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Sample records for electron tomography tilt-series

  1. Marker-free image registration of electron tomography tilt-series

    PubMed Central

    Sorzano, Carlos Oscar Sanchez; Messaoudi, Cédric; Eibauer, Matthias; Bilbao-Castro, JR; Hegerl, R; Nickell, S; Marco, S; Carazo, JM

    2009-01-01

    Background Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal. Results In this paper we introduce an algorithm to find regions of the tilt series which can be tracked within a subseries of the tilt series. These regions act as landmarks allowing the determination of the alignment parameters. We show our results with synthetic data as well as experimental cryo electron tomography. Conclusion Our algorithm is able to correctly align a single-tilt tomographic series without the help of fiducial markers thanks to the detection of thousands of small image patches that can be tracked over a short number of images in the series. PMID:19397789

  2. Fast auto-acquisition tomography tilt series by using HD video camera in ultra-high voltage electron microscope.

    PubMed

    Nishi, Ryuji; Cao, Meng; Kanaji, Atsuko; Nishida, Tomoki; Yoshida, Kiyokazu; Isakozawa, Shigeto

    2014-11-01

    The ultra-high voltage electron microscope (UHVEM) H-3000 with the world highest acceleration voltage of 3 MV can observe remarkable three dimensional microstructures of microns-thick samples[1]. Acquiring a tilt series of electron tomography is laborious work and thus an automatic technique is highly desired. We proposed the Auto-Focus system using image Sharpness (AFS)[2,3] for UHVEM tomography tilt series acquisition. In the method, five images with different defocus values are firstly acquired and the image sharpness are calculated. The sharpness are then fitted to a quasi-Gaussian function to decide the best focus value[3]. Defocused images acquired by the slow scan CCD (SS-CCD) camera (Hitachi F486BK) are of high quality but one minute is taken for acquisition of five defocused images.In this study, we introduce a high-definition video camera (HD video camera; Hamamatsu Photonics K. K. C9721S) for fast acquisition of images[4]. It is an analog camera but the camera image is captured by a PC and the effective image resolution is 1280×1023 pixels. This resolution is lower than that of the SS-CCD camera of 4096×4096 pixels. However, the HD video camera captures one image for only 1/30 second. In exchange for the faster acquisition the S/N of images are low. To improve the S/N, 22 captured frames are integrated so that each image sharpness is enough to become lower fitting error. As countermeasure against low resolution, we selected a large defocus step, which is typically five times of the manual defocus step, to discriminate different defocused images.By using HD video camera for autofocus process, the time consumption for each autofocus procedure was reduced to about six seconds. It took one second for correction of an image position and the total correction time was seven seconds, which was shorter by one order than that using SS-CCD camera. When we used SS-CCD camera for final image capture, it took 30 seconds to record one tilt image. We can obtain a tilt

  3. 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.

  4. A method for 3D-reconstruction of a muscle thick filament using the tilt series images of a single filament electron tomogram.

    PubMed

    Márquez, G; Pinto, A; Alamo, L; Baumann, B; Ye, F; Winkler, H; Taylor, K; Padrón, R

    2014-05-01

    Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament - calculated without any image averaging and/or imposition of helical symmetry - only reveals MIH motifs infrequently. This is - to our knowledge - the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms.

  5. A method for 3D-reconstruction of a muscle thick filament using the tilt series images of a single filament electron tomogram.

    PubMed

    Márquez, G; Pinto, A; Alamo, L; Baumann, B; Ye, F; Winkler, H; Taylor, K; Padrón, R

    2014-05-01

    Myosin interacting-heads (MIH) motifs are visualized in 3D-reconstructions of thick filaments from striated muscle. These reconstructions are calculated by averaging methods using images from electron micrographs of grids prepared using numerous filament preparations. Here we propose an alternative method to calculate the 3D-reconstruction of a single thick filament using only a tilt series images recorded by electron tomography. Relaxed thick filaments, prepared from tarantula leg muscle homogenates, were negatively stained. Single-axis tilt series of single isolated thick filaments were obtained with the electron microscope at a low electron dose, and recorded on a CCD camera by electron tomography. An IHRSR 3D-recontruction was calculated from the tilt series images of a single thick filament. The reconstruction was enhanced by including in the search stage dual tilt image segments while only single tilt along the filament axis is usually used, as well as applying a band pass filter just before the back projection. The reconstruction from a single filament has a 40 Å resolution and clearly shows the presence of MIH motifs. In contrast, the electron tomogram 3D-reconstruction of the same thick filament - calculated without any image averaging and/or imposition of helical symmetry - only reveals MIH motifs infrequently. This is - to our knowledge - the first application of the IHRSR method to calculate a 3D reconstruction from tilt series images. This single filament IHRSR reconstruction method (SF-IHRSR) should provide a new tool to assess structural differences between well-ordered thick (or thin) filaments in a grid by recording separately their electron tomograms. PMID:24727133

  6. Atomic resolution tomography reconstruction of tilt series based on a GPU accelerated hybrid input-output algorithm using polar Fourier transform.

    PubMed

    Lu, Xiangwen; Gao, Wenpei; Zuo, Jian-Min; Yuan, Jiabin

    2015-02-01

    Advances in diffraction and transmission electron microscopy (TEM) have greatly improved the prospect of three-dimensional (3D) structure reconstruction from two-dimensional (2D) images or diffraction patterns recorded in a tilt series at atomic resolution. Here, we report a new graphics processing unit (GPU) accelerated iterative transformation algorithm (ITA) based on polar fast Fourier transform for reconstructing 3D structure from 2D diffraction patterns. The algorithm also applies to image tilt series by calculating diffraction patterns from the recorded images using the projection-slice theorem. A gold icosahedral nanoparticle of 309 atoms is used as the model to test the feasibility, performance and robustness of the developed algorithm using simulations. Atomic resolution in 3D is achieved for the 309 atoms Au nanoparticle using 75 diffraction patterns covering 150° rotation. The capability demonstrated here provides an opportunity to uncover the 3D structure of small objects of nanometers in size by electron diffraction.

  7. 4D Electron Tomography

    NASA Astrophysics Data System (ADS)

    Kwon, Oh-Hoon; Zewail, Ahmed H.

    2010-06-01

    Electron tomography provides three-dimensional (3D) imaging of noncrystalline and crystalline equilibrium structures, as well as elemental volume composition, of materials and biological specimens, including those of viruses and cells. We report the development of 4D electron tomography by integrating the fourth dimension (time resolution) with the 3D spatial resolution obtained from a complete tilt series of 2D projections of an object. The different time frames of tomograms constitute a movie of the object in motion, thus enabling studies of nonequilibrium structures and transient processes. The method was demonstrated using carbon nanotubes of a bracelet-like ring structure for which 4D tomograms display different modes of motion, such as breathing and wiggling, with resonance frequencies up to 30 megahertz. Applications can now make use of the full space-time range with the nanometer-femtosecond resolution of ultrafast electron tomography.

  8. CTF Determination and Correction for Low Dose Tomographic Tilt Series

    PubMed Central

    Xiong, Quanren; Morphew, Mary K.; Schwartz, Cindi L.; Hoenger, Andreas H.; Mastronarde, David N.

    2009-01-01

    The resolution of cryo-electron tomography can be limited by the first zero of the microscope’s contrast transfer function (CTF). To achieve higher resolution, it is critical to determine the CTF and correct its phase inversions. However, the extremely low signal-to-noise ratio (SNR) and the defocus gradient in the projections of tilted specimens make this process challenging. Two programs, CTFPLOTTER and CTFPHASEFLIP, have been developed to address these issues. CTFPLOTTER obtains a 1D power spectrum by periodogram averaging and rotational averaging and it estimates the noise background with a novel approach, which uses images taken with no specimen. The background-subtracted 1D power spectra from image regions at different defocus values are then shifted to align their first zeros and averaged together. This averaging improves the SNR sufficiently that it becomes possible to determine the defocus for subsets of the tilt series rather than just the entire series. CTFPHASEFLIP corrects images line-by-line by inverting phases appropriately in thin strips of the image at nearly constant defocus. CTF correction by these methods is shown to improve the resolution of aligned, averaged particles extracted from tomograms. However, some restoration of Fourier amplitudes at high frequencies is important for seeing the benefits from CTF correction. PMID:19732834

  9. Rapid low dose electron tomography using a direct electron detection camera

    PubMed Central

    Migunov, Vadim; Ryll, Henning; Zhuge, Xiaodong; Simson, Martin; Strüder, Lothar; Batenburg, K. Joost; Houben, Lothar; Dunin-Borkowski, Rafal E.

    2015-01-01

    We demonstrate the ability to record a tomographic tilt series containing 3487 images in only 3.5 s by using a direct electron detector in a transmission electron microscope. The electron dose is lower by at least one order of magnitude when compared with that used to record a conventional tilt series of fewer than 100 images in 15–60 minutes and the overall signal-to-noise ratio is greater than 4. Our results, which are illustrated for an inorganic nanotube, are important for ultra-low-dose electron tomography of electron-beam-sensitive specimens and real-time dynamic electron tomography of nanoscale objects with sub-ms temporal resolution. PMID:26434767

  10. Rapid low dose electron tomography using a direct electron detection camera.

    PubMed

    Migunov, Vadim; Ryll, Henning; Zhuge, Xiaodong; Simson, Martin; Strüder, Lothar; Batenburg, K Joost; Houben, Lothar; Dunin-Borkowski, Rafal E

    2015-01-01

    We demonstrate the ability to record a tomographic tilt series containing 3487 images in only 3.5 s by using a direct electron detector in a transmission electron microscope. The electron dose is lower by at least one order of magnitude when compared with that used to record a conventional tilt series of fewer than 100 images in 15-60 minutes and the overall signal-to-noise ratio is greater than 4. Our results, which are illustrated for an inorganic nanotube, are important for ultra-low-dose electron tomography of electron-beam-sensitive specimens and real-time dynamic electron tomography of nanoscale objects with sub-ms temporal resolution. PMID:26434767

  11. Rapid low dose electron tomography using a direct electron detection camera

    NASA Astrophysics Data System (ADS)

    Migunov, Vadim; Ryll, Henning; Zhuge, Xiaodong; Simson, Martin; Strüder, Lothar; Batenburg, K. Joost; Houben, Lothar; Dunin-Borkowski, Rafal E.

