleus integral refractive index profile is calculated. We demonstrate the new technique on cancer cells, obtaining nucleus refractive index values that are lower than those of the cytoplasm, coinciding with recent findings. We believe that the proposed technique has the potential to be used for flow cytometry, where full 3-D refractive index tomography is too slow to be implemented during flow.

Quantitative phase-contrast digital holographic microscopy for cell dynamic evaluation

NASA Astrophysics Data System (ADS)

Yu, Lingfeng; Mohanty, Samarendra; Berns, Michael W.; Chen, Zhongping

2009-02-01

The laser microbeam uses lasers to alter and/or to ablate intracellular organelles and cellular and tissue samples, and, today, has become an important tool for cell biologists to study the molecular mechanism of complex biological systems by removing individual cells or sub-cellular organelles. However, absolute quantitation of the localized alteration/damage to transparent phase objects, such as the cell membrane or chromosomes, was not possible using conventional phase-contrast or differential interference contrast microscopy. We report the development of phase-contrast digital holographic microscopy for quantitative evaluation of cell dynamic changes in real time during laser microsurgery. Quantitative phase images are recorded during the process of laser microsurgery and thus, the dynamic change in phase can be continuously evaluated. Out-of-focus organelles are re-focused by numerical reconstruction algorithms.

Detection of secondary phases in duplex stainless steel by magnetic force microscopy and scanning Kelvin probe force microscopy

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

Ramírez-Salgado, J.; Domínguez-Aguilar, M.A., E-mail: madoming@imp.mx; Castro-Domínguez, B.

2013-12-15

The secondary phase transformations in a commercial super duplex stainless steel were investigated by micro-chemical analyses and high resolution scanning probe microscopy. Energy dispersive X-ray and electron probe detected ferrite and austenite as well as secondary phases in unetched aged duplex stainless steel type 25Cr-7Ni-3Mo. Volta potential indicated that nitride and sigma appeared more active than ferrite, while secondary austenite and austenite presented a nobler potential. Reversal order in nobility is thought to be attributable to the potential ranking provided by oxide nature diversity as a result of secondary phase surface compositions on steel. After eutectoid transformation, secondary austenite wasmore » detected by electron probe microanalysis, whereas atomic force microscopy distinguished this phase from former austenite by image contrast. Magnetic force microscopy revealed a “ghosted” effect on the latter microstructure probably derived from metal memory reminiscence of mechanical polishing at passivity and long range magnetic forces of ferrite phase. - Highlights: • Nobility detection of secondary phases by SKPFM in DSS particles is not a straightforward procedure. • As Volta potential and contrast are not always consistent SKPFM surface oxides is thought played an important role in detection. • AFM distinguished secondary austenite from former austenite by image contrast though SEM required EPMA.« less

Numerical modeling of two-photon focal modulation microscopy with a sinusoidal phase filter.

PubMed

Chen, Rui; Shen, Shuhao; Chen, Nanguang

2018-05-01

A spatiotemporal phase modulator (STPM) is theoretically investigated using the vectorial diffraction theory. The STPM is equivalent to a time-dependent phase-only pupil filter that alternates between a homogeneous filter and a stripe-shaped filter with a sinusoidal phase distribution. It is found that two-photon focal modulation microscopy (TPFMM) using this STPM can significantly suppress the background contribution from out-of-focus ballistic excitation and achieve almost the same resolution as two-photon microscopy. The modulation depth is also evaluated and a compromise exists between the signal-to-background ratio and signal-to-noise ratio. The theoretical investigations provide important insights into future implementations of TPFMM and its potential to further extend the penetration depth of nonlinear microscopy in imaging multiple-scattering biological tissues. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Frequency domain phase-shifted confocal microscopy (FDPCM) with array detection

NASA Astrophysics Data System (ADS)

Ge, Baoliang; Huang, Yujia; Fang, Yue; Kuang, Cuifang; Xiu, Peng; Liu, Xu

2017-09-01

We proposed a novel method to reconstruct images taken by array detected confocal microscopy without prior knowledge about its detector distribution. The proposed frequency domain phase-shifted confocal microscopy (FDPCM) shifts the image from each detection channel to its corresponding place by substituting the phase information in Fourier domain. Theoretical analysis shows that our method could approach the resolution nearly twofold of wide-field microscopy. Simulation and experiment results are also shown to verify the applicability and effectiveness of our method. Compared to Airyscan, our method holds the advantage of simplicity and convenience to be applied to array detectors with different structure, which makes FDPCM have great potential in the application of biomedical observation in the future.

Multislice coronary computed tomographic angiography in emergency department presentations of unsuspected acute myocardial infarction.

PubMed

Hecht, Harvey S; Bhatti, Tandeep

2009-01-01

Coronary computed tomographic angiography (CCTA) is not indicated in the setting of acute myocardial infarction in the emergency department (ED). Nonetheless, acute coronary syndromes may have atypical presentations, and CCTA may be inadvertently performed in this setting. This study was designed to determine the frequency and characteristics of CCTA imaging of unsuspected acute myocardial infarction in the ED. All CCTAs performed in the ED at Lenox Hill Hospital were reviewed for clinical indications and subsequent course; patients with documented acute myocardial infarction were identified. Of the 500 CCTAs performed on ED patients in the Lenox Hill laboratory, 5 patients (1%) were imaged during the initial phase of an unsuspected acute myocardial infarction; in all cases the CCTAs were key to the diagnosis. The imaging characteristics were (1) total or subtotal occlusion and (2) transmural hypodensity in the infarct area. Although acute myocardial infarction on CCTA in ED patients is an infrequent event, proper and prompt recognition is critical for appropriate patient care, particularly as applications to the ED increase.

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders

PubMed Central

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J.

2014-01-01

Abstract. Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed. PMID:26157976

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders.

PubMed

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J

2014-10-01

Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed.

Tomographic diagnostics of nonthermal plasmas

NASA Astrophysics Data System (ADS)

Denisova, Natalia

2009-10-01

In the previous work [1], we discussed a ``technology'' of tomographic method and relations between the tomographic diagnostics in thermal (equilibrium) and nonthermal (nonequilibrium) plasma sources. The conclusion has been made that tomographic reconstruction in thermal plasma sources is the standard procedure at present, which can provide much useful information on the plasma structure and its evolution in time, while the tomographic reconstruction of nonthermal plasma has a great potential at making a contribution to understanding the fundamental problem of substance behavior in strongly nonequilibrium conditions. Using medical terminology, one could say, that tomographic diagnostics of the equilibrium plasma sources studies their ``anatomic'' structure, while reconstruction of the nonequilibrium plasma is similar to the ``physiological'' examination: it is directed to study the physical mechanisms and processes. The present work is focused on nonthermal plasma research. The tomographic diagnostics is directed to study spatial structures formed in the gas discharge plasmas under the influence of electrical and gravitational fields. The ways of plasma ``self-organization'' in changing and extreme conditions are analyzed. The analysis has been made using some examples from our practical tomographic diagnostics of nonthermal plasma sources, such as low-pressure capacitive and inductive discharges. [0pt] [1] Denisova N. Plasma diagnostics using computed tomography method // IEEE Trans. Plasma Sci. 2009 37 4 502.

Direct observation of dopant distribution in GaAs compound semiconductors using phase-shifting electron holography and Lorentz microscopy.

PubMed

Sasaki, Hirokazu; Otomo, Shinya; Minato, Ryuichiro; Yamamoto, Kazuo; Hirayama, Tsukasa

2014-06-01

Phase-shifting electron holography and Lorentz microscopy were used to map dopant distributions in GaAs compound semiconductors with step-like dopant concentration. Transmission electron microscope specimens were prepared using a triple beam focused ion beam (FIB) system, which combines a Ga ion beam, a scanning electron microscope, and an Ar ion beam to remove the FIB damaged layers. The p-n junctions were clearly observed in both under-focused and over-focused Lorentz microscopy images. A phase image was obtained by using a phase-shifting reconstruction method to simultaneously achieve high sensitivity and high spatial resolution. Differences in dopant concentrations between 1 × 10(19) cm(-3) and 1 × 10(18) cm(-3) regions were clearly observed by using phase-shifting electron holography. We also interpreted phase profiles quantitatively by considering inactive layers induced by ion implantation during the FIB process. The thickness of an inactive layer at different dopant concentration area can be measured from the phase image. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding

PubMed Central

Bykov, Yury S; Sprenger, Simon; Pakdel, Mehrshad; Vogel, Georg F; Jih, Gloria; Skillern, Wesley; Behrouzi, Reza; Babst, Markus; Schmidt, Oliver; Hess, Michael W; Briggs, John AG

2017-01-01

The ESCRT machinery mediates reverse membrane scission. By quantitative fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III subunits polymerize rapidly on yeast endosomes, together with the recruitment of at least two Vps4 hexamers. During their 3–45 s lifetimes, the ESCRT-III assemblies accumulated 75–200 Snf7 and 15–50 Vps24 molecules. Productive budding events required at least two additional Vps4 hexamers. Membrane budding was associated with continuous, stochastic exchange of Vps4 and ESCRT-III components, rather than steady growth of fixed assemblies, and depended on Vps4 ATPase activity. An all-or-none step led to final release of ESCRT-III and Vps4. Tomographic electron microscopy demonstrated that acute disruption of Vps4 recruitment stalled membrane budding. We propose a model in which multiple Vps4 hexamers (four or more) draw together several ESCRT-III filaments. This process induces cargo crowding and inward membrane buckling, followed by constriction of the nascent bud neck and ultimately ILV generation by vesicle fission. PMID:29019322

Cryo-transmission electron tomography of native casein micelles from bovine milk.

PubMed

Trejo, R; Dokland, T; Jurat-Fuentes, J; Harte, F

2011-12-01

Caseins are the principal protein components in milk and an important ingredient in the food industry. In liquid milk, caseins are found as micelles of casein proteins and colloidal calcium nanoclusters. Casein micelles were isolated from raw skim milk by size exclusion chromatography and suspended in milk protein-free serum produced by ultrafiltration (molecular weight cut-off of 3 kDa) of raw skim milk. The micelles were imaged by cryo-electron microscopy and subjected to tomographic reconstruction methods to visualize the 3-dimensional and internal organization of native casein micelles. This provided new insights into the internal architecture of the casein micelle that had not been apparent from prior cryo-transmission electron microscopy studies. This analysis demonstrated the presence of water-filled cavities (∼20 to 30 nm in diameter), channels (diameter greater than ∼5 nm), and several hundred high-density nanoclusters (6 to 12 nm in diameter) within the interior of the micelles. No spherical protein submicellar structures were observed. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Neutron tomography of axially symmetric objects using 14 MeV neutrons from a portable neutron generator

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

Andersson, P., E-mail: peter.andersson@physics.uu.se; Andersson-Sunden, E.; Sjöstrand, H.

2014-08-01

In nuclear boiling water reactor cores, the distribution of water and steam (void) is essential for both safety and efficiency reasons. In order to enhance predictive capabilities, void distribution assessment is performed in two-phase test-loops under reactor-relevant conditions. This article proposes the novel technique of fast-neutron tomography using a portable deuterium-tritium neutron generator to determine the time-averaged void distribution in these loops. Fast neutrons have the advantage of high transmission through the metallic structures and pipes typically concealing a thermal-hydraulic test loop, while still being fairly sensitive to the water/void content. However, commercially available fast-neutron generators also have the disadvantagemore » of a relatively low yield and fast-neutron detection also suffers from relatively low detection efficiency. Fortunately, some loops are axially symmetric, a property which can be exploited to reduce the amount of data needed for tomographic measurement, thus limiting the interrogation time needed. In this article, three axially symmetric test objects depicting a thermal-hydraulic test loop have been examined; steel pipes with outer diameter 24 mm, thickness 1.5 mm, and with three different distributions of the plastic material POM inside the pipes. Data recorded with the FANTOM fast-neutron tomography instrument have been used to perform tomographic reconstructions to assess their radial material distribution. Here, a dedicated tomographic algorithm that exploits the symmetry of these objects has been applied, which is described in the paper. Results are demonstrated in 20 rixel (radial pixel) reconstructions of the interior constitution and 2D visualization of the pipe interior is demonstrated. The local POM attenuation coefficients in the rixels were measured with errors (RMS) of 0.025, 0.020, and 0.022 cm{sup −1}, solid POM attenuation coefficient. The accuracy and precision is high enough to provide a useful indication on the flow mode, and a visualization of the radial material distribution can be obtained. A benefit of this system is its potential to be mounted at any axial height of a two-phase test section without requirements for pre-fabricated entrances or windows. This could mean a significant increase in flexibility of the void distribution assessment capability at many existing two-phase test loops.« less

Neutron tomography of axially symmetric objects using 14 MeV neutrons from a portable neutron generator.

PubMed

Andersson, P; Andersson-Sunden, E; Sjöstrand, H; Jacobsson-Svärd, S

2014-08-01

In nuclear boiling water reactor cores, the distribution of water and steam (void) is essential for both safety and efficiency reasons. In order to enhance predictive capabilities, void distribution assessment is performed in two-phase test-loops under reactor-relevant conditions. This article proposes the novel technique of fast-neutron tomography using a portable deuterium-tritium neutron generator to determine the time-averaged void distribution in these loops. Fast neutrons have the advantage of high transmission through the metallic structures and pipes typically concealing a thermal-hydraulic test loop, while still being fairly sensitive to the water/void content. However, commercially available fast-neutron generators also have the disadvantage of a relatively low yield and fast-neutron detection also suffers from relatively low detection efficiency. Fortunately, some loops are axially symmetric, a property which can be exploited to reduce the amount of data needed for tomographic measurement, thus limiting the interrogation time needed. In this article, three axially symmetric test objects depicting a thermal-hydraulic test loop have been examined; steel pipes with outer diameter 24 mm, thickness 1.5 mm, and with three different distributions of the plastic material POM inside the pipes. Data recorded with the FANTOM fast-neutron tomography instrument have been used to perform tomographic reconstructions to assess their radial material distribution. Here, a dedicated tomographic algorithm that exploits the symmetry of these objects has been applied, which is described in the paper. Results are demonstrated in 20 rixel (radial pixel) reconstructions of the interior constitution and 2D visualization of the pipe interior is demonstrated. The local POM attenuation coefficients in the rixels were measured with errors (RMS) of 0.025, 0.020, and 0.022 cm(-1), solid POM attenuation coefficient. The accuracy and precision is high enough to provide a useful indication on the flow mode, and a visualization of the radial material distribution can be obtained. A benefit of this system is its potential to be mounted at any axial height of a two-phase test section without requirements for pre-fabricated entrances or windows. This could mean a significant increase in flexibility of the void distribution assessment capability at many existing two-phase test loops.

Four dimensional material movies: High speed phase-contrast tomography by backprojection along dynamically curved paths.

PubMed

Ruhlandt, A; Töpperwien, M; Krenkel, M; Mokso, R; Salditt, T

2017-07-26

We present an approach towards four dimensional (4d) movies of materials, showing dynamic processes within the entire 3d structure. The method is based on tomographic reconstruction on dynamically curved paths using a motion model estimated by optical flow techniques, considerably reducing the typical motion artefacts of dynamic tomography. At the same time we exploit x-ray phase contrast based on free propagation to enhance the signal from micron scale structure recorded with illumination times down to a millisecond (ms). The concept is demonstrated by observing the burning process of a match stick in 4d, using high speed synchrotron phase contrast x-ray tomography recordings. The resulting movies reveal the structural changes of the wood cells during the combustion.

Nonlinear dynamic phase contrast microscopy for microfluidic and microbiological applications

NASA Astrophysics Data System (ADS)

Denz, C.; Holtmann, F.; Woerdemann, M.; Oevermann, M.

2008-08-01

In live sciences, the observation and analysis of moving living cells, molecular motors or motion of micro- and nano-objects is a current field of research. At the same time, microfluidic innovations are needed for biological and medical applications on a micro- and nano-scale. Conventional microscopy techniques are reaching considerable limits with respect to these issues. A promising approach for this challenge is nonlinear dynamic phase contrast microscopy. It is an alternative full field approach that allows to detect motion as well as phase changes of living unstained micro-objects in real-time, thereby being marker free, without contact and non destructive, i.e. fully biocompatible. The generality of this system allows it to be combined with several other microscope techniques such as conventional bright field or fluorescence microscopy. In this article we will present the dynamic phase contrast technique and its applications in analysis of micro organismic dynamics, micro flow velocimetry and micro-mixing analysis.

Understanding the optics to aid microscopy image segmentation.

PubMed

Yin, Zhaozheng; Li, Kang; Kanade, Takeo; Chen, Mei

2010-01-01

Image segmentation is essential for many automated microscopy image analysis systems. Rather than treating microscopy images as general natural images and rushing into the image processing warehouse for solutions, we propose to study a microscope's optical properties to model its image formation process first using phase contrast microscopy as an exemplar. It turns out that the phase contrast imaging system can be relatively well explained by a linear imaging model. Using this model, we formulate a quadratic optimization function with sparseness and smoothness regularizations to restore the "authentic" phase contrast images that directly correspond to specimen's optical path length without phase contrast artifacts such as halo and shade-off. With artifacts removed, high quality segmentation can be achieved by simply thresholding the restored images. The imaging model and restoration method are quantitatively evaluated on two sequences with thousands of cells captured over several days.

Biological imaging by soft X-ray diffraction microscopy

NASA Astrophysics Data System (ADS)

Shapiro, David

We have developed a microscope for soft x-ray diffraction imaging of dry or frozen hydrated biological specimens. This lensless imaging system does not suffer from the resolution or specimen thickness limitations that other short wavelength microscopes experience. The microscope, currently situated at beamline 9.0.1 of the Advanced Light Source, can collect diffraction data to 12 nm resolution with 750 eV photons and 17 nm resolution with 520 eV photons. The specimen can be rotated with a precision goniometer through an angle of 160 degrees allowing for the collection of nearly complete three-dimensional diffraction data. The microscope is fully computer controlled through a graphical user interface and a scripting language automates the collection of both two-dimensional and three-dimensional data. Diffraction data from a freeze-dried dwarf yeast cell, Saccharomyces cerevisiae carrying the CLN3-1 mutation, was collected to 12 run resolution from 8 specimen orientations spanning a total rotation of 8 degrees. The diffraction data was phased using the difference map algorithm and the reconstructions provide real space images of the cell to 30 nm resolution from each of the orientations. The agreement of the different reconstructions provides confidence in the recovered, and previously unknown, structure and indicates the three dimensionality of the cell. This work represents the first imaging of the natural complex refractive contrast from a whole unstained cell by the diffraction microscopy method and has achieved a resolution superior to lens based x-ray tomographic reconstructions of similar specimens. Studies of the effects of exposure to large radiation doses were also carried out. It was determined that the freeze-dried cell suffers from an initial collapse, which is followed by a uniform, but slow, shrinkage. This structural damage to the cell is not accompanied by a diminished ability to see small features in the specimen. Preliminary measurements on frozen-hydrated yeast indicate that the frozen specimens do not exhibit these changes even with doses as high as 5 x 109 Gray.

White-light diffraction phase microscopy at doubled space-bandwidth product.

PubMed

Shan, Mingguang; Kandel, Mikhail E; Majeed, Hassaan; Nastasa, Viorel; Popescu, Gabriel

2016-12-12

White light diffraction microscopy (wDPM) is a quantitative phase imaging method that benefits from both temporal and spatial phase sensitivity, granted, respectively, by the common-path geometry and white light illumination. However, like all off-axis quantitative phase imaging methods, wDPM is characterized by a reduced space-bandwidth product compared to phase shifting approaches. This happens essentially because the ultimate resolution of the image is governed by the period of the interferogram and not just the diffraction limit. As a result, off-axis techniques generates single-shot, i.e., high time-bandwidth, phase measurements, at the expense of either spatial resolution or field of view. Here, we show that combining phase-shifting and off-axis, the original space-bandwidth is preserved. Specifically, we developed phase-shifting diffraction phase microscopy with white light, in which we measure and combine two phase shifted interferograms. Due to the white light illumination, the phase images are characterized by low spatial noise, i.e., <1nm pathlength. We illustrate the operation of the instrument with test samples, blood cells, and unlabeled prostate tissue biopsy.

Orbital angular momentum light in microscopy

PubMed Central

2017-01-01

Light with a helical phase has had an impact on optical imaging, pushing the limits of resolution or sensitivity. Here, special emphasis will be given to classical light microscopy of phase samples and to Fourier filtering techniques with a helical phase profile, such as the spiral phase contrast technique in its many variants and areas of application. This article is part of the themed issue ‘Optical orbital angular momentum’. PMID:28069768

Three-dimensional bright-field scanning transmission electron microscopy elucidate novel nanostructure in microbial biofilms.

PubMed

Hickey, William J; Shetty, Ameesha R; Massey, Randall J; Toso, Daniel B; Austin, Jotham

2017-01-01

Bacterial biofilms play key roles in environmental and biomedical processes, and understanding their activities requires comprehension of their nanoarchitectural characteristics. Electron microscopy (EM) is an essential tool for nanostructural analysis, but conventional EM methods are limited in that they either provide topographical information alone, or are suitable for imaging only relatively thin (<300 nm) sample volumes. For biofilm investigations, these are significant restrictions. Understanding structural relations between cells requires imaging of a sample volume sufficiently large to encompass multiple cells and the capture of both external and internal details of cell structure. An emerging EM technique with such capabilities is bright-field scanning transmission electron microscopy (BF-STEM) and in the present report BF-STEM was coupled with tomography to elucidate nanostructure in biofilms formed by the polycyclic aromatic hydrocarbon-degrading soil bacterium, Delftia acidovorans Cs1-4. Dual-axis BF-STEM enabled high-resolution 3-D tomographic recontructions (6-10 nm) visualization of thick (1250 and 1500 nm) sections. The 3-D data revealed that novel extracellular structures, termed nanopods, were polymorphic and formed complex networks within cell clusters. BF-STEM tomography enabled visualization of conduits formed by nanopods that could enable intercellular movement of outer membrane vesicles, and thereby enable direct communication between cells. This report is the first to document application of dual-axis BF-STEM tomography to obtain high-resolution 3-D images of novel nanostructures in bacterial biofilms. Future work with dual-axis BF-STEM tomography combined with correlative light electron microscopy may provide deeper insights into physiological functions associated with nanopods as well as other nanostructures. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies.

PubMed

Lanzavecchia, S; Bellon, P L; Tosoni, L

1993-12-01

FT3D is a self-contained package of tools for three-dimensional Fourier analysis, written in the C language for Unix workstations. It can evaluate direct transforms of three-dimensional real functions, inverse transforms, auto- and cross-correlations and spectra. The library has been developed to support three-dimensional reconstructions of biological structures from projections obtained in the electron microscope. This paper discusses some features of the library, which has been implemented in such a way as to profit from the resources of modern workstations. A table of elapsed times for jobs of different dimensions with different RAM buffers is reported for the particular hardware used in the authors' laboratory.

Big data in cryoEM: automated collection, processing and accessibility of EM data.

PubMed

Baldwin, Philip R; Tan, Yong Zi; Eng, Edward T; Rice, William J; Noble, Alex J; Negro, Carl J; Cianfrocco, Michael A; Potter, Clinton S; Carragher, Bridget

2018-06-01

The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing. Copyright © 2017 Elsevier Ltd. All rights reserved.

Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

PubMed Central

Bui, Khanh Huy; Pigino, Gaia; Ishikawa, Takashi

2011-01-01

Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed. PMID:21169680

Differentiation of nonneoplastic and neoplastic gallbladder polyps 1 cm or bigger with multi-detector row computed tomography.

PubMed

Park, Ko Woon; Kim, Seong Hyun; Choi, Seong Ho; Lee, Won Jae

2010-01-01

To evaluate useful computed tomographic features to differentiate nonneoplastic and neoplastic gallbladder polyps 1 cm or bigger. Thirty-one patients with 32 nonneoplastic polyps and 67 patients with 73 neoplastic polyps 1 cm or bigger underwent unenhanced and dual-phase (arterial and portal venous phases) multi-detector row computed tomography. Gallbladder polyps were diagnosed by cholecystectomy. Computed tomographic features including size (1.5 cm), surface (smooth or irregular), shape (pedunculated or sessile), accompanying wall thickening, basal indentation, perception on unenhanced images, and enhancement pattern between 2 groups were compared using univariate and multivariate analyses. On univariate analysis, age 55 years or older (P = 0.0019), size bigger than 1.5 cm (P < 0.0001), irregular surface (P = 0.0033), sessile shape (P = 0.0016), accompanying wall thickening (P = 0.0056), basal indentation (P = 0.0236), and perception on unenhanced images (P < 0.0001) were significantly more frequent in neoplastic polyps as compared with nonneoplastic polyps. On multivariate analysis, size bigger than 1.5 cm (P = 0.0260), sessile shape (P = 0.0397), and perception on unenhanced images (P < 0.0001) were statistically significant. Size bigger than 1.5 cm, sessile shape, and perception on unenhanced images are the main factors that differentiate neoplastic from nonneoplastic gallbladder polyps 1 cm or bigger.

Confirmation of a change in the global shear velocity pattern at around 1,000 km depth

NASA Astrophysics Data System (ADS)

Debayle, E.; Durand, S.; Ricard, Y. R.; Zaroli, C.; Lambotte, S.

2017-12-01

In this study, we confirm the existence of a change in the shear velocity spectrum around 1,000 km depth based on a new shear velocity tomographic model of the Earth's mantle, SEISGLOB2. This model is based on Rayleigh surface wave phase velocities, self- and cross- coupling structure coefficients of spheroidal normal modes and body wave travel times which are, for the first time, combined in a tomographic inversion. SEISGLOB2 is developed up to spherical harmonic degree 40 and in 21 radial spline functions. The spectrum of SEISGLOB2 is the flattest (i.e., richest in "short" wavelengths corresponding to spherical harmonic degrees greater than 10) around 1,000 km depth and this flattening occurs between 670 and 1,500 km depth. We also confirm various changes in the continuity of slabs and mantle plumes all around 1,000 km depth where we also observed the upper boundary of LLSVPs. The existence of a flatter spectrum, richer in short wavelength heterogeneities, in a region of the mid-mantle can have great impacts on our understanding of the mantle dynamics and should thus be better understood in the future. Although a viscosity increase, a phase change or a compositional change can all concur to induce this change of pattern, its precise origin is still very uncertain.

Joint 3-D tomographic imaging of Vp, Vs and Vp/Vs and hypocenter relocation at Sinabung volcano, Indonesia from November to December 2013

USGS Publications Warehouse

Nugraha, Andri Dian; Indrastuti, Novianti; Kusnandar, Ridwan; Gunawan, Hendra; McCausland, Wendy A.; Aulia, Atin Nur; Harlianti, Ulvienin

2018-01-01

We conducted travel time tomography using P- and S-wave arrival times of volcanic-tectonic (VT) events that occurred between November and December 2013 to determine the three-dimensional (3D) seismic velocity structure (Vp, Vs, and Vp/Vs) beneath Sinabung volcano, Indonesia in order to delineate geological subsurface structure and to enhance our understanding of the volcanism itself. This was a time period when phreatic explosions became phreatomagmatic and then magma migrated to the surface forming a summit lava dome. We used 4846 VT events with 16,138 P- and 16,138 S-wave arrival time phases recorded by 6 stations for the tomographic inversion. The relocated VTs collapse into three clusters at depths from the surface to sea level, from 2 to 4 km below sea level, and from 5 to 8.5 km below sea level. The tomographic inversion results show three prominent regions of high Vp/Vs (~ 1.8) beneath Sinabung volcano at depths consistent with the relocated earthquake clusters. We interpret these anomalies as intrusives associated with previous eruptions and possibly surrounding the magma conduit, which we cannot resolve with this study. One anomalous region might contain partial melt, at sea level and below the eventual eruption site at the summit. Our results are important for the interpretation of a conceptual model of the “plumbing system” of this hazardous volcano.

Use of the bolus tracking technique for the tomographic evaluation of the uretero-vesicular junction in dogs and assessment of dose records.

PubMed

Longo, Maurizio; Andreis, Maria Elena; Pettinato, Cinzia; Ravasio, Giuliano; Rabbogliatti, Vanessa; De Zani, Donatella; Di Giancamillo, Mauro; Zani, Davide Danilo

2016-03-29

The aim of the work is the application of a bolus tracking technique for tomographic evaluation of the uretero-vesicular junction in dogs. Ten adult dogs (8-14 years) with variable body weight (2,8-32 kg) were enrolled in the prospective study. The patients were placed in sternal recumbency with a 10° elevated pelvis and the visualization of the uretero-vesicular junction was obtained with the bolus tracking technique after intravenous administration of non-ionic contrast medium. In the post-contrast late phase a region of interest was placed within the lumen of the distal ureters and the density values were monitored before starting the helical scan. The uretero-vesicular junction was clearly visible in 100% of patients with the visualization of the endoluminal ureteral contrast enhancement and bladder washout. At the end of the tomographic study an evaluation of the dose records was performed and compared to human exposures reported in literature for the pelvic region. The effective dose estimated for each patient (37,5-138 mSv) proved to be elevated, when compared to those reported in human patients. The bolus tracking technique could be applied for the visualization of the uretero-vesicular junction in non-pathological patients, placing the region of interest in the distal ureters. The high effective doses recorded in our study support the need of specific thresholds for veterinary patients, pointing out the attention for paediatric patient's exposure also in veterinary imaging.

Ultraviolet Microscopy of Candida albicans

PubMed Central

Balish, Edward; Svihla, George

1966-01-01

Balish, Edward (Argonne National Laboratory, Argonne, Ill.), and George Svihla. Ultraviolet microscopy of Candida albicans. J. Bacteriol. 92:1812–1820. 1966.—Yeast and mycelial strains of Candida albicans were grown in medium supplemented with sulfur amino acids in an effort to determine factors that control the morphology and pathogenicity of the organism. Ultraviolet microscopy revealed a greater concentration of S-adenosylmethionine in the vacuoles of the mycelial phase than in those of yeast phases. Supplementation with amino acids greatly increased the concentration of S-adenosylmethionine in the mycelial phase, and made these cells more sensitive to the lytic action of snail gut enzymes than two yeast phase strains. This indicates a difference in cell wall structure that may be related to the pathogenicity of the mycelial phase. Images PMID:5958110

Atomic Force Microscopy Studies of Functional and Dysfunctional Pulmonary Surfactant Films. I. Micro- and Nanostructures of Functional Pulmonary Surfactant Films and the Effect of SP-A

PubMed Central

Zuo, Yi Y.; Keating, Eleonora; Zhao, Lin; Tadayyon, Seyed M.; Veldhuizen, Ruud A. W.; Petersen, Nils O.; Possmayer, Fred

2008-01-01

Monolayers of a functional pulmonary surfactant (PS) can reach very low surface tensions well below their equilibrium value. The mechanism by which PS monolayers reach such low surface tensions and maintain film stability remains unknown. As shown previously by fluorescence microscopy, phospholipid phase transition and separation seem to be important for the normal biophysical properties of PS. This work studied phospholipid phase transitions and separations in monolayers of bovine lipid extract surfactant using atomic force microscopy. Atomic force microscopy showed phospholipid phase separation on film compression and a monolayer-to-multilayer transition at surface pressure 40–50 mN/m. The tilted-condensed phase consisted of domains not only on the micrometer scale, as detected previously by fluorescence microscopy, but also on the nanometer scale, which is below the resolution limits of conventional optical methods. The nanodomains were embedded uniformly within the liquid-expanded phase. On compression, the microdomains broke up into nanodomains, thereby appearing to contribute to tilted-condensed and liquid-expanded phase remixing. Addition of surfactant protein A altered primarily the nanodomains and promoted the formation of multilayers. We conclude that the nanodomains play a predominant role in affecting the biophysical properties of PS monolayers and the monolayer-to-multilayer transition. PMID:18212010

Tomographic digital subtraction angiography for lung perfusion estimation in rodents.

PubMed

Badea, Cristian T; Hedlund, Laurence W; De Lin, Ming; Mackel, Julie S Boslego; Samei, Ehsan; Johnson, G Allan

2007-05-01

In vivo measurements of perfusion present a challenge to existing small animal imaging techniques such as magnetic resonance microscopy, micro computed tomography, micro positron emission tomography, and microSPECT, due to combined requirements for high spatial and temporal resolution. We demonstrate the use of tomographic digital subtraction angiography (TDSA) for estimation of perfusion in small animals. TDSA augments conventional digital subtraction angiography (DSA) by providing three-dimensional spatial information using tomosynthesis algorithms. TDSA is based on the novel paradigm that the same time density curves can be reproduced in a number of consecutive injections of microL volumes of contrast at a series of different angles of rotation. The capabilities of TDSA are established in studies on lung perfusion in rats. Using an imaging system developed in-house, we acquired data for four-dimensional (4D) imaging with temporal resolution of 140 ms, in-plane spatial resolution of 100 microm, and slice thickness on the order of millimeters. Based on a structured experimental approach, we optimized TDSA imaging providing a good trade-off between slice thickness, the number of injections, contrast to noise, and immunity to artifacts. Both DSA and TDSA images were used to create parametric maps of perfusion. TDSA imaging has potential application in a number of areas where functional perfusion measurements in 4D can provide valuable insight into animal models of disease and response to therapeutics.

Mantle-driven geodynamo features - accounting for non-thermal lower mantle features

NASA Astrophysics Data System (ADS)

Choblet, G.; Amit, H.

2011-12-01

Lower mantle heterogeneity responsible for spatial variations of the CMB heat flux could control long term geodynamo properties such as deviations from axial symmetry in the magnetic field and the core flow, frequency of geomagnetic reversals and anisotropic growth of the inner core. In this context, a classical interpretation of tomographic mapping of the lowermost mantle is to correlate linearly seismic velocities to heat flux anomalies. This implicitly assumes that temperature alone controls the tomographic anomalies. In addition, the limited spatial resolution of tomographic images precludes modeling sharp CMB heat flux structures.. There has been growing evidence however that non-thermal origins are also be expected for seismic velocity anomalies: the three main additional control parameters are (i) compositional anomalies possibly associated to the existence of a deep denser layer, (ii) the phase transition in magnesium perovskite believed to occur in the lowermost mantle and (iii) the possible presence of partial melts. Numerical models of mantle dynamics have illustrated how the first two parameters could distort the linear relationship between shear wave velocity anomalies and CMB heat flux (Nakagawa and Tackley, 2008). In this presentation we will consider the effect of such alternative interpretations of seismic velocity anomalies in order to prescribe CMB heat flux as an outer boundary for dynamo simulations. We first focus on the influence of post-perovskite. Taking into account this complexity could result in an improved agreement between the long term average properties of simulated dynamos and geophysical observations, including the Atlantic/Pacific hemispherical dichotomy in core flow activity, the single intense paleomagnetic field structure in the southern hemisphere, and possibly degree 1 dominant mode of inner-core seismic heterogeneity. We then account for sharp anomalies that are not resolved by the global tomographic probe. For instance, Ultra Low Velocity Zones (ULVZs) have been identified by dedicated seismic tools that cannot be observed by global tomographic models. These are likely associated to the hottest regions in the lowermost mantle. We thus model anomalies of the CMB heat flux where narrow ridges with low heat flux are juxtaposed to a large scale degree 2 pattern which represents the dominant component of tomographic observations. We find that hot ridges located with a large-scale positive heat flux anomaly to the east produce a time-average narrow elongated upwelling which acts as a flow barrier at the top of the core and results in intensified low-latitudes magnetic flux patches. This is found to have a clear signature on the meridional component of the thermal wind balance. Based on the lower mantle seismic tomography pattern, time average intense geomagnetic flux patches are expected below east Asia and Oceania and below the Americas.

Tomographic Imaging of a Forested Area By Airborne Multi-Baseline P-Band SAR.

PubMed

Frey, Othmar; Morsdorf, Felix; Meier, Erich

2008-09-24

In recent years, various attempts have been undertaken to obtain information about the structure of forested areas from multi-baseline synthetic aperture radar data. Tomographic processing of such data has been demonstrated for airborne L-band data but the quality of the focused tomographic images is limited by several factors. In particular, the common Fourierbased focusing methods are susceptible to irregular and sparse sampling, two problems, that are unavoidable in case of multi-pass, multi-baseline SAR data acquired by an airborne system. In this paper, a tomographic focusing method based on the time-domain back-projection algorithm is proposed, which maintains the geometric relationship between the original sensor positions and the imaged target and is therefore able to cope with irregular sampling without introducing any approximations with respect to the geometry. The tomographic focusing quality is assessed by analysing the impulse response of simulated point targets and an in-scene corner reflector. And, in particular, several tomographic slices of a volume representing a forested area are given. The respective P-band tomographic data set consisting of eleven flight tracks has been acquired by the airborne E-SAR sensor of the German Aerospace Center (DLR).

Total internal reflection holographic microscopy (TIRHM) for quantitative phase characterization of cell-substrate adhesion

NASA Astrophysics Data System (ADS)

Ash, William Mason, III

Total Internal Reflection Holographic Microscopy (TIRHM) combines near-field microscopy with digital holography to produce a new form of near-field phase microscopy. Using a prism in TIR as a near-field imager, the presence of microscopic organisms, cell-substrate interfaces, and adhesions, causes relative refractive index (RRI) and frustrated TIR (f-TIR) to modulate the object beam's evanescent wave phase front. Quantitative phase images of test specimens such as Amoeba proteus, Dictyostelium Discoideum and cells such as SKOV-3 ovarian cancer and 3T3 fibroblasts are produced without the need to introduce stains or fluorophores. The angular spectrum method of digital holography to compensate for tilt anamorphism due to the inclined TIR plane is also discussed. The results of this work conclusively demonstrate, for the first time, the integration of near-field microscopy with digital holography. The cellular images presented show a correlation between the physical extent of the Amoeba proteus plasma membrane and the adhesions that are quantitatively profiled by phase cross-sectioning of the holographic images obtained by digital holography. With its ability to quantitatively characterise cellular adhesion and motility, it is anticipated that TIRHM can be a tool for characterizing and combating cancer metastasis, as well as improving our understanding of morphogenesis and embryogenesis itself.