    2015-10-01

    We demonstrate the ability to record a tomographic tilt series containing 3487 images in only 3.5 s by using a direct electron detector in a transmission electron microscope. The electron dose is lower by at least one order of magnitude when compared with that used to record a conventional tilt series of fewer than 100 images in 15-60 minutes and the overall signal-to-noise ratio is greater than 4. Our results, which are illustrated for an inorganic nanotube, are important for ultra-low-dose electron tomography of electron-beam-sensitive specimens and real-time dynamic electron tomography of nanoscale objects with sub-ms temporal resolution.

  12. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    PubMed Central

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  13. Cryo-electron tomography for structural characterization of macromolecular complexes.

    PubMed

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-08-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological matter embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions.

  14. EPiK-a Workflow for Electron Tomography in Kepler*

    PubMed Central

    Wang, Jianwu; Crawl, Daniel; Phan, Sébastien; Lawrence, Albert; Ellisman, Mark

    2015-01-01

    Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility. PMID:25621086

  15. Three-Dimensional Imaging of the Local Structure of Materials at Atomic Resolution by Electron Tomography

    NASA Astrophysics Data System (ADS)

    Zhu, Chun

    Electron tomography was originally developed in 1968, and has been primarily applied to determine the three-dimensional (3D) structure of biological systems. In the last decade, the application of electron tomography in materials science and nanoscience has revived due to the utilization of scanning transmission electron microscopy (STEM) in the high-angle annular dark-field (HAADF) mode, and a highest resolution of ˜1 nm3 has been achieved. However, improving the resolution from ˜1 nm 3 to the atomic level remains a challenging task, which requires new tomographic reconstruction algorithms, better projection alignment methods, state-of-the-art STEM instruments, and more accurate data-acquisition procedures. In this thesis, important progress has been made in all these four areas. First, a novel tomographic method, termed equally sloped tomography (EST), was developed and allows the 3D image reconstruction of tilt series with a limited number projections and a "missing wedge" (i.e. specimens cannot usually be tilted beyond +/-70°). Second, an alignment method which can be used to align the projections of a tilt series at atomic-level resolution was developed based on center of mass. Finally, by using a Titan 80-300 STEM instrument at the California NanoSystems Institute, UCLA, more accurate data acquisition procedures were developed and a number of tomographic tilt series of atomic resolution projections from different nanoparticles have been obtained. With all these combinations, the 3D structure of a 10 nm gold nanoparticle was determined at 2.4 A resolution, the highest resolution ever achieved in any general tomography method. More recently, this novel electron tomography method has been applied to observe nearly all the atoms in a Pt nanoparticle, and imaged for the first time the 3D core structure of edge and screw dislocations at atomic resolution. Furthermore, through numerical simulations the feasibility of determining the 3D atomic structure of

  16. Electron tomography of cells.

    PubMed

    Gan, Lu; Jensen, Grant J

    2012-02-01

    The electron microscope has contributed deep insights into biological structure since its invention nearly 80 years ago. Advances in instrumentation and methodology in recent decades have now enabled electron tomography to become the highest resolution three-dimensional (3D) imaging technique available for unique objects such as cells. Cells can be imaged either plastic-embedded or frozen-hydrated. Then the series of projection images are aligned and back-projected to generate a 3D reconstruction or 'tomogram'. Here, we review how electron tomography has begun to reveal the molecular organization of cells and how the existing and upcoming technologies promise even greater insights into structural cell biology. PMID:22082691

  17. Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

    PubMed Central

    Levin, Barnaby D.A.; Padgett, Elliot; Chen, Chien-Chun; Scott, M.C.; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D.; Robinson, Richard D.; Ercius, Peter; Kourkoutis, Lena F.; Miao, Jianwei; Muller, David A.; Hovden, Robert

    2016-01-01

    Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data. PMID:27272459

  18. Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.

    PubMed

    Levin, Barnaby D A; Padgett, Elliot; Chen, Chien-Chun; Scott, M C; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D; Robinson, Richard D; Ercius, Peter; Kourkoutis, Lena F; Miao, Jianwei; Muller, David A; Hovden, Robert

    2016-01-01

    Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data. PMID:27272459

  19. Nanomaterial datasets to advance tomography in scanning transmission electron microscopy.

    PubMed

    Levin, Barnaby D A; Padgett, Elliot; Chen, Chien-Chun; Scott, M C; Xu, Rui; Theis, Wolfgang; Jiang, Yi; Yang, Yongsoo; Ophus, Colin; Zhang, Haitao; Ha, Don-Hyung; Wang, Deli; Yu, Yingchao; Abruña, Hector D; Robinson, Richard D; Ercius, Peter; Kourkoutis, Lena F; Miao, Jianwei; Muller, David A; Hovden, Robert

    2016-06-07

    Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

  20. Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography.

    PubMed

    Eibauer, Matthias; Hoffmann, Christian; Plitzko, Jürgen M; Baumeister, Wolfgang; Nickell, Stephan; Engelhardt, Harald

    2012-12-01

    Cryo-electron tomography in combination with subtomogram averaging allows to investigate the structure of protein assemblies in their natural environment in a close to live state. To make full use of the structural information contained in tomograms it is necessary to analyze the contrast transfer function (CTF) of projections and to restore the phases of higher spatial frequencies. CTF correction is however hampered by the difficulty of determining the actual defocus values from tilt series data, which is due to the low signal-to-noise ratio of electron micrographs. In this study, an extended acquisition scheme is introduced that enables an independent CTF determination. Two high-dose images are recorded along the tilt axis on both sides of each projection, which allow an accurate determination of the defocus values of these images. These values are used to calculate the CTF for each image of the tilt series. We applied this scheme to the mycobacterial outer membrane protein MspA reconstituted in lipid vesicles and tested several variants of CTF estimation in combination with subtomogram averaging and correction of the modulation transfer function (MTF). The 3D electron density map of MspA was compared with a structure previously determined by X-ray crystallography. We were able to demonstrate that structural information up to a resolution of 16.8Å can be recovered using our CTF correction approach, whereas the uncorrected 3D map had a resolution of only 26.2Å.

  1. Compressed Sensing Electron Tomography for Determining Biological Structure

    NASA Astrophysics Data System (ADS)

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-06-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets.

  2. Compressed Sensing Electron Tomography for Determining Biological Structure

    PubMed Central

    Guay, Matthew D.; Czaja, Wojciech; Aronova, Maria A.; Leapman, Richard D.

    2016-01-01

    There has been growing interest in applying compressed sensing (CS) theory and practice to reconstruct 3D volumes at the nanoscale from electron tomography datasets of inorganic materials, based on known sparsity in the structure of interest. Here we explore the application of CS for visualizing the 3D structure of biological specimens from tomographic tilt series acquired in the scanning transmission electron microscope (STEM). CS-ET reconstructions match or outperform commonly used alternative methods in full and undersampled tomogram recovery, but with less significant performance gains than observed for the imaging of inorganic materials. We propose that this disparity stems from the increased structural complexity of biological systems, as supported by theoretical CS sampling considerations and numerical results in simulated phantom datasets. A detailed analysis of the efficacy of CS-ET for undersampled recovery is therefore complicated by the structure of the object being imaged. The numerical nonlinear decoding process of CS shares strong connections with popular regularized least-squares methods, and the use of such numerical recovery techniques for mitigating artifacts and denoising in reconstructions of fully sampled datasets remains advantageous. This article provides a link to the software that has been developed for CS-ET reconstruction of electron tomographic data sets. PMID:27291259

  3. The Caltech Tomography Database and Automatic Processing Pipeline.

    PubMed

    Ding, H Jane; Oikonomou, Catherine M; Jensen, Grant J

    2015-11-01

    Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user's "Inbox" and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups.

  4. The Caltech Tomography Database and Automatic Processing Pipeline

    PubMed Central

    Ding, H. Jane; Oikonomou, Catherine M.; Jensen, Grant J.

    2015-01-01

    Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user’s “Inbox” and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups. PMID:26087141

  5. The Caltech Tomography Database and Automatic Processing Pipeline.

    PubMed

    Ding, H Jane; Oikonomou, Catherine M; Jensen, Grant J

    2015-11-01

    Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user's "Inbox" and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups. PMID:26087141

  6. A fast cross-validation method for alignment of electron tomography 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

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

  7. A fast cross-validation method for alignment of electron tomography 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

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography.

  8. Electron tomography of dislocation structures

    SciTech Connect

    Liu, G.S.; House, S.D.; Kacher, J.; Tanaka, M.; Higashida, K.; Robertson, I.M.

    2014-01-15

    Recent developments in the application of electron tomography for characterizing microstructures in crystalline solids are described. The underlying principles for electron tomography are presented in the context of typical challenges in adapting the technique to crystalline systems and in using diffraction contrast imaging conditions. Methods for overcoming the limitations associated with the angular range, the number of acquired images, and uniformity of image contrast are introduced. In addition, a method for incorporating the real space coordinate system into the tomogram is presented. As the approach emphasizes development of experimental solutions to the challenges, the solutions developed and implemented are presented in the form of examples.

  9. Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series

    SciTech Connect

    Dahmen, Tim; Baudoin, Jean-Pierre G; Lupini, Andrew R; Kubel, Christian; Slusallek, Phillip; De Jonge, Niels

    2014-01-01

    In this study, a combined tilt- and focal series is proposed as a new recording scheme for high-angle annular dark-field scanning transmission electron microscopy (STEM) tomography. Three-dimensional (3D) data were acquired by mechanically tilting the specimen, and recording a through-focal series at each tilt direction. The sample was a whole-mount macrophage cell with embedded gold nanoparticles. The tilt focal algebraic reconstruction technique (TF-ART) is introduced as a new algorithm to reconstruct tomograms from such combined tilt- and focal series. The feasibility of TF-ART was demonstrated by 3D reconstruction of the experimental 3D data. The results were compared with a conventional STEM tilt series of a similar sample. The combined tilt- and focal series led to smaller missing wedge artifacts, and a higher axial resolution than obtained for the STEM tilt series, thus improving on one of the main issues of tilt series-based electron tomography.

  10. Whole-cell imaging of the budding yeast Saccharomyces cerevisiae by high-voltage scanning transmission electron tomography.

    PubMed

    Murata, Kazuyoshi; Esaki, Masatoshi; Ogura, Teru; Arai, Shigeo; Yamamoto, Yuta; Tanaka, Nobuo

    2014-11-01

    Electron tomography using a high-voltage electron microscope (HVEM) provides three-dimensional information about cellular components in sections thicker than 1 μm, although in bright-field mode image degradation caused by multiple inelastic scattering of transmitted electrons limit the attainable resolution. Scanning transmission electron microscopy (STEM) is believed to give enhanced contrast and resolution compared to conventional transmission electron microscopy (CTEM). Samples up to 1 μm in thickness have been analyzed with an intermediate-voltage electron microscope because inelastic scattering is not a critical limitation, and probe broadening can be minimized. Here, we employed STEM at 1 MeV high-voltage to extend the useful specimen thickness for electron tomography, which we demonstrate by a seamless tomographic reconstruction of a whole, budding Saccharomyces cerevisiae yeast cell, which is ~3 μm in thickness. High-voltage STEM tomography, especially in the bright-field mode, demonstrated sufficiently enhanced contrast and intensity, compared to CTEM tomography, to permit segmentation of major organelles in the whole cell. STEM imaging also reduced specimen shrinkage during tilt-series acquisition. The fidelity of structural preservation was limited by cytoplasmic extraction, and the spatial resolution was limited by the relatively large convergence angle of the scanning probe. However, the new technique has potential to solve longstanding problems of image blurring in biological specimens beyond 1 μm in thickness, and may facilitate new research in cellular structural biology.

  11. Visualization of ATP Synthase Dimers in Mitochondria by Electron Cryo-tomography

    PubMed Central

    Davies, Karen M.; Daum, Bertram; Gold, Vicki A. M.; Mühleip, Alexander W.; Brandt, Tobias; Blum, Thorsten B.; Mills, Deryck J.; Kühlbrandt, Werner

    2014-01-01

    Electron cryo-tomography is a powerful tool in structural biology, capable of visualizing the three-dimensional structure of biological samples, such as cells, organelles, membrane vesicles, or viruses at molecular detail. To achieve this, the aqueous sample is rapidly vitrified in liquid ethane, which preserves it in a close-to-native, frozen-hydrated state. In the electron microscope, tilt series are recorded at liquid nitrogen temperature, from which 3D tomograms are reconstructed. The signal-to-noise ratio of the tomographic volume is inherently low. Recognizable, recurring features are enhanced by subtomogram averaging, by which individual subvolumes are cut out, aligned and averaged to reduce noise. In this way, 3D maps with a resolution of 2 nm or better can be obtained. A fit of available high-resolution structures to the 3D volume then produces atomic models of protein complexes in their native environment. Here we show how we use electron cryo-tomography to study the in situ organization of large membrane protein complexes in mitochondria. We find that ATP synthases are organized in rows of dimers along highly curved apices of the inner membrane cristae, whereas complex I is randomly distributed in the membrane regions on either side of the rows. By subtomogram averaging we obtained a structure of the mitochondrial ATP synthase dimer within the cristae membrane. PMID:25285856

  12. Accurate measurement of relative tilt and azimuth angles in electron tomography: A comparison of fiducial marker method with electron diffraction

    NASA Astrophysics Data System (ADS)

    Hayashida, Misa; Malac, Marek; Bergen, Michael; Egerton, Ray F.; Li, Peng

    2014-08-01

    Electron tomography is a method whereby a three-dimensional reconstruction of a nanoscale object is obtained from a series of projected images measured in a transmission electron microscope. We developed an electron-diffraction method to measure the tilt and azimuth angles, with Kikuchi lines used to align a series of diffraction patterns obtained with each image of the tilt series. Since it is based on electron diffraction, the method is not affected by sample drift and is not sensitive to sample thickness, whereas tilt angle measurement and alignment using fiducial-marker methods are affected by both sample drift and thickness. The accuracy of the diffraction method benefits reconstructions with a large number of voxels, where both high spatial resolution and a large field of view are desired. The diffraction method allows both the tilt and azimuth angle to be measured, while fiducial marker methods typically treat the tilt and azimuth angle as an unknown parameter. The diffraction method can be also used to estimate the accuracy of the fiducial marker method, and the sample-stage accuracy. A nano-dot fiducial marker measurement differs from a diffraction measurement by no more than ±1°.

  13. Accurate measurement of relative tilt and azimuth angles in electron tomography: A comparison of fiducial marker method with electron diffraction

    SciTech Connect

    Hayashida, Misa; Malac, Marek; Egerton, Ray F.; Bergen, Michael; Li, Peng

    2014-08-15

    Electron tomography is a method whereby a three-dimensional reconstruction of a nanoscale object is obtained from a series of projected images measured in a transmission electron microscope. We developed an electron-diffraction method to measure the tilt and azimuth angles, with Kikuchi lines used to align a series of diffraction patterns obtained with each image of the tilt series. Since it is based on electron diffraction, the method is not affected by sample drift and is not sensitive to sample thickness, whereas tilt angle measurement and alignment using fiducial-marker methods are affected by both sample drift and thickness. The accuracy of the diffraction method benefits reconstructions with a large number of voxels, where both high spatial resolution and a large field of view are desired. The diffraction method allows both the tilt and azimuth angle to be measured, while fiducial marker methods typically treat the tilt and azimuth angle as an unknown parameter. The diffraction method can be also used to estimate the accuracy of the fiducial marker method, and the sample-stage accuracy. A nano-dot fiducial marker measurement differs from a diffraction measurement by no more than ±1°.

  14. Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research

    PubMed Central

    Alaidi, Osama; Rames, Matthew J.

    2016-01-01

    Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated. PMID:26087941

  15. Using size-selected gold clusters on graphene oxide films to aid cryo-transmission electron tomography alignment

    NASA Astrophysics Data System (ADS)

    Arkill, Kenton P.; Mantell, Judith M.; Plant, Simon R.; Verkade, Paul; Palmer, Richard E.

    2015-03-01

    A three-dimensional reconstruction of a nano-scale aqueous object can be achieved by taking a series of transmission electron micrographs tilted at different angles in vitreous ice: cryo-Transmission Electron Tomography. Presented here is a novel method of fine alignment for the tilt series. Size-selected gold clusters of ~2.7 nm (Au561 +/- 14), ~3.2 nm (Au923 +/- 22), and ~4.3 nm (Au2057 +/- 45) in diameter were deposited onto separate graphene oxide films overlaying holes on amorphous carbon grids. After plunge freezing and subsequent transfer to cryo-Transmission Electron Tomography, the resulting tomograms have excellent (de-)focus and alignment properties during automatic acquisition. Fine alignment is accurate when the evenly distributed 3.2 nm gold particles are used as fiducial markers, demonstrated with a reconstruction of a tobacco mosaic virus. Using a graphene oxide film means the fiducial markers are not interfering with the ice bound sample and that automated collection is consistent. The use of pre-deposited size-selected clusters means there is no aggregation and a user defined concentration. The size-selected clusters are mono-dispersed and can be produced in a wide size range including 2-5 nm in diameter. The use of size-selected clusters on a graphene oxide films represents a significant technical advance for 3D cryo-electron microscopy.

  16. Feasibility study for mega-electron-volt electron beam tomography

    SciTech Connect

    Hampel, U.; Baertling, Y.; Hoppe, D.; Kuksanov, N.; Fadeev, S.; Salimov, R.

    2012-09-15

    Electron beam tomography is a promising imaging modality for the study of fast technical processes. But for many technical objects of interest x rays of several hundreds of keV energy are required to achieve sufficient material penetration. In this article we report on a feasibility study for fast electron beam computed tomography with a 1 MeV electron beam. The experimental setup comprises an electrostatic accelerator with beam optics, transmission target, and a single x-ray detector. We employed an inverse fan-beam tomography approach with radiographic projections being generated from the linearly moving x-ray source. Angular projections were obtained by rotating the object.

  17. Feasibility study for mega-electron-volt electron beam tomography.

    PubMed

    Hampel, U; Bärtling, Y; Hoppe, D; Kuksanov, N; Fadeev, S; Salimov, R

    2012-09-01

    Electron beam tomography is a promising imaging modality for the study of fast technical processes. But for many technical objects of interest x rays of several hundreds of keV energy are required to achieve sufficient material penetration. In this article we report on a feasibility study for fast electron beam computed tomography with a 1 MeV electron beam. The experimental setup comprises an electrostatic accelerator with beam optics, transmission target, and a single x-ray detector. We employed an inverse fan-beam tomography approach with radiographic projections being generated from the linearly moving x-ray source. Angular projections were obtained by rotating the object.