Phase behavior and transitions of self-assembling nano-structured materials

NASA Astrophysics Data System (ADS)

Duan, Hu

Homologous series of supramolecular nanostructures have been investigated by a combination of transmission electron microscopy (TEM), electron diffraction (ED), thermal polarized optical microscopy and X-ray diffraction (XRD). Materials include amphiphilic oligomers and polymer such as charged complexes, dipeptide dendrons semi-fluorinated dendron and polyethyleneimines. Upon microphase separation, they self-assemble into either cylindrical or spherical shapes, which co-organize into a 2D P6mm hexagonal columnar phase or 3D Pm 3¯ n and Im 3¯ m cubic phases. Correlation between the phase selection and molecular architecture is established accordingly. The order-disorder transition (ODT) is explored by rheometry and rheo-optical microscopy in a model polymeric compound poly(N-[3,4-bis(n-dodecan-1-yloxy)benzoyl]ethyleneimine). Shear alignment of the hexagonal columnar liquid crystalline phase along the velocity direction at low temperature and shear disordering in the vicinity of the ODT were observed. After cessation of shear, transformation back to the stable columnar phase follows a row-nucleation mechanism. The order-order transition process is explored in a monodendron that exhibits a hexagonal columnar and a weakly birefringent mesophase. Polarized DIC microscopy strongly supports an epitaxial relationship between them.

Fourier phase in Fourier-domain optical coherence tomography.

PubMed

Uttam, Shikhar; Liu, Yang

2015-12-01

Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided.

A cost-utility analysis of the use of preoperative computed tomographic angiography in abdomen-based perforator flap breast reconstruction.

PubMed

Offodile, Anaeze C; Chatterjee, Abhishek; Vallejo, Sergio; Fisher, Carla S; Tchou, Julia C; Guo, Lifei

2015-04-01

Computed tomographic angiography is a diagnostic tool increasingly used for preoperative vascular mapping in abdomen-based perforator flap breast reconstruction. This study compared the use of computed tomographic angiography and the conventional practice of Doppler ultrasonography only in postmastectomy reconstruction using a cost-utility model. Following a comprehensive literature review, a decision analytic model was created using the three most clinically relevant health outcomes in free autologous breast reconstruction with computed tomographic angiography versus Doppler ultrasonography only. Cost and utility estimates for each health outcome were used to derive the quality-adjusted life-years and incremental cost-utility ratio. One-way sensitivity analysis was performed to scrutinize the robustness of the authors' results. Six studies and 782 patients were identified. Cost-utility analysis revealed a baseline cost savings of $3179, a gain in quality-adjusted life-years of 0.25. This yielded an incremental cost-utility ratio of -$12,716, implying a dominant choice favoring preoperative computed tomographic angiography. Sensitivity analysis revealed that computed tomographic angiography was costlier when the operative time difference between the two techniques was less than 21.3 minutes. However, the clinical advantage of computed tomographic angiography over Doppler ultrasonography only showed that computed tomographic angiography would still remain the cost-effective option even if it offered no additional operating time advantage. The authors' results show that computed tomographic angiography is a cost-effective technology for identifying lower abdominal perforators for autologous breast reconstruction. Although the perfect study would be a randomized controlled trial of the two approaches with true cost accrual, the authors' results represent the best available evidence.

Quantitative phase-digital holographic microscopy: a new imaging modality to identify original cellular biomarkers of diseases

NASA Astrophysics Data System (ADS)

Marquet, P.; Rothenfusser, K.; Rappaz, B.; Depeursinge, C.; Jourdain, P.; Magistretti, P. J.

2016-03-01

Quantitative phase microscopy (QPM) has recently emerged as a powerful label-free technique in the field of living cell imaging allowing to non-invasively measure with a nanometric axial sensitivity cell structure and dynamics. Since the phase retardation of a light wave when transmitted through the observed cells, namely the quantitative phase signal (QPS), is sensitive to both cellular thickness and intracellular refractive index related to the cellular content, its accurate analysis allows to derive various cell parameters and monitor specific cell processes, which are very likely to identify new cell biomarkers. Specifically, quantitative phase-digital holographic microscopy (QP-DHM), thanks to its numerical flexibility facilitating parallelization and automation processes, represents an appealing imaging modality to both identify original cellular biomarkers of diseases as well to explore the underlying pathophysiological processes.

Phase aberration compensation of digital holographic microscopy based on least squares surface fitting

NASA Astrophysics Data System (ADS)

Di, Jianglei; Zhao, Jianlin; Sun, Weiwei; Jiang, Hongzhen; Yan, Xiaobo

2009-10-01

Digital holographic microscopy allows the numerical reconstruction of the complex wavefront of samples, especially biological samples such as living cells. In digital holographic microscopy, a microscope objective is introduced to improve the transverse resolution of the sample; however a phase aberration in the object wavefront is also brought along, which will affect the phase distribution of the reconstructed image. We propose here a numerical method to compensate for the phase aberration of thin transparent objects with a single hologram. The least squares surface fitting with points number less than the matrix of the original hologram is performed on the unwrapped phase distribution to remove the unwanted wavefront curvature. The proposed method is demonstrated with the samples of the cicada wings and epidermal cells of garlic, and the experimental results are consistent with that of the double exposure method.

Direct observation of anti-phase boundaries in heteroepitaxy of GaSb thin films grown on Si(001) by transmission electron microscopy

NASA Astrophysics Data System (ADS)

Woo, S. Y.; Hosseini Vajargah, S.; Ghanad-Tavakoli, S.; Kleiman, R. N.; Botton, G. A.

2012-10-01

Unambiguous identification of anti-phase boundaries (APBs) in heteroepitaxial films of GaSb grown on Si has been so far elusive. In this work, we present conventional transmission electron microscopy (TEM) diffraction contrast imaging using superlattice reflections, in conjunction with convergent beam electron diffraction analysis, to determine a change in polarity across APBs in order to confirm the presence of anti-phase disorder. In-depth analysis of anti-phase disorder is further supported with atomic resolution high-angle annular dark-field scanning transmission electron microscopy. The nature of APBs in GaSb is further elucidated by a comparison to previous results for GaAs epilayers grown on Si.

Influence of sample preparation and identification of subcelluar structures in quantitative holographic phase contrast microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Schmidt, Lisa; Przibilla, Sabine; Rommel, Christina; Vollmer, Angelika; Ketelhut, Steffi; Schnekenburger, Jürgen; von Bally, Gert

2010-04-01

Digital holographic microscopy (DHM) provides label-free quantitative phase contrast with low demands on sample preparation. Nevertheless, for DHM measurements on fixed cells the mounting medium has to be considered while the phase contrast of living cells may be influenced by the used buffer solution. To quantify these effects, the maximum cell caused phase contrast and the visibility of the nucleoli were analyzed. A second aim of the study was to identify subcellular components in DHM phase contrast images. Therefore, comparative investigations using bright field imaging, DHM and fluorescence microscopy with 4',6- Diamidino-2-phenylindol (DAPI) staining were performed. DAPI-staining visualizes cell components containing DNA. The obtained results demonstrate exemplarily for two tumor cell lines that from DHM phase contrast images of fixed cells in phosphate buffer saline (PBS) cell thickness values are obtained which are comparable to living cells. Furthermore, it is shown that in many cases nucleus components can be identified only by DHM phase contrast.

High-pressure freezing and freeze substitution of Arabidopsis for electron microscopy.

PubMed

Austin, Jotham R

2014-01-01

The objectives of electron microscopy ultrastructural studies are to examine cellular architecture and relate the cell's structural machinery to dynamic functional roles. This aspiration is difficult to achieve if specimens have not been adequately preserved in a "living state"; hence specimen preparation is of the utmost importance for the success of any electron micrographic study. High-pressure freezing (HPF)/freeze substitution (FS) has long been recognized as the primer technique for the preservation of ultrastructure in biological samples. In most cases a basic HPF/freeze substitution protocol is sufficient to obtain superior ultrastructural preservation and structural contrast, which allows one to use more advanced microscopy techniques such as 3D electron tomography. However, for plant tissues, which have a thick cell wall, large water-filled vacuoles, and air spaces (all of which are detrimental to cryopreservation), these basic HPF/FS protocols often yield undesirable results. In particular, ice crystal artifacts and the staining of membrane systems are often poorly or negatively stained, which make 3D segmentation of a tomogram difficult. To overcome these problems, various aspects of the HPF/FS protocol can be altered, including the cryo-filler(s) used, freeze substitution cocktail, and the resin infiltration process. This chapter will describe these modifications for the preparation of plant tissues for routine electron microscopic studies, immunocytochemistry, and 3D tomographic electron imaging.

New Developments in Hard X-ray Fluorescence Microscopy for In-situ Investigations of Trace Element Distributions in Aqueous Systems of Soil Colloids

NASA Astrophysics Data System (ADS)

Gleber, Sophie-Charlotte; Weinhausen, Britta; Köster, Sarah; Ward, Jesse; Vine, David; Finney, Lydia; Vogt, Stefan

2013-10-01

The distribution, binding and release of trace elements on soil colloids determine matter transport through the soil matrix, and necessitates an aqueous environment and short length and time scales for their study. However, not many microscopy techniques allow for that. We previously showed hard x-ray fluorescence microscopy capabilities to image aqueous colloidal soil samples [1]. As this technique provides attogram sensitivity for transition elements like Cu, Zn, and other geochemically relevant trace elements at sub micrometer spatial resolution (currently down to 150 nm at 2-ID-E [2]; below 50nm at Bionanoprobe, cf. G.Woloschak et al, this volume) combined with the capability to penetrate tens of micrometer of water, it is ideally suited for imaging the elemental content of soil colloids. To address the question of binding and release processes of trace elements on the surface of soil colloids, we developed a microfluidics based XRF flow cytometer, and expanded the applied methods of hard x-ray fluorescence microscopy towards three dimensional imaging. Here, we show (a) the 2-D imaged distributions of Si, K and Fe on soil colloids of Pseudogley samples; (b) how the trace element distribution is a dynamic, pH-dependent process; and (c) x-ray tomographic applications to render the trace elemental distributions in 3-D. We conclude that the approach presented here shows the remarkable potential to image and quantitate elemental distributions from samles within their natural aqueous microenvironment, particularly important in the environmental, medical, and biological sciences.

HANFORD WASTE MINERALOGY REFERENCE REPORT

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

DISSELKAMP RS

2010-06-29

This report lists the observed mineral phases present in the Hanford tanks. This task was accomplished by performing a review of numerous reports that used experimental techniques including, but not limited to: x-ray diffraction, polarized light microscopy, scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, electron energy loss spectroscopy, and particle size distribution analyses. This report contains tables that can be used as a quick reference to identify the crystal phases observed in Hanford waste.

Status of holographic interferometry at University of Michigan

NASA Technical Reports Server (NTRS)

Vest, Charles

1987-01-01

Reflection holograms were taken of a jet of air injected traverse to a subsonic stream. The technique of reflection holograms allowed maximum viewing angle and minimum distance to the jet. Holographic interferometry is being used to measure the temperature distribution in a growing crystal. Computations of the temperatures are being made. A phase shift interferometer was used to study flows with very weak changes in refractive index, of the order of 1 shift. Tomographic techniques are being developed for strong refractive cases.

Revising the lower statistical limit of x-ray grating-based phase-contrast computed tomography.

PubMed

Marschner, Mathias; Birnbacher, Lorenz; Willner, Marian; Chabior, Michael; Herzen, Julia; Noël, Peter B; Pfeiffer, Franz

2017-01-01

Phase-contrast x-ray computed tomography (PCCT) is currently investigated as an interesting extension of conventional CT, providing high soft-tissue contrast even if examining weakly absorbing specimen. Until now, the potential for dose reduction was thought to be limited compared to attenuation CT, since meaningful phase retrieval fails for scans with very low photon counts when using the conventional phase retrieval method via phase stepping. In this work, we examine the statistical behaviour of the reverse projection method, an alternative phase retrieval approach and compare the results to the conventional phase retrieval technique. We investigate the noise levels in the projections as well as the image quality and quantitative accuracy of the reconstructed tomographic volumes. The results of our study show that this method performs better in a low-dose scenario than the conventional phase retrieval approach, resulting in lower noise levels, enhanced image quality and more accurate quantitative values. Overall, we demonstrate that the lower statistical limit of the phase stepping procedure as proposed by recent literature does not apply to this alternative phase retrieval technique. However, further development is necessary to overcome experimental challenges posed by this method which would enable mainstream or even clinical application of PCCT.

Quantitative X-ray Differential Interference Contrast Microscopy

NASA Astrophysics Data System (ADS)

Nakamura, Takashi

Full-field soft x-ray microscopes are widely used in many fields of sciences. Advances in nanofabrication technology enabled short wavelength focusing elements with significantly improved spatial resolution. In the soft x-ray spectral region, samples as small as 12 nm can be resolved using micro zone-plates as the objective lens. In addition to conventional x-ray microscopy in which x-ray absorption difference provides the image contrast, phase contrast mechanisms such as differential phase contrast (DIC) and Zernike phase contrast have also been demonstrated These phase contrast imaging mechanisms are especially attractive at the x-ray wavelengths where phase contrast of most materials is typically 10 times stronger than the absorption contrast. With recent progresses in plasma-based x- ray sources and increasing accessibility to synchrotron user facilities, x-ray microscopes are quickly becoming standard measurement equipment in the laboratory. To further the usefulness of x-ray DIC microscopy this thesis explicitly addresses three known issues with this imaging modality by introducing new techniques and devices First, as opposed to its visible-light counterpart, no quantitative phase imaging technique exists for x-ray DIC microscopy. To address this issue, two nanoscale x-ray quantitative phase imaging techniques, using exclusive OR (XOR) patterns and zone-plate doublets, respectively, are proposed. Unlike existing x-ray quantitative phase imaging techniques such as Talbot interferometry and ptychography, no dedicated experimental setups or stringent illumination coherence are needed for quantitative phase retrieval. Second, to the best of our knowledge, no quantitative performance characterization of DIC microscopy exists to date. Therefore the imaging system's response to sample's spatial frequency is not known In order to gain in-depth understanding of this imaging modality, performance of x-ray DIC microscopy is quantified using modulation transfer function. A new illumination apparatus required for the transfer function analysis under partially coherent illumination is also proposed. Such a characterization is essential for a proper selection of DIC optics for various transparent samples under study. Finally, optical elements used for x-ray DIC microscopy are highly absorptive and high brilliance x-ray sources such as synchrotrons are generally needed for image contrast. To extend the use of x-ray DIC microscopy to a wider variety of applications, a high efficiency large numerical aperture optical element consisting of high reflective Bragg reflectors is proposed. Using Bragg reflectors, which have 70% ˜99% reflectivity at extreme ultraviolet and soft x-rays for all angles of glancing incidence, the first order focusing efficiency is expected to increase by ˜ 8 times compared to that of a typical Fresnel zone-plate. This thesis contributes to current nanoscale x-ray phase contrast imaging research and provides new insights for biological, material, and magnetic sciences

Single particle analysis based on Zernike phase contrast transmission electron microscopy.

PubMed

Danev, Radostin; Nagayama, Kuniaki

2008-02-01

We present the first application of Zernike phase-contrast transmission electron microscopy to single-particle 3D reconstruction of a protein, using GroEL chaperonin as the test specimen. We evaluated the performance of the technique by comparing 3D models derived from Zernike phase contrast imaging, with models from conventional underfocus phase contrast imaging. The same resolution, about 12A, was achieved by both imaging methods. The reconstruction based on Zernike phase contrast data required about 30% fewer particles. The advantages and prospects of each technique are discussed.

High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography

NASA Astrophysics Data System (ADS)

Larsson, Daniel H.; Vågberg, William; Yaroshenko, Andre; Yildirim, Ali Önder; Hertz, Hans M.

2016-12-01

X-ray computed tomography of small animals and their organs is an essential tool in basic and preclinical biomedical research. In both phase-contrast and absorption tomography high spatial resolution and short exposure times are of key importance. However, the observable spatial resolutions and achievable exposure times are presently limited by system parameters rather than more fundamental constraints like, e.g., dose. Here we demonstrate laboratory tomography with few-ten μm spatial resolution and few-minute exposure time at an acceptable dose for small-animal imaging, both with absorption contrast and phase contrast. The method relies on a magnifying imaging scheme in combination with a high-power small-spot liquid-metal-jet electron-impact source. The tomographic imaging is demonstrated on intact mouse, phantoms and excised lungs, both healthy and with pulmonary emphysema.

Three-dimensional molecular mapping of a multiple emulsion by means of CARS microscopy.

PubMed

Meyer, Tobias; Akimov, Denis; Tarcea, Nicolae; Chatzipapadopoulos, Susana; Muschiolik, Gerald; Kobow, Jens; Schmitt, Michael; Popp, Jürgen

2008-02-07

Multiple emulsions consisting of water droplets dispersed in an oil phase containing emulsifier which is emulsified in an outer water phase (W/O/W) are of great interest in pharmacology for developing new drugs, in the nutrition sciences for designing functional food, and in biology as model systems for cell organelles such as liposomes. In the food industry multiple emulsions with high sugar content in the aqueous phase can be used for the production of sweets, because the high sugar content prevents deterioration. However, for these emulsions the refractive indexes of oil and aqueous phase are very similar. This seriously impedes the analysis of these emulsions, e.g., for process monitoring, because microscopic techniques based on transmission or reflection do not provide sufficient contrast. We have characterized the inner dispersed phase of concentrated W/O/W emulsions with the same refractive index of the three phases by micro Raman spectroscopy and investigated the composition and molecular distribution in water-oil-water emulsions by means of three-dimensional laser scanning CARS (coherent anti-Stokes Raman scattering) microscopy. CARS microscopy has been used to study water droplets dispersed in oil droplets at different Raman resonances to visualize different molecular species. Water droplets with a diameter of about 700 nm could clearly be visualized. The advantages of CARS microscopy for studying this particular system are emphasized by comparing this microscopic technique with conventional confocal reflection and transmission microscopies.

Multimodal imaging of human cerebellum - merging X-ray phase microtomography, magnetic resonance microscopy and histology

NASA Astrophysics Data System (ADS)

Schulz, Georg; Waschkies, Conny; Pfeiffer, Franz; Zanette, Irene; Weitkamp, Timm; David, Christian; Müller, Bert

2012-11-01

Imaging modalities including magnetic resonance imaging and X-ray computed tomography are established methods in daily clinical diagnosis of human brain. Clinical equipment does not provide sufficient spatial resolution to obtain morphological information on the cellular level, essential for applying minimally or non-invasive surgical interventions. Therefore, generic data with lateral sub-micrometer resolution have been generated from histological slices post mortem. Sub-cellular spatial resolution, lost in the third dimension as a result of sectioning, is obtained using magnetic resonance microscopy and micro computed tomography. We demonstrate that for human cerebellum grating-based X-ray phase tomography shows complementary contrast to magnetic resonance microscopy and histology. In this study, the contrast-to-noise values of magnetic resonance microscopy and phase tomography were comparable whereas the spatial resolution in phase tomography is an order of magnitude better. The registered data with their complementary information permit the distinct segmentation of tissues within the human cerebellum.

Tomographic Reconstruction from a Few Views: A Multi-Marginal Optimal Transport Approach

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

Abraham, I., E-mail: isabelle.abraham@cea.fr; Abraham, R., E-mail: romain.abraham@univ-orleans.fr; Bergounioux, M., E-mail: maitine.bergounioux@univ-orleans.fr

2017-02-15

In this article, we focus on tomographic reconstruction. The problem is to determine the shape of the interior interface using a tomographic approach while very few X-ray radiographs are performed. We use a multi-marginal optimal transport approach. Preliminary numerical results are presented.

Wide-field imaging through scattering media by scattered light fluorescence microscopy

NASA Astrophysics Data System (ADS)

Zhou, Yulan; Li, Xun

2017-08-01

To obtain images through scattering media, scattered light fluorescence (SLF) microscopy that utilizes the optical memory effect has been developed. However, the small field of view (FOV) of SLF microscopy limits its application. In this paper, we have introduced a re-modulation method to achieve wide-field imaging through scattering media by SLF microscopy. In the re-modulation method, to raster scan the focus across the object plane, the incident wavefront is re-modulated via a spatial light modulator (SLM) in the updated phase compensation calculated using the optimized iterative algorithm. Compared with the conventional optical memory effect method, the re-modulation method can greatly increase the FOV of a SLF microscope. With the phase compensation theoretically calculated, the process of updating the phase compensation of a high speed SLM is fast. The re-modulation method does not increase the imaging time. The re-modulation method is, therefore, expected to make SLF microscopy have much wider applications in biology, medicine and physiology.

Global-scale Joint Body and Surface Wave Tomography with Vertical Transverse Isotropy for Seismic Monitoring Applications

NASA Astrophysics Data System (ADS)

Simmons, Nathan; Myers, Steve

2017-04-01

We continue to develop more advanced models of Earth's global seismic structure with specific focus on improving predictive capabilities for future seismic events. Our most recent version of the model combines high-quality P and S wave body wave travel times and surface-wave group and phase velocities into a joint (simultaneous) inversion process to tomographically image Earth's crust and mantle. The new model adds anisotropy (known as vertical transverse isotropy) to the model, which is necessitated by the addition of surface waves to the tomographic data set. Like previous versions of the model the new model consists of 59 surfaces and 1.6 million model nodes from the surface to the core-mantle boundary, overlaying a 1-D outer and inner core model. The model architecture is aspherical and we directly incorporate Earth's expected hydrostatic shape (ellipticity and mantle stretching). We also explicitly honor surface undulations including the Moho, several internal crustal units, and the upper mantle transition zone undulations as predicated by previous studies. The explicit Earth model design allows for accurate travel time computation using our unique 3-D ray tracing algorithms, capable of 3-D ray tracing more than 20 distinct seismic phases including crustal, regional, teleseismic, and core phases. Thus, we can now incorporate certain secondary (and sometimes exotic) phases into source location determination and other analyses. New work on model uncertainty quantification assesses the error covariance of the model, which when completed will enable calculation of path-specific estimates of uncertainty for travel times computed using our previous model (LLNL-G3D-JPS) which is available to the monitoring and broader research community and we encourage external evaluation and validation. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Quantitative DIC microscopy using an off-axis self-interference approach.

PubMed

Fu, Dan; Oh, Seungeun; Choi, Wonshik; Yamauchi, Toyohiko; Dorn, August; Yaqoob, Zahid; Dasari, Ramachandra R; Feld, Michael S

2010-07-15

Traditional Normarski differential interference contrast (DIC) microscopy is a very powerful method for imaging nonstained biological samples. However, one of its major limitations is the nonquantitative nature of the imaging. To overcome this problem, we developed a quantitative DIC microscopy method based on off-axis sample self-interference. The digital holography algorithm is applied to obtain quantitative phase gradients in orthogonal directions, which leads to a quantitative phase image through a spiral integration of the phase gradients. This method is practically simple to implement on any standard microscope without stringent requirements on polarization optics. Optical sectioning can be obtained through enlarged illumination NA.

Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Wolf, Sharon G; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef; Urban, Knut

2008-03-01

We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomic-scale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2-3 A. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subångström resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm3, preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scale at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.

Quantitative phase imaging of human red blood cells using phase-shifting white light interference microscopy with colour fringe analysis

NASA Astrophysics Data System (ADS)

Singh Mehta, Dalip; Srivastava, Vishal

2012-11-01

We report quantitative phase imaging of human red blood cells (RBCs) using phase-shifting interference microscopy. Five phase-shifted white light interferograms are recorded using colour charge coupled device camera. White light interferograms were decomposed into red, green, and blue colour components. The phase-shifted interferograms of each colour were then processed by phase-shifting analysis and phase maps for red, green, and blue colours were reconstructed. Wavelength dependent refractive index profiles of RBCs were computed from the single set of white light interferogram. The present technique has great potential for non-invasive determination of refractive index variation and morphological features of cells and tissues.

Constraints on Lateral S Wave Velocity Gradients around the Pacific Superplume

NASA Astrophysics Data System (ADS)

To, A.; Romanowicz, B.

2006-12-01

Global shear velocity tomographic models show two large-scale low velocity structures in the lower mantle, under southern Africa and under the mid-Pacific. While tomographic models show the shape of the structures, the gradient and amplitude of the anomalies are yet to be constrained. By forward modelling of Sdiffracted phases using the Coupled Spectral ELement Method (C-SEM, Capdeville et al., 2003), we have previously shown that observed secondary phases following the Sdiff can be explained by interaction of the wavefield with sharp boundaries of the superplumes in the south Indian and south Pacific ocean (To et al., 2005). Here, we search for further constrains on velocity gradients at the border of the Pacific superplume all around the Pacific using a multi-step approach applied to a large dataset of Sdiffracted travel times and waveforms which are sensitive to the lower most mantle. We first apply our finite frequency tomographic inversion methodology (NACT, Li and Romanowicz, 1996) which provides a good starting 3D model, which in particular allows us to position the fast and slow anomalies and their boundaries quite well, as has been shown previously, but underestimates the gradients and velocity contrasts. We then perform forward modelling of Sdiff travel times, taking into account finite frequency effects, to refine the velocity contrasts and gradients and provides the next iteration 3D model. We then perform forward modelling of waveforms, down to a frequency of 0.06Hz, using C-SEM which provides final adjustments to the model. We present a model which shows that we can constrain sharp gradients on the southern and northern edges of the Pacific Superplume. To, A., B. Romanowicz, Y. Capdeville and N. Takeuchi (2005) 3D effects of sharp boundaries at the borders of the African and Pacific Superplumes: Observation and modeling. Earth and Planetary Sceince Letters, 233: 137-153 Capdeville, Y., A. To and B. Romanowicz (2003) Coupling spectral elements and modes in a spherical earth: an extension to the "sandwich" case. Geophys. J. Int., 154: 44-57 Li, X.D. and B. Romanowicz (1996) Global mantle shear velocity model developed using nonlinear asymptotic coupling theory, J. Geophys. Res., 101, 22,245-22,273

Tomographic Reconstruction of Mercury's Exosphere from MESSENGER Flyby Data

NASA Technical Reports Server (NTRS)

Killen, Rosemary M.; McClintock, William E.; Slavin, James A.; Solomon, Sean C.; Vervack, Ronald J., Jr.

2011-01-01

The exosphere of Mercury is among the best-studied examples of a common type of atmosphere, a surface-bounded exosphere. Mercury's exosphere was probed in 2008-2009 with Ultraviolet and Visible Spectrometer (UVVS) measurements obtained during three planetary flybys by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft [1-3]. The measurements detailed the distribution of two previously known metallic constituents of Mercury's exosphere, Na and Ca, and indicated the presence in the gas phase of yet another metallic species, Mg. Such measurements can answer fundamental scientific questions regarding the relative importance of possible source and loss processes for exospheric species ejected from a surface boundary [4]. The trajectory of MESSENGER during the last of its three flybys provided the best spatial coverage prior to orbit insertion. The measurements by MESSENGER of Na, Ca, and Mg during the third flyby have been analyzed with a novel tomographic method. This approach maximizes the amount of information that can be extracted from line-of-sight measurements because it yields three-dimensional distributions of neutrals consistent with the data.

Evaluation of hepatic arterial anatomy by multidetector computed tomographic angiography in living donor liver transplantation.

PubMed

Keles, Papatya; Yuce, Ihsan; Keles, Sait; Kantarci, Mecit

2016-06-01

The aim of this study was to define the different courses and percentages of hepatic artery that were detected during preoperative evaluation of living liver donors by multidetector computed tomographic angiography (MDCTA). We evaluated 150 donors before hepatic transplantation. All of the donors were evaluated by multislice CT scan with 256 detectors. For each patient, arterial, portal and venous phase images were obtained. The hepatic arterial variations were evaluated by the same radiologist according to Michels' classification. Common hepatic arterial anatomy (type I) was observed in 95 donors (63.3%). Other arterial variations were determined in the remaining 55 donors (36.6%). The second common variation was type XI which did not match with the description of Michels' classification variation in 15 donors (10%). The remaining variations described in Michels' classification were seen at lower rates. Type VII or X variation was not seen. MDCTA is a useful method to identify the blood supply of the liver before the liver transplantations, and surgeons can make their plan on the basis of CT data.

Optimizing single-nanoparticle two-photon microscopy by in situ adaptive control of femtosecond pulses

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

Li, Donghai; Deng, Yongkai; Chu, Saisai

2016-07-11

Single-nanoparticle two-photon microscopy shows great application potential in super-resolution cell imaging. Here, we report in situ adaptive optimization of single-nanoparticle two-photon luminescence signals by phase and polarization modulations of broadband laser pulses. For polarization-independent quantum dots, phase-only optimization was carried out to compensate the phase dispersion at the focus of the objective. Enhancement of the two-photon excitation fluorescence intensity under dispersion-compensated femtosecond pulses was achieved. For polarization-dependent single gold nanorod, in situ polarization optimization resulted in further enhancement of two-photon photoluminescence intensity than phase-only optimization. The application of in situ adaptive control of femtosecond pulse provides a way for object-orientedmore » optimization of single-nanoparticle two-photon microscopy for its future applications.« less

Optical mesoscopy without the scatter: broadband multispectral optoacoustic mesoscopy

PubMed Central

Chekkoury, Andrei; Gateau, Jérôme; Driessen, Wouter; Symvoulidis, Panagiotis; Bézière, Nicolas; Feuchtinger, Annette; Walch, Axel; Ntziachristos, Vasilis

2015-01-01

Optical mesoscopy extends the capabilities of biological visualization beyond the limited penetration depth achieved by microscopy. However, imaging of opaque organisms or tissues larger than a few hundred micrometers requires invasive tissue sectioning or chemical treatment of the specimen for clearing photon scattering, an invasive process that is regardless limited with depth. We developed previously unreported broadband optoacoustic mesoscopy as a tomographic modality to enable imaging of optical contrast through several millimeters of tissue, without the need for chemical treatment of tissues. We show that the unique combination of three-dimensional projections over a broad 500 kHz–40 MHz frequency range combined with multi-wavelength illumination is necessary to render broadband multispectral optoacoustic mesoscopy (2B-MSOM) superior to previous optical or optoacoustic mesoscopy implementations. PMID:26417486

Cellular internalization of polycation-coated microparticles and its dependence on their zeta potential

NASA Astrophysics Data System (ADS)

Kato, Noritaka; Kondo, Ryosuke

2018-03-01

By applying microparticles to HeLa cells, the number of particles adhered on the cell and that of the ones internalized in the cells were evaluated. Three-dimensional tomographic images of the cells with the particles were obtained by multiphoton excitation laser scanning microscopy, and the adhered and internalized particles were counted separately. When the surface charge of the particles was reversed from negative to positive by coating the particles with polycations, both numbers significantly increased owing to the electrostatic attraction between the cells and the polycation-coated particles. Four different positively charged particles were prepared using four different polycations, and the numbers of adhered and internalized particles were compared. Our results suggest that these numbers depended on the zeta potential rather than the molecular structure of the polycation.

Fourier phase in Fourier-domain optical coherence tomography

PubMed Central

Uttam, Shikhar; Liu, Yang

2015-01-01

Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided. PMID:26831383

SU-E-J-189: Determination of Markerless Lung Tumor Position in Real Time: A Feasibility Study Using a Novel Tomo-Cinegraphy Imaging

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

Yi, B; Hu, E; Yu, C

2015-06-15

Purpose: A Tomo-Cinegraphy (TC) is a method to generate a series of temporal tomographic images from projection images of the on-board imager (OBI) while gantry is moving. It is to test if this technique is useful to determine a lung tumor position during treatments. Methods: Tomographic image via background subtraction, TIBS uses a priori anatomical information from a previous CT scan to isolate a SOI from a planar kV image by factoring out the attenuations by tissues outside the SOI (background). This idea was extended to a TC, which enables to generate tomographic images of same geometry from the projectionmore » of different gantry angles and different breathing phases. Projection images of a lung patient for CBCT acquisition are used to generate TC images. A region of interest (ROI) is selected around a tumor adding 2cm margins. Center of mass (COM) of the ROI is traced to determine tumor position for every projection images. Results: Tumor is visible in the TC images while the OBI projections are not. The coordinates of the COMs represent the temporal tumor positions. While, it is not possible to trace the tumor motion using the projection images. A source of time delay is the time to acquire projection images, which is always less than a second. Conclusion: TC allows tracking the tumor positions without fiducial markers in real time for some lung patients, if the projection images are acquired during treatments. Partially supported by NIH R01CA133539.« less

Spectroscopic AC Susceptibility Imaging (sASI) of Magnetic Nanoparticles

PubMed Central

Ficko, Bradley W.; Nadar, Priyanka M.; Diamond, Solomon G.

2014-01-01

This study demonstrates a method for alternating current (AC) susceptibility imaging (ASI) of magnetic nanoparticles (mNPs) using low cost instrumentation. The ASI method uses AC magnetic susceptibility measurement to create tomographic images using an array of drive coils, compensation coils and fluxgate magnetometers. Using a spectroscopic approach in conjunction with ASI, a series of tomographic images can be created for each frequency measurement and is termed sASI. The advantage of sASI is that mNPs can be simultaneously characterized and imaged in a biological medium. System calibration was performed by fitting the in-phase and out-of-phase susceptibility measurements of an mNP sample with a hydrodynamic diameter of 100 nm to a Brownian relaxation model (R2 = 0.96). Samples of mNPs with core diameters of 10 and 40 nm and a sample of 100 nm hydrodynamic diameter were prepared in 0.5 ml tubes. Three mNP samples were arranged in a randomized array and then scanned using sASI with six frequencies between 425 and 925 Hz. The sASI scans showed the location and quantity of the mNP samples (R2 = 0.97). Biological compatibility of the sASI method was demonstrated by scanning mNPs that were injected into a pork sausage. The mNP response in the biological medium was found to correlate with a calibration sample (R2 = 0.97, p <0.001). These results demonstrate the concept of ASI and advantages of sASI. PMID:25477704

Tomographic separation of composite spectra. 2: The components of 29 UW Canis Majoris

NASA Technical Reports Server (NTRS)

Bagnuolo, William G., Jr.; Gies, Douglas R.; Hahula, Michael E.; Wiemker, Rafael; Wiggs, Michael S.

1994-01-01

We have analyzed the UV photospheric lines of 29 CMa, a 4.39 day period, double-lined O-type spectroscopic binary. Archival data from International Ultraviolet Explorer (IUE)(28 spectra well distributed in oribital phase) were analyzed with several techniques. We find that the mass ratio is q = 1.20 +/- 0.16 (secondary more massive) based on three independent arguments. A tomography algorithm was used to produce the separate spectra of the two stars in six UV spectral regions. The MK spectral classifications of the primary and secondary, O7.5-8 Iab and O9.7 Ib, respectively, were estimated through a comparison of UV line ratios with those in spectral standard stars. The flux ratio of the stars in the UV is 0.36 +/- 0.07 (primary brighter). The primary has a strong P Cygni NIV wavelength 1718 feature, indicating a strong stellar wind. We also present tomographic reconstructions of visual spectral data in the range 4300-4950 A, based on seven observations of differing orbital phases, which confirm the UV classifications, and show that the primary is an Of star. From the spectral classifications, we estimate the temperatures of the stars to be 33,750 K and 29,000 K for primary and secondary, respectively. We then fit visual and UV light curves and show that reasonably good fits can be obtained with these temperatures, a semicontact configuration, an inclination of 74 deg. +/- 2 deg., and an intensity ratio r is less than 0.5.

System and method for generating motion corrected tomographic images

DOEpatents

Gleason, Shaun S [Knoxville, TN; Goddard, Jr., James S.

2012-05-01

A method and related system for generating motion corrected tomographic images includes the steps of illuminating a region of interest (ROI) to be imaged being part of an unrestrained live subject and having at least three spaced apart optical markers thereon. Simultaneous images are acquired from a first and a second camera of the markers from different angles. Motion data comprising 3D position and orientation of the markers relative to an initial reference position is then calculated. Motion corrected tomographic data obtained from the ROI using the motion data is then obtained, where motion corrected tomographic images obtained therefrom.

Propagation-based phase-contrast x-ray tomography of cochlea using a compact synchrotron source.

PubMed

Töpperwien, Mareike; Gradl, Regine; Keppeler, Daniel; Vassholz, Malte; Meyer, Alexander; Hessler, Roland; Achterhold, Klaus; Gleich, Bernhard; Dierolf, Martin; Pfeiffer, Franz; Moser, Tobias; Salditt, Tim

2018-03-21

We demonstrate that phase retrieval and tomographic imaging at the organ level of small animals can be advantageously carried out using the monochromatic radiation emitted by a compact x-ray light source, without further optical elements apart from source and detector. This approach allows to carry out microtomography experiments which - due to the large performance gap with respect to conventional laboratory instruments - so far were usually limited to synchrotron sources. We demonstrate the potential by mapping the functional soft tissue within the guinea pig and marmoset cochlea, including in the latter case an electrical cochlear implant. We show how 3d microanatomical studies without dissection or microscopic imaging can enhance future research on cochlear implants.

Optical tomographic memories: algorithms for the efficient information readout

NASA Astrophysics Data System (ADS)

Pantelic, Dejan V.

1990-07-01

Tomographic alogithms are modified in order to reconstruct the inf ormation previously stored by focusing laser radiation in a volume of photosensitive media. Apriori information about the position of bits of inf ormation is used. 1. THE PRINCIPLES OF TOMOGRAPHIC MEMORIES Tomographic principles can be used to store and reconstruct the inf ormation artificially stored in a bulk of a photosensitive media 1 The information is stored by changing some characteristics of a memory material (e. g. refractive index). Radiation from the two independent light sources (e. g. lasers) is f ocused inside the memory material. In this way the intensity of the light is above the threshold only in the localized point where the light rays intersect. By scanning the material the information can be stored in binary or nary format. When the information is stored it can be read by tomographic methods. However the situation is quite different from the classical tomographic problem. Here a lot of apriori information is present regarding the p0- sitions of the bits of information profile representing single bit and a mode of operation (binary or n-ary). 2. ALGORITHMS FOR THE READOUT OF THE TOMOGRAPHIC MEMORIES Apriori information enables efficient reconstruction of the memory contents. In this paper a few methods for the information readout together with the simulation results will be presented. Special attention will be given to the noise considerations. Two different

Characterization of Polymer Blends: Optical Microscopy (*Polarized, Interference and Phase Contrast Microscopy*) and Confocal Microscopy

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

Ramanathan, Nathan Muruganathan; Darling, Seth B.

2015-01-01

Chapter 15 surveys the characterization of macro, micro and meso morphologies of polymer blends by optical microscopy. Confocal Microscopy offers the ability to view the three dimensional morphology of polymer blends, popular in characterization of biological systems. Confocal microscopy uses point illumination and a spatial pinhole to eliminate out-of focus light in samples that are thicker than the focal plane.

Confocal raman microscopy as a non-invasive tool to investigate the phase composition of frozen complex cryopreservation media.

PubMed

Kreiner-Møller, A; Stracke, F; Zimmermann, H

2013-01-01

Various cryoprotective agents (CPA) are added to cell media in order to avoid cell injury during cryo preservation. The resulting complex environment of the preserved cell, consisting of crystalline and liquid phases can however not be investigated non-invasively by established methods in cryobiology. This study shows how scanning confocal Raman microscopy can non-invasively extract information on chemical composition, phase domain and distribution at cryogenic temperatures. The formation of the salt hydrate, hydrohalite NaCl∙H2O, in solutions comprised of phosphate buffered saline (PBS) and dimethyl sulphoxide (DMSO) is studied in particular. Scanning confocal Raman microscopy can be used to unambiguously identify hydrohalite in a medium containing DMSO and saline. The confocal Raman microscopy imaging along with differential scanning calorimetric measurements further show that the hydrohalite is formed without eutectic formation. This method also allows for discrimination between closely packed hydrohalite crystals that are oriented differently.

Flipping interferometry and its application for quantitative phase microscopy in a micro-channel.

PubMed

Roitshtain, Darina; Turko, Nir A; Javidi, Bahram; Shaked, Natan T

2016-05-15

We present a portable, off-axis interferometric module for quantitative phase microscopy of live cells, positioned at the exit port of a coherently illuminated inverted microscope. The module creates on the digital camera an interference pattern between the image of the sample and its flipped version. The proposed simplified module is based on a retro-reflector modification in an external Michelson interferometer. The module does not contain any lenses, pinholes, or gratings and its alignment is straightforward. Still, it allows full control of the off-axis angle and does not suffer from ghost images. As experimentally demonstrated, the module is useful for quantitative phase microscopy of live cells rapidly flowing in a micro-channel.

Optical nanoscopy of high T c cuprate nanoconstriction devices patterned by helium ion beams

DOE PAGES

Gozar, Adrian; Litombe, N. E.; Hoffman, Jennifer E.; ...

2017-02-06

Helium ion beams (HIB) focused to subnanometer scales have emerged as powerful tools for high-resolution imaging as well as nanoscale lithography, ion milling, or deposition. Quantifying irradiation effects is an essential step toward reliable device fabrication, but most of the depth profiling information is provided by computer simulations rather than the experiment. Here, we demonstrate the use of atomic force microscopy (AFM) combined with scanning near-field optical microscopy (SNOM) to provide three-dimensional (3D) dielectric characterization of high-temperature superconductor devices fabricated by HIB. By imaging the infrared dielectric response obtained from light demodulation at multiple harmonics of the AFM tapping frequency,more » we find that amorphization caused by the nominally 0.5 nm HIB extends throughout the entire 26.5 nm thickness of the cuprate film and by ~500 nm laterally. This unexpectedly widespread damage in morphology and electronic structure can be attributed to a helium depth distribution substantially modified by the internal device interfaces. Lastly, our study introduces AFM-SNOM as a quantitative tomographic technique for noninvasive 3D characterization of irradiation damage in a wide variety of nanoscale devices.« less

On the retrieval of crystallographic information from atom probe microscopy data via signal mapping from the detector coordinate space.

PubMed

Wallace, Nathan D; Ceguerra, Anna V; Breen, Andrew J; Ringer, Simon P

2018-06-01

Atom probe tomography is a powerful microscopy technique capable of reconstructing the 3D position and chemical identity of millions of atoms within engineering materials, at the atomic level. Crystallographic information contained within the data is particularly valuable for the purposes of reconstruction calibration and grain boundary analysis. Typically, analysing this data is a manual, time-consuming and error prone process. In many cases, the crystallographic signal is so weak that it is difficult to detect at all. In this study, a new automated signal processing methodology is demonstrated. We use the affine properties of the detector coordinate space, or the 'detector stack', as the basis for our calculations. The methodological framework and the visualisation tools are shown to be superior to the standard method of crystallographic pole visualisation directly from field evaporation images and there is no requirement for iterations between a full real-space initial tomographic reconstruction and the detector stack. The mapping approaches are demonstrated for aluminium, tungsten, magnesium and molybdenum. Implications for reconstruction calibration, accuracy of crystallographic measurements, reliability and repeatability are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Quantitative Analysis of Three-dimensional Microstructure of Li-ion Battery Electrodes

NASA Astrophysics Data System (ADS)

Liu, Zhao

Li-ion batteries (LIBs) have attracted considerable attention in the past two decades due to their widespread applications in portable electronics, and their growing use in electric vehicles and large-scale grid storage. Increasing battery energy density and powder density while maintaining long life, along with battery safety, are the biggest challenges that limit their further development. Various approaches with materials and chemistry have been employed to improve performance. However, one less-studied aspect that also impacts performance is the electrode microstructure. In particular, three-dimensional (3D) electrode microstructural data for LIB electrodes, which were not widely available prior to this thesis, can provide important input for understanding and improving LIB performance. The focus of this thesis is to apply 3D tomographic techniques, together with electrochemical performance data, to obtain LIB microstructure-performance correlations. Two advanced 3D structural analysis techniques, focused ion beam-scanning electron microscopy (FIB-SEM) and transmission X-ray microscopy (TXM) nanotomography, are used to quantify LIB electrode microstructure. 3D characterization of LIB electrode microstructure is used to obtain a deeper understanding of mechanisms that limit LIB performance. Microstructural characterization before and after cycling is used to explore capacity loss mechanisms. It is hoped that the results can guide electrode microstructures design to improve performance and stability. Two types of commercial electrodes, LiCoO2 and LiCoO 2/Li(Ni1/3Mn1/3Co1/3)O2, are studied using FIB-SEM and TXM. Both methods were found to be applicable to quantifying the oxide particle microstructure, including volume fraction, surface area, and particle size distribution, and results agreed well. However, structural inhomogeneity found in these commercial samples, limited the capability to resolve microstructural changes during cycling. In order to also quantify carbonaceous phases in the electrodes, which strongly correlate with LIB transport properties, a three-phase FIB-SEM method was developed where silicone resin was infiltrated into electrode pores, providing good image contrast with the carbon particles. Structural parameters including phase connectivity and tortuosity are quantified for commercial LiCoO 2 and laboratory-made LiFePO4 electrodes to help understand the transport process in these electrodes. For LiCoO2 electrodes, a heterogeneous tortuosity distribution observed in the electrolyte phase may result in inhomogeneous charge/discharge states, and consequently cause battery degradation. For LiFePO4 electrodes, highly percolated and less tortuous carbon found in a templated electrode explain its better high-C-rate performance. Finally, laboratory-made LiMn2O4 electrodes were electrochemically cycled with different operation parameters, including cycle number, temperature, and operating voltage. Quantitative analyses on 3D TXM data sets indicate particle fracture, mainly due to tetragonal to cubic phase transformations induced by the Jahn-Teller effect, resulting in electrode degradation. Moreover, high temperature operation is found to enhance active material dissolution and can also accelerate cell degradation. This ex-situ method, which combines electrochemical cycling and statistical analysis, proved to be an effective approach to provide insight for the interpretation of complex mechanical and electrochemical interactions within the electrodes.

High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography

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

Larsson, Daniel H.; Vågberg, William; Yaroshenko, Andre

X-ray computed tomography of small animals and their organs is an essential tool in basic and preclinical biomedical research. In both phase-contrast and absorption tomography high spatial resolution and short exposure times are of key importance. However, the observable spatial resolutions and achievable exposure times are presently limited by system parameters rather than more fundamental constraints like, e.g., dose. Here we demonstrate laboratory tomography with few-ten μm spatial resolution and few-minute exposure time at an acceptable dose for small-animal imaging, both with absorption contrast and phase contrast. The method relies on a magnifying imaging scheme in combination with a high-powermore » small-spot liquid-metal-jet electron-impact source. Lastly, the tomographic imaging is demonstrated on intact mouse, phantoms and excised lungs, both healthy and with pulmonary emphysema.« less

Feasibility study of a layer-oriented wavefront sensor for solar telescopes.

PubMed

Marino, Jose; Wöger, Friedrich

2014-02-01

Solar multiconjugate adaptive optics systems rely on several wavefront sensors, which measure the incoming turbulent phase along several field directions to produce a tomographic reconstruction of the turbulent phase. In this paper, we explore an alternative wavefront sensing approach that attempts to directly measure the turbulent phase present at a particular height in the atmosphere: a layer-oriented cross-correlating Shack-Hartmann wavefront sensor (SHWFS). In an experiment at the Dunn Solar Telescope, we built a prototype layer-oriented cross-correlating SHWFS system conjugated to two separate atmospheric heights. We present the data obtained in the observations and complement these with ray-tracing computations to achieve a better understanding of the instrument's performance and limitations. The results obtained in this study strongly indicate that a layer-oriented cross-correlating SHWFS is not a practical design to measure the wavefront at a high layer in the atmosphere.

High-resolution short-exposure small-animal laboratory x-ray phase-contrast tomography

DOE PAGES

Larsson, Daniel H.; Vågberg, William; Yaroshenko, Andre; ...

2016-12-13

X-ray computed tomography of small animals and their organs is an essential tool in basic and preclinical biomedical research. In both phase-contrast and absorption tomography high spatial resolution and short exposure times are of key importance. However, the observable spatial resolutions and achievable exposure times are presently limited by system parameters rather than more fundamental constraints like, e.g., dose. Here we demonstrate laboratory tomography with few-ten μm spatial resolution and few-minute exposure time at an acceptable dose for small-animal imaging, both with absorption contrast and phase contrast. The method relies on a magnifying imaging scheme in combination with a high-powermore » small-spot liquid-metal-jet electron-impact source. Lastly, the tomographic imaging is demonstrated on intact mouse, phantoms and excised lungs, both healthy and with pulmonary emphysema.« less

Reconstruction methods for phase-contrast tomography

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

Raven, C.

Phase contrast imaging with coherent x-rays can be distinguished in outline imaging and holography, depending on the wavelength {lambda}, the object size d and the object-to-detector distance r. When r << d{sup 2}{lambda}, phase contrast occurs only in regions where the refractive index fastly changes, i.e. at interfaces and edges in the sample. With increasing object-to-detector distance we come in the area of holographic imaging. The image contrast outside the shadow region of the object is due to interference of the direct, undiffracted beam and a beam diffracted by the object, or, in terms of holography, the interference of amore » reference wave with the object wave. Both, outline imaging and holography, offer the possibility to obtain three dimensional information of the sample in conjunction with a tomographic technique. But the data treatment and the kind of information one can obtain from the reconstruction is different.« less

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.

DEVELOPMENTAL PALEOBIOLOGY OF THE VERTEBRATE SKELETON.

PubMed

Rücklin, Martin; Donoghue, Philip C J; Cunningham, John A; Marone, Federica; Stampanoni, Marco

2014-07-01

Studies of the development of organisms can reveal crucial information on homology of structures. Developmental data are not peculiar to living organisms, and they are routinely preserved in the mineralized tissues that comprise the vertebrate skeleton, allowing us to obtain direct insight into the developmental evolution of this most formative of vertebrate innovations. The pattern of developmental processes is recorded in fossils as successive stages inferred from the gross morphology of multiple specimens and, more reliably and routinely, through the ontogenetic stages of development seen in the skeletal histology of individuals. Traditional techniques are destructive and restricted to a 2-D plane with the third dimension inferred. Effective non-invasive methods of visualizing paleohistology to reconstruct developmental stages of the skeleton are necessary. In a brief survey of paleohistological techniques we discuss the pros and cons of these methods. The use of tomographic methods to reconstruct development of organs is exemplified by the study of the placoderm dentition. Testing evidence for the presence of teeth in placoderms, the first jawed vertebrates, we compare the methods that have been used. These include inferring the development from morphology, and using serial sectioning, microCT or synchrotron X-ray tomographic microscopy (SRXTM) to reconstruct growth stages and directions of growth. The ensuing developmental interpretations are biased by the methods and degree of inference. The most direct and reliable method is using SRXTM data to trace sclerochronology. The resulting developmental data can be used to resolve homology and test hypotheses on the origin of evolutionary novelties.

Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC).

PubMed

Phillips, Zachary F; Chen, Michael; Waller, Laura

2017-01-01

We present a new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. Our system consists of a commercial brightfield microscope with one hardware modification-an inexpensive 3D printed condenser insert. The method, color-multiplexed Differential Phase Contrast (cDPC), is a single-shot variant of Differential Phase Contrast (DPC), which recovers the phase of a sample from images with asymmetric illumination. We employ partially coherent illumination to achieve resolution corresponding to 2× the objective NA. Quantitative phase can then be used to synthesize DIC and phase contrast images or extract shape and density. We demonstrate amplitude and phase recovery at camera-limited frame rates (50 fps) for various in vitro cell samples and c. elegans in a micro-fluidic channel.

Transverse Phase Space Reconstruction and Emittance Measurement of Intense Electron Beams using a Tomography Technique

NASA Astrophysics Data System (ADS)

Stratakis, D.; Kishek, R. A.; Li, H.; Bernal, S.; Walter, M.; Tobin, J.; Quinn, B.; Reiser, M.; O'Shea, P. G.

2006-11-01

Tomography is the technique of reconstructing an image from its projections. It is widely used in the medical community to observe the interior of the human body by processing multiple x-ray images taken at different angles, A few pioneering researchers have adapted tomography to reconstruct detailed phase space maps of charged particle beams. Some questions arise regarding the limitations of tomography technique for space charge dominated beams. For instance is the linear space charge force a valid approximation? Does tomography equally reproduce phase space for complex, experimentally observed, initial particle distributions? Does tomography make any assumptions about the initial distribution? This study explores the use of accurate modeling with the particle-in-cell code WARP to address these questions, using a wide range of different initial distributions in the code. The study also includes a number of experimental results on tomographic phase space mapping performed on the University of Maryland Electron Ring (UMER).

Global multiresolution models of surface wave propagation: comparing equivalently regularized Born and ray theoretical solutions

NASA Astrophysics Data System (ADS)

Boschi, Lapo

2006-10-01

I invert a large set of teleseismic phase-anomaly observations, to derive tomographic maps of fundamental-mode surface wave phase velocity, first via ray theory, then accounting for finite-frequency effects through scattering theory, in the far-field approximation and neglecting mode coupling. I make use of a multiple-resolution pixel parametrization which, in the assumption of sufficient data coverage, should be adequate to represent strongly oscillatory Fréchet kernels. The parametrization is finer over North America, a region particularly well covered by the data. For each surface-wave mode where phase-anomaly observations are available, I derive a wide spectrum of plausible, differently damped solutions; I then conduct a trade-off analysis, and select as optimal solution model the one associated with the point of maximum curvature on the trade-off curve. I repeat this exercise in both theoretical frameworks, to find that selected scattering and ray theoretical phase-velocity maps are coincident in pattern, and differ only slightly in amplitude.

Advanced electron microscopy methods for the analysis of MgB2 superconductor

NASA Astrophysics Data System (ADS)

Birajdar, B.; Peranio, N.; Eibl, O.

2008-02-01

Advanced electron microscopy methods used for the analysis of superconducting MgB2 wires and tapes are described. The wires and tapes were prepared by the powder in tube method using different processing technologies and thoroughly characterised for their superconducting properties within the HIPERMAG project. Microstructure analysis on μm to nm length scales is necessary to understand the superconducting properties of MgB2. For the MgB2 phase analysis on μm scale an analytical SEM, and for the analysis on nm scale a energy-filtered STEM is used. Both the microscopes were equipped with EDX detector and field emission gun. Electron microscopy and spectroscopy of MgB2 is challenging because of the boron analysis, carbon and oxygen contamination, and the presence of large number of secondary phases. Advanced electron microscopy involves, combined SEM, EPMA and TEM analysis with artefact free sample preparation, elemental mapping and chemical quantification of point spectra. Details of the acquisition conditions and achieved accuracy are presented. Ex-situ wires show oxygen-free MgB2 colonies (a colony is a dense arrangement of several MgB2 grains) embedded in a porous and oxygen-rich matrix, introducing structural granularity. In comparison, in-situ wires are generally more dense, but show inhibited MgB2 phase formation with significantly higher fraction of B-rich secondary phases. SiC additives in the in-situ wires forms Mg2Si secondary phases. The advanced electron microscopy has been used to extract the microstructure parameters like colony size, B-rich secondary phase fraction, O mole fraction and MgB2 grain size, and establish a microstructure-critical current density model [1]. In summary, conventional secondary electron imaging in SEM and diffraction contrast imaging in the TEM are by far not sufficient and advanced electron microscopy methods are essential for the analysis of superconducting MgB2 wires and tapes.

Effect of Annealing Temperature on the Mechanical and Corrosion Behavior of a Newly Developed Novel Lean Duplex Stainless Steel.

PubMed

Guo, Yanjun; Hu, Jincheng; Li, Jin; Jiang, Laizhu; Liu, Tianwei; Wu, Yanping

2014-09-12

The effect of annealing temperature (1000-1150 °C) on the microstructure evolution, mechanical properties, and pitting corrosion behavior of a newly developed novel lean duplex stainless steel with 20.53Cr-3.45Mn-2.08Ni-0.17N-0.31Mo was studied by means of optical metallographic microscopy (OMM), scanning electron microscopy (SEM), magnetic force microscopy (MFM), scanning Kelvin probe force microscopy (SKPFM), energy dispersive X-ray spectroscopy (EDS), uniaxial tensile tests (UTT), and potentiostatic critical pitting temperature (CPT). The results showed that tensile and yield strength, as well as the pitting corrosion resistance, could be degraded with annealing temperature increasing from 1000 up to 1150 °C. Meanwhile, the elongation at break reached the maximum of 52.7% after annealing at 1050 °C due to the effect of martensite transformation induced plasticity (TRIP). The localized pitting attack preferentially occurred at ferrite phase, indicating that the ferrite phase had inferior pitting corrosion resistance as compared to the austenite phase. With increasing annealing temperature, the pitting resistance equivalent number (PREN) of ferrite phase dropped, while that of the austenite phase rose. Additionally, it was found that ferrite possessed a lower Volta potential than austenite phase. Moreover, the Volta potential difference between ferrite and austenite increased with the annealing temperature, which was well consistent with the difference of PREN.

Effect of Annealing Temperature on the Mechanical and Corrosion Behavior of a Newly Developed Novel Lean Duplex Stainless Steel

PubMed Central

Guo, Yanjun; Hu, Jincheng; Li, Jin; Jiang, Laizhu; Liu, Tianwei; Wu, Yanping

2014-01-01

The effect of annealing temperature (1000–1150 °C) on the microstructure evolution, mechanical properties, and pitting corrosion behavior of a newly developed novel lean duplex stainless steel with 20.53Cr-3.45Mn-2.08Ni-0.17N-0.31Mo was studied by means of optical metallographic microscopy (OMM), scanning electron microscopy (SEM), magnetic force microscopy (MFM), scanning Kelvin probe force microscopy (SKPFM), energy dispersive X-ray spectroscopy (EDS), uniaxial tensile tests (UTT), and potentiostatic critical pitting temperature (CPT). The results showed that tensile and yield strength, as well as the pitting corrosion resistance, could be degraded with annealing temperature increasing from 1000 up to 1150 °C. Meanwhile, the elongation at break reached the maximum of 52.7% after annealing at 1050 °C due to the effect of martensite transformation induced plasticity (TRIP). The localized pitting attack preferentially occurred at ferrite phase, indicating that the ferrite phase had inferior pitting corrosion resistance as compared to the austenite phase. With increasing annealing temperature, the pitting resistance equivalent number (PREN) of ferrite phase dropped, while that of the austenite phase rose. Additionally, it was found that ferrite possessed a lower Volta potential than austenite phase. Moreover, the Volta potential difference between ferrite and austenite increased with the annealing temperature, which was well consistent with the difference of PREN. PMID:28788201

New developments in multimodal clinical multiphoton tomography

NASA Astrophysics Data System (ADS)

König, Karsten

2011-03-01

80 years ago, the PhD student Maria Goeppert predicted in her thesis in Goettingen, Germany, two-photon effects. It took 30 years to prove her theory, and another three decades to realize the first two-photon microscope. With the beginning of this millennium, first clinical multiphoton tomographs started operation in research institutions, hospitals, and in the cosmetic industry. The multiphoton tomograph MPTflexTM with its miniaturized flexible scan head became the Prism-Award 2010 winner in the category Life Sciences. Multiphoton tomographs with its superior submicron spatial resolution can be upgraded to 5D imaging tools by adding spectral time-correlated single photon counting units. Furthermore, multimodal hybrid tomographs provide chemical fingerprinting and fast wide-field imaging. The world's first clinical CARS studies have been performed with a hybrid multimodal multiphoton tomograph in spring 2010. In particular, nonfluorescent lipids and water as well as mitochondrial fluorescent NAD(P)H, fluorescent elastin, keratin, and melanin as well as SHG-active collagen have been imaged in patients with dermatological disorders. Further multimodal approaches include the combination of multiphoton tomographs with low-resolution imaging tools such as ultrasound, optoacoustic, OCT, and dermoscopy systems. Multiphoton tomographs are currently employed in Australia, Japan, the US, and in several European countries for early diagnosis of skin cancer (malignant melanoma), optimization of treatment strategies (wound healing, dermatitis), and cosmetic research including long-term biosafety tests of ZnO sunscreen nanoparticles and the measurement of the stimulated biosynthesis of collagen by anti-ageing products.

Chamber dimensions and functional assessment with coronary computed tomographic angiography as compared to echocardiography using American Society of Echocardiography guidelines

PubMed Central

Rose, Michael; Rubal, Bernard; Hulten, Edward; Slim, Jennifer N; Steel, Kevin; Furgerson, James L; Villines, Todd C

2014-01-01

Background: The correlation between normal cardiac chamber linear dimensions measured during retrospective coronary computed tomographic angiography as compared to transthoracic echocardiography using the American Society of Echocardiography guidelines is not well established. Methods: We performed a review from January 2005 to July 2011 to identify subjects with retrospective electrocardiogram-gated coronary computed tomographic angiography scans for chest pain and transthoracic echocardiography with normal cardiac structures performed within 90 days. Dimensions were manually calculated in both imaging modalities in accordance with the American Society of Echocardiography published guidelines. Left ventricular ejection fraction was calculated on echocardiography manually using the Simpson’s formula and by coronary computed tomographic angiography using the end-systolic and end-diastolic volumes. Results: We reviewed 532 studies, rejected 412 and had 120 cases for review with a median time between studies of 7 days (interquartile range (IQR25,75) = 0–22 days) with no correlation between the measurements made by coronary computed tomographic angiography and transthoracic echocardiography using Bland–Altman analysis. We generated coronary computed tomographic angiography cardiac dimension reference ranges for both genders for our population. Conclusion: Our findings represent a step towards generating cardiac chamber dimensions’ reference ranges for coronary computed tomographic angiography as compared to transthoracic echocardiography in patients with normal cardiac morphology and function using the American Society of Echocardiography guideline measurements that are commonly used by cardiologists. PMID:26770706

Airborne asbestos in Colorado public schools.

PubMed

Chadwick, D A; Buchan, R M; Beaulieu, H J

1985-02-01

Levels of airborne asbestos for six Colorado public school facilities with sprayed-on asbestos materials were documented using three analytical techniques. Phase contrast microscopy showed levels up to the thousandths of a fiber per cubic centimeter (f/cc), scanning electron microscopy (SEM) up to the hundredths of a f/cc, and transmission electron microscopy coupled to selected area electron diffraction and energy dispersive X-ray analysis (TEM-SAED-EDXA) up to the tenths of an asbestos f/cc. Phase contrast microscopy was found to be an inadequate analytical technique for documenting the levels of airborne asbestos fibers in the schools: only large fibers which were not embedded in the filter were counted, and asbestos fibers were not distinguished from nonasbestos.

Signal detectability in diffusive media using phased arrays in conjunction with detector arrays.

PubMed

Kang, Dongyel; Kupinski, Matthew A

2011-06-20

We investigate Hotelling observer performance (i.e., signal detectability) of a phased array system for tasks of detecting small inhomogeneities and distinguishing adjacent abnormalities in uniform diffusive media. Unlike conventional phased array systems where a single detector is located on the interface between two sources, we consider a detector array, such as a CCD, on a phantom exit surface for calculating the Hotelling observer detectability. The signal detectability for adjacent small abnormalities (2 mm displacement) for the CCD-based phased array is related to the resolution of reconstructed images. Simulations show that acquiring high-dimensional data from a detector array in a phased array system dramatically improves the detectability for both tasks when compared to conventional single detector measurements, especially at low modulation frequencies. It is also observed in all studied cases that there exists the modulation frequency optimizing CCD-based phased array systems, where detectability for both tasks is consistently high. These results imply that the CCD-based phased array has the potential to achieve high resolution and signal detectability in tomographic diffusive imaging while operating at a very low modulation frequency. The effect of other configuration parameters, such as a detector pixel size, on the observer performance is also discussed.

Mechanical Behavior of Three-Dimensional Braided Nickel-Based Superalloys Synthesized via Pack Cementation

NASA Astrophysics Data System (ADS)

Lippitz, Nicolas; Erdeniz, Dinc; Sharp, Keith W.; Dunand, David C.

2018-03-01

Braided tubes of Ni-based superalloys are fabricated via three-dimensional (3-D) braiding of ductile Ni-20Cr (wt pct) wires followed by post-textile gas-phase alloying with Al and Ti to create, after homogenization and aging, γ/ γ' strengthened lightweight, porous structures. Tensile tests reveal an increase in strength by 100 MPa compared to as-braided Ni-20Cr (wt pct). An interrupted tensile test, combined with X-ray tomographic scans between each step, sheds light on the failure behavior of the braided superalloy tubes.

Combined multi-plane phase retrieval and super-resolution optical fluctuation imaging for 4D cell microscopy

NASA Astrophysics Data System (ADS)

Descloux, A.; Grußmayer, K. S.; Bostan, E.; Lukes, T.; Bouwens, A.; Sharipov, A.; Geissbuehler, S.; Mahul-Mellier, A.-L.; Lashuel, H. A.; Leutenegger, M.; Lasser, T.

2018-03-01

Super-resolution fluorescence microscopy provides unprecedented insight into cellular and subcellular structures. However, going `beyond the diffraction barrier' comes at a price, since most far-field super-resolution imaging techniques trade temporal for spatial super-resolution. We propose the combination of a novel label-free white light quantitative phase imaging with fluorescence to provide high-speed imaging and spatial super-resolution. The non-iterative phase retrieval relies on the acquisition of single images at each z-location and thus enables straightforward 3D phase imaging using a classical microscope. We realized multi-plane imaging using a customized prism for the simultaneous acquisition of eight planes. This allowed us to not only image live cells in 3D at up to 200 Hz, but also to integrate fluorescence super-resolution optical fluctuation imaging within the same optical instrument. The 4D microscope platform unifies the sensitivity and high temporal resolution of phase imaging with the specificity and high spatial resolution of fluorescence microscopy.

Spectral interferometric microscopy reveals absorption by individual optical nanoantennas from extinction phase

PubMed Central

Gennaro, Sylvain D.; Sonnefraud, Yannick; Verellen, Niels; Van Dorpe, Pol; Moshchalkov, Victor V.; Maier, Stefan A.; Oulton, Rupert F.

2014-01-01

Optical antennas transform light from freely propagating waves into highly localized excitations that interact strongly with matter. Unlike their radio frequency counterparts, optical antennas are nanoscopic and high frequency, making amplitude and phase measurements challenging and leaving some information hidden. Here we report a novel spectral interferometric microscopy technique to expose the amplitude and phase response of individual optical antennas across an octave of the visible to near-infrared spectrum. Although it is a far-field technique, we show that knowledge of the extinction phase allows quantitative estimation of nanoantenna absorption, which is a near-field quantity. To verify our method we characterize gold ring-disk dimers exhibiting Fano interference. Our results reveal that Fano interference only cancels a bright mode’s scattering, leaving residual extinction dominated by absorption. Spectral interference microscopy has the potential for real-time and single-shot phase and amplitude investigations of isolated quantum and classical antennas with applications across the physical and life sciences. PMID:24781663

Procedures for analysis of debris relative to Space Shuttle systems

NASA Technical Reports Server (NTRS)

Kim, Hae Soo; Cummings, Virginia J.

1993-01-01

Debris samples collected from various Space Shuttle systems have been submitted to the Microchemical Analysis Branch. This investigation was initiated to develop optimal techniques for the analysis of debris. Optical microscopy provides information about the morphology and size of crystallites, particle sizes, amorphous phases, glass phases, and poorly crystallized materials. Scanning electron microscopy with energy dispersive spectrometry is utilized for information on surface morphology and qualitative elemental content of debris. Analytical electron microscopy with wavelength dispersive spectrometry provides information on the quantitative elemental content of debris.

Simultaneous fluorescence and quantitative phase microscopy with single-pixel detectors

NASA Astrophysics Data System (ADS)

Liu, Yang; Suo, Jinli; Zhang, Yuanlong; Dai, Qionghai

2018-02-01

Multimodal microscopy offers high flexibilities for biomedical observation and diagnosis. Conventional multimodal approaches either use multiple cameras or a single camera spatially multiplexing different modes. The former needs expertise demanding alignment and the latter suffers from limited spatial resolution. Here, we report an alignment-free full-resolution simultaneous fluorescence and quantitative phase imaging approach using single-pixel detectors. By combining reference-free interferometry with single-pixel detection, we encode the phase and fluorescence of the sample in two detection arms at the same time. Then we employ structured illumination and the correlated measurements between the sample and the illuminations for reconstruction. The recovered fluorescence and phase images are inherently aligned thanks to single-pixel detection. To validate the proposed method, we built a proof-of-concept setup for first imaging the phase of etched glass with the depth of a few hundred nanometers and then imaging the fluorescence and phase of the quantum dot drop. This method holds great potential for multispectral fluorescence microscopy with additional single-pixel detectors or a spectrometer. Besides, this cost-efficient multimodal system might find broad applications in biomedical science and neuroscience.

Microstructure and phase composition of hypoeutectic Te-Bi alloy as evaporation source for photoelectric cathode

NASA Astrophysics Data System (ADS)

Wang, Bao-guang; Yang, Wen-hui; Gao, Hong-ye; Tian, Wen-huai

2018-05-01

A hypoeutectic 60Te-40Bi alloy in mass percent was designed as a tellurium atom evaporation source instead of pure tellurium for an ultraviolet detection photocathode. The alloy was prepared by slow solidification at about 10-2 K·s-1. The microstructure, crystal structure, chemical composition, and crystallographic orientation of each phase in the as-prepared alloy were investigated by optical microscopy, scanning electron microscopy, X-ray diffraction, electron backscatter diffraction, and transmission electron microscopy. The experimental results suggest that the as-prepared 60Te-40Bi alloy consists of primary Bi2Te3 and eutectic Bi2Te3/Te phases. The primary Bi2Te3 phase has the characteristics of faceted growth. The eutectic Bi2Te3 phase is encased by the eutectic Te phase in the eutectic structure. The purity of the eutectic Te phase reaches 100wt% owing to the slow solidification. In the eutectic phases, the crystallographic orientation relationship between Bi2Te3 and Te is confirmed as {[0001]_{B{i_2}T{e_3}}}//{[1\\bar 21\\bar 3]_{Te}} and the direction of Te phase parallel to {[11\\bar 20]_{B{i_2}T{e_3}}} is deviated by 18° from Te N{(2\\bar 1\\bar 11)_{Te}}.

Observing Tin-Lead Alloys by Scanning Electron Microscopy: A Physical Chemistry Experiment Investigating Macro-Level Behaviors and Micro-Level Structures

ERIC Educational Resources Information Center

Wang, Yue; Xu, Xinhua; Wu, Meifen; Hu, Huikang; Wang, Xiaogang

2015-01-01

Scanning electron microscopy (SEM) was introduced into undergraduate physical chemistry laboratory curriculum to help students observe the phase composition and morphology characteristics of tin-lead alloys and thus further their understanding of binary alloy phase diagrams. The students were captivated by this visual analysis method, which…

X-ray diffraction tomography of polycrystalline materials: present and future (Conference Presentation)

NASA Astrophysics Data System (ADS)

Stock, Stuart R.; Almer, Jonathan D.; Birkedal, Henrik

2016-10-01

Scattered x-radiation can be used for computed tomographic reconstruction of the distribution of crystallographic phases within the interior of specimens, and diffraction patterns can be measured for each volume element (voxel) within a reconstructed slice. This modality has been applied to systems as diverse as mineralized tissues and inorganic composites. Use of high energy x-rays (E < 40 keV) offers advantages including the ability to study volumes deep with specimens and to sample large ranges of reciprocal space, i.e., many reflections. The bases of diffraction tomography are reviewed, and the power of the technique is illustrated by the results obtained for specimens containing: a) different materials (SiC/Al composite), b) different polytypes (calcite/aragonite in a bivalve attachment system); c) mixtures of nanocrystalline and amorphous phases; d) a single phase, but volumes with different lattice parameters (hydroxyapatite, hAp, the mineral in bone and tooth); e) a single phase containing a spatial distribution of crystallographic texture (bone); a single phase with a spatial distribution of strains produced by in situ loading (bone). Finally, challenges and future directions are discussed.

Sequential processing of quantitative phase images for the study of cell behaviour in real-time digital holographic microscopy.

PubMed

Zikmund, T; Kvasnica, L; Týč, M; Křížová, A; Colláková, J; Chmelík, R

2014-11-01

Transmitted light holographic microscopy is particularly used for quantitative phase imaging of transparent microscopic objects such as living cells. The study of the cell is based on extraction of the dynamic data on cell behaviour from the time-lapse sequence of the phase images. However, the phase images are affected by the phase aberrations that make the analysis particularly difficult. This is because the phase deformation is prone to change during long-term experiments. Here, we present a novel algorithm for sequential processing of living cells phase images in a time-lapse sequence. The algorithm compensates for the deformation of a phase image using weighted least-squares surface fitting. Moreover, it identifies and segments the individual cells in the phase image. All these procedures are performed automatically and applied immediately after obtaining every single phase image. This property of the algorithm is important for real-time cell quantitative phase imaging and instantaneous control of the course of the experiment by playback of the recorded sequence up to actual time. Such operator's intervention is a forerunner of process automation derived from image analysis. The efficiency of the propounded algorithm is demonstrated on images of rat fibrosarcoma cells using an off-axis holographic microscope. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Image recovery from defocused 2D fluorescent images in multimodal digital holographic microscopy.

PubMed

Quan, Xiangyu; Matoba, Osamu; Awatsuji, Yasuhiro

2017-05-01

A technique of three-dimensional (3D) intensity retrieval from defocused, two-dimensional (2D) fluorescent images in the multimodal digital holographic microscopy (DHM) is proposed. In the multimodal DHM, 3D phase and 2D fluorescence distributions are obtained simultaneously by an integrated system of an off-axis DHM and a conventional epifluorescence microscopy, respectively. This gives us more information of the target; however, defocused fluorescent images are observed due to the short depth of field. In this Letter, we propose a method to recover the defocused images based on the phase compensation and backpropagation from the defocused plane to the focused plane using the distance information that is obtained from a 3D phase distribution. By applying Zernike polynomial phase correction, we brought back the fluorescence intensity to the focused imaging planes. The experimental demonstration using fluorescent beads is presented, and the expected applications are suggested.

Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC)

PubMed Central

2017-01-01

We present a new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. Our system consists of a commercial brightfield microscope with one hardware modification—an inexpensive 3D printed condenser insert. The method, color-multiplexed Differential Phase Contrast (cDPC), is a single-shot variant of Differential Phase Contrast (DPC), which recovers the phase of a sample from images with asymmetric illumination. We employ partially coherent illumination to achieve resolution corresponding to 2× the objective NA. Quantitative phase can then be used to synthesize DIC and phase contrast images or extract shape and density. We demonstrate amplitude and phase recovery at camera-limited frame rates (50 fps) for various in vitro cell samples and c. elegans in a micro-fluidic channel. PMID:28152023

Solid-state transformation of Fe-rich intermetallic phases in Al–5.0Cu–0.6Mn squeeze cast alloy with variable Fe contents during solution heat treatment

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

Lin, Bo; School of Mechanical Engineering, Gui Zhou University, Guiyang 550000; Zhang, Weiwen, E-mail: mewzhang@scut.edu.cn

2015-06-15

The Al–5.0 wt.% Cu–0.6 wt.% Mn alloys with a variable Fe content were prepared by squeeze casting. Optical microscopy (OM), Deep etching technique, scanning electron microscopy(SEM), X-ray diffraction (XRD) and transmission electron microscopy (TEM) were used to examine the solid-state transformation of Fe-rich intermetallics during the solution heat treatment. The results showed that the Chinese script-like α-Fe, Al{sub 6}(FeMn) and needle-like Al{sub 3}(FeMn) phases transform to a new Cu-rich β-Fe (Al{sub 7}Cu{sub 2}(FeMn)) phase during solution heat treatment. The possible reaction and overall transformation kinetics of the solid-state phase transformation for the Fe-rich intermetallics were investigated. - Graphical abstract: Displaymore » Omitted - Highlights: • The α-Fe, Al{sub 6}(FeMn) and Al{sub 3}(FeMn) phases change to the β-Fe phases. • Possible reactions of Fe phases during solution heat treatment are discussed. • The overall fractional transformation rate follows an Avrami curve.« less

Towards in vivo breast skin characterization using multiphoton microscopy

NASA Astrophysics Data System (ADS)

Batista, Ana; Uchugonova, Aisada; Breunig, Hans Georg; König, Karsten

2017-02-01

Breast cancer, the most common type of cancer in women worldwide, as well as its treatment (e.g. radiation therapy) can affect the human skin. Multiphoton imaging could provide new insights into these skin alterations non-invasively and with high-resolution. As a preparation for a later investigation involving patients, areas of the breast and forearm skin of healthy volunteers were imaged using the clinically certified multiphoton imaging tomograph MPTflex based on endogenous skin autofluorescence and second-harmonic signals. Depth-resolved image stacks were acquired in consecutive weeks to explore the influence of hormonal variations on the skin properties. Both breasts were considered and up to three different areas were imaged per session. Acquisition parameters were optimized to minimize artifacts caused by breathing-motion. As a first result, skin properties, such as the epidermal thickness, appear to be influenced by hormonal variations.

FLIM FRET Technology for Drug Discovery: Automated Multiwell-Plate High-Content Analysis, Multiplexed Readouts and Application in Situ**

PubMed Central

Kumar, Sunil; Alibhai, Dominic; Margineanu, Anca; Laine, Romain; Kennedy, Gordon; McGinty, James; Warren, Sean; Kelly, Douglas; Alexandrov, Yuriy; Munro, Ian; Talbot, Clifford; Stuckey, Daniel W; Kimberly, Christopher; Viellerobe, Bertrand; Lacombe, Francois; Lam, Eric W-F; Taylor, Harriet; Dallman, Margaret J; Stamp, Gordon; Murray, Edward J; Stuhmeier, Frank; Sardini, Alessandro; Katan, Matilda; Elson, Daniel S; Neil, Mark A A; Dunsby, Chris; French, Paul M W

2011-01-01

A fluorescence lifetime imaging (FLIM) technology platform intended to read out changes in Förster resonance energy transfer (FRET) efficiency is presented for the study of protein interactions across the drug-discovery pipeline. FLIM provides a robust, inherently ratiometric imaging modality for drug discovery that could allow the same sensor constructs to be translated from automated cell-based assays through small transparent organisms such as zebrafish to mammals. To this end, an automated FLIM multiwell-plate reader is described for high content analysis of fixed and live cells, tomographic FLIM in zebrafish and FLIM FRET of live cells via confocal endomicroscopy. For cell-based assays, an exemplar application reading out protein aggregation using FLIM FRET is presented, and the potential for multiple simultaneous FLIM (FRET) readouts in microscopy is illustrated. PMID:21337485

Time-resolved imaging refractometry of microbicidal films using quantitative phase microscopy.