  18. Morphology of organic electronic materials imaged via electron tomography.

    PubMed

    Andersson, B V; Masich, S; Solin, N; Inganäs, O

    2012-09-01

    Organic electronic materials and nanostructures have been studied with the use of electron tomography. Nanostructured materials including contrast enhancing features have been studied and double tilt data collection has been employed to improve reconstructions. Tomography reconstructions of active layers of organic solar cells, where various preparation techniques have been used, have been analysed and compared to device behaviour. Small changes in preparation procedures may lead to large differences in morphology and device performance, and the results also indicate a complex relation between these.

  19. Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography.

    PubMed

    Morado, Dustin R; Hu, Bo; Liu, Jun

    2016-01-30

    Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native context at a molecular level. The technique involves initially preserving the sample in its native state by rapidly freezing the specimen in vitreous ice, then collecting a series of micrographs from different angles at high magnification, and finally computationally reconstructing a 3-D density map. The frozen-hydrated specimen is extremely sensitive to the electron beam and so micrographs are collected at very low electron doses to limit the radiation damage. As a result, the raw cryo-tomogram has a very low signal to noise ratio characterized by an intrinsically noisy image. To better visualize subjects of interest, conventional imaging analysis and sub-tomogram averaging in which sub-tomograms of the subject are extracted from the initial tomogram and aligned and averaged are utilized to improve both contrast and resolution. Large datasets of tilt-series are essential to understanding and resolving the complexes at different states, conditions, or mutations as well as obtaining a large enough collection of sub-tomograms for averaging and classification. Collecting and processing this data can be a major obstacle preventing further analysis. Here we describe a high-throughput cryo-ET protocol based on a computer-controlled 300kV cryo-electron microscope, a direct detection device (DDD) camera and a highly effective, semi-automated image-processing pipeline software wrapper library tomoauto developed in-house. This protocol has been effectively utilized to visualize the intact type III secretion system (T3SS) in Shigella flexneri minicells. It can be applicable to any project suitable for cryo-ET.

  20. A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

    PubMed

    Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

    2015-12-01

    Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction.

  1. Calibration method of tilt and azimuth angles for alignment of TEM tomographic tilt series.

    PubMed

    Hayashida, Misa; Terauchi, Shinya; Fujimoto, Toshiyuki

    2011-10-01

    This paper describes the calibration method of the tilt and azimuth angles of specimen using a digital protractor and a laser autocollimator for alignment of electron tomography. It also suggests an easy method to check whether the specimen is tilted by 180.0°, and whether the azimuth angle is 0.0°; the method involves the use of two images of a rod-shaped specimen collected before and after a 180.0° tilt. The method is based on the assumption that these images are symmetric about the tilt axis when the azimuth angle is 0.0°. In addition, we used an experiment to demonstrate the effect of the incorrect angles on reconstructed images and simulated the image quality against distance away from tilt axis.

  2. Calibration method of tilt and azimuth angles for alignment of TEM tomographic tilt series

    SciTech Connect

    Hayashida, Misa; Terauchi, Shinya; Fujimoto, Toshiyuki

    2011-10-15

    This paper describes the calibration method of the tilt and azimuth angles of specimen using a digital protractor and a laser autocollimator for alignment of electron tomography. It also suggests an easy method to check whether the specimen is tilted by 180.0 deg., and whether the azimuth angle is 0.0 deg.; the method involves the use of two images of a rod-shaped specimen collected before and after a 180.0 deg. The method is based on the assumption that these images are symmetric about the tilt axis when the azimuth angle is 0.0 deg. In addition, we used an experiment to demonstrate the effect of the incorrect angles on reconstructed images and simulated the image quality against distance away from tilt axis.

  3. Using tomoauto – a protocol for high-throughput automated cryo-electron tomography

    PubMed Central

    Morado, Dustin R.; Hu, Bo; Liu, Jun

    2016-01-01

    We present a protocol on how to utilize high-throughput cryo-electron tomography to determine high resolution in situ structures of molecular machines. The protocol permits large amounts of data to be processed, avoids common bottlenecks and reduces resource downtime, allowing the user to focus on important biological questions. Cryo-electron tomography (Cryo-ET) is a powerful three-dimensional (3-D) imaging technique for visualizing macromolecular complexes in their native context at a molecular level. The technique involves initially preserving the sample in its native state by rapidly freezing the specimen in vitreous ice, then collecting a series of micrographs from different angles at high magnification, and finally computationally reconstructing a 3-D density map. The frozen-hydrated specimen is extremely sensitive to the electron beam and so micrographs are collected at very low electron doses to limit the radiation damage. As a result, the raw cryo-tomogram has a very low signal to noise ratio characterized by an intrinsically noisy image. To better visualize subjects of interest, conventional imaging analysis and sub-tomogram averaging in which sub-tomograms of the subject are extracted from the initial tomogram and aligned and averaged are utilized to improve both contrast and resolution. Large datasets of tilt-series are essential to understanding and resolving the complexes at different states, conditions, or mutations as well as obtaining a large enough collection of sub-tomograms for averaging and classification. Collecting and processing this data can be a major obstacle preventing further analysis. Here we describe a high-throughput cryo-ET protocol based on a computer-controlled 300kV cryo-electron microscope, a direct detection device (DDD) camera and a highly effective, semi-automated image-processing pipeline software wrapper library tomoauto developed in-house. This protocol has been effectively utilized to visualize the intact type III

  4. Local electron tomography using angular variations of surface tangents: Stomo version 2

    NASA Astrophysics Data System (ADS)

    Petersen, T. C.; Ringer, S. P.

    2012-03-01

    In a recent publication, we investigated the prospect of measuring the outer three-dimensional (3D) shapes of nano-scale atom probe specimens from tilt-series of images collected in the transmission electron microscope. For this purpose alone, an algorithm and simplified reconstruction theory were developed to circumvent issues that arise in commercial "back-projection" computations in this context. In our approach, we give up the difficult task of computing the complete 3D continuum structure and instead seek only the 3D morphology of internal and external scattering interfaces. These interfaces can be described as embedded 2D surfaces projected onto each image in a tilt series. Curves and other features in the images are interpreted as inscribed sets of tangent lines, which intersect the scattering interfaces at unknown locations along the direction of the incident electron beam. Smooth angular variations of the tangent line abscissa are used to compute the surface tangent intersections and hence the 3D morphology as a "point cloud". We have published the explicit details of our alternative algorithm along with the source code entitled "stomo_version_1". For this work, we have further modified the code to efficiently handle rectangular image sets, perform much faster tangent-line "edge detection" and smoother tilt-axis image alignment using simple bi-linear interpolation. We have also adapted the algorithm to detect tangent lines as "ridges", based upon 2nd order partial derivatives of the image intensity; the magnitude and orientation of which is described by a Hessian matrix. Ridges are more appropriate descriptors for tangent-line curves in phase contrast images outlined by Fresnel fringes or absorption contrast data from fine-scale objects. Improved accuracy, efficiency and speed for "stomo_version_2" is demonstrated in this paper using both high resolution electron tomography data of a nano-sized atom probe tip and simulated absorption-contrast images

  5. Using size-selected gold clusters on graphene oxide films to aid cryo-transmission electron tomography alignment.

    PubMed

    Arkill, Kenton P; Mantell, Judith M; Plant, Simon R; Verkade, Paul; Palmer, Richard E

    2015-01-01

    A three-dimensional reconstruction of a nano-scale aqueous object can be achieved by taking a series of transmission electron micrographs tilted at different angles in vitreous ice: cryo-Transmission Electron Tomography. Presented here is a novel method of fine alignment for the tilt series. Size-selected gold clusters of ~2.7 nm (Au₅₆₁±₁₄ ), ~3.2 nm (Au₉₂₃± ₂₂ ), and ~4.3 nm (Au₂₀₅₇±₄₅) in diameter were deposited onto separate graphene oxide films overlaying holes on amorphous carbon grids. After plunge freezing and subsequent transfer to cryo-Transmission Electron Tomography, the resulting tomograms have excellent (de-)focus and alignment properties during automatic acquisition. Fine alignment is accurate when the evenly distributed 3.2 nm gold particles are used as fiducial markers, demonstrated with a reconstruction of a tobacco mosaic virus. Using a graphene oxide film means the fiducial markers are not interfering with the ice bound sample and that automated collection is consistent. The use of pre-deposited size-selected clusters means there is no aggregation and a user defined concentration. The size-selected clusters are mono-dispersed and can be produced in a wide size range including 2-5 nm in diameter. The use of size-selected clusters on a graphene oxide films represents a significant technical advance for 3D cryo-electron microscopy. PMID:25783049

  6. Electron Tomography: Seeing Atoms in Three Dimensions

    SciTech Connect

    Arslan, Ilke; Stach, Eric A.