PubMed

Rinehart, Matthew T; Drake, Tyler K; Robles, Francisco E; Rohan, Lisa C; Katz, David; Wax, Adam

2011-12-01

Quantitative phase microscopy is applied to image temporal changes in the refractive index (RI) distributions of solutions created by microbicidal films undergoing hydration. We present a novel method of using an engineered polydimethylsiloxane structure as a static phase reference to facilitate calibration of the absolute RI across the entire field. We present a study of dynamic structural changes in microbicidal films during hydration and subsequent dissolution. With assumptions about the smoothness of the phase changes induced by these films, we calculate absolute changes in the percentage of film in regions across the field of view.

Time-resolved imaging refractometry of microbicidal films using quantitative phase microscopy

PubMed Central

Rinehart, Matthew T.; Drake, Tyler K.; Robles, Francisco E.; Rohan, Lisa C.; Katz, David; Wax, Adam

2011-01-01

Quantitative phase microscopy is applied to image temporal changes in the refractive index (RI) distributions of solutions created by microbicidal films undergoing hydration. We present a novel method of using an engineered polydimethylsiloxane structure as a static phase reference to facilitate calibration of the absolute RI across the entire field. We present a study of dynamic structural changes in microbicidal films during hydration and subsequent dissolution. With assumptions about the smoothness of the phase changes induced by these films, we calculate absolute changes in the percentage of film in regions across the field of view. PMID:22191912

Imaging Coronal Mass Ejections and Large-Scale Solar Wind Structure Using IPS and Thomson-Scattered Sunlight (Invited)

NASA Astrophysics Data System (ADS)

Clover, J. M.; Jackson, B. V.; Buffington, A.; Hick, P. P.; Bisi, M. M.; Tokumaru, M.; Fujiki, K.

2010-12-01

The Solar Mass Ejection Imager (SMEI) observes Thomson-scattered white light from heliospheric electrons across almost all of the sky nearly all of the time since early 2003. Interplanetary scintillation (IPS) observations of velocity and g-level provide similar structure information but with a less-complete sky-and-time coverage. The Solar TErrestrial RElations Observatory (STEREO) twin spacecraft outer Heliospheric Imagers (HI-2) currently image the heliosphere in Thomson-scattered light near the ecliptic plane far from Earth. The Solar-Terrestrial Environment Laboratory (STELab) IPS observations provide IPS velocity and g-level values, which in conjunction with our tomographic reconstruction program, yield velocities and densities of the inner heliosphere in three dimensions. The same tomographic program substitutes SMEI Thomson-scattering brightness information for the g-level values to derive heliospheric densities from these data alone. We look at the global structure of the heliosphere concentrating mainly on three events from 2007 through the rise phase of Solar Cycle 24. The first event, observed in both the IPS and SMEI defines the three-dimensional velocity and density structure around the time of the shock observed at Earth on 02:02 UT 17 December 2007. The second event, seen only by SMEI, is that of the 23-26 April 2008 coronal mass ejection (CME) and its interplanetary counterpart. The third event is the CME (and its interplanetary counterpart) that took place 17 January 2010 and arrived at STEREO-B about four days later. For each event, we isolate the particular portion of the heliosphere attributed to the transient density structure using our tomographic technique, and then estimate its extent.

Tomographic imaging of Central Java, Indonesia: Preliminary result of joint inversion of the MERAMEX and MCGA earthquake data

NASA Astrophysics Data System (ADS)

Rohadi, Supriyanto; Widiyantoro, Sri; Nugraha, Andri Dian; Masturyono

2013-09-01

The realization of local earthquake tomography is usually conducted by removing distant events outside the study region, because these events may increase errors. In this study, tomographic inversion has been conducted using the travel time data of local and regional events in order to improve the structural resolution, especially for deep structures. We used the local MERapi Amphibious EXperiments (MERAMEX) data catalog that consists of 292 events from May to October 2004. The additional new data of regional events in the Java region were taken from the Meteorological, Climatological, and Geophysical Agency (MCGA) of Indonesia, which consist of 882 events, having at least 10 recording phases at each seismographic station from April 2009 to February 2011. We have conducted joint inversions of the combined data sets using double-difference tomography to invert for velocity structures and to conduct hypocenter relocation simultaneously. The checkerboard test results of Vp and Vs structures demonstrate a significantly improved spatial resolution from the shallow crust down to a depth of 165 km. Our tomographic inversions reveal a low velocity anomaly beneath the Lawu - Merapi zone, which is consistent with the results from previous studies. A strong velocity anomaly zone with low Vp, low Vs and low Vp/Vs is also identified between Cilacap and Banyumas. We interpret this anomaly as a fluid content material with large aspect ratio or sediment layer. This anomaly zone is in a good agreement with the existence of a large dome containing sediment in this area as proposed by previous geological studies. A low velocity anomaly zone is also detected in Kebumen, where it may be related to the extensional oceanic basin toward the land.

SXR measurement and W transport survey using GEM tomographic system on WEST

NASA Astrophysics Data System (ADS)

Mazon, D.; Jardin, A.; Malard, P.; Chernyshova, M.; Coston, C.; Malard, P.; O'Mullane, M.; Czarski, T.; Malinowski, K.; Faisse, F.; Ferlay, F.; Verger, J. M.; Bec, A.; Larroque, S.; Kasprowicz, G.; Wojenski, A.; Pozniak, K.

2017-11-01

Measuring Soft X-Ray (SXR) radiation (0.1-20 keV) of fusion plasmas is a standard way of accessing valuable information on particle transport. Since heavy impurities like tungsten (W) could degrade plasma core performances and cause radiative collapses, it is necessary to develop new diagnostics to be able to monitor the impurity distribution in harsh fusion environments like ITER. A gaseous detector with energy discrimination would be a very good candidate for this purpose. The design and implementation of a new SXR diagnostic developed for the WEST project, based on a triple Gas Electron Multiplier (GEM) detector is presented. This detector works in photon counting mode and presents energy discrimination capabilities. The SXR system is composed of two 1D cameras (vertical and horizontal views respectively), located in the same poloidal cross-section to allow for tomographic reconstruction. An array (20 cm × 2 cm) consists of up to 128 detectors in front of a beryllium pinhole (equipped with a 1 mm diameter diaphragm) inserted at about 50 cm depth inside a cooled thimble in order to retrieve a wide plasma view. Acquisition of low energy spectrum is insured by a helium buffer installed between the pinhole and the detector. Complementary cooling systems (water) are used to maintain a constant temperature (25oC) inside the thimble. Finally a real-time automatic extraction system has been developed to protect the diagnostic during baking phases or any overheating unwanted events. Preliminary simulations of plasma emissivity and W distribution have been performed for WEST using a recently developed synthetic diagnostic coupled to a tomographic algorithm based on the minimum Fisher information (MFI) inversion method. First GEM acquisitions are presented as well as estimation of transport effect in presence of ICRH on W density reconstruction capabilities of the GEM.

Tomographic imaging of Central Java, Indonesia: Preliminary result of joint inversion of the MERAMEX and MCGA earthquake data

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

Rohadi, Supriyanto; Widiyantoro, Sri; Nugraha, Andri Dian

The realization of local earthquake tomography is usually conducted by removing distant events outside the study region, because these events may increase errors. In this study, tomographic inversion has been conducted using the travel time data of local and regional events in order to improve the structural resolution, especially for deep structures. We used the local MERapi Amphibious EXperiments (MERAMEX) data catalog that consists of 292 events from May to October 2004. The additional new data of regional events in the Java region were taken from the Meteorological, Climatological, and Geophysical Agency (MCGA) of Indonesia, which consist of 882 events,more » having at least 10 recording phases at each seismographic station from April 2009 to February 2011. We have conducted joint inversions of the combined data sets using double-difference tomography to invert for velocity structures and to conduct hypocenter relocation simultaneously. The checkerboard test results of Vp and Vs structures demonstrate a significantly improved spatial resolution from the shallow crust down to a depth of 165 km. Our tomographic inversions reveal a low velocity anomaly beneath the Lawu - Merapi zone, which is consistent with the results from previous studies. A strong velocity anomaly zone with low Vp, low Vs and low Vp/Vs is also identified between Cilacap and Banyumas. We interpret this anomaly as a fluid content material with large aspect ratio or sediment layer. This anomaly zone is in a good agreement with the existence of a large dome containing sediment in this area as proposed by previous geological studies. A low velocity anomaly zone is also detected in Kebumen, where it may be related to the extensional oceanic basin toward the land.« less

Quantitative X-ray dark-field and phase tomography using single directional speckle scanning technique

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

Wang, Hongchang, E-mail: hongchang.wang@diamond.ac.uk; Kashyap, Yogesh; Sawhney, Kawal

2016-03-21

X-ray dark-field contrast tomography can provide important supplementary information inside a sample to the conventional absorption tomography. Recently, the X-ray speckle based technique has been proposed to provide qualitative two-dimensional dark-field imaging with a simple experimental arrangement. In this letter, we deduce a relationship between the second moment of scattering angle distribution and cross-correlation degradation of speckle and establish a quantitative basis of X-ray dark-field tomography using single directional speckle scanning technique. In addition, the phase contrast images can be simultaneously retrieved permitting tomographic reconstruction, which yields enhanced contrast in weakly absorbing materials. Such complementary tomography technique can allow systematicmore » investigation of complex samples containing both soft and hard materials.« less

First results from the ionospheric tomography experiment using beacon TEC data obtained by means of a network along a longitude of 136°E over Japan

NASA Astrophysics Data System (ADS)

Thampi, Smitha V.; Yamamoto, Mamoru

2010-03-01

A chain of newly designed GNU (GNU is not UNIX) Radio Beacon Receivers (GRBR) has recently been established over Japan, primarily for tomographic imaging of the ionosphere over this region. Receivers installed at Shionomisaki (33.45°N, 135.8°E), Shigaraki (34.8°N, 136.1°E), and Fukui (36°N, 136°E) continuously track low earth orbiting satellites (LEOS), mainly OSCAR, Cosmos, and FORMOSAT-3/COSMIC, to obtain simultaneous total electron content (TEC) data from these three locations, which are then used for the tomographic reconstruction of ionospheric electron densities. This is the first GRBR network established for TEC observations, and the first beacon-based tomographic imaging in Japanese longitudes. The first tomographic images revealed the temporal evolution with all of the major features in the ionospheric electron density distribution over Japan. A comparison of the tomographically reconstructed electron densities with the ƒ o F 2 data from Kokubunji (35°N, 139°E) revealed that there was good agreement between the datasets. These first results show the potential of GRBR and its network for making continuous, unattended ionospheric TEC measurements and for tomographic imaging of the ionosphere.

On the feasibility of tomographic-PIV with low pulse energy illumination in a lifted turbulent jet flame

NASA Astrophysics Data System (ADS)

Boxx, I.; Carter, C. D.; Meier, W.

2014-08-01

Tomographic particle image velocimetry (tomographic-PIV) is a recently developed measurement technique used to acquire volumetric velocity field data in liquid and gaseous flows. The technique relies on line-of-sight reconstruction of the rays between a 3D particle distribution and a multi-camera imaging system. In a turbulent flame, however, index-of-refraction variations resulting from local heat-release may inhibit reconstruction and thereby render the technique infeasible. The objective of this study was to test the efficacy of tomographic-PIV in a turbulent flame. An additional goal was to determine the feasibility of acquiring usable tomographic-PIV measurements in a turbulent flame at multi-kHz acquisition rates with current-generation laser and camera technology. To this end, a setup consisting of four complementary metal oxide semiconductor cameras and a dual-cavity Nd:YAG laser was implemented to test the technique in a lifted turbulent jet flame. While the cameras were capable of kHz-rate image acquisition, the laser operated at a pulse repetition rate of only 10 Hz. However, use of this laser allowed exploration of the required pulse energy and thus power for a kHz-rate system. The imaged region was 29 × 28 × 2.7 mm in size. The tomographic reconstruction of the 3D particle distributions was accomplished using the multiplicative algebraic reconstruction technique. The results indicate that volumetric velocimetry via tomographic-PIV is feasible with pulse energies of 25 mJ, which is within the capability of current-generation kHz-rate diode-pumped solid-state lasers.

Large-scale tomographic particle image velocimetry using helium-filled soap bubbles

NASA Astrophysics Data System (ADS)

Kühn, Matthias; Ehrenfried, Klaus; Bosbach, Johannes; Wagner, Claus

2011-04-01

To measure large-scale flow structures in air, a tomographic particle image velocimetry (tomographic PIV) system for measurement volumes of the order of one cubic metre is developed, which employs helium-filled soap bubbles (HFSBs) as tracer particles. The technique has several specific characteristics compared to most conventional tomographic PIV systems, which are usually applied to small measurement volumes. One of them is spot lights on the HFSB tracers, which slightly change their position, when the direction of observation is altered. Further issues are the large particle to voxel ratio and the short focal length of the used camera lenses, which result in a noticeable variation of the magnification factor in volume depth direction. Taking the specific characteristics of the HFSBs into account, the feasibility of our large-scale tomographic PIV system is demonstrated by showing that the calibration errors can be reduced down to 0.1 pixels as required. Further, an accurate and fast implementation of the multiplicative algebraic reconstruction technique, which calculates the weighting coefficients when needed instead of storing them, is discussed. The tomographic PIV system is applied to measure forced convection in a convection cell at a Reynolds number of 530 based on the inlet channel height and the mean inlet velocity. The size of the measurement volume and the interrogation volumes amount to 750 mm × 450 mm × 165 mm and 48 mm × 48 mm × 24 mm, respectively. Validation of the tomographic PIV technique employing HFSBs is further provided by comparing profiles of the mean velocity and of the root mean square velocity fluctuations to respective planar PIV data.

Clinical, radiographic, ultrasonographic and computed tomographic features of nonseptic osteitis of the axial border of the proximal sesamoid bones.

PubMed

Vanderperren, K; Bergman, H J; Spoormakers, T J P; Pille, F; Duchateau, L; Puchalski, S M; Saunders, J H

2014-07-01

Lysis of the axial aspect of equine proximal sesamoid bones (PSBs) is a rare condition reported to have septic or traumatic origins. Limited information exists regarding imaging of nonseptic axial osteitis of a PSB. To report the clinical, radiographic, ultrasonographic, computed tomographic and intra-arterial contrast-enhanced computed tomographic abnormalities in horses with axial nonseptic osteitis of a PSB. Retrospective clinical study. Eighteen horses diagnosed with nonseptic osteitis of the axial border of a PSB between 2007 and 2012 were reviewed retrospectively. Case details, clinical examination, radiographic, ultrasonographic, computed tomographic and intra-arterial/intra-articular contrast-enhanced computed tomographic features were recorded, when available. Radiographic, ultrasonographic and computed tomographic evaluations of the fetlock region had been performed on 18, 15 and 9 horses, respectively. The effect of the degree of lysis on the grade and duration of lameness was determined. All horses had chronic unilateral lameness, 4 with forelimb and 14 with hindlimb signs. On radiographs, lysis was identified in both PSBs in 14 horses, one PSB in 3 horses and in one horse no lysis was identified. The degree of osteolysis was variable. Ultrasonography identified variably sized irregularities of the bone surface and alteration in echogenicity of the palmar/plantar ligament (PL). All horses undergoing computed tomographic examination (n = 9) had biaxial lysis. The lesions were significantly longer and deeper on computed tomographic images compared with radiographic images. Intra-arterial contrast-enhanced computed tomography may reveal moderate to marked contrast enhancement of the PL. There was no significant effect of the degree of lysis on the grade and duration of lameness. Lesions of nonseptic axial osteitis of a PSB can be identified using a combination of radiography and ultrasonography. Computed tomography provides additional information regarding the extent of the pathology. © 2013 EVJ Ltd.

Analysis of rolling fracture of the conticasted and tandem rolled blanks of low alloyed aluminum

NASA Astrophysics Data System (ADS)

Li, Yong; Zeng, Lingping; Jiao Xie, Xian

2018-01-01

Optical microscopy, electron microscopy and energy spectrum were used to test the morphology of grains, as-cast microstructure and secondary phases in confiscated and tandem rolled planks of 8011 low alloying aluminum alloy. It can be concluded that the existence of inhomogeneous secondary FeSiAl phases lead to the fracture of planks during rolling.

Crystal morphology of sunflower wax in soybean oil organogel

USDA-ARS?s Scientific Manuscript database

While sunflower wax has been recognized as an excellent organogelator for edible oil, the detailed morphology of sunflower wax crystals formed in an edible oil organogel has not been fully understood. In this study, polarized light microscopy, phase contrast microscopy, scanning electron microscopy ...

Tomographic reflection modelling of quasi-periodic oscillations in the black hole binary H 1743-322

NASA Astrophysics Data System (ADS)

Ingram, Adam; van der Klis, Michiel; Middleton, Matthew; Altamirano, Diego; Uttley, Phil

2017-01-01

Accreting stellar mass black holes (BHs) routinely exhibit Type-C quasi-periodic oscillations (QPOs). These are often interpreted as Lense-Thirring precession of the inner accretion flow, a relativistic effect whereby the spin of the BH distorts the surrounding space-time, inducing nodal precession. The best evidence for the precession model is the recent discovery, using a long joint XMM-Newton and NuSTAR observation of H 1743-322, that the centroid energy of the iron florescence line changes systematically with QPO phase. This was interpreted as the inner flow illuminating different azimuths of the accretion disc as it precesses, giving rise to a blueshifted/redshifted iron line when the approaching/receding disc material is illuminated. Here, we develop a physical model for this interpretation, including a self-consistent reflection continuum, and fit this to the same H 1743-322 data. We use an analytic function to parametrize the asymmetric illumination pattern on the disc surface that would result from inner flow precession, and find that the data are well described if two bright patches rotate about the disc surface. This model is preferred to alternatives considering an oscillating disc ionization parameter, disc inner radius and radial emissivity profile. We find that the reflection fraction varies with QPO phase (3.5σ), adding to the now formidable body of evidence that Type-C QPOs are a geometric effect. This is the first example of tomographic QPO modelling, initiating a powerful new technique that utilizes QPOs in order to map the dynamics of accreting material close to the BH.

High-resolution imaging of biological tissue with full-field optical coherence tomography

NASA Astrophysics Data System (ADS)

Zhu, Yue; Gao, Wanrong

2015-03-01

A new full-field optical coherence tomography system with high-resolution has been developed for imaging of cells and tissues. Compared with other FF-OCT (Full-field optical coherence tomography, FF-OCT) systems illuminated with optical fiber bundle, the improved Köhler illumination arrangement with a halogen lamp was used in the proposed FF-OCT system. High numerical aperture microscopic objectives were used for imaging and a piezoelectric ceramic transducer (PZT) was used for phase-shifting. En-face tomographic images can be obtained by applying the five-step phase-shifting algorithm to a series of interferometric images which are recorded by a smart camera. Three-dimensional images can be generated from these tomographic images. Imaging of the chip of Intel Pentium 4 processor demonstrated the ultrahigh resolution of the system (lateral resolution is 0.8μm ), which approaches the theoretical resolution 0.7 μm× 0.5 μm (lateral × axial). En-face images of cells of onion show an excellent performance of the system in generating en-face images of biological tissues. Then, unstained pig stomach was imaged as a tissue and gastric pits could be easily recognized using FF-OCT system. Our study provides evidence for the potential ability of FFOCT in identifying gastric pits from pig stomach tissue. Finally, label-free and unstained ex vivo human liver tissues from both normal and tumor were imaged with this FFOCT system. The results show that the setup has the potential for medical diagnosis applications such liver cancer diagnosis.

Advances in Urine Microscopy.

PubMed

Becker, Gavin J; Garigali, Giuseppe; Fogazzi, Giovanni B

2016-06-01

Urine microscopy is an important tool for the diagnosis and management of several conditions affecting the kidneys and urinary tract. In this review, we describe the automated instruments, based either on flow cytometry or digitized microscopy, that are currently in use in large clinical laboratories. These tools allow the examination of large numbers of samples in short periods. We also discuss manual urinary microscopy commonly performed by nephrologists, which we encourage. After discussing the advantages of phase contrast microscopy over bright field microscopy, we describe the advancements of urine microscopy in various clinical conditions. These include persistent isolated microscopic hematuria (which can be classified as glomerular or nonglomerular on the basis of urinary erythrocyte morphology), drug- and toxin-related cystalluria (which can be a clue for the diagnosis of acute kidney injury associated with intrarenal crystal precipitation), and some inherited conditions (eg, adenine phosphoribosyltransferase deficiency, which is associated with 2,8-dihydroxyadenine crystalluria, and Fabry disease, which is characterized by unique urinary lamellated fatty particles). Finally, we describe the utility of identifying "decoy cells" and atypical malignant cells, which can be easily done with phase contrast microscopy in unfixed samples. Copyright © 2016 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Quantitative assessment of cancer cell morphology and motility using telecentric digital holographic microscopy and machine learning.

PubMed

Lam, Van K; Nguyen, Thanh C; Chung, Byung M; Nehmetallah, George; Raub, Christopher B

2018-03-01

The noninvasive, fast acquisition of quantitative phase maps using digital holographic microscopy (DHM) allows tracking of rapid cellular motility on transparent substrates. On two-dimensional surfaces in vitro, MDA-MB-231 cancer cells assume several morphologies related to the mode of migration and substrate stiffness, relevant to mechanisms of cancer invasiveness in vivo. The quantitative phase information from DHM may accurately classify adhesive cancer cell subpopulations with clinical relevance. To test this, cells from the invasive breast cancer MDA-MB-231 cell line were cultured on glass, tissue-culture treated polystyrene, and collagen hydrogels, and imaged with DHM followed by epifluorescence microscopy after staining F-actin and nuclei. Trends in cell phase parameters were tracked on the different substrates, during cell division, and during matrix adhesion, relating them to F-actin features. Support vector machine learning algorithms were trained and tested using parameters from holographic phase reconstructions and cell geometric features from conventional phase images, and used to distinguish between elongated and rounded cell morphologies. DHM was able to distinguish between elongated and rounded morphologies of MDA-MB-231 cells with 94% accuracy, compared to 83% accuracy using cell geometric features from conventional brightfield microscopy. This finding indicates the potential of DHM to detect and monitor cancer cell morphologies relevant to cell cycle phase status, substrate adhesion, and motility. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

The influence of shear-velocity heterogeneity on ScS2/ScS amplitude ratios and estimates of Q in the mantle

NASA Astrophysics Data System (ADS)

Ritsema, J.; Chaves, C. A. M.

2016-12-01

Regional waveforms of deep-focus Tonga-Fiji earthquakes indicate anomalous traveltime differences (ScS2-ScS) and amplitude ratios (ScS2/ScS) of the phases ScS and ScS2. The correlation between the ScS2-ScS delay time and the ScS2/ScS amplitude ratio suggests that shear-wave apparent Q in the mantle below the Tonga-Fiji region is highest when shear-wave velocities are lowest. This observation is unexpected if temperature variations were responsible for the seismic anomalies. Using spectral-element-method waveform simulations for four tomographic models we demonstrate that focusing and scattering of shear waves by long-wavelength 3D heterogeneity in the mantle may overwhelm the signal from intrinsic attenuation in long-period ScS2/ScS amplitude ratios. The tomographic models reproduce the variability in recorded ScS2-ScS difference times and ScS2/ScS amplitude ratios. Variations in shear-wave attenuation (i.e., the quality factor Q) are not necessary to explain the data. An explanation for slow shear wave propagation without intrinsic attenuation does not require a creative solution from mineral physics.

The influence of shear-velocity heterogeneity on ScS2/ScS amplitude ratios and estimates of Q in the mantle

NASA Astrophysics Data System (ADS)

Chaves, Carlos A. M.; Ritsema, Jeroen

2016-08-01

Regional waveforms of deep-focus Tonga-Fiji earthquakes indicate anomalous traveltime differences (ScS2-ScS) and amplitude ratios (ScS2/ScS) of the phases ScS and ScS2. The correlation between the ScS2-ScS delay time and the ScS2/ScS amplitude ratio suggests that shear wave apparent Q in the mantle below the Tonga-Fiji region is highest when shear wave velocities are lowest. This observation is unexpected if temperature variations were responsible for the seismic anomalies. Using spectral element method waveform simulations for four tomographic models, we demonstrate that focusing and scattering of shear waves by long-wavelength 3-D heterogeneity in the mantle may overwhelm the signal from intrinsic attenuation in long-period ScS2/ScS amplitude ratios. The tomographic models reproduce the trends in recorded ScS2-ScS difference times and ScS2/ScS amplitude ratios. Although they cannot be ruled out, variations in shear wave attenuation (i.e., the quality factor Q) are not necessary to explain the data.

Cerebral blood flow tomography with xenon-133

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

Lassen, N.A.

1985-10-01

Cerebral blood flow (CBF) can be measured tomographically by inhalation of Xenon-/sup 133/. The calculation is based on taking a sequence of tomograms during the wash-in and wash-out phase of the tracer. Due to the dynamic nature of the process, a highly sensitive and fast moving single photon emission computed tomograph (SPECT) is required. Two brain-dedicated SPECT systems designed for this purpose are mentioned, and the method is described with special reference to the limitations inherent in the soft energy of the 133Xe primary photons. CBF tomography can be used for a multitude of clinical and investigative purposes. This articlemore » discusses in particular its use for the selection of patients with carotid occlusion for extracranial/intracranial bypass surgery, for detection of severe arterial spasm after aneurysm bleeding, and for detection of low flow areas during severe migraine attacks. The use of other tracers for CBF tomography using SPECT is summarized with emphasis on the /sup 99m/Tc chelates that freely pass the intact blood-brain barrier. The highly sensitive brain-dedicated SPECT systems described are a prerequisite for achieving high resolution tomograms with such tracers.« less

Configuration optimization of laser guide stars and wavefront correctors for multi-conjugation adaptive optics

NASA Astrophysics Data System (ADS)

Xuan, Li; He, Bin; Hu, Li-Fa; Li, Da-Yu; Xu, Huan-Yu; Zhang, Xing-Yun; Wang, Shao-Xin; Wang, Yu-Kun; Yang, Cheng-Liang; Cao, Zhao-Liang; Mu, Quan-Quan; Lu, Xing-Hai

2016-09-01

Multi-conjugation adaptive optics (MCAOs) have been investigated and used in the large aperture optical telescopes for high-resolution imaging with large field of view (FOV). The atmospheric tomographic phase reconstruction and projection of three-dimensional turbulence volume onto wavefront correctors, such as deformable mirrors (DMs) or liquid crystal wavefront correctors (LCWCs), is a very important step in the data processing of an MCAO’s controller. In this paper, a method according to the wavefront reconstruction performance of MCAO is presented to evaluate the optimized configuration of multi laser guide stars (LGSs) and the reasonable conjugation heights of LCWCs. Analytical formulations are derived for the different configurations and are used to generate optimized parameters for MCAO. Several examples are given to demonstrate our LGSs configuration optimization method. Compared with traditional methods, our method has minimum wavefront tomographic error, which will be helpful to get higher imaging resolution at large FOV in MCAO. Project supported by the National Natural Science Foundation of China (Grant Nos. 11174274, 11174279, 61205021, 11204299, 61475152, and 61405194) and the State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences.

Nanoscale quantification of intracellular element concentration by X-ray fluorescence microscopy combined with X-ray phase contrast nanotomography

NASA Astrophysics Data System (ADS)

Gramaccioni, Chiara; Yang, Yang; Procopio, Alessandra; Pacureanu, Alexandra; Bohic, Sylvain; Malucelli, Emil; Iotti, Stefano; Farruggia, Giovanna; Bukreeva, Inna; Notargiacomo, Andrea; Fratini, Michela; Valenti, Piera; Rosa, Luigi; Berlutti, Francesca; Cloetens, Peter; Lagomarsino, Stefano

2018-01-01

We present here a correlative X-ray microscopy approach for quantitative single cell imaging of molar concentrations. By combining the elemental content provided by X-ray fluorescence microscopy and the morphology information extracted from X-ray phase nanotomography, we determine the intracellular molarity distributions. This correlative method was demonstrated on a freeze-dried human phagocytic cell to obtain the absolute elemental concentration maps of K, P, and Fe. The cell morphology results showed a very good agreement with atomic-force microscopy measurements. This work opens the way for non-destructive single cell chemical analysis down to the sub-cellular level using exclusively synchrotron radiation techniques. It will be of high interest in the case where it is difficult to access the morphology using atomic-force microscopy, for example, on frozen-hydrated cells or tissues.

Quantification of synthesized hydration products using synchrotron microtomography and spectral analysis

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

Deboodt, Tyler; Ideker, Jason H.; Isgor, O. Burkan

2017-12-01

The use of x-ray computed tomography (CT) as a standalone method has primarily been used to characterize pore structure, cracking and mechanical damage in cementitious systems due to low contrast in the hydrated phases. These limitations have resulted in the inability to extract quantifiable information on such phases. The goal of this research was to address the limitations caused by low contrast and improving the ability to distinguish the four primary hydrated phases in portland cement; C-S-H, calcium hydroxide, monosulfate, and ettringite. X-ray CT on individual layers, binary mixtures of phases, and quaternary mixtures of phases to represent a hydratedmore » portland cement paste were imaged with synchrotron radiation. Known masses of each phase were converted to a volume and compared to the segmented image volumes. It was observed that adequate contrast in binary mixing of phases allowed for segmentation, and subsequent image analysis indicated quantifiable volumes could be extracted from the tomographic volume. However, low contrast was observed when C-S-H and monosulfate were paired together leading to difficulties segmenting in an unbiased manner. Quantification of phases in quaternary mixtures included larger errors than binary mixes due to histogram overlaps of monosulfate, C-S-H, and calcium hydroxide.« less

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

Buck, E.C.; Cunnane, J.C.; Brown, N.R.

A combination of optical microscopy, scanning electron microscopy with backscattered electron detection (SEM/BSE), and analytical electron microscopy (AEM) is being used to determine the nature of uranium in soils from the Fernald Environmental Management Project. The information gained from these studies is being used to develop and test remediation technologies. Investigations using SEM have shown that uranium is contained within particles that are typically 1 to 100 {mu}m in diameter. Further analysis with AEM has shown that these uranium-rich regions are made up of discrete uranium-bearing phases. The distribution of these uranium phases was found to be inhomogeneous at themore » microscopic level.« less

SIRT-FILTER v1.0.0

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

PELT, DANIEL

2017-04-21

Small Python package to compute tomographic reconstructions using a reconstruction method published in: Pelt, D.M., & De Andrade, V. (2017). Improved tomographic reconstruction of large-scale real-world data by filter optimization. Advanced Structural and Chemical Imaging 2: 17; and Pelt, D. M., & Batenburg, K. J. (2015). Accurately approximating algebraic tomographic reconstruction by filtered backprojection. In Proceedings of The 13th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine (pp. 158-161).

Shining X-rays on catalysts at work

NASA Astrophysics Data System (ADS)

Grunwaldt, J.-D.

2009-11-01

Structure-performance relationships gained by studying catalysts at work are considered the key to further development of catalysts underlined here by a brief overview on our research in this area. The partial oxidation of methane to hydrogen and carbon monoxide over Pt- and Rh-based catalysts and the total combustion of hydrocarbons demonstrate the importance of structural identification of catalysts in its working state and the measurement of the catalytic performance at the same time. Moreover, proper cell design is a key both here and in liquid phase reactions including preparation or high pressure reactions. In several cases structural changes during preparation, activation and reaction occur on a subminute scale or the catalyst structure varies inside a reactor as a result of temperature or concentration gradients. This, additionally, requires time and spatial resolution. Examples from time-resolved QEXAFS studies during the partial oxidation of methane over Pt- and Rh-based catalysts demonstrate some of the recent developments of the technique (use not only of Si(111) but also Si(311) crystals, angular encoder, full EXAFS spectra at subsecond recording time, and modulation excitation spectroscopy). In order to obtain spectroscopic information on the oxidation state inside a microreactor, scanning and full field X-ray microscopy with X-ray absorption spectroscopic contrast were achieved under reaction conditions. If a microbeam is applied, fast scanning techniques like QEXAFS are required. In this way, even X-ray absorption spectroscopic tomographic images of a slice of a microreactor were obtained. The studies were recently extended to spatiotemporal studies that give important insight into the dynamics of the catalyst structure in a spatial manner with subsecond time-resolution.

Microstructures and microhardness evolutions of melt-spun Al-8Ni-5Nd-4Si alloy

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

Karakoese, Ercan, E-mail: ekarakose@karatekin.edu.tr; Keskin, Mustafa

2012-03-15

Al-Ni-Nd-Si alloy with nominal composition of Al-8 wt.%Ni-5 wt.%Nd-4 wt.%Si was rapidly solidified by using melt-spinning technique to examine the influence of the cooling rate/conditions on microstructure and mechanical properties. The resulting conventional cast (ingot) and melt-spun ribbons were characterized by X-ray diffraction, optical microscopy, scanning electron microscopy together with energy dispersive spectroscopy, differential scanning calorimetry, differential thermal analysis and Vickers microhardness tester. The ingot alloys consists of four phases namely {alpha}-Al, intermetallic Al{sub 3}Ni, Al{sub 11}Nd{sub 3} and fcc Si. Melt-spun ribbons are completely composed of {alpha}-Al phase. The optical microscopy and scanning electron microscopy results show that themore » microstructures of rapidly solidified ribbons are clearly different from their ingot alloy. The change in microhardness is discussed based on the microstructural observations. - Highlights: Black-Right-Pointing-Pointer Rapid solidification allows a reduction in grain size, extended solid solution ranges. Black-Right-Pointing-Pointer We observed the matrix lattice parameter increases with increasing wheel speed. Black-Right-Pointing-Pointer Melt-spun ribbons consist of partly amorphous phases embedded in crystalline phases. Black-Right-Pointing-Pointer The solidification rate is high enough to retain most of alloying elements in the Al matrix. Black-Right-Pointing-Pointer The rapid solidification has effect on the phase constitution.« less

A review of US anthropometric reference data (1971 2000) with comparisons to both stylized and tomographic anatomic models

NASA Astrophysics Data System (ADS)

Huh, C.; Bolch, W. E.

2003-10-01

Two classes of anatomic models currently exist for use in both radiation protection and radiation dose reconstruction: stylized mathematical models and tomographic voxel models. The former utilize 3D surface equations to represent internal organ structure and external body shape, while the latter are based on segmented CT or MR images of a single individual. While tomographic models are clearly more anthropomorphic than stylized models, a given model's characterization as being anthropometric is dependent upon the reference human to which the model is compared. In the present study, data on total body mass, standing/sitting heights and body mass index are collected and reviewed for the US population covering the time interval from 1971 to 2000. These same anthropometric parameters are then assembled for the ORNL series of stylized models, the GSF series of tomographic models (Golem, Helga, Donna, etc), the adult male Zubal tomographic model and the UF newborn tomographic model. The stylized ORNL models of the adult male and female are found to be fairly representative of present-day average US males and females, respectively, in terms of both standing and sitting heights for ages between 20 and 60-80 years. While the ORNL adult male model provides a reasonably close match to the total body mass of the average US 21-year-old male (within ~5%), present-day 40-year-old males have an average total body mass that is ~16% higher. For radiation protection purposes, the use of the larger 73.7 kg adult ORNL stylized hermaphrodite model provides a much closer representation of average present-day US females at ages ranging from 20 to 70 years. In terms of the adult tomographic models from the GSF series, only Donna (40-year-old F) closely matches her age-matched US counterpart in terms of average body mass. Regarding standing heights, the better matches to US age-correlated averages belong to Irene (32-year-old F) for the females and Golem (38-year-old M) for the males. Both Helga (27-year-old F) and Donna, however, provide good matches to average US sitting heights for adult females, while Golem and Otoko (male of unknown age) yield sitting heights that are slightly below US adult male averages. Finally, Helga is seen as the only GSF tomographic female model that yields a body mass index in line with her average US female counterpart at age 26. In terms of dose reconstruction activities, however, all current tomographic voxel models are valuable assets in attempting to cover the broad distribution of individual anthropometric parameters representative of the current US population. It is highly recommended that similar attempts to create a broad library of tomographic models be initiated in the United States and elsewhere to complement and extend the limited number of tomographic models presently available for these efforts.

In search of the elusive IrB 2: Can mechanochemistry help?

DOE PAGES

Xie, Zhilin; Blair, Richard G.; Orlovskaya, Nina; ...

2015-10-20

We produced hexagonal ReB 2-type IrB 2 diboride and orthorhombic IrB monoboride phases, that were previously unknown and saw them produced by mechanochemical syntheses. High energy ball milling of elemental Ir and B powder for 30 h, followed by annealing of the powder at 1050 °C for 48 h, resulted in the formation of the desired phases. Both traditional laboratory and high resolution synchrotron X-ray diffraction (XRD) analyses were used for phase identification of the synthesized powder. Additionally, scanning electron microscopy and transmission electron microscopy were employed, along with XRD, to further characterize the microstructure of the phases produced.

Electron microscopy of a Gd-Ba-Cu-O superconductor

NASA Technical Reports Server (NTRS)

Ramesh, R.; Thomas, G.; Meng, R. L.; Hor, P. H.; Chu, C. W.

1989-01-01

An electron microscopy study has been carried out to characterize the microstructure of a sintered Gd-Ba-Cu-O superconductor alloy. The GdBa2Cu3O(7-x) phase in the oxygen annealed sample is orthorhombic, while in the vacuum annealed sample it is tetragonal. It is shown that the details of the fine structure in the 001-line zone axis convergent beam patterns can be used to distinguish between the orthorhombic form and the tetragonal form. In addition to this matrix phase, an amorphous phase is frequently observed at the triple grain junctions. Gd-rich inclusions have been observed inside the matrix phase.

Artifact-free dynamic atomic force microscopy reveals monotonic dissipation for a simple confined liquid

NASA Astrophysics Data System (ADS)

Kaggwa, G. B.; Kilpatrick, J. I.; Sader, J. E.; Jarvis, S. P.

2008-07-01

We present definitive interaction measurements of a simple confined liquid (octamethylcyclotetrasiloxane) using artifact-free frequency modulation atomic force microscopy. We use existing theory to decouple the conservative and dissipative components of the interaction, for a known phase offset from resonance (90° phase shift), that has been deliberately introduced into the experiment. Further we show the qualitative influence on the conservative and dissipative components of the interaction of a phase error deliberately introduced into the measurement, highlighting that artifacts, such as oscillatory dissipation, can be readily observed when the phase error is not compensated for in the force analysis.

In search of the elusive IrB 2: Can mechanochemistry help?

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

Xie, Zhilin; Blair, Richard G.; Orlovskaya, Nina

We produced hexagonal ReB 2-type IrB 2 diboride and orthorhombic IrB monoboride phases, that were previously unknown and saw them produced by mechanochemical syntheses. High energy ball milling of elemental Ir and B powder for 30 h, followed by annealing of the powder at 1050 °C for 48 h, resulted in the formation of the desired phases. Both traditional laboratory and high resolution synchrotron X-ray diffraction (XRD) analyses were used for phase identification of the synthesized powder. Additionally, scanning electron microscopy and transmission electron microscopy were employed, along with XRD, to further characterize the microstructure of the phases produced.

Multimodal quantitative phase and fluorescence imaging of cell apoptosis

NASA Astrophysics Data System (ADS)

Fu, Xinye; Zuo, Chao; Yan, Hao

2017-06-01

Fluorescence microscopy, utilizing fluorescence labeling, has the capability to observe intercellular changes which transmitted and reflected light microscopy techniques cannot resolve. However, the parts without fluorescence labeling are not imaged. Hence, the processes simultaneously happen in these parts cannot be revealed. Meanwhile, fluorescence imaging is 2D imaging where information in the depth is missing. Therefore the information in labeling parts is also not complete. On the other hand, quantitative phase imaging is capable to image cells in 3D in real time through phase calculation. However, its resolution is limited by the optical diffraction and cannot observe intercellular changes below 200 nanometers. In this work, fluorescence imaging and quantitative phase imaging are combined to build a multimodal imaging system. Such system has the capability to simultaneously observe the detailed intercellular phenomenon and 3D cell morphology. In this study the proposed multimodal imaging system is used to observe the cell behavior in the cell apoptosis. The aim is to highlight the limitations of fluorescence microscopy and to point out the advantages of multimodal quantitative phase and fluorescence imaging. The proposed multimodal quantitative phase imaging could be further applied in cell related biomedical research, such as tumor.

3D Tomographic SAR Imaging in Densely Vegetated Mountainous Rural Areas in China and Sweden

NASA Astrophysics Data System (ADS)

Feng, L.; Muller, J. P., , Prof

2017-12-01

3D SAR Tomography (TomoSAR) and 4D SAR Differential Tomography (Diff-TomoSAR) exploit multi-baseline SAR data stacks to create an important new innovation of SAR Interferometry, to unscramble complex scenes with multiple scatterers mapped into the same SAR cell. In addition to this 3-D shape reconstruction and deformation solution in complex urban/infrastructure areas, and recent cryospheric ice investigations, emerging tomographic remote sensing applications include forest applications, e.g. tree height and biomass estimation, sub-canopy topographic mapping, and even search, rescue and surveillance. However, these scenes are characterized by temporal decorrelation of scatterers, orbital, tropospheric and ionospheric phase distortion and an open issue regarding possible height blurring and accuracy losses for TomoSAR applications particularly in densely vegetated mountainous rural areas. Thus, it is important to develop solutions for temporal decorrelation, orbital, tropospheric and ionospheric phase distortion.We report here on 3D imaging (especially in vertical layers) over densely vegetated mountainous rural areas using 3-D SAR imaging (SAR tomography) derived from data stacks of X-band COSMO-SkyMed Spotlight and L band ALOS-1 PALSAR data stacks over Dujiangyan Dam, Sichuan, China and L and P band airborne SAR data (BioSAR 2008 - ESA) in the Krycklan river catchment, Northern Sweden. The new TanDEM-X 12m DEM is used to assist co - registration of all the data stacks over China first. Then, atmospheric correction is being assessed using weather model data such as ERA-I, MERRA, MERRA-2, WRF; linear phase-topography correction and MODIS spectrometer correction will be compared and ionospheric correction methods are discussed to remove tropospheric and ionospheric delay. Then the new TomoSAR method with the TanDEM-X 12m DEM is described to obtain the number of scatterers inside each pixel, the scattering amplitude and phase of each scatterer and finally extract tomograms (imaging), their 3D positions and motion parameters (deformation). A progress report will be shown on these different aspects.This work is partially supported by the CSC and UCL MAPS Dean prize through a PhD studentship at UCL-MSSL.

Multi-scale mantle structure underneath the Americas from a new tomographic model of seismic shear velocity

NASA Astrophysics Data System (ADS)

Porritt, R. W.; Becker, T. W.; Auer, L.; Boschi, L.

2017-12-01

We present a whole-mantle, variable resolution, shear-wave tomography model based on newly available and existing seismological datasets including regional body-wave delay times and multi-mode Rayleigh and Love wave phase delays. Our body wave dataset includes 160,000 S wave delays used in the DNA13 regional tomographic model focused on the western and central US, 86,000 S and SKS delays measured on stations in western South America (Porritt et al., in prep), and 3,900,000 S+ phases measured by correlation between data observed at stations in the IRIS global networks (IU, II) and stations in the continuous US, against synthetic data generated with IRIS Syngine. The surface wave dataset includes fundamental mode and overtone Rayleigh wave data from Schaeffer and Levedev (2014), ambient noise derived Rayleigh wave and Love wave measurements from Ekstrom (2013), newly computed fundamental mode ambient noise Rayleigh wave phase delays for the continuous US up to July 2017, and other, previously published, measurements. These datasets, along with a data-adaptive parameterization utilized for the SAVANI model (Auer et al., 2014), should allow significantly finer-scale imaging than previous global models, rivaling that of regional-scale approaches, under the USArray footprint in the continuous US, while seamlessly integrating into a global model. We parameterize the model for both vertically (vSV) and horizontally (vSH) polarized shear velocities by accounting for the different sensitivities of the various phases and wave types. The resulting, radially anisotropic model should allow for a range of new geodynamic analysis, including estimates of mantle flow induced topography or seismic anisotropy, without generating artifacts due to edge effects, or requiring assumptions about the structure of the region outside the well resolved model space. Our model shows a number of features, including indications of the effects of edge-driven convection in the Cordillera and along the eastern margin and larger-scale convection due to the subduction of the Farallon slab and along the edge of the Laurentia cratonic margin.

Time-lapse ultrasonic imaging of elastic anisotropy in saturated sandstone under polyaxial stress state

NASA Astrophysics Data System (ADS)

Tabari, Mehdi Sherveen Ghofrani

Although true-triaxial test (TTT) of rocks is now more extensive worldwide, stress-induced heterogeneity is not accounted for and usually simplified anisotropic models are used. Data from a TTT on a cubic sample of Fontainebleau sandstone is used in this study to evaluate our velocity imaging methodology. An anisotropic P wave velocity tomography method was developed using a geometrical approach based on an ellipsoidal P wavefront surface. During the two non-damaging phases of the experiment, saturation of the rock sample with water resulted in inaccurate tomographic images; however, during the final elasto-plastic phase of the experiment comprising major AE activities, tomographic images demonstrated reasonable anomalies. Thus, the P-S1-S2 velocity survey was utilized to obtain an accurate and reliable velocity image of the sample during the two non-damaging phases. This was accomplished using a numerical investigation by FLAC3D on the non-uniform distribution of stress over the sample to estimate the compaction pseudo-boundary surfaces within the rock. Thus, the problem of breakdown in the expected symmetry of shear wave velocities was resolved. It was discovered that a homogeneous anisotropic core in the center of the sample is formed under the standard polyaxial setup where elastic parameters could be computed. Off-diagonal elastic tensor parameters were obtained by a combination of various velocity survey data and justified the ellipsoidal model as being the most appropriate and facilitated the calculation of Thomsen parameters. The ellipsoidal heterogeneous velocity model was also verified by AE event location of transducer shots through the cubic rock specimen especially at the final phase of the experiment consisting lower-velocity zones bearing partially saturated fractures. AE of the rock during the whole experiment recorded by the surrounding transducers were investigated by location methods developed for anisotropic heterogeneous medium. AE events occurred in the vicinity of the dilation pseudo-boundaries where, a relatively large velocity gradient was formed and along parallel fractures in the sigma1/sigma2 plane. This research facilitated the computation of anisotropic parameters for rock during polyaxial tests contributing to enhanced AE interpretation of fracture growth processes in the rock under laboratory true-triaxial stress conditions.

Characterisation of phases in nanostructured, multilayered titanium alloys by analytical and high-resolution electron microscopy.

PubMed

Czyrska-Filemonowicz, A; Buffat, P A

2009-01-01

Surface processing of a Ti-6Al-4V alloy led to a complex multilayered microstructure containing several phases of the Ni-Ti-P-Al-O system, which improves the mechanical and tribological surface properties. The microstructure, chemical and phase compositions of the hard layer formed on the surface were investigated by LM, XRD, SEM as well as analytical/high-resolution TEM, STEM, EDS, electron diffraction and FIB. Phase identification based on electron diffraction, HRTEM and EDS microanalysis revealed the presence of several binary and ternary phases in the system Ti-Ni-P, sometimes with partial substitution of Ti by Al. However some phases, mainly nanoparticles, still remain not identified satisfactorily. Electron microscopy techniques used for identification of phases present in surface multilayers and some practical limits to their routine application are reminded here.

Interference Confocal Microscope Integrated with Spatial Phase Shifter.

PubMed

Wang, Weibo; Gu, Kang; You, Xiaoyu; Tan, Jiubin; Liu, Jian

2016-08-24

We present an interference confocal microscope (ICM) with a new single-body four-step simultaneous phase-shifter device designed to obtain high immunity to vibration. The proposed ICM combines the respective advantages of simultaneous phase shifting interferometry and bipolar differential confocal microscopy to obtain high axis resolution, large dynamic range, and reduce the sensitivity to vibration and reflectance disturbance seamlessly. A compact single body spatial phase shifter is added to capture four phase-shifted interference signals simultaneously without time delay and construct a stable and space-saving simplified interference confocal microscope system. The test result can be obtained by combining the interference phase response and the bipolar property of differential confocal microscopy without phase unwrapping. Experiments prove that the proposed microscope is capable of providing stable measurements with 1 nm of axial depth resolution for either low- or high-numerical aperture objective lenses.

Three phase crystallography and solute distribution analysis during residual austenite decomposition in tempered nanocrystalline bainitic steels

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

Caballero, F.G.; Yen, Hung-Wei; Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006

2014-02-15

Interphase carbide precipitation due to austenite decomposition was investigated by high resolution transmission electron microscopy and atom probe tomography in tempered nanostructured bainitic steels. Results showed that cementite (θ) forms by a paraequilibrium transformation mechanism at the bainitic ferrite–austenite interface with a simultaneous three phase crystallographic orientation relationship. - Highlights: • Interphase carbide precipitation due to austenite decomposition • Tempered nanostructured bainitic steels • High resolution transmission electron microscopy and atom probe tomography • Paraequilibrium θ with three phase crystallographic orientation relationship.

A comparison of newborn stylized and tomographic models for dose assessment in paediatric radiology

NASA Astrophysics Data System (ADS)

Staton, R. J.; Pazik, F. D.; Nipper, J. C.; Williams, J. L.; Bolch, W. E.

2003-04-01

Establishment of organ doses from diagnostic and interventional examinations is a key component to quantifying the radiation risks from medical exposures and for formulating corresponding dose-reduction strategies. Radiation transport models of human anatomy provide a convenient method for simulating radiological examinations. At present, two classes of models exist: stylized mathematical models and tomographic voxel models. In the present study, organ dose comparisons are made for projection radiographs of both a stylized and a tomographic model of the newborn patient. Sixteen separate radiographs were simulated for each model at x-ray technique factors typical of newborn examinations: chest, abdomen, thorax and head views in the AP, PA, left LAT and right LAT projection orientation. For AP and PA radiographs of the torso (chest, abdomen and thorax views), the effective dose assessed for the tomographic model exceeds that for the stylized model with per cent differences ranging from 19% (AP abdominal view) to 43% AP chest view. In contrast, the effective dose for the stylized model exceeds that for the tomographic model for all eight lateral views including those of the head, with per cent differences ranging from 9% (LLAT chest view) to 51% (RLAT thorax view). While organ positioning differences do exist between the models, a major factor contributing to differences in effective dose is the models' exterior trunk shape. In the tomographic model, a more elliptical shape is seen thus providing for less tissue shielding for internal organs in the AP and PA directions, with corresponding increased tissue shielding in the lateral directions. This observation is opposite of that seen in comparisons of stylized and tomographic models of the adult.

Prospects and Techniques for Eddy-Resolving Acoustic Tomography in the Eastern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Caruthers, J. W.; Nechaev, D.; Roman, D. A.; Sidorovskaia, N. A.; Ioup, G. E.; Ioup, J.; Yaremchuk, M.

2007-05-01

For several decades monitoring and modeling the dynamics and physical structure of the Gulf of Mexico have been major efforts undertaken by oceanographers of the United States and other American countries. There are very interesting physical oceanographic features in the Gulf, not the least of which are the Gulf Loop Current and the eddies it spawns. Satellite sensing of IR and altimeter imagery has been a major input to modeling those features. Such efforts are very important to the economy and well being of much of the United States and Mexico, including fisheries, mineral economies, hurricane strengths and paths in the summer, and severe snow storms in the eastern US in the winter. A major shortcoming of the present monitoring of the Gulf is the lack of subsurface input to the dynamic models of the Gulf. Acoustic tomography is a viable means of providing that missing input. Several universities have come together to investigate the prospects for establishing a Gulf Eddy Monitoring System (GEMS) for the deep eastern half of the Gulf using acoustic tomography. The group has conducted several acoustics experiments and propagation studies to determine the feasibility of long-range propagation in the eastern Gulf and the mitigation of adverse effects on marine mammal populations in that region under the Office of Naval Research project entitled the Littoral Acoustic Demonstration Center (LADC). The group has also convened an invited session for the 9th World Multiconference on Systemics, Cybernetics and Informatics (WMSCI 2005) Orlando, FL, July 2005. This paper discusses prospects for establishing the GEMS tomographic system, its technical characteristics, and its contributions to advancing the knowledge of the dynamics of the Gulf. This presentation will concentrate on the characteristics of a single-slice tomographic system, called GEMS Phase I, across the approaches to the DeSoto Canyon in the northeastern Gulf and its prospect for monitoring the movements of eddies into the canyon. It will also touch on the prospects for expanding the network to include the entire eastern Gulf with a moored system on the Campeche Bank and several along the US Gulf shelf. This projected tomographic system is called GEMS Phase II. The paper will invite the participation of Mexican organizations to help plan and develop this proposed extensive project.

Phase development in a U-7 wt.% Mo vs. Al-7 wt.% Ge diffusion couple

NASA Astrophysics Data System (ADS)

Perez, E.; Keiser, D. D.; Sohn, Y. H.

2013-10-01

Fuel development for the Reduced Enrichment for Research and Test Reactors (RERTR) program has demonstrated that U-Mo alloys in contact with Al develop interaction regions with phases that have poor irradiation behavior. The addition of Si to the Al has been considered with positive results. In this study, compositional modification is considered by replacing Si with Ge to determine the effect on the phase development in the system. The microstructural and phase development of a diffusion couple of U-7 wt.% Mo in contact with Al-7 wt.% Ge was examined by transmission electron microscopy, scanning electron microscopy and energy dispersive spectroscopy. The interdiffusion zone developed a microstructure that included the cubic-UGe3 phase and amorphous phases. The UGe3 phase was observed with and without Mo and Al solid solution developing a (U,Mo)(Al,Ge)3 phase.

Parallel-quadrature phase-shifting digital holographic microscopy using polarization beam splitter

PubMed Central

Das, Bhargab; Yelleswarapu, Chandra S; Rao, DVGLN

2012-01-01

We present a digital holography microscopy technique based on parallel-quadrature phase-shifting method. Two π/2 phase-shifted holograms are recorded simultaneously using polarization phase-shifting principle, slightly off-axis recording geometry, and two identical CCD sensors. The parallel phase-shifting is realized by combining circularly polarized object beam with a 45° degree polarized reference beam through a polarizing beam splitter. DC term is eliminated by subtracting the two holograms from each other and the object information is reconstructed after selecting the frequency spectrum of the real image. Both amplitude and phase object reconstruction results are presented. Simultaneous recording eliminates phase errors caused by mechanical vibrations and air turbulences. The slightly off-axis recording geometry with phase-shifting allows a much larger dimension of the spatial filter for reconstruction of the object information. This leads to better reconstruction capability than traditional off-axis holography. PMID:23109732

Spectro-microscopic Characterization of Physical Properties and Phase Separations in Individual Atmospheric Particles

NASA Astrophysics Data System (ADS)

OBrien, R. E.; Wang, B.; Neu, A.; Kelly, S. T.; Lundt, N.; Epstein, S. A.; MacMillan, A.; You, Y.; Laskin, A.; Nizkorodov, S.; Bertram, A. K.; Moffet, R.; Gilles, M.

2013-12-01

The phase state and liquid-liquid phase separations of ambient and laboratory generated aerosol particles were investigated using (1) scanning transmission x-ray microscopy/near-edge x-ray absorption fine structure spectroscopy (STXM/NEXAFS) coupled to a relative humidity (RH) controlled in-situ chamber and (2) environmental scanning electron microscopy (ESEM). The phase states of the particles were determined from measurements of their size and optical density. A comparison is made between the observed phase states of ambient samples and of laboratory generated aerosols to determine how well laboratory samples represent the phase of ambient samples. In addition, liquid-liquid phase separations in laboratory generated particles were investigated. Preliminary results showing that liquid-liquid phase separations occur at RH's between the deliquescence and efflorescence points and that the organic phase surrounds the inorganic phase will be presented. The STXM/NEXAFS technique provides insight into the degree of mixing at the deliquescence point and the degree of phase separation for particles of atmospherically relevant sizes.

High-Energy, High-Pulse-Rate Light Sources for Enhanced Time-Resolved Tomographic PIV of Unsteady and Turbulent Flows

DTIC Science & Technology

2017-07-31

Report: High-Energy, High-Pulse-Rate Light Sources for Enhanced Time -Resolved Tomographic PIV of Unsteady & Turbulent Flows The views, opinions and/or...reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching...High-Energy, High-Pulse-Rate Light Sources for Enhanced Time -Resolved Tomographic PIV of Unsteady & Turbulent Flows Report Term: 0-Other Email

Accurate modelling of single-particle cryo-EM images quantifies the benefits expected from using Zernike phase contrast

PubMed Central

Hall, R. J.; Nogales, E.; Glaeser, R. M.

2011-01-01

The use of a Zernike-type phase plate in biological cryo-electron microscopy allows the imaging, without using defocus, of what are predominantly phase objects. It is thought that such phase-plate implementations might result in higher quality images, free from the problems of CTF correction that occur when images must be recorded at extremely high values of defocus. In single-particle cryo-electron microscopy it is hoped that these improvements in image quality will facilitate work on structures that have proved difficult to study, either because of their relatively small size or because the structures are not completely homogeneous. There is still a need, however, to quantify how much improvement can be gained by using a phase plate for single-particle cryo-electron microscopy. We present a method for quantitatively modelling the images recorded with 200 keV electrons, for single particles embedded in vitreous ice. We then investigate what difference the use of a phase-plate device could have on the processing of single-particle data. We confirm that using a phase plate results in single-particle datasets in which smaller molecules can be detected, particles can be more accurately aligned and problems of heterogeneity can be more easily addressed. PMID:21463690

Advantages of intermediate X-ray energies in Zernike phase contrast X-ray microscopy.

PubMed

Wang, Zhili; Gao, Kun; Chen, Jian; Hong, Youli; Ge, Xin; Wang, Dajiang; Pan, Zhiyun; Zhu, Peiping; Yun, Wenbing; Jacobsen, Chris; Wu, Ziyu

2013-01-01

Understanding the hierarchical organizations of molecules and organelles within the interior of large eukaryotic cells is a challenge of fundamental interest in cell biology. Light microscopy is a powerful tool for observations of the dynamics of live cells, its resolution attainable is limited and insufficient. While electron microscopy can produce images with astonishing resolution and clarity of ultra-thin (<1 μm thick) sections of biological specimens, many questions involve the three-dimensional organization of a cell or the interconnectivity of cells. X-ray microscopy offers superior imaging resolution compared to light microscopy, and unique capability of nondestructive three-dimensional imaging of hydrated unstained biological cells, complementary to existing light and electron microscopy. Until now, X-ray microscopes operating in the "water window" energy range between carbon and oxygen k-shell absorption edges have produced outstanding 3D images of cryo-preserved cells. The relatively low X-ray energy (<540 eV) of the water window imposes two important limitations: limited penetration (<10 μm) not suitable for imaging larger cells or tissues, and small depth of focus (DoF) for high resolution 3D imaging (e.g., ~1 μm DoF for 20 nm resolution). An X-ray microscope operating at intermediate energy around 2.5 keV using Zernike phase contrast can overcome the above limitations and reduces radiation dose to the specimen. Using a hydrated model cell with an average chemical composition reported in literature, we calculated the image contrast and the radiation dose for absorption and Zernike phase contrast, respectively. The results show that an X-ray microscope operating at ~2.5 keV using Zernike phase contrast offers substantial advantages in terms of specimen size, radiation dose and depth-of-focus. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantitative tracking of tumor cells in phase-contrast microscopy exploiting halo artifact pattern

NASA Astrophysics Data System (ADS)

Kang, Mi-Sun; Song, Soo-Min; Lee, Hana; Kim, Myoung-Hee

2012-03-01

Tumor cell morphology is closely related to its invasiveness characteristics and migratory behaviors. An invasive tumor cell has a highly irregular shape, whereas a spherical cell is non-metastatic. Thus, quantitative analysis of cell features is crucial to determine tumor malignancy or to test the efficacy of anticancer treatment. We use phase-contrast microscopy to analyze single cell morphology and to monitor its change because it enables observation of long-term activity of living cells without photobleaching and phototoxicity, which is common in other fluorescence-labeled microscopy. Despite this advantage, there are image-level drawbacks to phase-contrast microscopy, such as local light effect and contrast interference ring, among others. Thus, we first applied a local filter to compensate for non-uniform illumination. Then, we used intensity distribution information to detect the cell boundary. In phase-contrast microscopy images, the cell normally appears as a dark region surrounded by a bright halo. As the halo artifact around the cell body is minimal and has an asymmetric diffusion pattern, we calculated the cross-sectional plane that intersected the center of each cell and was orthogonal to the first principal axis. Then, we extracted the dark cell region by level set. However, a dense population of cultured cells still rendered single-cell analysis difficult. Finally, we measured roundness and size to classify tumor cells into malignant and benign groups. We validated segmentation accuracy by comparing our findings with manually obtained results.

Electron tomographic analysis of gap junctions in lateral giant fibers of crayfish.

PubMed

Ohta, Yasumi; Nishikawa, Kouki; Hiroaki, Yoko; Fujiyoshi, Yoshinori

2011-07-01

Innexin-gap junctions in crayfish lateral giant fibers (LGFs) have an important role in escape behavior as a key component of rapid signal transduction. Knowledge of the structure and function of characteristic vesicles on the both sides of the gap junction, however, is limited. We used electron tomography to analyze the three-dimensional structure of crayfish gap junctions and gap junctional vesicles (GJVs). Tomographic analyses showed that some vesicles were anchored to innexons and almost all vesicles were connected by thin filaments. High densities inside the GJVs and projecting densities on the GJV membranes were observed in fixed and stained samples. Because the densities inside synaptic vesicles were dependent on the fixative conditions, different fixative conditions were used to elucidate the molecules included in the GJVs. The projecting densities on the GJVs were studied by immunoelectron microscopy with anti-vesicular monoamine transporter (anti-VMAT) and anti-vesicular nucleotide transporter (anti-VNUT) antibodies. Some of the projecting densities were labeled by anti-VNUT, but not anti-VMAT. Three-dimensional analyses of GJVs and excitatory chemical synaptic vesicles (CSVs) revealed clear differences in their sizes and central densities. Furthermore, the imaging data obtained under different fixative conditions and the immunolabeling results, in which GJVs were positively labeled for anti-VNUT but excitatory CSVs were not, support our model that GJVs contain nucleotides and excitatory CSVs do not. We propose a model in which characteristic GJVs containing nucleotides play an important role in the signal processing in gap junctions of crayfish LGFs. Copyright © 2011 Elsevier Inc. All rights reserved.

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. PMID:26433027

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. Copyright © 2015 Elsevier Inc. All rights reserved.

Tomographic imaging of OH laser-induced fluorescence in laminar and turbulent jet flames

NASA Astrophysics Data System (ADS)

Li, Tao; Pareja, Jhon; Fuest, Frederik; Schütte, Manuel; Zhou, Yihui; Dreizler, Andreas; Böhm, Benjamin

2018-01-01

In this paper a new approach for 3D flame structure diagnostics using tomographic laser-induced fluorescence (Tomo-LIF) of the OH radical was evaluated. The approach combined volumetric illumination with a multi-camera detection system of eight views. Single-shot measurements were performed in a methane/air premixed laminar flame and in a non-premixed turbulent methane jet flame. 3D OH fluorescence distributions in the flames were reconstructed using the simultaneous multiplicative algebraic reconstruction technique. The tomographic measurements were compared and validated against results of OH-PLIF in the laminar flame. The effects of the experimental setup of the detection system and the size of the volumetric illumination on the quality of the tomographic reconstructions were evaluated. Results revealed that the Tomo-LIF is suitable for volumetric reconstruction of flame structures with acceptable spatial resolution and uncertainty. It was found that the number of views and their angular orientation have a strong influence on the quality and accuracy of the tomographic reconstruction while the illumination volume thickness influences mainly the spatial resolution.

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry

DOE PAGES

Ophus, Colin; Ciston, Jim; Pierce, Jordan; ...

2016-02-29

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, makingmore » it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Ultimately, simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals.« less

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry.

PubMed

Ophus, Colin; Ciston, Jim; Pierce, Jordan; Harvey, Tyler R; Chess, Jordan; McMorran, Benjamin J; Czarnik, Cory; Rose, Harald H; Ercius, Peter

2016-02-29

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, making it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals.

Efficient linear phase contrast in scanning transmission electron microscopy with matched illumination and detector interferometry

PubMed Central

Ophus, Colin; Ciston, Jim; Pierce, Jordan; Harvey, Tyler R.; Chess, Jordan; McMorran, Benjamin J.; Czarnik, Cory; Rose, Harald H.; Ercius, Peter

2016-01-01

The ability to image light elements in soft matter at atomic resolution enables unprecedented insight into the structure and properties of molecular heterostructures and beam-sensitive nanomaterials. In this study, we introduce a scanning transmission electron microscopy technique combining a pre-specimen phase plate designed to produce a probe with structured phase with a high-speed direct electron detector to generate nearly linear contrast images with high efficiency. We demonstrate this method by using both experiment and simulation to simultaneously image the atomic-scale structure of weakly scattering amorphous carbon and strongly scattering gold nanoparticles. Our method demonstrates strong contrast for both materials, making it a promising candidate for structural determination of heterogeneous soft/hard matter samples even at low electron doses comparable to traditional phase-contrast transmission electron microscopy. Simulated images demonstrate the extension of this technique to the challenging problem of structural determination of biological material at the surface of inorganic crystals. PMID:26923483

Precipitation and Phase Transformations in 2101 Lean Duplex Stainless Steel During Isothermal Aging

NASA Astrophysics Data System (ADS)

Maetz, Jean-Yves; Cazottes, Sophie; Verdu, Catherine; Kleber, Xavier

2016-01-01

The effect of isothermal aging at 963 K (690 °C) on the microstructure of a 2101 lean duplex stainless steel, with the composition Fe-21.5Cr-5Mn-1.6Ni-0.22N-0.3Mo, was investigated using a multi-technique and multi-scale approach. The kinetics of phase transformation and precipitation was followed from a few minutes to thousands of hours using thermoelectric power measurements; based on these results, certain aging states were selected for electron microscopy characterization. Scanning electron microscopy, electron back-scattered diffraction, and transmission electron microscopy were used to quantitatively describe the microstructural evolution through crystallographic analysis, chemical analysis, and volume fraction measurements from the macroscopic scale down to the nanometric scale. During aging, the precipitation of M23C6 carbides, Cr2N nitrides, and σ phase as well as the transformation of ferrite into austenite and austenite into martensite was observed. These complex microstructural changes are controlled by Cr volume diffusion. The precipitation and phase transformation mechanisms are described.

Threshold automatic selection hybrid phase unwrapping algorithm for digital holographic microscopy

NASA Astrophysics Data System (ADS)

Zhou, Meiling; Min, Junwei; Yao, Baoli; Yu, Xianghua; Lei, Ming; Yan, Shaohui; Yang, Yanlong; Dan, Dan

2015-01-01

Conventional quality-guided (QG) phase unwrapping algorithm is hard to be applied to digital holographic microscopy because of the long execution time. In this paper, we present a threshold automatic selection hybrid phase unwrapping algorithm that combines the existing QG algorithm and the flood-filled (FF) algorithm to solve this problem. The original wrapped phase map is divided into high- and low-quality sub-maps by selecting a threshold automatically, and then the FF and QG unwrapping algorithms are used in each level to unwrap the phase, respectively. The feasibility of the proposed method is proved by experimental results, and the execution speed is shown to be much faster than that of the original QG unwrapping algorithm.

Optimal joule heating of the subsurface

DOEpatents

Berryman, James G.; Daily, William D.

1994-01-01

A method for simultaneously heating the subsurface and imaging the effects of the heating. This method combines the use of tomographic imaging (electrical resistance tomography or ERT) to image electrical resistivity distribution underground, with joule heating by electrical currents injected in the ground. A potential distribution is established on a series of buried electrodes resulting in energy deposition underground which is a function of the resistivity and injection current density. Measurement of the voltages and currents also permits a tomographic reconstruction of the resistivity distribution. Using this tomographic information, the current injection pattern on the driving electrodes can be adjusted to change the current density distribution and thus optimize the heating. As the heating changes conditions, the applied current pattern can be repeatedly adjusted (based on updated resistivity tomographs) to affect real time control of the heating.

Smectite flocculation structure modified by Al13 macro-molecules--as revealed by the transmission X-ray microscopy (TXM).

PubMed

Zbik, Marek S; Martens, Wayde N; Frost, Ray L; Song, Yen-Fang; Chen, Yi-Ming; Chen, Jian-Hua

2010-05-01

The aggregate structure which occurs in aqueous smectitic suspensions is responsible for poor water clarification, difficulties in sludge dewatering and the unusual rheological behaviour of smectite rich soils. These macroscopic properties are dictated by the 3D structural arrangement of smectite finest fraction within flocculated aggregates. Here, we report results from a relatively new technique, transmission X-ray microscopy (TXM), which makes it possible to investigate the internal structure and 3D tomographic reconstruction of the smectite clay aggregates modified by Al(13) Keggin macro-molecule [Al(13)(O)(4)(OH)(24)(H(2)O)(12)](7+). Three different treatment methods were shown resulted in three different micro-structural environments of the resulting flocculation. In case of smectite sample prepared in Methods 1 and 3 particles fall into the primary minimum where Van der Waals forces act between FF oriented smectite flakes and aggregates become approach irreversible flocculation. In case of sample prepared using Method 2, particles contacting by edges (EE) and edge to face (EF) orientation fell into secondary minimum and weak flocculation resulted in severe gelation and formation of the micelle-like texture in fringe superstructure, which was first time observed in smectite based gel. Copyright 2010 Elsevier Inc. All rights reserved.

Three-dimensional full-field X-ray orientation microscopy

PubMed Central

Viganò, Nicola; Tanguy, Alexandre; Hallais, Simon; Dimanov, Alexandre; Bornert, Michel; Batenburg, Kees Joost; Ludwig, Wolfgang

2016-01-01

A previously introduced mathematical framework for full-field X-ray orientation microscopy is for the first time applied to experimental near-field diffraction data acquired from a polycrystalline sample. Grain by grain tomographic reconstructions using convex optimization and prior knowledge are carried out in a six-dimensional representation of position-orientation space, used for modelling the inverse problem of X-ray orientation imaging. From the 6D reconstruction output we derive 3D orientation maps, which are then assembled into a common sample volume. The obtained 3D orientation map is compared to an EBSD surface map and local misorientations, as well as remaining discrepancies in grain boundary positions are quantified. The new approach replaces the single orientation reconstruction scheme behind X-ray diffraction contrast tomography and extends the applicability of this diffraction imaging technique to material micro-structures exhibiting sub-grains and/or intra-granular orientation spreads of up to a few degrees. As demonstrated on textured sub-regions of the sample, the new framework can be extended to operate on experimental raw data, thereby bypassing the concept of orientation indexation based on diffraction spot peak positions. This new method enables fast, three-dimensional characterization with isotropic spatial resolution, suitable for time-lapse observations of grain microstructures evolving as a function of applied strain or temperature. PMID:26868303

[The role of multidetector computer tomography in diagnosis of acute pancreatitis].

PubMed

Lohanikhina, K Iu; Hordiienko, K P; Kozarenko, T M

2014-10-01

With the objective to improve the diagnostic semiotics of an acute pancreatitis (AP) 35 patients were examined, using 64-cut computeric tomograph Lightspeed VCT (GE, USA) with intravenous augmentation in arterial and portal phases. Basing on analysis of the investigations conducted, using multidetector computeric tomography (MDCT), the AP semiotics was systematized, which is characteristic for oedematous and destructive forms, diagnosed in 19 (44.2%) and 16 (45.8%) patients, accordingly. The procedure for estimation of preservation of the organ functional capacity in pancreonecrosis pres- ence was elaborated, promoting rising of the method diagnostic efficacy by 5.3 - 9.4%.

Synchrotron radiation microtomography of Taylor bubbles in capillary two-phase flow

NASA Astrophysics Data System (ADS)

Boden, Stephan; dos Santos Rolo, Tomy; Baumbach, Tilo; Hampel, Uwe

2014-07-01

We report on a study to measure the three-dimensional shape of Taylor bubbles in capillaries using synchrotron radiation in conjunction with ultrafast radiographic imaging. Moving Taylor bubbles in 2-mm round and square capillaries were radiographically scanned with an ultrahigh frame rate of up to 36,000 fps and 5.6-µm pixel separation. Consecutive images were properly processed to yield 2D transmission radiographs of high contrast-to-noise ratio. Application of 3D tomographic image reconstruction disclosed the 3D bubble shape. The results provide a reference data base for development of sophisticated interface resolving CFD computations.

Direct Observations of Nucleation in a Nondilute Multicomponent Alloy

NASA Technical Reports Server (NTRS)

Sudbrack, Chantal K.; Noebe, Ronald D.; Seidman, David N.

2006-01-01

The chemical pathways leading to gamma'(L1(sub 2)) nucleation from nondilute Ni-5.2 Al-14.2 Cr at. %, gama(fcc), at 873 K are followed with radial distribution functions and isoconcentration surface analyses of direct-space atom-probe tomographic images. Although Cr atoms initially are randomly distributed, a distribution of congruent Ni3Al short-range-order domains (SRO), [R] approx. equals 0.6 nm, results from Al diffusion during quenching. Domain site occupancy develops as their number density increases leading to Al-rich phase separation by gamma'-nucleation, [R]=0.75 nm, after SRO occurs.

30 CFR 56.5001 - Exposure limits for airborne contaminants.

Code of Federal Regulations, 2012 CFR

2012-07-01

... concentration shall be determined by phase contrast microscopy (PCM) using the OSHA Reference Method in OSHA's.../cc excursion limit, samples shall be further analyzed using transmission electron microscopy...

30 CFR 56.5001 - Exposure limits for airborne contaminants.

Code of Federal Regulations, 2013 CFR

2013-07-01

... concentration shall be determined by phase contrast microscopy (PCM) using the OSHA Reference Method in OSHA's.../cc excursion limit, samples shall be further analyzed using transmission electron microscopy...

30 CFR 56.5001 - Exposure limits for airborne contaminants.

Code of Federal Regulations, 2014 CFR

2014-07-01

... concentration shall be determined by phase contrast microscopy (PCM) using the OSHA Reference Method in OSHA's.../cc excursion limit, samples shall be further analyzed using transmission electron microscopy...

30 CFR 56.5001 - Exposure limits for airborne contaminants.

Code of Federal Regulations, 2011 CFR

2011-07-01

... concentration shall be determined by phase contrast microscopy (PCM) using the OSHA Reference Method in OSHA's.../cc excursion limit, samples shall be further analyzed using transmission electron microscopy...

Label-free imaging of intracellular motility by low-coherent quantitative phase microscope in reflection geometry

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2011-11-01

We demonstrate tomographic imaging of intracellular activity of living cells by a low-coherent quantitative phase microscope. The intracellular organelles, such as the nucleus, nucleolus, and mitochondria, are moving around inside living cells, driven by the cellular physiological activity. In order to visualize the intracellular motility in a label-free manner we have developed a reflection-type quantitative phase microscope which employs the phase shifting interferometric technique with a low-coherent light source. The phase shifting interferometry enables us to quantitatively measure the intensity and phase of the optical field, and the low-coherence interferometry makes it possible to selectively probe a specific sectioning plane in the cell volume. The results quantitatively revealed the depth-resolved fluctuations of intracellular surfaces so that the plasma membrane and the membranes of intracellular organelles were independently measured. The transversal and the vertical spatial resolutions were 0.56 μm and 0.93 μm, respectively, and the mechanical sensitivity of the phase measurement was 1.2 nanometers. The mean-squared displacement was applied as a statistical tool to analyze the temporal fluctuation of the intracellular organelles. To the best of our knowledge, our system visualized depth-resolved intracellular organelles motion for the first time in sub-micrometer resolution without contrast agents.