    2012-11-01

    Our eyes - a parallel lens system - have the phenomenal ability to observe and "reconstruct" the three-dimensional world, relaying a 3-D image to our brains. Imaging of the nanoworld is best done with electrons rather than photons because of their lower wavelengths and higher resolution. The advent of aberration-correction has led to transmission electron microscopes with sub-Angstrom resolution that can resolve single atoms. Yet, no matter what detector is used, the resulting images are only two-dimensional projections of three-dimensional objects. Electron tomography is a technique that allows reconstruction of the three-dimensional structure and morphology of nanomaterials from such projections. X-ray tomography has been used in many branches of science for nearly half a century, and in the biological sciences electron tomography has been a powerful tool for understanding ultrastructure. However, for many years crystalline materials posed a challenge to electron tomography because diffraction contrast (a change in intensity in the image at particular crystal orientations) creates artifacts in the 3-D reconstruction. In 2003, with advances in scanning transmission electron microscopy, Midgley and colleagues obtained the first electron tomograms of crystalline materials. Shortly thereafter, Arslan et al. showed that the spatial resolution could be improved to 1 nm in all three spatial dimensions and visualized the formation of faceted 3.5-nm quantum dots embedded in a Si matrix. However, with that work existing reconstruction algorithms appeared to have reached their limit. To attain a resolution of 1 nm, a total of 140 images over ±78 degrees of tilt were needed. Writing in Nature Materials, Goris et al. now report a novel algorithm for 3-D reconstruction of the atomic structure of free-standing Au nanorods, using only four projection images. I.A. acknowledges collaboration with J.D. Roehling, K.J. Batenburg, B.C. Gates and A. Katz for Figure 1, supported in

  7. Single particle and molecular assembly analysis of polyribosomes by single- and double-tilt cryo electron tomography.

    PubMed

    Myasnikov, Alexander G; Afonina, Zhanna A; Klaholz, Bruno P

    2013-03-01

    Cryo electron tomography (cryo-ET) can provide cellular and molecular structural information on various biological samples. However, the detailed interpretation of tomograms reconstructed from single-tilt data tends to suffer from low signal-to-noise ratio and artefacts caused by some systematically missing angular views. While these can be overcome by sub-tomogram averaging, they remain limiting for the analysis of unique structures. Double-tilt ET can improve the tomogram quality by acquiring a second tilt series after an in-plane rotation, but its usage is not widespread yet because it is considered technically demanding and it is rarely used under cryo conditions. Here we show that double-tilt cryo-ET improves the quality of 3D reconstructions so significantly that even single particle analysis can be envisaged despite of the intrinsically low image contrast obtained from frozen-hydrated specimens. This is illustrated by the analysis of eukaryotic polyribosomes in which individual ribosomes were reconstructed using single-tilt, partial and full double-tilt geometries. The improved tomograms favour the faster convergence of iterative sub-tomogram averaging and allow a better 3D classification using multivariate statistical analysis. Our study of single particles and molecular assemblies within polysomes illustrates that the dual-axis approach is particularly useful for cryo applications of ET, both for unique objects and for structures that can be classified and averaged.

  8. Cryo-electron tomography of bacterial viruses

    SciTech Connect

    Guerrero-Ferreira, Ricardo C.; Wright, Elizabeth R.

    2013-01-05

    Bacteriophage particles contain both simple and complex macromolecular assemblages and machines that enable them to regulate the infection process under diverse environmental conditions with a broad range of bacterial hosts. Recent developments in cryo-electron tomography (cryo-ET) make it possible to observe the interactions of bacteriophages with their host cells under native-state conditions at unprecedented resolution and in three-dimensions. This review describes the application of cryo-ET to studies of bacteriophage attachment, genome ejection, assembly and egress. Current topics of investigation and future directions in the field are also discussed.

  9. Atom Probe Tomography of Nanoscale Electronic Materials

    SciTech Connect

    Larson, David J.; Prosa, Ty J.; Perea, Daniel E.; Inoue, Hidekazu; Mangelinck, D.

    2016-01-01

    Atom probe tomography (APT) is a mass spectrometry based on time-of-flight measurements which also concurrently produces 3D spatial information. The reader is referred to any of the other papers in this volume or to the following references for further information 4–8. The current capabilities of APT, such as detecting a low number of dopant atoms in nanoscale devices or segregation at a nanoparticle interface, make this technique an important component in the nanoscale metrology toolbox. In this manuscript, we review some of the applications of APT to nanoscale electronic materials, including transistors and finFETs, silicide contact microstructures, nanowires, and nanoparticles.

  10. Structural relations between collagen and mineral in bone as determined by high voltage electron microscopic tomography

    NASA Technical Reports Server (NTRS)

    Landis, W. J.; Hodgens, K. J.; Arena, J.; Song, M. J.; McEwen, B. F.

    1996-01-01

    Aspects of the ultrastructural interaction between collagen and mineral crystals in embryonic chick bone have been examined by the novel technique of high voltage electron microscopic tomography to obtain three-dimensional information concerning extracellular calcification in this tissue. Newly mineralizing osteoid along periosteal surfaces of mid-diaphyseal regions from normal chick tibiae was embedded, cut into 0.25 microns thick sections, and documented at 1.0 MV in the Albany AEI-EM7 high voltage electron microscope. The areas of the tissue studied contained electron dense mineral crystals associated with collagen fibrils, some marked by crystals disposed along their cylindrically shaped lengths. Tomographic reconstructions of one site with two mineralizing fibrils were computed from a 5 degrees tilt series of micrographs over a +/- 60 degrees range. Reconstructions showed that the mineral crystals were platelets of irregular shape. Their sizes were variable, measured here up to 80 x 30 x 8 nm in length, width, and thickness, respectively. The longest crystal dimension, corresponding to the c-axis crystallographically, was generally parallel to the collagen fibril long axis. Individual crystals were oriented parallel to one another in each fibril examined. They were also parallel in the neighboring but apparently spatially separate fibrils. Crystals were periodically (approximately 67 nm repeat distance) arranged along the fibrils and their location appeared to correspond to collagen hole and overlap zones defined by geometrical imaging techniques. The crystals appeared to be continuously distributed along a fibril, their size and number increasing in a tapered fashion from a relatively narrow tip containing smaller and infrequent crystals to wider regions having more densely packed and larger crystals. Defined for the first time by direct visual 3D imaging, these data describe the size, shape, location, orientation, and development of early crystals in normal

  11. Combined scanning transmission electron microscopy tilt- and focal series.

    PubMed

    Dahmen, Tim; Baudoin, Jean-Pierre; Lupini, Andrew R; Kübel, Christian; Slusallek, Philipp; de Jonge, Niels

    2014-04-01

    In this study, a combined tilt- and focal series is proposed as a new recording scheme for high-angle annular dark-field scanning transmission electron microscopy (STEM) tomography. Three-dimensional (3D) data were acquired by mechanically tilting the specimen, and recording a through-focal series at each tilt direction. The sample was a whole-mount macrophage cell with embedded gold nanoparticles. The tilt-focal algebraic reconstruction technique (TF-ART) is introduced as a new algorithm to reconstruct tomograms from such combined tilt- and focal series. The feasibility of TF-ART was demonstrated by 3D reconstruction of the experimental 3D data. The results were compared with a conventional STEM tilt series of a similar sample. The combined tilt- and focal series led to smaller "missing wedge" artifacts, and a higher axial resolution than obtained for the STEM tilt series, thus improving on one of the main issues of tilt series-based electron tomography.

  12. Resolving Presynaptic Structure by Electron Tomography

    PubMed Central

    Perkins, Guy A.; Jackson, Dakota R.; Spirou, George A.

    2016-01-01

    A key goal in neurobiology is to generate a theoretical framework that merges structural, physiological and molecular explanations of brain function. These categories of explanation do not advance in synchrony; advances in one category define new experiments in other categories. For example, the synapse was defined physiologically and biochemically before it was visualized using electron microscopy. Indeed, the original descriptions of synapses in the 1950s were lent credence by the presence of spherical vesicles in presynaptic terminals that were considered to be the substrate for quantal neurotransmission. In the last few decades, our understanding of synaptic function has again been driven by physiological and molecular techniques. The key molecular players for synaptic vesicle structure, mobility and fusion were identified and applications of the patch clamp technique permitted physiological estimation of neurotransmitter release and receptor properties. These advances demand higher resolution structural images of synapses. During the 1990s a second renaissance in cell biology driven by EM was fueled by improved techniques for electron tomography (ET) with the ability to compute virtual images with nm resolution between image planes. Over the last fifteen years, ET has been applied to the presynaptic terminal with special attention to the active zone and organelles of the nerve terminal. In this review, we first summarize the technical improvements that have led to a resurgence in utilization of ET and then we summarize new insights gained by the application of ET to reveal the high-resolution structure of the nerve terminal. PMID:25683026

  13. Fully Mechanically Controlled Automated Electron Microscopic Tomography

    PubMed Central

    Liu, Jinxin; Li, Hongchang; Zhang, Lei; Rames, Matthew; Zhang, Meng; Yu, Yadong; Peng, Bo; Celis, César Díaz; Xu, April; Zou, Qin; Yang, Xu; Chen, Xuefeng; Ren, Gang

    2016-01-01

    Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins’ functions; but their structures are difficult to determine. Electron tomography (ET) provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional (3D) reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification (approximately 50,000–160,000×) and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisition without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral (PI) control algorithm. The validations by both negative staining (NS) and cryo-electron microscopy (cryo-EM) suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging. PMID:27403922

  14. Fully Mechanically Controlled Automated Electron Microscopic Tomography

    NASA Astrophysics Data System (ADS)

    Liu, Jinxin; Li, Hongchang; Zhang, Lei; Rames, Matthew; Zhang, Meng; Yu, Yadong; Peng, Bo; Celis, César Díaz; Xu, April; Zou, Qin; Yang, Xu; Chen, Xuefeng; Ren, Gang

    2016-07-01

    Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins’ functions; but their structures are difficult to determine. Electron tomography (ET) provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional (3D) reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification (approximately 50,000–160,000×) and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisition without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral (PI) control algorithm. The validations by both negative staining (NS) and cryo-electron microscopy (cryo-EM) suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging.