Quantitative tomographic measurements of opaque multiphase flows

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

GEORGE,DARIN L.; TORCZYNSKI,JOHN R.; SHOLLENBERGER,KIM ANN

2000-03-01

An electrical-impedance tomography (EIT) system has been developed for quantitative measurements of radial phase distribution profiles in two-phase and three-phase vertical column flows. The EIT system is described along with the computer algorithm used for reconstructing phase volume fraction profiles. EIT measurements were validated by comparison with a gamma-densitometry tomography (GDT) system. The EIT system was used to accurately measure average solid volume fractions up to 0.05 in solid-liquid flows, and radial gas volume fraction profiles in gas-liquid flows with gas volume fractions up to 0.15. In both flows, average phase volume fractions and radial volume fraction profiles from GDTmore » and EIT were in good agreement. A minor modification to the formula used to relate conductivity data to phase volume fractions was found to improve agreement between the methods. GDT and EIT were then applied together to simultaneously measure the solid, liquid, and gas radial distributions within several vertical three-phase flows. For average solid volume fractions up to 0.30, the gas distribution for each gas flow rate was approximately independent of the amount of solids in the column. Measurements made with this EIT system demonstrate that EIT may be used successfully for noninvasive, quantitative measurements of dispersed multiphase flows.« less

Shear Wave Velocity Structure beneath the African-Anatolian Subduction Zone in Southwestern Turkey from Inversions of Rayleigh Waves

NASA Astrophysics Data System (ADS)

Teoman, U. M.; Sandvol, E. A.; Kahraman, M.; Sahin, S.; Turkelli, N.

2011-12-01

The ongoing subduction of the African Plate under western Anatolia results in a highly complex tectonic structure especially beneath Isparta Angle (IA) and the surroundings where the Hellenic and Cyprian slabs with different subduction geometries intersect. The primary objective is to accurately image the lithospheric structure at this convergent plate boundary and further understand the reasons responsible for the active deformation. Data was gathered from a temporary seismic network consisting of 10 broadband stations that was installed in August 2006 with the support from University of Missouri and nine more stations deployed in March 2007 with the support from Bogazici Research Fund (project ID:07T203). In addition, 21 permanent stations of Kandilli Observatory and Earthquake Research Institute (KOERI) and two from Süleyman Demirel University (SDU) together with five stations from IRIS/Geofon Network were also included to extend the station coverage. We used earthquakes in a distance range of 30-120 degrees with body wave magnitudes larger than 5.5. Depending on the signal to noise ratio, azimuthal coverage of events, and coherence from station, 81 events provided high-quality data for our analysis. The distribution of events shows a good azimuthal coverage, which is important for resolving both lateral heterogeneity and azimuthal anisotropy. We adopted a two-plane-wave inversion technique of Forsyth and Li (2003) to simultaneously solve for the incoming wave field and phase velocity. This relatively simpler representation of a more complex wavefield provided quite stable patterns of amplitude variations in many cases. To begin with, an average phase velocity dispersion curve was obtained and used as an input for tomographic inversions. Two-dimensional tomographic maps of isotropic and azimuthally anisotropic phase velocity variations were generated. Phase velocities can only tell us integrated information about the upper mantle. Furthermore, we inverted phase velocities for shear wave velocities (Saito,1988) in order to obtain direct information at a depth range of 30-300 km that can be interpreted in terms of major tectonic processes such as extension, slab detachment/tearing, STEP faults, volcanism, temperature anomalies, the presence of melt or dissolved water, etc. Resulting tomograms along horizontal and vertical depth sections provided valuable insights on the crustal and upper mantle structure beneath Southwestern Turkey down to almost 300 km.

Necrosis and apoptosis pathways of cell death at photodynamic treatment in vitro as revealed by digital holographic microscopy

NASA Astrophysics Data System (ADS)

Semenova, I. V.; Belashov, A. V.; Belyaeva, T. N.; Kornilova, E. S.; Salova, A. V.; Zhikhoreva, A. A.; Vasyutinskii, O. S.

2018-02-01

Monitoring of variations in morphological characteristics of cultured HeLa cells after photodynamic treatment with Radachlorin photosensitizer is performed by means of digital holographic microscopy. The observed dose-dependent post-treatment variations of phase shift evidence threshold effect of photodynamic treatment and allow for distinguishing between necrotic or apoptotic pathways of cell death. Results obtained by holographic microscopy were confirmed by means of far-field optical microscopy and confocal fluorescence microscopy with commonly used test assays.

Insights into intermediate phases of human intestinal fluids visualized by atomic force microscopy and cryo-transmission electron microscopy ex vivo.

PubMed

Müllertz, Anette; Fatouros, Dimitrios G; Smith, James R; Vertzoni, Maria; Reppas, Christos

2012-02-06

The current work aims to study at the ultrastructural level the morphological development of colloidal intermediate phases of human intestinal fluids (HIFs) produced during lipid digestion. HIFs were aspirated near the ligament of Treitz early (30 min), Aspirate(early), and 1 h, Aspirate(1h)(ave,comp), after the administration of a heterogeneous liquid meal into the antrum. The composition of the sample aspirated 1 h after meal administration was similar to the average lumenal composition 1 h after meal administration (Aspirate(1h)(ave,comp)). The colloidal structures of individual aspirates and supernatants of aspirates after ultracentrifugation (micellar phase) were characterized by means of atomic force microscopy (AFM) and cryogenic transmission electron microscopy (Cryo-TEM). AFM revealed domain-like structures in Aspirate(early) and both vesicles and large aggregates Aspirate(1h)(ave,comp). Rough surfaces and domains varying in size were frequently present in the micellar phase of both Aspirate(early) and Aspirate(1h)(ave,comp). Cryo-TEM revealed an abundance of spherical micelles and occasionally presented worm-like micelles coexisting with faceted and less defined vesicles in Aspirate(early) and Aspirate(1h)(ave,comp). In Aspirate(1h)(ave,comp) oil droplets were visualized with bilayers closely located to their surface suggesting lipolytic product phases accumulated on the surface of the oil droplet. In the micellar phase of Aspirate(early), Cryo-TEM revealed the presence of spherical micelles, small vesicles, membrane fragments, oil droplets and plate-like structures. In the micellar phase of Aspirate(1h)(ave,comp) the only difference was the absence of oil droplets. Visualization studies previously performed with biorelevant media revealed structural features with many similarities as presented in the current investigation. The impression of the complexity and diversion of these phases has been reinforced with the excessive variation of structural features visualized ex vivo in the current study offering insights at the ultrastuctural level of intermediate phases which impact drug solubilization.

Business aspects of cardiovascular computed tomography: tackling the challenges.

PubMed

Bateman, Timothy M

2008-01-01

The purpose of this article is to provide a comprehensive understanding of the business issues surrounding provision of dedicated cardiovascular computed tomographic imaging. Some of the challenges include high up-front costs, current low utilization relative to scanner capability, and inadequate payments. Cardiovascular computed tomographic imaging is a valuable clinical modality that should be offered by cardiovascular centers-of-excellence. With careful consideration of the business aspects, moderate-to-large size cardiology programs should be able to implement an economically viable cardiovascular computed tomographic service.

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

Improved cancer risk stratification and diagnosis via quantitative phase microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Liu, Yang; Uttam, Shikhar; Pham, Hoa V.; Hartman, Douglas J.

2017-02-01

Pathology remains the gold standard for cancer diagnosis and in some cases prognosis, in which trained pathologists examine abnormality in tissue architecture and cell morphology characteristic of cancer cells with a bright-field microscope. The limited resolution of conventional microscope can result in intra-observer variation, missed early-stage cancers, and indeterminate cases that often result in unnecessary invasive procedures in the absence of cancer. Assessment of nanoscale structural characteristics via quantitative phase represents a promising strategy for identifying pre-cancerous or cancerous cells, due to its nanoscale sensitivity to optical path length, simple sample preparation (i.e., label-free) and low cost. I will present the development of quantitative phase microscopy system in transmission and reflection configuration to detect the structural changes in nuclear architecture, not be easily identifiable by conventional pathology. Specifically, we will present the use of transmission-mode quantitative phase imaging to improve diagnostic accuracy of urine cytology and the nuclear dry mass is progressively correlate with negative, atypical, suspicious and positive cytological diagnosis. In a second application, we will present the use of reflection-mode quantitative phase microscopy for depth-resolved nanoscale nuclear architecture mapping (nanoNAM) of clinically prepared formalin-fixed, paraffin-embedded tissue sections. We demonstrated that the quantitative phase microscopy system detects a gradual increase in the density alteration of nuclear architecture during malignant transformation in animal models of colon carcinogenesis and in human patients with ulcerative colitis, even in tissue that appears histologically normal according to pathologists. We evaluated the ability of nanoNAM to predict "future" cancer progression in patients with ulcerative colitis.

Clinical multiphoton and CARS microscopy

NASA Astrophysics Data System (ADS)

Breunig, H. G.; Weinigel, M.; Darvin, M. E.; Lademann, J.; König, K.

2012-03-01

We report on clinical CARS imaging of human skin in vivo with the certified hybrid multiphoton tomograph CARSDermaInspect. The CARS-DermaInspect provides simultaneous imaging of non-fluorescent intradermal lipid and water as well as imaging of two-photon excited fluorescence from intrinsic molecules. Two different excitation schemes for CARS imaging have been realized: In the first setup, a combination of fs oscillator and optical parametric oscillator provided fs-CARS pump and Stokes pulses, respectively. In the second setup a fs oscillator was combined with a photonic crystal fiber which provided a broadband spectrum. A spectral range out of the broadband-spectrum was selected and used for CARS excitation in combination with the residual fs-oscillator output. In both setups, in addition to CARS, single-beam excitation was used for imaging of two-photon excited fluorescence and second harmonic generation signals. Both CARS-excitation systems were successfully used for imaging of lipids inside the skin in vivo.

A reversible component of mitochondrial respiratory dysfunction in apoptosis can be rescued by exogenous cytochrome c

PubMed Central

Mootha, Vamsi K.; Wei, Michael C.; Buttle, Karolyn F.; Scorrano, Luca; Panoutsakopoulou, Vily; Mannella, Carmen A.; Korsmeyer, Stanley J.

2001-01-01

Multiple apoptotic pathways release cytochrome c from the mitochondrial intermembrane space, resulting in the activation of downstream caspases. In vivo activation of Fas (CD95) resulted in increased permeability of the mitochondrial outer membrane and depletion of cytochrome c stores. Serial measurements of oxygen consumption, NADH redox state and membrane potential revealed a loss of respiratory state transitions. This tBID-induced respiratory failure did not require any caspase activity. At early time points, re-addition of exogenous cytochrome c markedly restored respiratory functions. Over time, however, mitochondria showed increasing irreversible respiratory dysfunction as well as diminished calcium buffering. Electron microscopy and tomographic reconstruction revealed asymmetric mitochondria with blebs of herniated matrix, distended inner membrane and partial loss of cristae structure. Thus, apoptogenic redistribution of cytochrome c is responsible for a distinct program of mitochondrial respiratory dysfunction, in addition to the activation of downstream caspases. PMID:11179211

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

PubMed Central

Chen, F.-R.; Van Dyck, D.; Kisielowski, C.

2016-01-01

Resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we report a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose rate electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. We apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances. PMID:26887849

Algorithmic structural segmentation of defective particle systems: a lithium-ion battery study.

PubMed

Westhoff, D; Finegan, D P; Shearing, P R; Schmidt, V

2018-04-01

We describe a segmentation algorithm that is able to identify defects (cracks, holes and breakages) in particle systems. This information is used to segment image data into individual particles, where each particle and its defects are identified accordingly. We apply the method to particle systems that appear in Li-ion battery electrodes. First, the algorithm is validated using simulated data from a stochastic 3D microstructure model, where we have full information about defects. This allows us to quantify the accuracy of the segmentation result. Then we show that the algorithm can successfully be applied to tomographic image data from real battery anodes and cathodes, which are composed of particle systems with very different morpohological properties. Finally, we show how the results of the segmentation algorithm can be used for structural analysis. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Vectorization with SIMD extensions speeds up reconstruction in electron tomography.

PubMed

Agulleiro, J I; Garzón, E M; García, I; Fernández, J J

2010-06-01

Electron tomography allows structural studies of cellular structures at molecular detail. Large 3D reconstructions are needed to meet the resolution requirements. The processing time to compute these large volumes may be considerable and so, high performance computing techniques have been used traditionally. This work presents a vector approach to tomographic reconstruction that relies on the exploitation of the SIMD extensions available in modern processors in combination to other single processor optimization techniques. This approach succeeds in producing full resolution tomograms with an important reduction in processing time, as evaluated with the most common reconstruction algorithms, namely WBP and SIRT. The main advantage stems from the fact that this approach is to be run on standard computers without the need of specialized hardware, which facilitates the development, use and management of programs. Future trends in processor design open excellent opportunities for vector processing with processor's SIMD extensions in the field of 3D electron microscopy.

Imaging samples larger than the field of view: the SLS experience

NASA Astrophysics Data System (ADS)

Vogiatzis Oikonomidis, Ioannis; Lovric, Goran; Cremona, Tiziana P.; Arcadu, Filippo; Patera, Alessandra; Schittny, Johannes C.; Stampanoni, Marco

2017-06-01

Volumetric datasets with micrometer spatial and sub-second temporal resolutions are nowadays routinely acquired using synchrotron X-ray tomographic microscopy (SRXTM). Although SRXTM technology allows the examination of multiple samples with short scan times, many specimens are larger than the field-of-view (FOV) provided by the detector. The extension of the FOV in the direction perpendicular to the rotation axis remains non-trivial. We present a method that can efficiently increase the FOV merging volumetric datasets obtained by region-of-interest tomographies in different 3D positions of the sample with a minimal amount of artefacts and with the ability to handle large amounts of data. The method has been successfully applied for the three-dimensional imaging of a small number of mouse lung acini of intact animals, where pixel sizes down to the micrometer range and short exposure times are required.

Advanced SLMs for microscopy

NASA Astrophysics Data System (ADS)

Linnenberger, A.

2018-02-01

Wavefront shaping devices such as deformable mirrors, liquid crystal spatial light modulators (SLMs), and active lenses are of considerable interest in microscopy for aberration correction, volumetric imaging, and programmable excitation. Liquid crystal SLMs are high resolution phase modulators capable of creating complex phase profiles to reshape, or redirect light within a three-dimensional (3D) volume. Recent advances in Meadowlark Optics (MLO) SLMs reduce losses by increasing fill factor from 83.4% to 96%, and improving resolution from 512 x 512 pixels to 1920 x 1152 pixels while maintaining a liquid crystal response time of 300 Hz at 1064 nm. This paper summarizes new SLM capabilities, and benefits for microscopy.

Evaluation of Airborne l- Band Multi-Baseline Pol-Insar for dem Extraction Beneath Forest Canopy

NASA Astrophysics Data System (ADS)

Li, W. M.; Chen, E. X.; Li, Z. Y.; Jiang, C.; Jia, Y.

2018-04-01

DEM beneath forest canopy is difficult to extract with optical stereo pairs, InSAR and Pol-InSAR techniques. Tomographic SAR (TomoSAR) based on different penetration and view angles could reflect vertical structure and ground structure. This paper aims at evaluating the possibility of TomoSAR for underlying DEM extraction. Airborne L-band repeat-pass Pol-InSAR collected in BioSAR 2008 campaign was applied to reconstruct the 3D structure of forest. And sum of kronecker product and algebraic synthesis algorithm were used to extract ground structure, and phase linking algorithm was applied to estimate ground phase. Then Goldstein cut-branch approach was used to unwrap the phases and then estimated underlying DEM. The average difference between the extracted underlying DEM and Lidar DEM is about 3.39 m in our test site. And the result indicates that it is possible for underlying DEM estimation with airborne L-band repeat-pass TomoSAR technique.

Electron microscopy characterization of Ni-Cr-B-Si-C laser deposited coatings.

PubMed

Hemmati, I; Rao, J C; Ocelík, V; De Hosson, J Th M

2013-02-01

During laser deposition of Ni-Cr-B-Si-C alloys with high amounts of Cr and B, various microstructures and phases can be generated from the same chemical composition that results in heterogeneous properties in the clad layer. In this study, the microstructure and phase constitution of a high-alloy Ni-Cr-B-Si-C coating deposited by laser cladding were analyzed by a combination of several microscopy characterization techniques including scanning electron microscopy in secondary and backscatter imaging modes, energy dispersive spectroscopy (EDS), electron backscatter diffraction (EBSD), and transmission electron microscopy (TEM). The combination of EDS and EBSD allowed unequivocal identification of micron-sized precipitates as polycrystalline orthorhombic CrB, single crystal tetragonal Cr5B3, and single crystal hexagonal Cr7C3. In addition, TEM characterization showed various equilibrium and metastable Ni-B, Ni-Si, and Ni-Si-B eutectic products in the alloy matrix. The findings of this study can be used to explain the phase formation reactions and to tune the microstructure of Ni-Cr-B-Si-C coatings to obtain the desired properties.

Fast photoacoustic imaging system based on 320-element linear transducer array.

PubMed

Yin, Bangzheng; Xing, Da; Wang, Yi; Zeng, Yaguang; Tan, Yi; Chen, Qun

2004-04-07

A fast photoacoustic (PA) imaging system, based on a 320-transducer linear array, was developed and tested on a tissue phantom. To reconstruct a test tomographic image, 64 time-domain PA signals were acquired from a tissue phantom with embedded light-absorption targets. A signal acquisition was accomplished by utilizing 11 phase-controlled sub-arrays, each consisting of four transducers. The results show that the system can rapidly map the optical absorption of a tissue phantom and effectively detect the embedded light-absorbing target. By utilizing the multi-element linear transducer array and phase-controlled imaging algorithm, we thus can acquire PA tomography more efficiently, compared to other existing technology and algorithms. The methodology and equipment thus provide a rapid and reliable approach to PA imaging that may have potential applications in noninvasive imaging and clinic diagnosis.

Using digital inline holographic microscopy and quantitative phase contrast imaging to assess viability of cultured mammalian cells

NASA Astrophysics Data System (ADS)

Missan, Sergey; Hrytsenko, Olga

2015-03-01

Digital inline holographic microscopy was used to record holograms of mammalian cells (HEK293, B16, and E0771) in culture. The holograms have been reconstructed using Octopus software (4Deep inwater imaging) and phase shift maps were unwrapped using the FFT-based phase unwrapping algorithm. The unwrapped phase shifts were used to determine the maximum phase shifts in individual cells. Addition of 0.5 mM H2O2 to cell media produced rapid rounding of cultured cells, followed by cell membrane rupture. The cell morphology changes and cell membrane ruptures were detected in real time and were apparent in the unwrapped phase shift images. The results indicate that quantitative phase contrast imaging produced by the digital inline holographic microscope can be used for the label-free real time automated determination of cell viability and confluence in mammalian cell cultures.

Estimation of the Above Ground Biomass of Tropical Forests using Polarimetric and Tomographic SAR Data Acquired at P Band and 3-D Imaging Techniques

NASA Astrophysics Data System (ADS)

Ferro-Famil, L.; El Hajj Chehade, B.; Ho Tong Minh, D.; Tebaldini, S.; LE Toan, T.

2016-12-01

Developing and improving methods to monitor forest biomass in space and time is a timely challenge, especially for tropical forests, for which SAR imaging at larger wavelength presents an interesting potential. Nevertheless, directly estimating tropical forest biomass from classical 2-D SAR images may reveal a very complex and ill-conditioned problem, since a SAR echo is composed of numerous contributions, whose features and importance depend on many geophysical parameters, such has ground humidity, roughness, topography… that are not related to biomass. Recent studies showed that SAR modes of diversity, i.e. polarimetric intensity ratios or interferometric phase centers, do not fully resolve this under-determined problem, whereas Pol-InSAR tree height estimates may be related to biomass through allometric relationships, with, in general over tropical forests, significant levels of uncertainty and lack of robustness. In this context, 3-D imaging using SAR tomography represents an appealing solution at larger wavelengths, for which wave penetration properties ensures a high quality mapping of a tropical forest reflectivity in the vertical direction. This paper presents a series of studies led, in the frame of the preparation of the next ESA mission BIOMASS, on the estimation of biomass over a tropical forest in French Guiana, using Polarimetric SAR Tomographic (Pol-TomSAR) data acquired at P band by ONERA. It is then shown that Pol-TomoSAR significantly improves the retrieval of forest above ground biomass (AGB) in a high biomass forest (200 up to 500 t/ha), with an error of only 10% at 1.5-ha resolution using a reflectivity estimates sampled at a predetermined elevation. The robustness of this technique is tested by applying the same approach over another site, and results show a similar relationship between AGB and tomographic reflectivity over both sites. The excellent ability of Pol-TomSAR to retrieve both canopy top heights and ground topography with an error of the order of 2m compared to LiDAR estimates, is then used to generalize this tomographic technique by selecting in an adaptive way the height at which reflectivity is estimated. Results indicate that this generalized techniques reduces the estimation error to values inferior to 10% and improve the representativity of the obtained AGB maps.

Characterization of Flow Dynamics and Reduced-Order Description of Experimental Two-Phase Pipe Flow

NASA Astrophysics Data System (ADS)

Viggiano, Bianca; SkjæRaasen, Olaf; Tutkun, Murat; Cal, Raul Bayoan

2017-11-01

Multiphase pipe flow is investigated using proper orthogonal decomposition for tomographic X-ray data, where holdup, cross sectional phase distributions and phase interface characteristics are obtained. Instantaneous phase fractions of dispersed flow and slug flow are analyzed and a reduced order dynamical description is generated. The dispersed flow displays coherent structures in the first few modes near the horizontal center of the pipe, representing the liquid-liquid interface location while the slug flow case shows coherent structures that correspond to the cyclical formation and breakup of the slug in the first 10 modes. The reconstruction of the fields indicate that main features are observed in the low order dynamical descriptions utilizing less than 1 % of the full order model. POD temporal coefficients a1, a2 and a3 show interdependence for the slug flow case. The coefficients also describe the phase fraction holdup as a function of time for both dispersed and slug flow. These flows are highly applicable to petroleum transport pipelines, hydroelectric power and heat exchanger tubes to name a few. The mathematical representations obtained via proper orthogonal decomposition will deepen the understanding of fundamental multiphase flow characteristics.

Phase sensitive optical coherence microscopy for photothermal imaging of gold nanorods

NASA Astrophysics Data System (ADS)

Hu, Yong; Podoleanu, Adrian G.; Dobre, George

2018-03-01

We describe a swept source based phase sensitive optical coherence microscopy (OCM) system for photothermal imaging of gold nanorods (GNR). The phase sensitive OCM system employed in the study has a displacement sensitivity of 0.17 nm to vibrations at single frequencies below 250 Hz. We demonstrate the generation of phase maps and confocal phase images. By displaying the difference between successive confocal phase images, we perform the confocal photothermal imaging of accumulated GNRs behind a glass coverslip and behind the scattering media separately. Compared with two-photon luminescence (TPL) detection techniques reported in literature, the technique in this study has the advantage of a simplified experimental setup and provides a more efficient method for imaging the aggregation of GNR. However, the repeatability performance of this technique suffers due to jitter noise from the swept laser source.

Microstructure of Haynes® 282® Superalloy after Vacuum Induction Melting and Investment Casting of Thin-Walled Components.

PubMed

Matysiak, Hubert; Zagorska, Malgorzata; Andersson, Joel; Balkowiec, Alicja; Cygan, Rafal; Rasinski, Marcin; Pisarek, Marcin; Andrzejczuk, Mariusz; Kubiak, Krzysztof; Kurzydlowski, Krzysztof J

2013-11-01

The aim of this work was to characterize the microstructure of the as-cast Haynes ® 282 ® alloy. Observations and analyses were carried out using techniques such as X-ray diffraction (XRD), light microscopy (LM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray spectroscopy (EDS), wave length dispersive X-ray spectroscopy (WDS), auger electron spectroscopy (AES) and electron energy-loss spectrometry (EELS). The phases identified in the as-cast alloy include: γ (gamma matrix), γ' (matrix strengthening phase), (TiMoCr)C (primary carbide), TiN (primary nitride), σ (sigma-TCP phase), (TiMo)₂SC (carbosulphide) and a lamellar constituent consisting of molybdenum and chromium rich secondary carbide phase together with γ phase. Within the dendrites the γ' appears mostly in the form of spherical, nanometric precipitates (74 nm), while coarser (113 nm) cubic γ' precipitates are present in the interdendritic areas. Volume fraction content of the γ' precipitates in the dendrites and interdendritic areas are 9.6% and 8.5%, respectively. Primary nitrides metallic nitrides (MN), are homogeneously dispersed in the as-cast microstructure, while primary carbides metallic carbides (MC), preferentially precipitate in interdendritic areas. Such preference is also observed in the case of globular σ phase. Lamellar constituents characterized as secondary carbides/γ phases were together with (TiMo)₂SC phase always observed adjacent to σ phase precipitates. Crystallographic relations were established in-between the MC, σ, secondary carbides and γ/γ' matrix.

Solid state amorphization of metastable Al 0.5TiZrPdCuNi high entropy alloy investigated by high voltage electron microscopy

DOE PAGES

Nagase, Takeshi; Takeuchi, Akira; Amiya, Kenji; ...

2017-07-18

Here, the phase stability of high entropy alloy (HEA), Al 0.5TiZrPdCuNi, under fast electron irradiation was studied by in-situ high voltage electron microscopy (HVEM). The initial phase of this alloy quenched from the melt was dependent on cooling rate. At high cooling rates an amorphous phase was obtained, whereas a body-centered cubic ( b.c.c.) phase were obtained at low cooling rates. By thermal crystallization of the amorphous phase b.c.c. phase nano-crystals were formed. Upon fast electron irradiation solid state amorphization (SSA) was observed in b.c.c. phase regardless of the initial microstructure (i.e., “coarse crystalline structure” or “nano-crystalline structure with grainmore » boundaries as a sink for point defects”). SSA behavior in the Al 0.5TiZrPdCuNi HEAs was investigated by in-situ transmission electron microscopy observations. Because the amorphization is very rarely achieved in a solid solution phase under fast electron irradiation in common metallic materials, this result suggests that the Al 0.5TiZrPdCuNi HEA from other common alloys and the other HEAs. The differences in phase stability against the irradiation between the Al 0.5TiZrPdCuNi HEA and the other HEAs were discussed. This is the first experimental evidence of SSA in HEAs stimulated by fast electron irradiation.« less

TEM studies of plasma nitrided austenitic stainless steel.

PubMed

Stróz, D; Psoda, M

2010-03-01

Cross-sectional transmission electron microscopy and X-ray phase analysis were used to study the structure of a layer formed during nitriding the AISI 316L stainless steel at temperature 440 degrees C. It was found that the applied treatment led to the formation of 6-microm-thick layer of the S-phase. There is no evidence of CrN precipitation. The X-ray diffraction experiments proved that the occurred austenite lattice expansion - due to nitrogen atoms - depended on the crystallographic direction. The cross-sectional transmission electron microscopy studies showed that the layer consisted of a single cubic phase that contained a lot of defects such as dislocations, stacking faults, slip bands and twins. The high-resolution electron microscopy observations were applied to study the defect formation due to the nitriding process. It was shown that the presence of great number of stacking faults leads to formation of nanotwins. Weak, forbidden {100} reflections were still another characteristic feature of the S-phase. These were not detected in the X-ray spectra of the phase. Basing on the high-resolution electron microscopy studies it can be suggested that the short-range ordering of the nitrogen atoms in the octahedral sites inside the f.c.c. matrix lattice takes place and gives rise to appearance of these spots. It is suggested that the cubic lattice undergoes not only expansion but also slight rombohedral distortion that explains differences in the lattice expansion for different crystallographic directions.

Optimal joule heating of the subsurface

DOEpatents

Berryman, J.G.; Daily, W.D.

1994-07-05

A method for simultaneously heating the subsurface and imaging the effects of the heating is disclosed. This method combines the use of tomographic imaging (electrical resistance tomography or ERT) to image electrical resistivity distribution underground, with joule heating by electrical currents injected in the ground. A potential distribution is established on a series of buried electrodes resulting in energy deposition underground which is a function of the resistivity and injection current density. Measurement of the voltages and currents also permits a tomographic reconstruction of the resistivity distribution. Using this tomographic information, the current injection pattern on the driving electrodes can be adjusted to change the current density distribution and thus optimize the heating. As the heating changes conditions, the applied current pattern can be repeatedly adjusted (based on updated resistivity tomographs) to affect real time control of the heating.

Lamb-Wave-Based Tomographic Imaging Techniques for Hole-Edge Corrosion Monitoring in Plate Structures

PubMed Central

Wang, Dengjiang; Zhang, Weifang; Wang, Xiangyu; Sun, Bo

2016-01-01

This study presents a novel monitoring method for hole-edge corrosion damage in plate structures based on Lamb wave tomographic imaging techniques. An experimental procedure with a cross-hole layout using 16 piezoelectric transducers (PZTs) was designed. The A0 mode of the Lamb wave was selected, which is sensitive to thickness-loss damage. The iterative algebraic reconstruction technique (ART) method was used to locate and quantify the corrosion damage at the edge of the hole. Hydrofluoric acid with a concentration of 20% was used to corrode the specimen artificially. To estimate the effectiveness of the proposed method, the real corrosion damage was compared with the predicted corrosion damage based on the tomographic method. The results show that the Lamb-wave-based tomographic method can be used to monitor the hole-edge corrosion damage accurately. PMID:28774041

DMD-based quantitative phase microscopy and optical diffraction tomography

NASA Astrophysics Data System (ADS)

Zhou, Renjie

2018-02-01

Digital micromirror devices (DMDs), which offer high speed and high degree of freedoms in steering light illuminations, have been increasingly applied to optical microscopy systems in recent years. Lately, we introduced DMDs into digital holography to enable new imaging modalities and break existing imaging limitations. In this paper, we will first present our progress in using DMDs for demonstrating laser-illumination Fourier ptychographic microscopy (FPM) with shotnoise limited detection. After that, we will present a novel common-path quantitative phase microscopy (QPM) system based on using a DMD. Building on those early developments, a DMD-based high speed optical diffraction tomography (ODT) system has been recently demonstrated, and the results will also be presented. This ODT system is able to achieve video-rate 3D refractive-index imaging, which can potentially enable observations of high-speed 3D sample structural changes.

Analytical Model of the Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions for Various Acoustic-Atomic Force Microscopies

NASA Technical Reports Server (NTRS)

Cantrell, John H., Jr.; Cantrell, Sean A.

2008-01-01

A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.

Application of Nomarski DIC and cathodoluminescence (CL) microscopy to building materials

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

Goetze, J., E-mail: goetze@mineral.tu-freiberg.de

2009-07-15

The present study discusses the potential of an integrated application of Nomarski differential interference contrast and cathodoluminescence microscopy for the investigation of building materials such as natural stone, cement, mortar and concrete. Nomarski differential interference contrast microscopy is a modern technique applied in materials sciences to visualize different phases and/or to image the surface relief on the scale of 50 nm. It is based on the principle of beam splitting by a double-crystal prism split, resulting in the superposition of laterally shifted wave fronts. In cathodoluminescence microscopy, the luminescence signal is excited by an electron beam and is generated bymore » different point defects within the material. Therefore, cathodoluminescence is a powerful method to characterize the defect structure of solid materials, to distinguish different phases and to reveal detailed information about their chemical composition. By combining Nomarski differential interference contrast and cathodoluminescence microscopy, textural, crystallographic and chemical information can be obtained from the same sample area in a polished thin section.« less

Identification of sigma and chi phases in duplex stainless steels

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

Llorca-Isern, Núria, E-mail: nullorca@ub.edu; López-Luque, Héctor, E-mail: hlopezlu7@alumnes.ub.edu; López-Jiménez, Isabel, E-mail: ilopezji9@alumnes.ub.edu

The aim of this work is to find out the most suitable method for detecting and analyzing accurately the formation conditions of secondary phases, particularly Sigma-phase (σ-phase) and Chi-phase (χ-phase) in duplex stainless steels (UNS S32205 and UNS S32750). The microstructure was characterized after a solution annealing at 1080 °C followed by an isothermal heating at 830 °C for different time ranges, ranging from 1 min to 9 h, in order to enlighten the controversial point concerning the mechanism of χ-phase nucleation in relation with the σ-phase. Etched samples were observed using optical microscopy (MO), and scanning electron microscopy (FESEM)more » with a backscattered electron detector (BSE) was used on unetched samples. Compositional microanalysis (EDS) was carried out for identifying the different phases present in the steels. Sigma phase was easily observed using different etching procedures, whereas χ-phase was only clearly detected with FESEM–BSE on unetched samples. The compositional analyses showed that the molybdenum content in χ-phase almost doubles the content of this element in σ-phase, and as a result the kinetics of nucleation and growth were also found to be remarkably faster when the alloy content in the steel is higher. In addition, chromium nitrides and carbides were also observed to precipitate as a result of the heat treatments and, in the case of the chromium nitrides, they act as a favorable site for the nucleation of σ-phase and χ-phase. - Highlights: • Microscopy was used on heat treated duplex steels for microstructure identification. • FESEM–BSE observation on unetched samples provided the best contrast between phases. • Analyses of carbides, nitrides, chi and sigma phases were possible by EDS and WDS. • Chromium nitrides act as favorable site for the nucleation of chi and sigma phases. • Secondary phases nucleation kinetics are faster in superduplex than in duplex steels.« less

Ultra-high resolution coded wavefront sensor.

PubMed

Wang, Congli; Dun, Xiong; Fu, Qiang; Heidrich, Wolfgang

2017-06-12

Wavefront sensors and more general phase retrieval methods have recently attracted a lot of attention in a host of application domains, ranging from astronomy to scientific imaging and microscopy. In this paper, we introduce a new class of sensor, the Coded Wavefront Sensor, which provides high spatio-temporal resolution using a simple masked sensor under white light illumination. Specifically, we demonstrate megapixel spatial resolution and phase accuracy better than 0.1 wavelengths at reconstruction rates of 50 Hz or more, thus opening up many new applications from high-resolution adaptive optics to real-time phase retrieval in microscopy.

Lung cancer diagnosis with quantitative DIC microscopy and support vector machine

NASA Astrophysics Data System (ADS)

Zheng, Longfei; Cai, Shuangshuang; Zeng, Bixin; Xu, Min

2017-01-01

We report the study of lung squamous cell carcinoma diagnosis using the TI-DIC microscopy and the scattering-phase theorem. The spatially resolved optical properties of tissue are computed from the 2D phase map via the scattering-phase theorem. The scattering coefficient, the reduced scattering coefficient, and the anisotropy factor are all found to increase with the grade of lung cancer. The retrieved optical parameters are shown to distinguish cancer cases from the normal cases with high accuracy. This label-free microscopic approach applicable to fresh tissues may be promising for in situ rapid cancer diagnosis.

Doppler flow imaging of cytoplasmic streaming using spectral domain phase microscopy

NASA Astrophysics Data System (ADS)

Choma, Michael A.; Ellerbee, Audrey K.; Yazdanfar, Siavash; Izatt, Joseph A.

2006-03-01

Spectral domain phase microscopy (SDPM) is a function extension of spectral domain optical coherence tomography. SDPM achieves exquisite levels of phase stability by employing common-path interferometry. We discuss the theory and limitations of Doppler flow imaging using SDPM, demonstrate monitoring the thermal contraction of a glass sample with nanometer per second velocity sensitivity, and apply this technique to measurement of cytoplasmic streaming in an Amoeba proteus pseudopod. We observe reversal of cytoplasmic flow induced by extracellular CaCl2, and report results that suggest parabolic flow of cytoplasm in the A. proteus pseudopod.

A 3D gantry single photon emission tomograph with hemispherical coverage for dedicated breast imaging

NASA Astrophysics Data System (ADS)

Tornai, Martin P.; Bowsher, James E.; Archer, Caryl N.; Peter, Jörg; Jaszczak, Ronald J.; MacDonald, Lawrence R.; Patt, Bradley E.; Iwanczyk, Jan S.

2003-01-01

A novel tomographic gantry was designed, built and initially evaluated for single photon emission imaging of metabolically active lesions in the pendant breast and near chest wall. Initial emission imaging measurements with breast lesions of various uptake ratios are presented. Methods: A prototype tomograph was constructed utilizing a compact gamma camera having a field-of-view of <13×13 cm 2 with arrays of 2×2×6 mm 3 quantized NaI(Tl) scintillators coupled to position sensitive PMTs. The camera was mounted on a radially oriented support with 6 cm variable radius-of-rotation. This unit is further mounted on a goniometric cradle providing polar motion, and in turn mounted on an azimuthal rotation stage capable of indefinite vertical axis-of-rotation about the central rotation axis (RA). Initial measurements with isotopic Tc-99 m (140 keV) to evaluate the system include acquisitions with various polar tilt angles about the RA. Tomographic measurements were made of a frequency and resolution cold-rod phantom filled with aqueous Tc-99 m. Tomographic and planar measurements of 0.6 and 1.0 cm diameter fillable spheres in an available ˜950 ml hemi-ellipsoidal (uncompressed) breast phantom attached to a life-size anthropomorphic torso phantom with lesion:breast-and-body:cardiac-and-liver activity concentration ratios of 11:1:19 were compared. Various photopeak energy windows from 10-30% widths were obtained, along with a 35% scatter window below a 15% photopeak window from the list mode data. Projections with all photopeak window and camera tilt conditions were reconstructed with an ordered subsets expectation maximization (OSEM) algorithm capable of reconstructing arbitrary tomographic orbits. Results: As iteration number increased for the tomographically measured data at all polar angles, contrasts increased while signal-to-noise ratios (SNRs) decreased in the expected way with OSEM reconstruction. The rollover between contrast improvement and SNR degradation of the lesion occurred at two to three iterations. The reconstructed tomographic data yielded SNRs with or without scatter correction that were >9 times better than the planar scans. There was up to a factor of ˜2.5 increase in total primary and scatter contamination in the photopeak window with increasing tilt angle from 15° to 45°, consistent with more direct line-of-sight of myocardial and liver activity with increased camera polar angle. Conclusion: This new, ultra-compact, dedicated tomographic imaging system has the potential of providing valuable, fully 3D functional information about small, otherwise indeterminate breast lesions as an adjunct to diagnostic mammography.

Laser Light-field Fusion for Wide-field Lensfree On-chip Phase Contrast Microscopy of Nanoparticles

NASA Astrophysics Data System (ADS)

Kazemzadeh, Farnoud; Wong, Alexander

2016-12-01

Wide-field lensfree on-chip microscopy, which leverages holography principles to capture interferometric light-field encodings without lenses, is an emerging imaging modality with widespread interest given the large field-of-view compared to lens-based techniques. In this study, we introduce the idea of laser light-field fusion for lensfree on-chip phase contrast microscopy for detecting nanoparticles, where interferometric laser light-field encodings acquired using a lensfree, on-chip setup with laser pulsations at different wavelengths are fused to produce marker-free phase contrast images of particles at the nanometer scale. As a proof of concept, we demonstrate, for the first time, a wide-field lensfree on-chip instrument successfully detecting 300 nm particles across a large field-of-view of ~30 mm2 without any specialized or intricate sample preparation, or the use of synthetic aperture- or shift-based techniques.

Laser Light-field Fusion for Wide-field Lensfree On-chip Phase Contrast Microscopy of Nanoparticles.