  15. Cryo-Electron Tomography and Subtomogram Averaging.

    PubMed

    Wan, W; Briggs, J A G

    2016-01-01

    Cryo-electron tomography (cryo-ET) allows 3D volumes to be reconstructed from a set of 2D projection images of a tilted biological sample. It allows densities to be resolved in 3D that would otherwise overlap in 2D projection images. Cryo-ET can be applied to resolve structural features in complex native environments, such as within the cell. Analogous to single-particle reconstruction in cryo-electron microscopy, structures present in multiple copies within tomograms can be extracted, aligned, and averaged, thus increasing the signal-to-noise ratio and resolution. This reconstruction approach, termed subtomogram averaging, can be used to determine protein structures in situ. It can also be applied to facilitate more conventional 2D image analysis approaches. In this chapter, we provide an introduction to cryo-ET and subtomogram averaging. We describe the overall workflow, including tomographic data collection, preprocessing, tomogram reconstruction, subtomogram alignment and averaging, classification, and postprocessing. We consider theoretical issues and practical considerations for each step in the workflow, along with descriptions of recent methodological advances and remaining limitations. PMID:27572733

  16. Cryo-Electron Tomography and Subtomogram Averaging.

    PubMed

    Wan, W; Briggs, J A G

    2016-01-01

    Cryo-electron tomography (cryo-ET) allows 3D volumes to be reconstructed from a set of 2D projection images of a tilted biological sample. It allows densities to be resolved in 3D that would otherwise overlap in 2D projection images. Cryo-ET can be applied to resolve structural features in complex native environments, such as within the cell. Analogous to single-particle reconstruction in cryo-electron microscopy, structures present in multiple copies within tomograms can be extracted, aligned, and averaged, thus increasing the signal-to-noise ratio and resolution. This reconstruction approach, termed subtomogram averaging, can be used to determine protein structures in situ. It can also be applied to facilitate more conventional 2D image analysis approaches. In this chapter, we provide an introduction to cryo-ET and subtomogram averaging. We describe the overall workflow, including tomographic data collection, preprocessing, tomogram reconstruction, subtomogram alignment and averaging, classification, and postprocessing. We consider theoretical issues and practical considerations for each step in the workflow, along with descriptions of recent methodological advances and remaining limitations.

  17. Fully Mechanically Controlled Automated Electron Microscopic Tomography.

    PubMed

    Liu, Jinxin; Li, Hongchang; Zhang, Lei; Rames, Matthew; Zhang, Meng; Yu, Yadong; Peng, Bo; Celis, César Díaz; Xu, April; Zou, Qin; Yang, Xu; Chen, Xuefeng; Ren, Gang

    2016-01-01

    Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins' functions; but their structures are difficult to determine. Electron tomography (ET) provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional (3D) reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification (approximately 50,000-160,000×) and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisition without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral (PI) control algorithm. The validations by both negative staining (NS) and cryo-electron microscopy (cryo-EM) suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging. PMID:27403922

  18. Cryo-Electron Tomography of Rubella Virus

    PubMed Central

    Battisti, Anthony J.; Yoder, Joshua D.; Plevka, Pavel; Winkler, Dennis C.; Mangala Prasad, Vidya; Kuhn, Richard J.; Frey, Teryl K.; Steven, Alasdair C.

    2012-01-01

    Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses. PMID:22855483

  19. Cryo-electron tomography in biology and medicine.

    PubMed

    Koning, Roman I; Koster, Abraham J

    2009-11-01

    During the last six decades electron microscopy (EM) has been essential to ultra-structural studies of the cell to understand the fundamentals of cellular morphology and processes underlying diseases. More recently, electron tomography (ET) has emerged as a novel approach able to provide three-dimensional (3D) information on cells and tissues at molecular level. Electron tomography is comparable to medical tomographic techniques like CAT, PET and MRI in the sense that it provides a 3D view of an object, yet it does so at a cellular scale and with nanometer resolution. Electron tomography has the unique ability to visualize molecular assemblies, cytoskeletal elements and organelles within cells. The three-dimensional perspective it provides has revised our understanding of cellular organization and its relation with morphological changes in normal development and disease. Cryo-electron tomography of vitrified samples at cryogenic temperatures combines excellent structural preservation with direct high-resolution imaging. The use of cryo-preparation and imaging techniques eliminates artifacts induced by plastic embedding and staining of the samples is circumvented. This review describes the technique of cryo-electron tomography, its basic principles, cryo-specimen preparation, tomographic data acquisition and image processing. A number of illustrative examples ranging from whole cells, cytoskeletal filaments, viruses and organelles are presented along with a comprehensive list of research articles employing cryo-electron tomography as the key ultrastuctural technique.

  20. Quantitative determination of the mineral distribution in different collagen zones of calcifying tendon using high voltage electron microscopic tomography

    NASA Technical Reports Server (NTRS)

    McEwen, B. F.; Song, M. J.; Landis, W. J.

    1991-01-01

    High voltage electron microscopic tomography was used to make the first quantitative determination of the distribution of mineral between different regions of collagen fibrils undergoing early calcification in normal leg tendons of the domestic turkey, Meleagris gallopavo. The tomographic 3-D reconstruction was computed from a tilt series of 61 different views spanning an angular range of +/- 60 degrees in 2 degrees intervals. Successive applications of an interactive computer operation were used to mask the collagen banding pattern of either hole or overlap zones into separate versions of the reconstruction. In such 3-D volumes, regions specified by the mask retained their original image density while the remaining volume was set to background levels. This approach was also applied to the mineral crystals present in the same volumes to yield versions of the 3-D reconstructions that were masked for both the crystal mass and the respective collagen zones. Density profiles from these volumes contained a distinct peak corresponding only to the crystal mass. A comparison of the integrated density of this peak from each profile established that 64% of the crystals observed were located in the collagen hole zones and 36% were found in the overlap zones. If no changes in crystal stability occur once crystals are formed, this result suggests the possibilities that nucleation of mineral is preferentially and initially associated with the hole zones, nucleation occurs more frequently in the hole zones, the rate of crystal growth is more rapid in the hole zones, or a combination of these alternatives. All lead to the conclusion that the overall accumulation of mineral mass is predominant in the collagen hole zones compared to overlap zones during early collagen fibril calcification.

  1. Cryo-scanning transmission electron tomography of vitrified cells.

    PubMed

    Wolf, Sharon Grayer; Houben, Lothar; Elbaum, Michael

    2014-04-01

    Cryo-electron tomography (CET) of fully hydrated, vitrified biological specimens has emerged as a vital tool for biological research. For cellular studies, the conventional imaging modality of transmission electron microscopy places stringent constraints on sample thickness because of its dependence on phase coherence for contrast generation. Here we demonstrate the feasibility of using scanning transmission electron microscopy for cryo-tomography of unstained vitrified specimens (CSTET). We compare CSTET and CET for the imaging of whole bacteria and human tissue culture cells, finding favorable contrast and detail in the CSTET reconstructions. Particularly at high sample tilts, the CSTET signals contain more informative data than energy-filtered CET phase contrast images, resulting in improved depth resolution. Careful control over dose delivery permits relatively high cumulative exposures before the onset of observable beam damage. The increase in acceptable specimen thickness broadens the applicability of electron cryo-tomography.

  2. Characterization of Septin Ultrastructure in Budding Yeast Using Electron Tomography

    PubMed Central

    Bertin, Aurélie; Nogales, Eva

    2015-01-01

    Summary Septins are essential for the completion of cytokinesis. In budding yeast, Saccharomyces cerevisiae, septins are located at the bud neck during mitosis and are closely connected to the inner plasma membrane. In vitro, yeast septins have been shown to self-assemble into a variety of filamentous structures, including rods, paired filaments, bundles and rings [1–3]. Using electron tomography of freeze-substituted section and cryo-electron tomography of frozen sections, we determined the three dimensional organization of the septin cytoskeleton in dividing budding yeast with molecular resolution [4,5]. Here we describe the detailed procedures used for our characterization of the septin cellular ultrastructure. PMID:26519309

  3. Microstructural characterization of an Al-li-mg-cu alloy by correlative electron tomography and atom probe tomography.

    PubMed

    Xiong, Xiangyuan; Weyland, Matthew

    2014-08-01

    Correlative electron tomography and atom probe tomography have been carried out successfully on the same region of a commercial 8090 aluminum alloy (Al-Li-Mg-Cu). The combination of the two techniques allows accurate geometric reconstruction of the atom probe tomography data verified by crystallographic information retrieved from the reconstruction. Quantitative analysis of the precipitate phase compositions and volume fractions of each phase have been obtained from the atom probe tomography and electron tomography at various scales, showing strong agreement between both techniques.

  4. Removing the effects of the "dark matter" in tomography.

    PubMed

    Gontard, Lionel C

    2015-07-01

    Electron tomography (ET) using different imaging modes has been progressively consolidating its position as a key tool in materials science. The fidelity of a tomographic reconstruction, or tomogram, is affected by several experimental factors. Most often, an unrealistic cloud of intensity that does not correspond to a real material phase of the specimen ("dark matter") blurs the tomograms and enhances artefacts arising from the missing wedge (MW). Here we show that by simple preprocessing of the background level of any tomographic tilt series, it is possible to minimise the negative effects of that "dark matter". Iterative reconstruction algorithms converge better, leading to tomograms with fewer streaking artefacts from the MW, more contrast, and increased accuracy. The conclusions are valid irrespective of the imaging mode used, and the methodology improves the segmentation and visualisation of tomograms of both crystalline and amorphous materials. We show examples of HAADF STEM and BF TEM tomography.

  5. Non-rigid alignment in electron tomography in materials science.

    PubMed

    Printemps, Tony; Bernier, Nicolas; Bleuet, Pierre; Mula, Guido; Hervé, Lionel

    2016-09-01

    Electron tomography is a key technique that enables the visualization of an object in three dimensions with a resolution of about a nanometre. High-quality 3D reconstruction is possible thanks to the latest compressed sensing algorithms and/or better alignment and preprocessing of the 2D projections. Rigid alignment of 2D projections is routine in electron tomography. However, it cannot correct misalignments induced by (i) deformations of the sample due to radiation damage or (ii) drifting of the sample during the acquisition of an image in scanning transmission electron microscope mode. In both cases, those misalignments can give rise to artefacts in the reconstruction. We propose a simple-to-implement non-rigid alignment technique to correct those artefacts. This technique is particularly suited for needle-shaped samples in materials science. It is initiated by a rigid alignment of the projections and it is then followed by several rigid alignments of different parts of the projections. Piecewise linear deformations are applied to each projection to force them to simultaneously satisfy the rigid alignments of the different parts. The efficiency of this technique is demonstrated on three samples, an intermetallic sample with deformation misalignments due to a high electron dose typical to spectroscopic electron tomography, a porous silicon sample with an extremely thin end particularly sensitive to electron beam and another porous silicon sample that was drifting during image acquisitions.

  6. Non-rigid alignment in electron tomography in materials science.

    PubMed

    Printemps, Tony; Bernier, Nicolas; Bleuet, Pierre; Mula, Guido; Hervé, Lionel

    2016-09-01

    Electron tomography is a key technique that enables the visualization of an object in three dimensions with a resolution of about a nanometre. High-quality 3D reconstruction is possible thanks to the latest compressed sensing algorithms and/or better alignment and preprocessing of the 2D projections. Rigid alignment of 2D projections is routine in electron tomography. However, it cannot correct misalignments induced by (i) deformations of the sample due to radiation damage or (ii) drifting of the sample during the acquisition of an image in scanning transmission electron microscope mode. In both cases, those misalignments can give rise to artefacts in the reconstruction. We propose a simple-to-implement non-rigid alignment technique to correct those artefacts. This technique is particularly suited for needle-shaped samples in materials science. It is initiated by a rigid alignment of the projections and it is then followed by several rigid alignments of different parts of the projections. Piecewise linear deformations are applied to each projection to force them to simultaneously satisfy the rigid alignments of the different parts. The efficiency of this technique is demonstrated on three samples, an intermetallic sample with deformation misalignments due to a high electron dose typical to spectroscopic electron tomography, a porous silicon sample with an extremely thin end particularly sensitive to electron beam and another porous silicon sample that was drifting during image acquisitions. PMID:27018779

  7. Tomography of Particle Plasmon Fields from Electron Energy Loss Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hörl, Anton; Trügler, Andreas; Hohenester, Ulrich

    2013-08-01

    We theoretically investigate electron energy loss spectroscopy (EELS) of metallic nanoparticles in the optical frequency domain. Using a quasistatic approximation scheme together with a plasmon eigenmode expansion, we show that EELS can be rephrased in terms of a tomography problem. For selected single and coupled nanoparticles we extract the three-dimensional plasmon fields from a collection of rotated EELS maps. Our results pave the way for a fully three-dimensional plasmon-field tomography and establish EELS as a quantitative measurement device for plasmonics.

  8. Application of transmission electron tomography for modeling the renal corpuscle.

    PubMed

    Cheng, Delfine; Shen, Sylvie; Chen, Xin-Ming; Pollock, Carol; Braet, Filip

    2013-11-01

    Structural alteration to the microanatomical organization of the glomerular filtration barrier results in proteinuria. Conventional transmission electron microscopy is an important diagnostic tool to assess the degree of ultrastructural damage of the corpusclar filtration unit. However, this approach lacks the ability to collect accurate stereological insights in a relative large tissue volume. Transmission electron tomography offers the ability to gather three-dimensional information with relative ease. Therefore, this contribution aims to highlight what electron tomography can bring to the pathologist in this challenging area of diagnostic practice. Kidney tissue was prepared for routine ultrastructural transmission electron microscopy investigation. Three-dimensional data stacks were automatically acquired by tilting semi-thin sections of 270 nm in an angular range of typically -60° to +60° with 1° increment. Subsequently, models of the filtration unit were produced by computer-assisted tracking of structures of interest. This short report illustrates the capability that transmission electron tomography can offer in the fine structure-function assessment of the porous fenestrated glomerular capillary endothelium, the underlying basement membrane and the podocyte filtration slits. Furthermore, this approach allows the generation of morphometric data about size, shape and volume alterations of the kidney's filtration barrier at the nanoscale.

  9. Cryo-electron tomography of vaccinia virus

    PubMed Central

    Cyrklaff, Marek; Risco, Cristina; Fernández, Jose Jesús; Jiménez, Maria Victoria; Estéban, Mariano; Baumeister, Wolfgang; Carrascosa, José L.

    2005-01-01

    The combination of cryo-microscopy and electron tomographic reconstruction has allowed us to determine the structure of one of the more complex viruses, intracellular mature vaccinia virus, at a resolution of 4–6 nm. The tomographic reconstruction allows us to dissect the different structural components of the viral particle, avoiding projection artifacts derived from previous microscopic observations. A surface-rendering representation revealed brick-shaped viral particles with slightly rounded edges and dimensions of ≈360 × 270 × 250 nm. The outer layer was consistent with a lipid membrane (5–6 nm thick), below which usually two lateral bodies were found, built up by a heterogeneous material without apparent ordering or repetitive features. The internal core presented an inner cavity with electron dense coils of presumptive DNA–protein complexes, together with areas of very low density. The core was surrounded by two layers comprising an overall thickness of ≈18–19 nm; the inner layer was consistent with a lipid membrane. The outer layer was discontinuous, formed by a periodic palisade built by the side interaction of T-shaped protein spikes that were anchored in the lower membrane and were arranged into small hexagonal crystallites. It was possible to detect a few pore-like structures that communicated the inner side of the core with the region outside the layer built by the T-shaped spike palisade. PMID:15699328

  10. Electronic hardware design of electrical capacitance tomography systems.

    PubMed

    Saied, I; Meribout, M

    2016-06-28

    Electrical tomography techniques for process imaging are very prominent for industrial applications, such as the oil and gas industry and chemical refineries, owing to their ability to provide the flow regime of a flowing fluid within a relatively high throughput. Among the various techniques, electrical capacitance tomography (ECT) is gaining popularity due to its non-invasive nature and its capability to differentiate between different phases based on their permittivity distribution. In recent years, several hardware designs have been provided for ECT systems that have improved its resolution of measurements to be around attofarads (aF, 10(-18) F), or the number of channels, that is required to be large for some applications that require a significant amount of data. In terms of image acquisition time, some recent systems could achieve a throughput of a few hundred frames per second, while data processing time could be achieved in only a few milliseconds per frame. This paper outlines the concept and main features of the most recent front-end and back-end electronic circuits dedicated for ECT systems. In this paper, multiple-excitation capacitance polling, a front-end electronic technique, shows promising results for ECT systems to acquire fast data acquisition speeds. A highly parallel field-programmable gate array (FPGA) based architecture for a fast reconstruction algorithm is also described. This article is part of the themed issue 'Supersensing through industrial process tomography'. PMID:27185964

  11. Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography.

    PubMed

    Schmid, Michael F; Paredes, Angel M; Khant, Htet A; Soyer, Ferda; Aldrich, Henry C; Chiu, Wah; Shively, Jessup M

    2006-12-01

    Carboxysomes are polyhedral bodies consisting of a proteinaceous shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO). They are found in the cytoplasm of all cyanobacteria and some chemoautotrophic bacteria. Previous studies of Halothiobacillus neapolitanus and Nitrobacter agilis carboxysomes suggest that the structures are either icosahedral or dodecahedral. To determine the protein shell structure more definitively, purified H. neapolitanus carboxysomes were re-examined by cryo-electron tomography and scanning transmission electron microscopy (STEM). Due to the limited tilt angles in the electron microscope, the tomographic reconstructions are distorted. Corrections were made in the 3D orientation searching and averaging of the computationally extracted carboxysomes to minimize the missing data effects. It was found that H. neapolitanus carboxysomes vary widely in size and mass as shown by cryo-electron tomography and STEM mass measurements, respectively. We have aligned and averaged carboxysomes in several size classes from the 3D tomographic reconstruction by methods that are not model-biased. The averages reveal icosahedral symmetry of the shell, but not of the density inside it, for all the size classes.

  12. Markov random field based automatic alignment for low SNR imagesfor cryo electron tomography

    SciTech Connect

    Amat, Fernando; Moussavi, Farshid; Comolli, Luis R.; Elidan, Gal; Horowitz, Mark

    2007-07-21

    We present a method for automatic full precision alignmentof the images in a tomographic tilt series. Full-precision automaticalignment of cryo electron microscopy images has remained a difficultchallenge to date, due to the limited electron dose and low imagecontrast. These facts lead to poor signal to noise ratio (SNR) in theimages, which causes automatic feature trackers to generate errors, evenwith high contrast gold particles as fiducial features. To enable fullyautomatic alignment for full-precision reconstructions, we frame theproblem probabilistically as finding the most likely particle tracksgiven a set of noisy images, using contextual information to make thesolution more robust to the noise in each image. To solve this maximumlikelihood problem, we use Markov Random Fields (MRF) to establish thecorrespondence of features in alignment and robust optimization forprojection model estimation. The resultingalgorithm, called RobustAlignment and Projection Estimation for Tomographic Reconstruction, orRAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as goodas the manual approach by an expert user. We are able to automaticallymap complete and partial marker trajectories and thus obtain highlyaccurate image alignment. Our method has been applied to challenging cryoelectron tomographic datasets with low SNR from intact bacterial cells,as well as several plastic section and x-ray datasets.