PubMed

Kazemzadeh, Farnoud; Wong, Alexander

2016-12-13

Wide-field lensfree on-chip microscopy, which leverages holography principles to capture interferometric light-field encodings without lenses, is an emerging imaging modality with widespread interest given the large field-of-view compared to lens-based techniques. In this study, we introduce the idea of laser light-field fusion for lensfree on-chip phase contrast microscopy for detecting nanoparticles, where interferometric laser light-field encodings acquired using a lensfree, on-chip setup with laser pulsations at different wavelengths are fused to produce marker-free phase contrast images of particles at the nanometer scale. As a proof of concept, we demonstrate, for the first time, a wide-field lensfree on-chip instrument successfully detecting 300 nm particles across a large field-of-view of ~30 mm 2 without any specialized or intricate sample preparation, or the use of synthetic aperture- or shift-based techniques.

A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source

PubMed Central

Atwood, Robert C.; Bodey, Andrew J.; Price, Stephen W. T.; Basham, Mark; Drakopoulos, Michael

2015-01-01

Tomographic datasets collected at synchrotrons are becoming very large and complex, and, therefore, need to be managed efficiently. Raw images may have high pixel counts, and each pixel can be multidimensional and associated with additional data such as those derived from spectroscopy. In time-resolved studies, hundreds of tomographic datasets can be collected in sequence, yielding terabytes of data. Users of tomographic beamlines are drawn from various scientific disciplines, and many are keen to use tomographic reconstruction software that does not require a deep understanding of reconstruction principles. We have developed Savu, a reconstruction pipeline that enables users to rapidly reconstruct data to consistently create high-quality results. Savu is designed to work in an ‘orthogonal’ fashion, meaning that data can be converted between projection and sinogram space throughout the processing workflow as required. The Savu pipeline is modular and allows processing strategies to be optimized for users' purposes. In addition to the reconstruction algorithms themselves, it can include modules for identification of experimental problems, artefact correction, general image processing and data quality assessment. Savu is open source, open licensed and ‘facility-independent’: it can run on standard cluster infrastructure at any institution. PMID:25939626

Automated classification of cell morphology by coherence-controlled holographic microscopy

NASA Astrophysics Data System (ADS)

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity.

Phase Contrast Microscopy Analysis of Breast Tissue

PubMed Central

Wells, Wendy A.; Wang, Xin; Daghlian, Charles P.; Paulsen, Keith D.; Pogue, Brian W.

2010-01-01

OBJECTIVE To assess how optical scatter properties in breast tissue, as measured by phase contrast microscopy and interpreted pathophysiologically, might be exploited as a diagnostic tool to differentiate cancer from benign tissue. STUDY DESIGN We evaluated frozen human breast tissue sections of adipose tissue, normal breast parenchyma, benign fibroadenoma tumors and noninvasive and invasive malignant cancers by phase contrast microscopy through quantification of grayscale values, using multiple regions of interest (ROI). Student’s t tests were performed on phase contrast measures across diagnostic categories testing data from individual cases; all ROI data were used as separate measures. RESULTS Stroma demonstrated significantly higher scatter intensity than did epithelium, with lower scattering in tumor-associated stroma as compared with normal or benign-associated stroma. Measures were comparable for invasive and noninvasive malignant tumors but were higher than those found in benign tumors and were lowest in adipose tissue. CONCLUSION Significant differences were found in scatter coefficient properties of epithelium and stroma across diagnostic categories of breast tissue, particularly between benign and malignant-associated stroma. Improved understanding of how scatter properties correlate with morphologic criteria used in routine pathologic diagnoses could have a significant clinical impact as developing optical technology allows macroscopic in situ phase contrast imaging. PMID:19736867

Automated classification of cell morphology by coherence-controlled holographic microscopy.

PubMed

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Tomographic inversion of satellite photometry. II

NASA Technical Reports Server (NTRS)

Solomon, S. C.; Hays, P. B.; Abreu, V. J.

1985-01-01

A method for combining nadir observations of emission features in the upper atmosphere with the result of a tomographic inversion of limb brightness measurements is presented. Simulated and actual results are provided, and error sensitivity is investigated.

Tomographic Image of a Seismically Active Volcano: Mammoth Mountain, California

NASA Astrophysics Data System (ADS)

Dawson, P. B.; Chouet, B. A.; Pitt, A. M.

2015-12-01

High-resolution tomographic P wave, S wave, and VP /VS velocity structure models are derived for Mammoth Mountain, California using phase data from the Northern California Seismic Network and a temporary deployment of broadband seismometers. An anomalous volume (˜50 km3) of low P and low S wave velocities is imaged beneath Mammoth Mountain, extending from near the surface to a depth of ˜2 km below sea level. We infer that the reduction in seismic wave velocities is primarily due to the presence of CO2 distributed in oblate-spheroid pores with mean aspect ratio α ˜8 x 10-4 (crack-like pores) and gas volume fraction φ ˜4 x 10-4. The pore density parameter κ = 3φ / (4πα) = na3 = 0.12, where n is the number of pores per cubic meter and a is the mean pore equatorial radius. The total mass of CO2 is estimated to range up to ˜1.6 x 1010 kg if the pores exclusively contain CO2, although he presence of an aqueous phase may lower this estimate by up to one order of magnitude. The local geological structure indicates that the CO2 contained in the pores is delivered to the surface through fractures controlled by faults and remnant foliation of the bedrock beneath Mammoth Mountain. The total volume of CO2 contained in the reservoir suggests that given an emission rate of 5 x 105 kg day-1, the reservoir could supply the emission of CO2 for ˜8 to ˜90 years before depletion. Continued supply of CO2 from an underlying magmatic system would significantly prolong the existence of the reservoir.

A 4-D dataset for validation of crystal growth in a complex three-phase material, ice cream

NASA Astrophysics Data System (ADS)

Rockett, P.; Karagadde, S.; Guo, E.; Bent, J.; Hazekamp, J.; Kingsley, M.; Vila-Comamala, J.; Lee, P. D.

2015-06-01

Four dimensional (4D, or 3D plus time) X-ray tomographic imaging of phase changes in materials is quickly becoming an accepted tool for quantifying the development of microstructures to both inform and validate models. However, most of the systems studied have been relatively simple binary compositions with only two phases. In this study we present a quantitative dataset of the phase evolution in a complex three-phase material, ice cream. The microstructure of ice cream is an important parameter in terms of sensorial perception, and therefore quantification and modelling of the evolution of the microstructure with time and temperature is key to understanding its fabrication and storage. The microstructure consists of three phases, air cells, ice crystals, and unfrozen matrix. We perform in situ synchrotron X-ray imaging of ice cream samples using in-line phase contrast tomography, housed within a purpose built cold-stage (-40 to +20oC) with finely controlled variation in specimen temperature. The size and distribution of ice crystals and air cells during programmed temperature cycling are determined using 3D quantification. The microstructural evolution of three-phase materials has many other important applications ranging from biological to structural and functional material, hence this dataset can act as a validation case for numerical investigations on faceted and non-faceted crystal growth in a range of materials.

Efficient control schemes with limited computation complexity for Tomographic AO systems on VLTs and ELTs

NASA Astrophysics Data System (ADS)

Petit, C.; Le Louarn, M.; Fusco, T.; Madec, P.-Y.

2011-09-01

Various tomographic control solutions have been proposed during the last decades to ensure efficient or even optimal closed-loop correction to tomographic Adaptive Optics (AO) concepts such as Laser Tomographic AO (LTAO), Multi-Conjugate AO (MCAO). The optimal solution, based on Linear Quadratic Gaussian (LQG) approach, as well as suboptimal but efficient solutions such as Pseudo-Open Loop Control (POLC) require multiple Matrix Vector Multiplications (MVM). Disregarding their respective performance, these efficient control solutions thus exhibit strong increase of on-line complexity and their implementation may become difficult in demanding cases. Among them, two cases are of particular interest. First, the system Real-Time Computer architecture and implementation is derived from past or present solutions and does not support multiple MVM. This is the case of the AO Facility which RTC architecture is derived from the SPARTA platform and inherits its simple MVM architecture, which does not fit with LTAO control solutions for instance. Second, considering future systems such as Extremely Large Telescopes, the number of degrees of freedom is twenty to one hundred times bigger than present systems. In these conditions, tomographic control solutions can hardly be used in their standard form and optimized implementation shall be considered. Single MVM tomographic control solutions represent a potential solution, and straightforward solutions such as Virtual Deformable Mirrors have been already proposed for LTAO but with tuning issues. We investigate in this paper the possibility to derive from tomographic control solutions, such as POLC or LQG, simplified control solutions ensuring simple MVM architecture and that could be thus implemented on nowadays systems or future complex systems. We theoretically derive various solutions and analyze their respective performance on various systems thanks to numerical simulation. We discuss the optimization of their performance and stability issues with respect to classic control solutions. We finally discuss off-line computation and implementation constraints.

Multi-scale invertigation of the relationship between the microstructure and mechanical properties in dual phase steels

NASA Astrophysics Data System (ADS)

Zhang, Fan

Dual phase steel alloys belong to the first generation of advanced high strength steels that are widely used in the automotive industry to form body structure and closure panels of vehicles. A deeper understanding of the microstructural features, such as phase orientation and morphology are needed in order to establish their effect on the mechanical performance and to design a material with optimized attributes. In this work, our goal is to establish what kind of relationship exist between the mechanical properties and the microstructural representation of dual phase steels obtained from experimental observations. Microstructure in different specimens are characterized with advanced experimental techniques as optical microscopy, scanning electron microscopy, transmission electron microscopy, electron backscatter diffraction pattern, scanning probe microscopy, and nanoindentation. Nanoindentation, Vickers hardness and tensile testing are conducted to reveal a multi-scale mechanical performance on original material and also specimens under a variety combinations of temperatures, cooling rates, and rolling conditions. To quantify the single phase properties in each sample, an inverse method is adopted using experimental nanoindentation load-depth curves to obtain tensile stress-strain curves for each phase, and the inverse results were verified with the true stress-strain curves from tensile tests. This work also provides the insight on spatial phase distribution of different phases through a 2-point correlation statistical methodology and relate to material strength and formability. The microstructure information is correlated with the results of mechanical tests. The broken surfaces from tensile testing are analyzed to discover the fracture mechanism in relation to martensite morphology and distribuion. Viscoplastic self-consistent fast Fourier Transformation simulations is also used to compute efficiently the local and the homogenized viscoplastic response of the polycrystalline microstructure. The specific objectives of this work are 1) the development of etching techniques and electron backscatter diffraction strategies to characterize ferrite and martensite phases in steel; 2) the uncovering of a relationship between strength/ductility and material microstructure, 3) a statistical description to quantify the spatial distributions of these phases; and finally 4) the simulation of the microstructural evolution using parameters obtained from the experiments.

Phase controlled homodyne infrared near-field microscopy and spectroscopy reveal inhomogeneity within and among individual boron nitride nanotubes.

PubMed

Xu, Xiaoji G; Tanur, Adrienne E; Walker, Gilbert C

2013-04-25

We propose a practical method to obtain near-field infrared absorption spectra in apertureless near-field scanning optical microscopy (aNSOM) through homodyne detection with a specific choice of reference phase. The underlying mechanism of the method is illustrated by theoretical and numeric models to show its ability to obtain absorptive rather than dispersive profiles in near-field infrared vibrational microscopy. The proposed near-field nanospectroscopic method is applied to obtain infrared spectra from regions of individual multiwall boron nitride nanotubes (BNNTs) in spatial regions smaller than the diffraction limit of the light source. The spectra suggest variations in interwall spacing within the individual tubes probed.

Mineralogy and Microstructures of Shock-Induced Melt Veins in Chondrites

NASA Technical Reports Server (NTRS)

Sharp, Thomas G.

2000-01-01

The applicability of phase equilibrium data to the interpretation of shock-induced melt veins can only be tested by a detailed study of melt- vein mineralogy to see how high-pressure assemblages vary as a function of shock conditions inferred from other indicators. We have used transmission electron microscopy (TEM), analytical electron microscopy (AEM), scanning electron microscopy (SEM), electron microprobe analysis (EMA) and optical petrography to characterize the mineralogy, microstructures, and compositions of melt veins and associated high-pressure minerals in shocked chondrites and SNC meteorites. In the processes, we have gained a better understanding of what melt veining can tell us about shock conditions and we have discovered new mineral phases in chondritic and SNC meteorites.

Phase contrast and DIC instrumentation and applications in cell, developmental, and marine biology

NASA Astrophysics Data System (ADS)

Gundlach, Heinz

1994-05-01

Nomarski's differential interference contrast (DIC) microscopy is discussed in comparison to Zernike's phase contrast (PhC) microscopy. The possibilities and limits of both are demonstrated by various applications. The high contrast and the use of the full numerical aperture of the DIC optics makes it possible to obtain a series of 'optical sections' through rather thick living specimens (e.g. head of water flea, salivary gland of Drosophila, Xenopus nucleolus, sea urchen egg, mouse embryo). PhC and DIC optics are today available for high resolution light microscopy until N.A. 1.4 Oil as well as for long working distance (LWD) optics, mainly combined with inverted biological microscopes.

Towards Seismic Tomography Based Upon Adjoint Methods

NASA Astrophysics Data System (ADS)

Tromp, J.; Liu, Q.; Tape, C.; Maggi, A.

2006-12-01

We outline the theory behind tomographic inversions based on 3D reference models, fully numerical 3D wave propagation, and adjoint methods. Our approach involves computing the Fréchet derivatives for tomographic inversions via the interaction between a forward wavefield, propagating from the source to the receivers, and an `adjoint' wavefield, propagating from the receivers back to the source. The forward wavefield is computed using a spectral-element method (SEM) and a heterogeneous wave-speed model, and stored as synthetic seismograms at particular receivers for which there is data. We specify an objective or misfit function that defines a measure of misfit between data and synthetics. For a given receiver, the differences between the data and the synthetics are time reversed and used as the source of the adjoint wavefield. For each earthquake, the interaction between the regular and adjoint wavefields is used to construct finite-frequency sensitivity kernels, which we call event kernel. These kernels may be thought of as weighted sums of measurement-specific banana-donut kernels, with weights determined by the measurements. The overall sensitivity is simply the sum of event kernels, which defines the misfit kernel. The misfit kernel is multiplied by convenient orthonormal basis functions that are embedded in the SEM code, resulting in the gradient of the misfit function, i.e., the Fréchet derivatives. The misfit kernel is multiplied by convenient orthonormal basis functions that are embedded in the SEM code, resulting in the gradient of the misfit function, i.e., the Fréchet derivatives. A conjugate gradient algorithm is used to iteratively improve the model while reducing the misfit function. Using 2D examples for Rayleigh wave phase-speed maps of southern California, we illustrate the construction of the gradient and the minimization algorithm, and consider various tomographic experiments, including source inversions, structural inversions, and joint source-structure inversions. We also illustrate the characteristics of these 3D finite-frequency kernels based upon adjoint simulations for a variety of global arrivals, e.g., Pdiff, P'P', and SKS, and we illustrate how the approach may be used to investigate body- and surface-wave anisotropy. In adjoint tomography any time segment in which the data and synthetics match reasonably well is suitable for measurement, and this implies a much greater number of phases per seismogram can be used compared to classical tomography in which the sensitivity of the measurements is determined analytically for specific arrivals, e.g., P. We use an automated picking algorithm based upon short-term/long-term averages and strict phase and amplitude anomaly criteria to determine arrivals and time windows suitable for measurement. For shallow global events the algorithm typically identifies of the order of 1000~windows suitable for measurement, whereas for a deep event the number can reach 4000. For southern California earthquakes the number of phases is of the order of 100 for a magnitude 4.0 event and up to 450 for a magnitude 5.0 event. We will show examples of event kernels for both global and regional earthquakes. These event kernels form the basis of adjoint tomography.

Structural studies of degradation process of zirconium dioxide tetragonal phase induced by grinding with dental bur

NASA Astrophysics Data System (ADS)

Piosik, A.; Żurowski, K.; Pietralik, Z.; Hędzelek, W.; Kozak, M.

2017-11-01

Zirconium dioxide has been widely used in dental prosthetics. However, the improper mechanical treatment can induce changes in the microstructure of zirconium dioxide. From the viewpoint of mechanical properties and performance, the phase transitions of ZrO2 from the tetragonal to the monoclinic phase induced by mechanical processing, are particularly undesirable. In this study, the phase transitions of yttrium stabilized zirconium dioxide (Y-TZP) induced by mechanical treatment are investigated by the scanning electron microscopy (SEM), atomic force microscopy (AFM) and powder diffraction (XRD). Mechanical stress was induced by different types of drills used presently in dentistry. At the same time the surface temperature was monitored during milling using a thermal imaging camera. Diffraction analysis allowed determination of the effect of temperature and mechanical processing on the scale of induced changes. The observed phase transition to the monoclinic phase was correlated with the methods of mechanical processing.

Assessing the resolution-dependent utility of tomograms for geostatistics

USGS Publications Warehouse

Day-Lewis, F. D.; Lane, J.W.

2004-01-01

Geophysical tomograms are used increasingly as auxiliary data for geostatistical modeling of aquifer and reservoir properties. The correlation between tomographic estimates and hydrogeologic properties is commonly based on laboratory measurements, co-located measurements at boreholes, or petrophysical models. The inferred correlation is assumed uniform throughout the interwell region; however, tomographic resolution varies spatially due to acquisition geometry, regularization, data error, and the physics underlying the geophysical measurements. Blurring and inversion artifacts are expected in regions traversed by few or only low-angle raypaths. In the context of radar traveltime tomography, we derive analytical models for (1) the variance of tomographic estimates, (2) the spatially variable correlation with a hydrologic parameter of interest, and (3) the spatial covariance of tomographic estimates. Synthetic examples demonstrate that tomograms of qualitative value may have limited utility for geostatistics; moreover, the imprint of regularization may preclude inference of meaningful spatial statistics from tomograms.

Subsurface PpIX imaging in vivo with ultrasound-guided tomographic spectroscopy: reconstruction vs. born-normalized data

NASA Astrophysics Data System (ADS)

Flynn, Brendan P.; D'Souza, Alisha V.; Kanick, Stephen C.; Maytin, Edward; Hasan, Tayyaba; Pogue, Brian W.

2013-03-01

Aminolevulinic acid (ALA)-induced Protoporphyrin IX (PpIX)-based photodynamic therapy (PDT) is an effective treatment for skin cancers including basal cell carcinoma (BCC). Topically applied ALA promotes PpIX production preferentially in tumors, and many strategies have been developed to increase PpIX distribution and PDT treatment efficacy at depths > 1mm is not fully understood. While surface imaging techniques provide useful diagnosis, dosimetry, and efficacy information for superficial tumors, these methods cannot interrogate deeper tumors to provide in situ insight into spatial PpIX distributions. We have developed an ultrasound-guided, white-light-informed, tomographics spectroscopy system for the spatial measurement of subsurface PpIX. Detailed imaging system specifications, methodology, and optical-phantom-based characterization will be presented separately. Here we evaluate preliminary in vivo results using both full tomographic reconstruction and by plotting individual tomographic source-detector pair data against US images.

An ensemble and single-molecule fluorescence microscopy investigation of phase-separated monolayer films stained with Nile Red.

PubMed

Lu, Yin; Porterfield, Robyn; Thunder, Terri; Paige, Matthew F

2011-01-01

Phase-separated Langmuir-Blodgett monolayer films prepared from mixtures of arachidic acid (C19H39COOH) and perfluorotetradecanoic acid (C13F27COOH) were stained via spin-casting with the polarity sensitive phenoxazine dye Nile Red, and characterized using a combination of ensemble and single-molecule fluorescence microscopy measurements. Ensemble fluorescence microscopy and spectromicroscopy showed that Nile Red preferentially associated with the hydrogenated domains of the phase-separated films, and was strongly fluorescent in these areas of the film. These measurements, in conjunction with single-molecule fluorescence imaging experiments, also indicated that a small sub-population of dye molecules localizes on the perfluorinated regions of the sample, but that this sub-population is spectroscopically indistinguishable from that associated with the hydrogenated domains. The relative importance of selective dye adsorption and local polarity sensitivity of Nile Red for staining applications in phase-separated LB films as well as in cellular environments is discussed in context of the experimental results. Copyright © 2010 Elsevier B.V. All rights reserved.

Structure of the European upper mantle revealed by adjoint tomography

NASA Astrophysics Data System (ADS)

Zhu, Hejun; Bozdağ, Ebru; Peter, Daniel; Tromp, Jeroen

2012-07-01

Images of the European crust and upper mantle, created using seismic tomography, identify the Cenozoic Rift System and related volcanism in central and western Europe. They also reveal subduction and slab roll back in the Mediterranean-Carpathian region. However, existing tomographic models are either high in resolution, but cover only a limited area, or low in resolution, and thus miss the finer-scale details of mantle structure. Here we simultaneously fit frequency-dependent phase anomalies of body and surface waveforms in complete three-component seismograms with an iterative inversion strategy involving adjoint methods, to create a tomographic model of the European upper mantle. We find that many of the smaller-scale structures such as slabs, upwellings and delaminations that emerge naturally in our model are consistent with existing images. However, we also derive some hitherto unidentified structures. Specifically, we interpret fast seismic-wave speeds beneath the Dinarides Mountains, southern Europe, as a signature of northeastward subduction of the Adria plate; slow seismic-wave speeds beneath the northern part of the Rhine Graben as a reservoir connected to the Eifel hotspot; and fast wave-speed anomalies beneath Scandinavia as a lithospheric drip, where the lithosphere is delaminating and breaking away. Our model sheds new light on the enigmatic palaeotectonic history of Europe.

Dynamic Computed Tomographic Features of Adult Renal Cell Carcinoma Associated With Xp11.2 Translocation/TFE3 Gene Fusions: Comparison With Clear Cell Renal Cell Carcinoma.

PubMed

He, Jian; Gan, Weidong; Liu, Song; Zhou, Kefeng; Zhang, Gutian; Guo, Hongqian; Zhu, Bin

2015-01-01

To investigate the dynamic contrast-enhanced computed tomography (CT) characteristics of renal cell carcinoma associated with Xp11.2 translocation and TFE gene fusion (Xp11.2 RCC) by comparison with clear cell renal cell carcinoma (CCRCC). Dynamic contrast-enhanced CT images and clinical and pathological records of 20 adult patients with Xp11.2 RCC confirmed by TFE3 immunohistochemical and fluorescence in situ hybridization assay were retrospectively analyzed and compared with the findings of 21 contemporary CCRCCs. Renal cell carcinoma associated with Xp11.2 translocation and TFE gene fusions often occurred in young (30.6 ± 8.6 years) patients with hematuria (9/20). They presented as well-defined (17/20) cystic-solid (17/20) mass with hemorrhage (8/20) and circular/rim calcifications (6/20). Dynamic contrast-enhanced CT showed heterogeneous moderate prolonged enhancement. A tumor-to-cortex attenuation ratio in corticomedullary phase less than 0.62 gave a sensitivity of 90.0% and a specificity of 92.9% in differentiating Xp11.2 RCC from CCRCC (area under the receiver operating characteristic curve = 0.957, P < 0.001). Computed tomographic characteristics and dynamic contrast-enhanced patterns and index can differentiate Xp11.2 RCC from CCRCC.

CoCrMo cellular structures made by Electron Beam Melting studied by local tomography and finite element modelling

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

Petit, Clémence; Maire, Eric, E-mail: eric.maire@insa-lyon.fr; Meille, Sylvain

The work focuses on the structural and mechanical characterization of Co-Cr-Mo cellular samples with cubic pore structure made by Electron Beam Melting (EBM). X-ray tomography was used to characterize the architecture of the sample. High resolution images were also obtained thanks to local tomography in which the specimen is placed close to the X-ray source. These images enabled to observe some defects due to the fabrication process: small pores in the solid phase, partially melted particles attached to the surface. Then, in situ compression tests were performed in the tomograph. The images of the deformed sample show a progressive bucklingmore » of the vertical struts leading to final fracture. The deformation initiated where the defects were present in the strut i.e. in regions with reduced local thickness. The finite element modelling confirmed the high stress concentrations of these weak points leading to the fracture of the sample. - Highlights: • CoCrMo samples fabricated by Electron Beam Melting (EBM) process are considered. • X-ray Computed Tomography is used to observe the structure of the sample. • The mechanical properties are tested thanks to an in situ test in the tomograph. • A finite element model is developed to model the mechanical behaviour.« less

Cone Beam Computed Tomographic imaging in orthodontics.

PubMed

Scarfe, W C; Azevedo, B; Toghyani, S; Farman, A G

2017-03-01

Over the last 15 years, cone beam computed tomographic (CBCT) imaging has emerged as an important supplemental radiographic technique for orthodontic diagnosis and treatment planning, especially in situations which require an understanding of the complex anatomic relationships and surrounding structures of the maxillofacial skeleton. CBCT imaging provides unique features and advantages to enhance orthodontic practice over conventional extraoral radiographic imaging. While it is the responsibility of each practitioner to make a decision, in tandem with the patient/family, consensus-derived, evidence-based clinical guidelines are available to assist the clinician in the decision-making process. Specific recommendations provide selection guidance based on variables such as phase of treatment, clinically-assessed treatment difficulty, the presence of dental and/or skeletal modifying conditions, and pathology. CBCT imaging in orthodontics should always be considered wisely as children have conservatively, on average, a three to five times greater radiation risk compared with adults for the same exposure. The purpose of this paper is to provide an understanding of the operation of CBCT equipment as it relates to image quality and dose, highlight the benefits of the technique in orthodontic practice, and provide guidance on appropriate clinical use with respect to radiation dose and relative risk, particularly for the paediatric patient. © 2017 Australian Dental Association.

Correlative multi-scale characterization of a fine grained Nd-Fe-B sintered magnet.

PubMed

Sasaki, T T; Ohkubo, T; Hono, K; Une, Y; Sagawa, M

2013-09-01

The Nd-rich phases in pressless processed fine grained Nd-Fe-B sintered magnets have been characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and three dimensional atom probe tomography (3DAP). The combination of the backscattered electron (BSE) and in-lens secondary electron (IL-SE) images in SEM led to an unambiguous identification of four types of Nd-rich phases, NdOx, Ia3 type phase, which is isostructural to Nd₂O₃, dhcp-Nd and Nd₁Fe₄B₄. In addition, the 3DAP analysis of thin Nd-rich grain boundary layer indicate that the coercivity has a close correlation with the chemistry of the grain boundary phase. Copyright © 2013 Elsevier B.V. All rights reserved.

Single-shot water-immersion microscopy platform for qualitative visualization and quantitative phase imaging of biosamples

NASA Astrophysics Data System (ADS)

Picazo-Bueno, José Ángel; Cojoc, Dan; Torre, Vincent; Micó, Vicente

2017-07-01

We present the combination of a single-shot water-immersion digital holographic microscopy with broadband illumination for simultaneous visualization of coherent and incoherent images using microbeads and different biosamples.

Wave front engineering by means of diffractive optical elements for applications in microscopy

NASA Astrophysics Data System (ADS)

Cojoc, Dan; Ferrari, Enrico; Garbin, Valeria; Cabrini, Stefano; Carpentiero, Alessandro; Prasciolu, Mauro; Businaro, Luca; Kaulich, Burchard; Di Fabrizio, Enzo

2006-05-01

We present a unified view regarding the use of diffractive optical elements (DOEs) for microscopy applications a wide range of electromagnetic spectrum. The unified treatment is realized through the design and fabrication of DOE through which wave front beam shaping is obtained. In particular we show applications ranging from micromanipulation using optical tweezers to X-ray differential interference contrast (DIC) microscopy. We report some details on the design and physical implementation of diffractive elements that beside focusing perform also other optical functions: beam splitting, beam intensity and phase redistribution or mode conversion. Laser beam splitting is used for multiple trapping and independent manipulation of spherical micro beads and for direct trapping and manipulation of biological cells with non-spherical shapes. Another application is the Gauss to Laguerre-Gaussian mode conversion, which allows to trap and transfer orbital angular momentum of light to micro particles with high refractive index and to trap and manipulate low index particles. These experiments are performed in an inverted optical microscope coupled with an infrared laser beam and a spatial light modulator for DOEs implementation. High resolution optics, fabricated by means of e-beam lithography, are demonstrated to control the intensity and the phase of the sheared beams in X-ray DIC microscopy. DIC experiments with phase objects reveal a dramatic increase in image contrast compared to bright-field X-ray microscopy.

Study of the Decomposition and Phase Transition of Uranium Nitride under UHV Conditions via TDS, XRD, SEM, and XPS.

PubMed

Wang, Xiaofang; Long, Zhong; Bin, Ren; Yang, Ruilong; Pan, Qifa; Li, Fangfang; Luo, Lizhu; Hu, Yin; Liu, Kezhao

2016-11-07

Uranium nitrides are among the most promising fuels for Generation IV nuclear reactors, but until now, very little has been known about their thermal stability properties under nonequilibrium conditions. In this work, thermal decomposition of nitrogen-rich uranium nitride (denoted as UN 2-x ) under ultrahigh-vacuum (UHV) conditions was investigated by thermal desorption spectroscopy (TDS). It has been shown that the nitrogen TDS spectrum consists of two peaks at about 723 and 1038 K. The X-ray diffraction, scanning electron microscopy, and X-ray photoelectron microscopy results indicate that UN 2-x (UN 2 phase) decomposed into the α-U 2 N 3 phase in the first step and the α-U 2 N 3 phase decomposed into the UN phase in the second step.

Characterization of Homopolymer and Polymer Blend Films by Phase Sensitive Acoustic Microscopy

NASA Astrophysics Data System (ADS)

Ngwa, Wilfred; Wannemacher, Reinhold; Grill, Wolfgang

2003-03-01

CHARACTERIZATION OF HOMOPOLYMER AND POLYMER BLEND FILMS BY PHASE SENSITIVE ACOUSTIC MICROSCOPY W Ngwa, R Wannemacher, W Grill Institute of Experimental Physics II, University of Leipzig, 04103 Leipzig, Germany Abstract We have used phase sensitive acoustic microscopy (PSAM) to study homopolymer thin films of polystyrene (PS) and poly (methyl methacrylate) (PMMA), as well as PS/PMMA blend films. We show from our results that PSAM can be used as a complementary and highly valuable technique for elucidating the three-dimensional (3D) morphology and micromechanical properties of thin films. Three-dimensional image acquisition with vector contrast provides the basis for: complex V(z) analysis (per image pixel), 3D image processing, height profiling, and subsurface image analysis of the polymer films. Results show good agreement with previous studies. In addition, important new information on the three dimensional structure and properties of polymer films is obtained. Homopolymer film structure analysis reveals (pseudo-) dewetting by retraction of droplets, resulting in a morphology that can serve as a starting point for the analysis of polymer blend thin films. The outcome of confocal laser scanning microscopy studies, performed on the same samples are correlated with the obtained results. Advantages and limitations of PSAM are discussed.

Dark-field optical coherence microscopy

NASA Astrophysics Data System (ADS)

Pache, C.; Villiger, M. L.; Lasser, T.

2010-02-01

Many solutions have been proposed to produce phase quantitative images of biological cell samples. Among these, Spectral Domain Phase Microscopy combines the fast imaging speed and high sensitivity of Optical Coherence Microscopy (OCM) in the Fourier domain with the high phase stability of common-path interferometry. We report on a new illumination scheme for OCM that enhances the sensitivity for backscattered light and detects the weak sample signal, otherwise buried by the signal from specular reflection. With the use of a Bessel-like beam, a dark-field configuration was realized. Sensitivity measurements for three different illumination configurations were performed to compare our method to standard OCM and extended focus OCM. Using a well-defined scattering and reflecting object, we demonstrated an attenuation of -40 dB of the DC-component and a relative gain of 30 dB for scattered light, compared to standard OCM. In a second step, we applied this technique, referred to as dark-field Optical Coherence Microscopy (dfOCM), to living cells. Chinese hamster ovarian cells were applied in a drop of medium on a coverslide. The cells of ~15 μm in diameter and even internal cell structures were visualized in the acquired tomograms.

Emerging optical nanoscopy techniques

PubMed Central

Montgomery, Paul C; Leong-Hoi, Audrey

2015-01-01

To face the challenges of modern health care, new imaging techniques with subcellular resolution or detection over wide fields are required. Far field optical nanoscopy presents many new solutions, providing high resolution or detection at high speed. We present a new classification scheme to help appreciate the growing number of optical nanoscopy techniques. We underline an important distinction between superresolution techniques that provide improved resolving power and nanodetection techniques for characterizing unresolved nanostructures. Some of the emerging techniques within these two categories are highlighted with applications in biophysics and medicine. Recent techniques employing wider angle imaging by digital holography and scattering lens microscopy allow superresolution to be achieved for subcellular and even in vivo, imaging without labeling. Nanodetection techniques are divided into four subcategories using contrast, phase, deconvolution, and nanomarkers. Contrast enhancement is illustrated by means of a polarized light-based technique and with strobed phase-contrast microscopy to reveal nanostructures. Very high sensitivity phase measurement using interference microscopy is shown to provide nanometric surface roughness measurement or to reveal internal nanometric structures. Finally, the use of nanomarkers is illustrated with stochastic fluorescence microscopy for mapping intracellular structures. We also present some of the future perspectives of optical nanoscopy. PMID:26491270

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

Bostroem, P.A.

In order to evaluate the therapeutic effects of metoprolol, nifedipine, and their combination, 11 patients with secondary angina pectoris and with thallium tomographic findings indicating coronary artery disease were studied before and after these three treatment regimes in a single-blind cross-over study. The therapeutic effect was measured by standardized working test and isotope angiocardiography, which enabled evaluation of left ventricular ejection fraction, stroke volume, and phase analysis of left ventricular contraction. Treatment with metoprolol and combination therapy increased work performance. Ejection fraction did not differentiate the treatment regimes, whereas stroke volume was significantly lower at work and heart rate highermore » at rest and at work during nifedipine treatment compared to either metoprolol or combination treatment (p less than 0.05). Cardiac output was significantly reduced during nifedipine and metoprolol treatment during work (p less than 0.05). Phase improved after all therapeutic regimes, but reached significance only during the metoprolol treatment period at rest (p less than 0.05).« less

Hugoniot Measurements at Low Pressures in Tin Using 800 MeV proton Radiography

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

Schwartz, Cynthia; Hogan, Gary E; King, Nicholas S. P.

2009-08-05

A 2cm long 8 mm diameter cylindrical tin target has been shocked to a pressure in the region of the {beta} {yields} {gamma} phase change using a small, low density PETN charge mounted on the opposite side of a stainless steel diaphragm. The density jump and shock velocity were measured radiographically as the shock wave moved through the sample and the pressure dropped, using the proton radiography facility at LANL. This provided a quasi-continuous record of the equations of state along the Hugoniot for the P1 wave from a shock velocity of 3.25 km/sec down to near the sound speed.more » Edge release effects were removed from the data using tomographic techniques. The data show evidence for a phase transition that extends over a broad pressure range. The data and analysis will be presented.« less

Observations and interpretation of fundamental mode Rayleigh wavefields recorded by the Transportable Array (USArray)

USGS Publications Warehouse

Pollitz, F.F.

2008-01-01

Broadband recordings of the dense Transportable Array (TA) in the western United States provide unparalleled detailed images of long-period seismic surface wavefields. With 400 stations spanning most of the western United States, wavefronts of fundamental mode Rayleigh waves may be visualized coherently across the array at periods ???40 s. In order to constrain the Rayleigh wave phase velocity structure in the western United States, I assemble a data set of vertical component seismograms from 53 teleseismic events recorded by the TA from April 2006 to October 2007. Complex amplitude spectra from these recordings at peni ods 27-100 s are interpreted using the multiplane wave tomographic method of Friederich and Wielandt (1995) and Pollitz (1999). This analysis yields detailed surface wave phase velocity and three-dimensional shear wave velocity patterns across the North American plate boundary zone, elucidating the active processes in the highly heterogeneous western U.S. upper mantle.

High-resolution corneal topography and tomography of fish eye using wide-field white light interference microscopy

NASA Astrophysics Data System (ADS)

Srivastava, Vishal; Nandy, Sreyankar; Singh Mehta, Dalip

2013-04-01

Topography and tomography of fish cornea is reconstructed using high resolution white light interference microscopy. White light interferograms at different depths were recorded by moving the object axially. For each depth position, five phase shifted interferograms were recorded and analyzed. From the reconstructed phase maps, the corneal topography and hence the refractive index was determined and from amplitude images the cross-sectional image of fish cornea was reconstructed. In the present method, we utilize a nearly common-path interference microscope and wide field illumination and hence do not require any mechanical B-scan. Therefore, the phase stability of the recorded data is improved.

Quantum tomography of a molecular bond in ice.

PubMed

Goldschleger, I U; Golschleger, I U; van Staveren, M N; Apkarian, V Ara

2013-07-21

We present the moving picture of a molecular bond, in phase-space, in real-time, at resolution limited by quantum uncertainty. The images are tomographically reconstructed Wigner distribution functions (WDF) obtained from four-wave mixing measurements on Br2-doped ice. The WDF completely characterizes the dissipative quantum evolution of the system, which despite coupling to the environment retains quantum coherence, as evidenced by its persistent negative Wigner hole. The spectral decomposition of the WDF allows a direct visualization of wavefunctions and spatiotemporal coherences of the system and the system-bath interaction. The measurements vividly illustrate nonclassical wave mechanics in a many-body system, in ordinary condensed matter.

Downstream Fabry-Perot interferometer for acoustic wave monitoring in photoacoustic tomography.

PubMed

Nuster, Robert; Gruen, Hubert; Reitinger, Bernhard; Burgholzer, Peter; Gratt, Sibylle; Passler, Klaus; Paltauf, Guenther

2011-03-15

An optical detection setup consisting of a focused laser beam fed into a downstream Fabry-Perot interferometer (FPI) for demodulation of acoustically generated optical phase variations is investigated for its applicability in photoacoustic tomography. The device measures the time derivative of acoustic signals integrated along the beam. Compared to a setup where the detection beam is part of a Mach-Zehnder interferometer, the signal-to-noise ratio of the FPI is lower, but the image quality of the two devices is similar. Using the FPI in a photoacoustic tomograph allows scanning the probe beam around the imaging object without moving the latter.

FPGA-based real time processing of the Plenoptic Wavefront Sensor

NASA Astrophysics Data System (ADS)

Rodríguez-Ramos, L. F.; Marín, Y.; Díaz, J. J.; Piqueras, J.; García-Jiménez, J.; Rodríguez-Ramos, J. M.

The plenoptic wavefront sensor combines measurements at pupil and image planes in order to obtain simultaneously wavefront information from different points of view, being capable to sample the volume above the telescope to extract the tomographic information of the atmospheric turbulence. The advantages of this sensor are presented elsewhere at this conference (José M. Rodríguez-Ramos et al). This paper will concentrate in the processing required for pupil plane phase recovery, and its computation in real time using FPGAs (Field Programmable Gate Arrays). This technology eases the implementation of massive parallel processing and allows tailoring the system to the requirements, maintaining flexibility, speed and cost figures.

Evaluating tooth restorations: micro-computed tomography in practical training for students in dentistry

NASA Astrophysics Data System (ADS)

Deyhle, Hans; Schmidli, Fredy; Krastl, Gabriel; Müller, Bert

2010-09-01

Direct composite fillings belong to widespread tooth restoration techniques in dental medicine. The procedure consists of successive steps, which include etching of the prepared tooth surface, bonding and placement of composite in incrementally built up layers. Durability and lifespan of the composite inlays strongly depend on the accurate completion of the individual steps to be also realized by students in dental medicine. Improper handling or nonconformity in the bonding procedure often lead to air enclosures (bubbles) as well as to significant gaps between the composite layers or at the margins of the restoration. Traditionally one analyzes the quality of the restoration cutting the tooth in an arbitrarily selected plane and inspecting this plane by conventional optical microscopy. Although the precision of this established method is satisfactory, it is restricted to the selected two-dimensional plane. Rather simple micro computed tomography (μCT) systems, such as SkyScan 1174™, allows for the non-destructive three-dimensional imaging of restored teeth ex vivo and virtually cutting the tomographic data in any desired direction, offering a powerful tool for inspection of the restored tooth with micrometer resolution before cutting and thus also to select a two-dimensional plane with potential defects. In order to study the influence of the individual steps on the resulted tooth restoration, direct composite fillings were placed in mod cavities of extracted teeth. After etching, an adhesive was applied in half of the specimens. From the tomographic datasets, it becomes clear that gaps occur more frequently when bonding is omitted. The visualization of air enclosures offers to determine the probability to find a micrometer-sized defect using an arbitrarily selected cutting plane for inspection.

Post-processing methods of rendering and visualizing 3-D reconstructed tomographic images

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

Wong, S.T.C.

The purpose of this presentation is to discuss the computer processing techniques of tomographic images, after they have been generated by imaging scanners, for volume visualization. Volume visualization is concerned with the representation, manipulation, and rendering of volumetric data. Since the first digital images were produced from computed tomography (CT) scanners in the mid 1970s, applications of visualization in medicine have expanded dramatically. Today, three-dimensional (3D) medical visualization has expanded from using CT data, the first inherently digital source of 3D medical data, to using data from various medical imaging modalities, including magnetic resonance scanners, positron emission scanners, digital ultrasound,more » electronic and confocal microscopy, and other medical imaging modalities. We have advanced from rendering anatomy to aid diagnosis and visualize complex anatomic structures to planning and assisting surgery and radiation treatment. New, more accurate and cost-effective procedures for clinical services and biomedical research have become possible by integrating computer graphics technology with medical images. This trend is particularly noticeable in current market-driven health care environment. For example, interventional imaging, image-guided surgery, and stereotactic and visualization techniques are now stemming into surgical practice. In this presentation, we discuss only computer-display-based approaches of volumetric medical visualization. That is, we assume that the display device available is two-dimensional (2D) in nature and all analysis of multidimensional image data is to be carried out via the 2D screen of the device. There are technologies such as holography and virtual reality that do provide a {open_quotes}true 3D screen{close_quotes}. To confine the scope, this presentation will not discuss such approaches.« less

Shaping ability of the conventional nickel-titanium and reciprocating nickel-titanium file systems: a comparative study using micro-computed tomography.

PubMed

Hwang, Young-Hye; Bae, Kwang-Shik; Baek, Seung-Ho; Kum, Kee-Yeon; Lee, WooCheol; Shon, Won-Jun; Chang, Seok Woo

2014-08-01

This study used micro-computed tomographic imaging to compare the shaping ability of Mtwo (VDW, Munich, Germany), a conventional nickel-titanium file system, and Reciproc (VDW), a reciprocating file system morphologically similar to Mtwo. Root canal shaping was performed on the mesiobuccal and distobuccal canals of extracted maxillary molars. In the RR group (n = 15), Reciproc was used in a reciprocating motion (150° counterclockwise/30° clockwise, 300 rpm); in the MR group, Mtwo was used in a reciprocating motion (150° clockwise/30° counterclockwise, 300 rpm); and in the MC group, Mtwo was used in a continuous rotating motion (300 rpm). Micro-computed tomographic images taken before and after canal shaping were used to analyze canal volume change and the degree of transportation at the cervical, middle, and apical levels. The time required for canal shaping was recorded. Afterward, each file was analyzed using scanning electron microscopy. No statistically significant differences were found among the 3 groups in the time for canal shaping or canal volume change (P > .05). Transportation values of the RR and MR groups were not significantly different at any level. However, the transportation value of the MC group was significantly higher than both the RR and MR groups at the cervical and apical levels (P < .05). In the scanning electron microscopic analysis, file deformation was observed for 1 file in group RR (1/15), 3 files in group MR (3/15), and 5 files in group MC (5/15). In terms of shaping ability, Mtwo used in a reciprocating motion was not significantly different from the Reciproc system. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Understanding External Cervical Resorption in Vital Teeth.

PubMed

Mavridou, Athina M; Hauben, Esther; Wevers, Martine; Schepers, Evert; Bergmans, Lars; Lambrechts, Paul

2016-12-01

The aim of this study was to investigate the 3-dimensional (3D) structure and the cellular and tissue characteristics of external cervical resorption (ECR) in vital teeth and to understand the phenomenon of ECR by combining histomorphological and radiographic findings. Twenty-seven cases of vital permanent teeth displaying ECR were investigated. ECR diagnosis was based on clinical and radiographic examination with cone-beam computed tomographic imaging. The extracted teeth were further analyzed by using nanofocus computed tomographic imaging, hard tissue histology, and scanning electron microscopy. All examined teeth showed some common characteristics. Based on the clinical and experimental findings, a 3-stage mechanism of ECR was proposed. At the first stage (ie, the initiation stage), ECR was initiated at the cementum below the gingival epithelial attachment. At the second stage (ie, the resorption stage), the resorption invaded the tooth structure 3-dimensionally toward the pulp space. However, it did not penetrate the pulp space because of the presence of a pericanalar resorption-resistant sheet. This layer was observed to consist of predentin, dentin, and occasionally reparative mineralized (bonelike) tissue, having a fluctuating thickness averaging 210 μm. At the last advanced stage (ie, the repair stage), repair took place by an ingrowth and apposition of bonelike tissue into the resorption cavity. During the reparative stage, repair and remodeling phenomena evolve simultaneously, whereas both resorption and reparative stages progress in parallel at different areas of the tooth. ECR is a dynamic and complex condition that involves periodontal and endodontic tissues. Using clinical, histologic, radiographic, and scanning microscopic analysis, a better understanding of the evolution of ECR is possible. Based on the experimental findings, a 3-stage mechanism for the initiation and growth of ECR is proposed. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Quantitative phase microscopy via optimized inversion of the phase optical transfer function.

PubMed

Jenkins, Micah H; Gaylord, Thomas K

2015-10-01

Although the field of quantitative phase imaging (QPI) has wide-ranging biomedical applicability, many QPI methods are not well-suited for such applications due to their reliance on coherent illumination and specialized hardware. By contrast, methods utilizing partially coherent illumination have the potential to promote the widespread adoption of QPI due to their compatibility with microscopy, which is ubiquitous in the biomedical community. Described herein is a new defocus-based reconstruction method that utilizes a small number of efficiently sampled micrographs to optimally invert the partially coherent phase optical transfer function under assumptions of weak absorption and slowly varying phase. Simulation results are provided that compare the performance of this method with similar algorithms and demonstrate compatibility with large phase objects. The accuracy of the method is validated experimentally using a microlens array as a test phase object. Lastly, time-lapse images of live adherent cells are obtained with an off-the-shelf microscope, thus demonstrating the new method's potential for extending QPI capability widely in the biomedical community.

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

Buck, E.C.; Dietz, N.L.; Bates, J.K.

Uranium contaminated soils from the Fernald Operation Site, Ohio, have been examined by a combination of optical microscopy, scanning electron microscopy with backscattered electron detection (SEM/BSE), and analytical electron microscopy (AEM). A method is described for preparing of transmission electron microscopy (TEM) thin sections by ultramicrotomy. By using these thin sections, SEM and TEM images can be compared directly. Uranium was found in iron oxides, silicates (soddyite), phosphates (autunites), and fluorite. Little uranium was associated with clays. The distribution of uranium phases was found to be inhomogeneous at the microscopic level.

TOmographic Remote Observer of Ionospheric Disturbances

DTIC Science & Technology

2007-11-15

ionosphere . The proposed spacecraft was an evolutionary design from the USUSat, Combat Sentinel, and USUSat II programs whose histories are shown in...Figure 1. The primary science instrument, TOROID for TOmographic Remote Observer of Ionospheric Disturbances, is a photometer for measuring the

Acoustic representation of tomographic data

NASA Astrophysics Data System (ADS)

Wampler, Cheryl; Zahrt, John D.; Hotchkiss, Robert S.; Zahrt, Rebecca; Kust, Mark

1993-04-01

Tomographic data and tomographic reconstructions are naturally periodic in the angle of rotation of the turntable and the polar angel of the coordinates in the object, respectively. Similarly, acoustic waves are periodic and have amplitude and wavelength as free parameters that can be fit to another representation. Work has been in progress for some time in bringing the acoustic senses to bear on large data sets rather than just the visual sense. We will provide several different acoustic representations of both raw data and density maps. Rather than graphical portrayal of the data and reconstructions, you will be presented various 'tone poems.'

Optical tomograph optimized for tumor detection inside highly absorbent organs

NASA Astrophysics Data System (ADS)

Boutet, Jérôme; Koenig, Anne; Hervé, Lionel; Berger, Michel; Dinten, Jean-Marc; Josserand, Véronique; Coll, Jean-Luc

2011-05-01

This paper presents a tomograph for small animal fluorescence imaging. The compact and cost-effective system described in this article was designed to address the problem of tumor detection inside highly absorbent heterogeneous organs, such as lungs. To validate the tomograph's ability to detect cancerous nodules inside lungs, in vivo tumor growth was studied on seven cancerous mice bearing murine mammary tumors marked with Alexa Fluor 700. They were successively imaged 10, 12, and 14 days after the primary tumor implantation. The fluorescence maps were compared over this time period. As expected, the reconstructed fluorescence increases with the tumor growth stage.

Lamb wave tomographic imaging system for aircraft structural health assessment

NASA Astrophysics Data System (ADS)

Schwarz, Willi G.; Read, Michael E.; Kremer, Matthew J.; Hinders, Mark K.; Smith, Barry T.

1999-01-01

A tomographic imaging system using ultrasonic Lamb waves for the nondestructive inspection of aircraft components such as wings and fuselage is being developed. The computer-based system provides large-area inspection capability by electronically scanning an array of transducers that can be easily attached to flat and curved surface without moving parts. Images of the inspected area are produced in near real time employing a tomographic reconstruction method adapted from seismological applications. Changes in material properties caused by structural flaws such as disbonds, corrosion, and fatigue cracks can be effectively detected and characterized utilizing this fast NDE technique.

Multiphase contrast medium injection for optimization of computed tomographic coronary angiography.

PubMed

Budoff, Matthew Jay; Shinbane, Jerold S; Child, Janis; Carson, Sivi; Chau, Alex; Liu, Stephen H; Mao, SongShou

2006-02-01

Electron beam angiography is a minimally invasive imaging technique. Adequate vascular opacification throughout the study remains a critical issue for image quality. We hypothesized that vascular image opacification and uniformity of vascular enhancement between slices can be improved using multiphase contrast medium injection protocols. We enrolled 244 consecutive patients who were randomized to three different injection protocols: single-phase contrast medium injection (Group 1), dual-phase contrast medium injection with each phase at a different injection rate (Group 2), and a three-phase injection with two phases of contrast medium injection followed by a saline injection phase (Group 3). Parameters measured were aortic opacification based on Hounsfield units and uniformity of aortic enhancement at predetermined slices (locations from top [level 1] to base [level 60]). In Group 1, contrast opacification differed across seven predetermined locations (scan levels: 1st versus 60th, P < .05), demonstrating significant nonuniformity. In Group 2, there was more uniform vascular enhancement, with no significant differences between the first 50 slices (P > .05). In Group 3, there was greater uniformity of vascular enhancement and higher mean Hounsfield units value across all 60 images, from the aortic root to the base of the heart (P < .05). The three-phase injection protocol improved vascular opacification at the base of the heart, as well as uniformity of arterial enhancement throughout the study.

Technical Note: Synchrotron-based high-energy x-ray phase sensitive microtomography for biomedical research

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

Liu, Huiqiang; Wu, Xizeng, E-mail: xwu@uabmc.edu, E-mail: tqxiao@sinap.ac.cn; Xiao, Tiqiao, E-mail: xwu@uabmc.edu, E-mail: tqxiao@sinap.ac.cn

Purpose: Propagation-based phase-contrast CT (PPCT) utilizes highly sensitive phase-contrast technology applied to x-ray microtomography. Performing phase retrieval on the acquired angular projections can enhance image contrast and enable quantitative imaging. In this work, the authors demonstrate the validity and advantages of a novel technique for high-resolution PPCT by using the generalized phase-attenuation duality (PAD) method of phase retrieval. Methods: A high-resolution angular projection data set of a fish head specimen was acquired with a monochromatic 60-keV x-ray beam. In one approach, the projection data were directly used for tomographic reconstruction. In two other approaches, the projection data were preprocessed bymore » phase retrieval based on either the linearized PAD method or the generalized PAD method. The reconstructed images from all three approaches were then compared in terms of tissue contrast-to-noise ratio and spatial resolution. Results: The authors’ experimental results demonstrated the validity of the PPCT technique based on the generalized PAD-based method. In addition, the results show that the authors’ technique is superior to the direct PPCT technique as well as the linearized PAD-based PPCT technique in terms of their relative capabilities for tissue discrimination and characterization. Conclusions: This novel PPCT technique demonstrates great potential for biomedical imaging, especially for applications that require high spatial resolution and limited radiation exposure.« less

Phase decomposition of γ-U (bcc) in U-10 wt% Mo fuel alloy during hot isostatic pressing of monolithic fuel plate

NASA Astrophysics Data System (ADS)

Park, Y.; Eriksson, N.; Newell, R.; Keiser, D. D.; Sohn, Y. H.

2016-11-01

Eutectoid decomposition of γ-phase (cI2) into α-phase (oC4) and γ‧-phase (tI6) during the hot isostatic pressing (HIP) of the U-10 wt% Mo (U10Mo) alloy was investigated using monolithic fuel plate samples consisting of U10Mo fuel alloy, Zr diffusion barrier and AA6061 cladding. The decomposition of the γ-phase was observed because the HIP process is carried out near the eutectoid temperature, 555 °C. Initially, a cellular structure, consisting of γ‧-phase surrounded by α-phase, developed from the destabilization of the γ-phase. The cellular structure further developed into an alternating lamellar structure of α- and γ‧-phases. Using scanning electron microscopy and transmission electron microscopy, qualitative and quantitative microstructural analyses were carried out to identify the phase constituents, and elucidate the microstructural development based on time-temperature-transformation diagram of the U10Mo alloy. The destabilization of γ -phase into α- and γ‧-phases would be minimized when HIP process was carried out with rapid ramping/cooling rate and dwell temperature higher than 560 °C.

Low cost label-free live cell imaging for biological samples

NASA Astrophysics Data System (ADS)

Seniya, C.; Towers, C. E.; Towers, D. P.

2017-02-01

This paper reports the progress to develop a practical phase measuring microscope offering new capabilities in terms of phase measurement accuracy and quantification of cell:cell interactions over the longer term. A novel, low cost phase interference microscope for imaging live cells (label-free) is described. The method combines the Zernike phase contrast approach with a dual mirror design to enable phase modulation between the scattered and un-scattered optical fields. Two designs are proposed and demonstrated, one of which retains the common path nature of Zernike's original microscopy concept. In both setups the phase shift is simple to control via a piezoelectric driven mirror in the back focal plane of the imaging system. The approach is significantly cheaper to implement than those based on spatial light modulators (SLM) at approximately 20% of the cost. A quantitative assessment of the performance of a set of phase shifting algorithms is also presented, specifically with regard to broad bandwidth illumination in phase contrast microscopy. The simulation results show that the phase measurement accuracy is strongly dependent on the algorithm selected and the optical path difference in the sample.

Thermal stability of intermetallic phases in Fe-rich Fe-Cr-Ni-Mo alloys

DOE PAGES

Yang, Ying; Tan, Lizhen; Busby, Jeremy T.

2015-06-12

Understanding the stability of precipitate phases in the Fe-rich Fe-Cr-Ni-Mo alloys is critical to the alloy design and application of Mo-containing Austenitic steels. Coupled with thermodynamic modeling, stability of the chi and Laves phases in two Fe-Cr-Ni-Mo alloys were investigated at 1000, 850 and 700 °C for different annealing time. The morphologies, compositions and crystal structures of the matrix and precipitate phases were carefully examined by Scanning Electron Microscopy, Electron Probe Microanalysis, X-ray diffraction and Transmission Electron Microscopy. The two key findings resulted from this work. One is that the chi phase is stable at high temperature and transformed intomore » the Laves phase at low temperature. The other is that both the chi and Laves phases have large solubilites of Cr, Mo and Ni, among which the Mo solubility has a major role on the relative stability of the precipitate phases. The developed thermodynamic models were then applied to evaluating the Mo effect on the stability of precipitate phases in AISI 316 and NF709 alloys.« less

Microscopy of biological sample through advanced diffractive optics from visible to X-ray wavelength regime.

PubMed

Di Fabrizio, Enzo; Cojoc, Dan; Emiliani, Valentina; Cabrini, Stefano; Coppey-Moisan, Maite; Ferrari, Enrico; Garbin, Valeria; Altissimo, Matteo

2004-11-01

The aim of this report is to demonstrate a unified version of microscopy through the use of advanced diffractive optics. The unified scheme derives from the technical possibility of realizing front wave engineering in a wide range of electromagnetic spectrum. The unified treatment is realized through the design and nanofabrication of phase diffractive elements (PDE) through which wave front beam shaping is obtained. In particular, we will show applications, by using biological samples, ranging from micromanipulation using optical tweezers to X-ray differential interference contrast (DIC) microscopy combined with X-ray fluorescence. We report some details on the design and physical implementation of diffractive elements that besides focusing also perform other optical functions: beam splitting, beam intensity, and phase redistribution or mode conversion. Laser beam splitting is used for multiple trapping and independent manipulation of micro-beads surrounding a cell as an array of tweezers and for arraying and sorting microscopic size biological samples. Another application is the Gauss to Laguerre-Gauss mode conversion, which allows for trapping and transfering orbital angular momentum of light to micro-particles immersed in a fluid. These experiments are performed in an inverted optical microscope coupled with an infrared laser beam and a spatial light modulator for diffractive optics implementation. High-resolution optics, fabricated by means of e-beam lithography, are demonstrated to control the intensity and the phase of the sheared beams in x-ray DIC microscopy. DIC experiments with phase objects reveal a dramatic increase in image contrast compared to bright-field x-ray microscopy. Besides the topographic information, fluorescence allows detection of certain chemical elements (Cl, P, Sc, K) in the same setup, by changing the photon energy of the x-ray beam. (c) 2005 Wiley-Liss, Inc.

Phase control of austenitic chrome-nickel steel

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

Korkh, M. K., E-mail: KorkhMK@imp.uran.ru; Davidov, D. I., E-mail: davidov@imp.uran.ru; Korkh, J. V., E-mail: Korkh@imp.uran.ru

2015-10-27

The paper presents the results of the comparative study of the possibilities of different structural and magnetic methods for detection and visualization of the strain-induced martensitic phase in low carbon austenitic chromium-nickel steel. Results of TEM, SEM, optical microscopy, atomic and magnetic force microscopy, and magnetic measurements are presented. Amount of the magnetic strain-induced martensite was estimated. We pioneered magnetic force microscopic images of the single domain cluster distribution of the strain-induced martensite in austenite-ferrite materials.

Simultaneous off-axis multiplexed holography and regular fluorescence microscopy of biological cells.

PubMed

Nygate, Yoav N; Singh, Gyanendra; Barnea, Itay; Shaked, Natan T

2018-06-01

We present a new technique for obtaining simultaneous multimodal quantitative phase and fluorescence microscopy of biological cells, providing both quantitative phase imaging and molecular specificity using a single camera. Our system is based on an interferometric multiplexing module, externally positioned at the exit of an optical microscope. In contrast to previous approaches, the presented technique allows conventional fluorescence imaging, rather than interferometric off-axis fluorescence imaging. We demonstrate the presented technique for imaging fluorescent beads and live biological cells.

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

Jana, S.; Devaraj, A.; Kovarik, L.

Transformation kinetics of metastable body-centered cubic γ-UMo phase in U-10 wt.percent Mo alloy during annealing at sub-eutectoid temperatures of 500C and 400C has been determined as a function of time using detailed microstructural characterization by scanning electron microscopy, X-ray diffraction analysis, scanning transmission electron microscopy, and atom probe tomography. Based on the results, we found that the phase transformation is initiated by cellular transformation at both the temperatures, which results in formation of a lamellar microstructure along prior γ-UMo grain boundaries.

Intracellular subsurface imaging using a hybrid shear-force feedback/scanning quantitative phase microscopy technique

NASA Astrophysics Data System (ADS)

Edward, Kert

Quantitative phase microscopy (QPM) allows for the imaging of translucent or transparent biological specimens without the need for exogenous contrast agents. This technique is usually applied towards the investigation of simple cells such as red blood cells which are typically enucleated and can be considered to be homogenous. However, most biological cells are nucleated and contain other interesting intracellular organelles. It has been established that the physical characteristics of certain subsurface structures such as the shape and roughness of the nucleus is well correlated with onset and progress of pathological conditions such as cancer. Although the acquired quantitative phase information of biological cells contains surface information as well as coupled subsurface information, the latter has been ignored up until now. A novel scanning quantitative phase imaging system unencumbered by 2pi ambiguities is hereby presented. This system is incorporated into a shear-force feedback scheme which allows for simultaneous phase and topography determination. It will be shown how subsequent image processing of these two data sets allows for the extraction of the subsurface component in the phase data and in vivo cell refractometry studies. Both fabricated samples and biological cells ranging from rat fibroblast cells to malaria infected human erythrocytes were investigated as part of this research. The results correlate quite well with that obtained via other microscopy techniques.

Phase contrast imaging with coherent high energy X-rays

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

Snigireva, I.

X-ray imaging concern high energy domain (>6 keV) like a contact radiography, projection microscopy and tomography is used for many years to discern the features of the internal structure non destructively in material science, medicine and biology. In so doing the main contrast formation is absorption that makes some limitations for imaging of the light density materials and what is more the resolution of these techniques is not better than 10-100 {mu}m. It was turned out that there is now way in which to overcome 1{mu}m or even sub-{mu}m resolution limit except phase contrast imaging. It is well known inmore » optics that the phase contrast is realised when interference between reference wave front and transmitted through the sample take place. Examples of this imaging are: phase contrast microscopy suggested by Zernike and Gabor (in-line) holography. Both of this techniques: phase contrast x-ray microscopy and holography are successfully progressing now in soft x-ray region. For imaging in the hard X-rays to enhance the contrast and to be able to resolve phase variations across the beam the high degree of the time and more importantly spatial coherence is needed. Because of this it was reasonable that the perfect crystal optics was involved like Bonse-Hart interferometry, double-crystal and even triple-crystal set-up using Laue and Bragg geometry with asymmetrically cut crystals.« less

Water-induced phase separation of miconazole-poly (vinylpyrrolidone-co-vinyl acetate) amorphous solid dispersions: Insights with confocal fluorescence microscopy.

PubMed

Saboo, Sugandha; Taylor, Lynne S

2017-08-30

The aim of this study was to evaluate the utility of confocal fluorescence microscopy (CFM) to study the water-induced phase separation of miconazole-poly (vinylpyrrolidone-co-vinyl acetate) (mico-PVPVA) amorphous solid dispersions (ASDs), induced during preparation, upon storage at high relative humidity (RH) and during dissolution. Different fluorescent dyes were added to drug-polymer films and the location of the dyes was evaluated using CFM. Orthogonal techniques, in particular atomic force microscopy (AFM) coupled with nanoscale infrared spectroscopy (AFM-nanoIR), were used to provide additional analysis of the drug-polymer blends. The initial miscibility of mico-PVPVA ASDs prepared under low humidity conditions was confirmed by AFM-nanoIR. CFM enabled rapid identification of drug-rich and polymer-rich phases in phase separated films prepared under high humidity conditions. The identity of drug- and polymer-rich domains was confirmed using AFM-nanoIR imaging and localized IR spectroscopy, together with Lorentz contact resonance (LCR) measurements. The CFM technique was then utilized successfully to further investigate phase separation in mico-PVPVA films exposed to high RH storage and to visualize phase separation dynamics following film immersion in buffer. CFM is thus a promising new approach to study the phase behavior of ASDs, utilizing drug and polymer specific dyes to visualize the evolution of heterogeneity in films exposed to water. Copyright © 2017 Elsevier B.V. All rights reserved.

Holographic microscopy studies of emulsions

NASA Technical Reports Server (NTRS)

Witherow, W. K.

1981-01-01

A holographic microscopy system that records and observes the dynamic properties of separation of dispersed immiscible fluids is described. The holographic construction system and reconstruction system that were used to obtain particle size and distribution information from the holograms are discussed. The holographic microscopy system is used to observed the phase separating processes in immiscible fluids that were isothermally cooled into the two phase region. Nucleation, growth rates, coalescence, and particle motion are successfully demonstrated with this system. Thus a holographic particle sizing system with a resolution of 2 micrometers and a field of view of 100 cu cm was developed that provides the capability of testing the theories of separating immiscible fluids for particle number densities in the range of 10 to 10 to the 7th power particles.

Speckle-field digital holographic microscopy.

PubMed

Park, YongKeun; Choi, Wonshik; Yaqoob, Zahid; Dasari, Ramachandra; Badizadegan, Kamran; Feld, Michael S

2009-07-20

The use of coherent light in conventional holographic phase microscopy (HPM) poses three major drawbacks: poor spatial resolution, weak depth sectioning, and fixed pattern noise due to unwanted diffraction. Here, we report a technique which can overcome these drawbacks, but maintains the advantage of phase microscopy - high contrast live cell imaging and 3D imaging. A speckle beam of a complex spatial pattern is used for illumination to reduce fixed pattern noise and to improve optical sectioning capability. By recording of the electric field of speckle, we demonstrate high contrast 3D live cell imaging without the need for axial scanning - neither objective lens nor sample stage. This technique has great potential in studying biological samples with improved sensitivity, resolution and optical sectioning capability.

Tomographic Image Compression Using Multidimensional Transforms.

ERIC Educational Resources Information Center

Villasenor, John D.

1994-01-01

Describes a method for compressing tomographic images obtained using Positron Emission Tomography (PET) and Magnetic Resonance (MR) by applying transform compression using all available dimensions. This takes maximum advantage of redundancy of the data, allowing significant increases in compression efficiency and performance. (13 references) (KRN)

Glandulocalyx upatoiensis, a fossil flower of Ericales (Actinidiaceae/Clethraceae) from the Late Cretaceous (Santonian) of Georgia, USA

PubMed Central

Schönenberger, Jürg; von Balthazar, Maria; Takahashi, Masamichi; Xiao, Xianghui; Crane, Peter R.; Herendeen, Patrick S.

2012-01-01

Background and Aims Ericales are a major group of extant asterid angiosperms that are well represented in the Late Cretaceous fossil record, mainly by flowers, fruits and seeds. Exceptionally well preserved fossil flowers, here described as Glandulocalyx upatoiensis gen. & sp. nov., from the Santonian of Georgia, USA, yield new detailed evidence of floral structure in one of these early members of Ericales and provide a secure basis for comparison with extant taxa. Methods The floral structure of several fossil specimens was studied by scanning electron microscopy (SEM), light microscopy of microtome thin sections and synchrotron-radiation X-ray tomographic microscopy (SRXTM). For direct comparisons with flowers of extant Ericales, selected floral features of Actinidiaceae and Clethraceae were studied with SEM. Key Results Flowers of G. upatoiensis have five sepals with quincuncial aestivation, five free petals with quincuncial aestivation, 20–28 stamens arranged in a single series, extrorse anther orientation in the bud, ventral anther attachment and a tricarpellate, syncarpous ovary with three free styles and numerous small ovules on axile, protruding-diffuse and pendant placentae. The calyx is characterized by a conspicuous indumentum of large, densely arranged, multicellular and possibly glandular trichomes. Conclusions Comparison with extant taxa provides clear evidence for a relationship with core Ericales comprised of the extant families Actinidiaceae, Roridulaceae, Sarraceniaceae, Clethraceae, Cyrillaceae and Ericaceae. Within this group, the most marked similarities are with extant Actinidiaceae and, to a lesser degree, with Clethraceae. More detailed analyses of the relationships of Glandulocalyx and other Ericales from the Late Cretaceous will require an improved understanding of the morphological features that diagnose particular extant groups defined on the basis of molecular data. PMID:22442339

From 2D slices to 3D volumes: image based reconstruction and morphological characterization of hippocampal cells on charged and uncharged surfaces using FIB/SEM serial sectioning.

PubMed

Schmidt, Franziska; Kühbacher, Markus; Gross, Ulrich; Kyriakopoulos, Antonius; Schubert, Helmut; Zehbe, Rolf

2011-03-01

3D imaging at a subcellular resolution is a powerful tool in the life sciences to investigate cells and their interactions with native tissues or artificial objects. While a tomographic experimental setup achieving a sufficient structural resolution can be established with either X-rays or electrons, the use of electrons is usually limited to very thin samples in transmission electron microscopy due to the poor penetration depths of electrons. The combination of a serial sectioning approach and scanning electron microscopy in state of the art dual beam experimental setups therefore offers a means to image highly resolved spatial details using a focused ion beam for slicing and an electron beam for imaging. The advantage of this technique over X-ray μCT or X-ray microscopy attributes to the fact that absorption is not a limiting factor in imaging and therefore even strong absorbing structures can be spatially reconstructed with a much higher possible resolution. This approach was used in this study to elucidate the effect of an electric potential on the morphology of cells from a hippocampal cell line (HT22) deposited on gold microelectrodes. While cells cultivated on two different controls (gold and polymer substrates) did show the expected stretched morphology, cells on both the anode and the cathode differed significantly. Cells deposited on the anode part of the electrode exhibited the most extreme deviation, being almost spherical and showed signs of chromatin condensation possibly indicating cell death. Furthermore, EDX was used as supplemental methodology for combined chemical and structural analyses. Copyright © 2010 Elsevier B.V. All rights reserved.

Invited Review Article: Methods for imaging weak-phase objects in electron microscopy

PubMed Central

Glaeser, Robert M.

2013-01-01

Contrast has traditionally been produced in electron-microscopy of weak phase objects by simply defocusing the objective lens. There now is renewed interest, however, in using devices that apply a uniform quarter-wave phase shift to the scattered electrons relative to the unscattered beam, or that generate in-focus image contrast in some other way. Renewed activity in making an electron-optical equivalent of the familiar “phase-contrast” light microscope is based in part on the improved possibilities that are now available for device microfabrication. There is also a better understanding that it is important to take full advantage of contrast that can be had at low spatial frequency when imaging large, macromolecular objects. In addition, a number of conceptually new phase-plate designs have been proposed, thus increasing the number of options that are available for development. The advantages, disadvantages, and current status of each of these options is now compared and contrasted. Experimental results that are, indeed, superior to what can be accomplished with defocus-based phase contrast have been obtained recently with two different designs of phase-contrast aperture. Nevertheless, extensive work also has shown that fabrication of such devices is inconsistent, and that their working lifetime is short. The main limitation, in fact, appears to be electrostatic charging of any device that is placed into the electron diffraction pattern. The challenge in fabricating phase plates that are practical to use for routine work in electron microscopy thus may be more in the area of materials science than in the area of electron optics. PMID:24289381

Trimodal low-dose X-ray tomography

PubMed Central

Zanette, I.; Bech, M.; Rack, A.; Le Duc, G.; Tafforeau, P.; David, C.; Mohr, J.; Pfeiffer, F.; Weitkamp, T.

2012-01-01

X-ray grating interferometry is a coherent imaging technique that bears tremendous potential for three-dimensional tomographic imaging of soft biological tissue and other specimens whose details exhibit very weak absorption contrast. It is intrinsically trimodal, delivering phase contrast, absorption contrast, and scattering (“dark-field”) contrast. Recently reported acquisition strategies for grating-interferometric phase tomography constitute a major improvement of dose efficiency and speed. In particular, some of these techniques eliminate the need for scanning of one of the gratings (“phase stepping”). This advantage, however, comes at the cost of other limitations. These can be a loss in spatial resolution, or the inability to fully separate the three imaging modalities. In the present paper we report a data acquisition and processing method that optimizes dose efficiency but does not share the main limitations of other recently reported methods. Although our method still relies on phase stepping, it effectively uses only down to a single detector frame per projection angle and yields images corresponding to all three contrast modalities. In particular, this means that dark-field imaging remains accessible. The method is also compliant with data acquisition over an angular range of only 180° and with a continuous rotation of the specimen. PMID:22699500

Four-dimensional ultrafast electron microscopy of phase transitions

PubMed Central

Grinolds, Michael S.; Lobastov, Vladimir A.; Weissenrieder, Jonas; Zewail, Ahmed H.

2006-01-01

Reported here is direct imaging (and diffraction) by using 4D ultrafast electron microscopy (UEM) with combined spatial and temporal resolutions. In the first phase of UEM, it was possible to obtain snapshot images by using timed, single-electron packets; each packet is free of space–charge effects. Here, we demonstrate the ability to obtain sequences of snapshots (“movies”) with atomic-scale spatial resolution and ultrashort temporal resolution. Specifically, it is shown that ultrafast metal–insulator phase transitions can be studied with these achieved spatial and temporal resolutions. The diffraction (atomic scale) and images (nanometer scale) we obtained manifest the structural phase transition with its characteristic hysteresis, and the time scale involved (100 fs) is now studied by directly monitoring coordinates of the atoms themselves. PMID:17130445

Fixture-abutment connection surface and micro-gap measurements by 3D micro-tomographic technique analysis.

PubMed

Meleo, Deborah; Baggi, Luigi; Di Girolamo, Michele; Di Carlo, Fabio; Pecci, Raffaella; Bedini, Rossella

2012-01-01

X-ray micro-tomography (micro-CT) is a miniaturized form of conventional computed axial tomography (CAT) able to investigate small radio-opaque objects at a-few-microns high resolution, in a non-destructive, non-invasive, and tri-dimensional way. Compared to traditional optical and electron microscopy techniques, which provide two-dimensional images, this innovative investigation technology enables a sample tri-dimensional analysis without cutting, coating or exposing the object to any particular chemical treatment. X-ray micro-tomography matches ideal 3D microscopy features: the possibility of investigating an object in natural conditions and without any preparation or alteration; non-invasive, non-destructive, and sufficiently magnified 3D reconstruction; reliable measurement of numeric data of the internal structure (morphology, structure and ultra-structure). Hence, this technique has multi-fold applications in a wide range of fields, not only in medical and odontostomatologic areas, but also in biomedical engineering, materials science, biology, electronics, geology, archaeology, oil industry, and semi-conductors industry. This study shows possible applications of micro-CT in dental implantology to analyze 3D micro-features of dental implant to abutment interface. Indeed, implant-abutment misfit is known to increase mechanical stress on connection structures and surrounding bone tissue. This condition may cause not only screw preload loss or screw fracture, but also biological issues in peri-implant tissues.

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Breaking the acoustic diffraction barrier with localization optoacoustic tomography

NASA Astrophysics Data System (ADS)

Deán-Ben, X. Luís.; Razansky, Daniel

2018-02-01

Diffraction causes blurring of high-resolution features in images and has been traditionally associated to the resolution limit in light microscopy and other imaging modalities. The resolution of an imaging system can be generally assessed via its point spread function, corresponding to the image acquired from a point source. However, the precision in determining the position of an isolated source can greatly exceed the diffraction limit. By combining the estimated positions of multiple sources, localization-based imaging has resulted in groundbreaking methods such as super-resolution fluorescence optical microscopy and has also enabled ultrasound imaging of microvascular structures with unprecedented spatial resolution in deep tissues. Herein, we introduce localization optoacoustic tomography (LOT) and discuss on the prospects of using localization imaging principles in optoacoustic imaging. LOT was experimentally implemented by real-time imaging of flowing particles in 3D with a recently-developed volumetric optoacoustic tomography system. Provided the particles were separated by a distance larger than the diffraction-limited resolution, their individual locations could be accurately determined in each frame of the acquired image sequence and the localization image was formed by superimposing a set of points corresponding to the localized positions of the absorbers. The presented results demonstrate that LOT can significantly enhance the well-established advantages of optoacoustic imaging by breaking the acoustic diffraction barrier in deep tissues and mitigating artifacts due to limited-view tomographic acquisitions.

Can organic matter hide from decomposers in the labyrinth of soil aggregates? Micro-engineered Soil Chips challenging foraging fungi

NASA Astrophysics Data System (ADS)

Hammer, Edith C.; Aleklett, Kristin; Arellano Caicedo, Carlos G.; Bengtsson, Martin; Micaela Mafla Endara, Paola; Ohlsson, Pelle

2017-04-01

From the point of view of microorganisms, the soil environment is an enormously complex labyrinth with paths and dead-end streets, where resources and shelters are unevenly distributed. We study foraging strategies of soil organisms, especially fungi, and the possibility of physio-spatial stabilization of organic matter by "hiding" in occluded soil spaces. We manipulate growth habitat microstructure with lab-on-a-chip techniques, where we designed complex environments with channels and obstacle at dimensions of the size of hyphae, and construct them in the transparent, gas-permeable polymer PDMS. We fill those with different nutrient solutions or combine with mineral nutrient gradients, and inoculate them with soil organisms. We analyze organisms and substrates with microscopy, fluorescence microscopy and analytical chemistry. We compared different soil litter decomposers and an arbuscular mycorrhizal fungus for their ability to forage through complex air-gap structures and attempt to classify them into functional traits concerning their mycelium directionality, space-exploring approach and ability to grow through acute angles and narrow constrictions. We identified structures which are very difficult to penetrate for most species, and compounds located behind such features may thus be spatially unavailable for decomposers. We discuss our approach in comparison to soil pore space tomographic analyses and findings we made in the pore space of colonized wood biochar.