  13. Nanoscale 3D cellular imaging by axial scanning transmission electron tomography

    PubMed Central

    Hohmann-Marriott, Martin F.; Sousa, Alioscka A.; Azari, Afrouz A.; Glushakova, Svetlana; Zhang, Guofeng; Zimmerberg, Joshua; Leapman, Richard D.

    2009-01-01

    Electron tomography provides three-dimensional structural information about supramolecular assemblies and organelles in a cellular context but image degradation, caused by scattering of transmitted electrons, limits applicability in specimens thicker than 300 nm. We show that scanning transmission electron tomography of 1000 nm thick samples using axial detection provides resolution comparable to conventional electron tomography. The method is demonstrated by reconstructing a human erythrocyte infected with the malaria parasite Plasmodium falciparum. PMID:19718033

  14. STEM electron tomography in the Scanning Electron Microscope

    NASA Astrophysics Data System (ADS)

    Ferroni, M.; Signoroni, A.; Sanzogni, A.; Sberveglieri, G.; Migliori, A.; Ortolani, L.; Christian, M.; Masini, L.; Morandi, V.

    2015-10-01

    The scanning-transmission imaging mode in the SEM allows for the threedimensional tomographic reconstruction of a specimen, starting from a set of projection images. Compressed sensing was used to solve the undetermined problem of structure reconstruction and was proven capable of overcoming the limitations arising from the sampling scheme. Reconstructions of cobalt particles within a carbon nanotube and collagen fibrils in a dermal tissue are presented, demonstrating the potential of this technique in the set of 3-D electron microscopy methods for both physical and biological science.

  15. TOM software toolbox: acquisition and analysis for electron tomography.

    PubMed

    Nickell, Stephan; Förster, Friedrich; Linaroudis, Alexandros; Net, William Del; Beck, Florian; Hegerl, Reiner; Baumeister, Wolfgang; Plitzko, Jürgen M

    2005-03-01

    Automated data acquisition procedures have changed the perspectives of electron tomography (ET) in a profound manner. Elaborate data acquisition schemes with autotuning functions minimize exposure of the specimen to the electron beam and sophisticated image analysis routines retrieve a maximum of information from noisy data sets. "TOM software toolbox" integrates established algorithms and new concepts tailored to the special needs of low dose ET. It provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis. Designed as a collection of computational procedures it is a complete software solution within a highly flexible framework. TOM represents a new way of working with the electron microscope and can serve as the basis for future high-throughput applications.

  16. Cellular structural biology as revealed by cryo-electron tomography.

    PubMed

    Irobalieva, Rossitza N; Martins, Bruno; Medalia, Ohad

    2016-02-01

    Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.

  17. Physically motivated global alignment method for electron tomography

    DOE PAGESBeta

    Sanders, Toby; Prange, Micah; Akatay, Cem; Binev, Peter

    2015-04-08

    Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop amore » new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.« less

  18. Physically motivated global alignment method for electron tomography

    SciTech Connect

    Sanders, Toby; Prange, Micah; Akatay, Cem; Binev, Peter

    2015-04-08

    Electron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop a new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.

  19. Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography.

    PubMed

    Chang, Yi-Wei; Chen, Songye; Tocheva, Elitza I; Treuner-Lange, Anke; Löbach, Stephanie; Søgaard-Andersen, Lotte; Jensen, Grant J

    2014-07-01

    Cryo-electron tomography (CET) produces three-dimensional images of cells in a near-native state at macromolecular resolution, but identifying structures of interest can be challenging. Here we describe a correlated cryo-PALM (photoactivated localization microscopy)-CET method for localizing objects within cryo-tomograms to beyond the diffraction limit of the light microscope. Using cryo-PALM-CET, we identified multiple and new conformations of the dynamic type VI secretion system in the crowded interior of Myxococcus xanthus.

  20. Understanding Cellulose Through Molecular Simulation and Electron Tomography

    SciTech Connect

    Matthews, J.

    2013-01-01

    High-resolution cellulose crystal structures have been determined from diffraction experiments using large diameter microfibrils as the sample material. However, cellulose microfibrils in plants are much smaller in diameter, and are more difficult to directly examine experimentally. Molecular dynamics simulation combined with quantum chemical calculations can help to elucidate the structure and dynamics of small diameter cellulose microfibrils. These simulation techniques also aid in the interpretation of electron tomography volumetric structural data from maize cell walls, where pretreatment with dilute acid or ammonia reveals microfibril geometry.

  1. Recent Advances in Electron Tomography: TEM and HAADF-STEM Tomography for Materials Science and IC Applications

    SciTech Connect

    Kubel, C; Voigt, A; Schoenmakers, R; Otten, M; Su, D; Lee, T; Carlsson, A; Engelmann, H; Bradley, J

    2005-11-09

    Electron tomograph tomography is a well y well-established technique for three-dimensional structure determination of (almost) amorphous specimens in life science applications. With the recent advances in nanotechnology and the semiconductor industry, there is also an increasing need for high-resolution 3D structural information in physical sciences. In this paper, we evaluate the capabilities and limitations of TEM and HAADF-STEM tomography for the 3D structural characterization of partially crystalline to highly crystalline materials. Our analysis of catalysts, a hydrogen storage material, and different semiconductor devices shows that features with a diameter as small as 1-2 nm can be resolved in 3D by electron tomography. For partially crystalline materials with small single crystalline domains, TEM tomography provides reliable 3D structural information. HAADF-STEM tomography is more versatile and can also be used for high-resolution 3D imaging of highly crystalline materials such as semiconductor devices.

  2. Mineral and organic matrix interaction in normally calcifying tendon visualized in three dimensions by high-voltage electron microscopic tomography and graphic image reconstruction

    NASA Technical Reports Server (NTRS)

    Landis, W. J.; Song, M. J.; Leith, A.; McEwen, L.; McEwen, B. F.

    1993-01-01

    To define the ultrastructural accommodation of mineral crystals by collagen fibrils and other organic matrix components during vertebrate calcification, electron microscopic 3-D reconstructions were generated from the normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo. Embedded specimens containing initial collagen mineralizing sites were cut into 0.5-micron-thick sections and viewed and photographed at 1.0 MV in the Albany AEI-EM7 high-voltage electron microscope. Tomographic 3-D reconstructions were computed from a 2 degree tilt series of micrographs taken over a minimum angular range of +/- 60 degrees. Reconstructions of longitudinal tendon profiles confirm the presence of irregularly shaped mineral platelets, whose crystallographic c-axes are oriented generally parallel to one another and directed along the collagen long axes. The reconstructions also corroborate observations of a variable crystal length (up to 170 nm measured along crystallographic c-axes), the presence of crystals initially in either the hole or overlap zones of collagen, and crystal growth in the c-axis direction beyond these zones into adjacent overlap and other hole regions. Tomography shows for the first time that crystal width varies (30-45 nm) but crystal thickness is uniform (approximately 4-6 nm at the resolution limit of tomography); more crystals are located in the collagen hole zones than in the overlap regions at the earliest stages of tendon mineralization; the crystallographic c-axes of the platelets lie within +/- 15-20 degrees of one another rather than being perfectly parallel; adjacent platelets are spatially separated by a minimum of 4.2 +/- 1.0 nm; crystals apparently fuse in coplanar alignment to form larger platelets; development of crystals in width occurs to dimensions beyond single collagen hole zones; and a thin envelope of organic origin may be present along or just beneath the surfaces of individual mineral platelets. Implicit in the

  3. Correlated Light and Electron Microscopy/Electron Tomography of Mitochondria In Situ

    PubMed Central

    Perkins, Guy A.; Sun, Mei G.; Frey, Terrence G.

    2009-01-01

    Three-dimensional light microscopy and three-dimensional electron microscopy (electron tomography) separately provide very powerful tools to study cellular structure and physiology, including the structure and physiology of mitochondria. Fluorescence microscopy allows one to study processes in live cells with specific labels and stains that follow the movement of labeled proteins and changes within cellular compartments but does not have sufficient resolution to define the ultrastructure of intracellular organelles such as mitochondria. Electron microscopy and electron tomography provide the highest resolution currently available to study mitochondrial ultrastructure but cannot follow processes in living cells. We describe the combination of these two techniques in which fluorescence confocal microscopy is used to study structural and physiologic changes in mitochondria within apoptotic HeLa cells to define the apoptotic timeframe. Cells can then be selected at various stages of the apoptotic timeframe for examination at higher resolution by electron microscopy and electron tomography. This is a form of “virtual” 4-dimensional electron microscopy that has revealed interesting structural changes in the mitochondria of HeLa cells during apoptosis. The same techniques can be applied, with modification, to study other dynamic processes within cells in other experimental contexts. PMID:19348881

  4. Local regularization of tilt projections reduces artifacts in electron tomography.

    PubMed

    Maiorca, Mauro; Millet, Coralie; Hanssen, Eric; Abbey, Brian; Kazmierczak, Edmund; Tilley, Leann

    2014-04-01

    Electron tomography produces very high resolution 3D image volumes useful for investigating the structure and function of cellular components. Unfortunately, unavoidable discontinuities and physical constraints in the acquisition geometry lead to a range of artifacts that can affect the reconstructed image. In particular, highly electron dense regions, such as gold nanoparticles, can hide proximal biological structures and degrade the overall quality of the reconstructed tomograms. In this work we introduce a pre-reconstruction non-conservative non-linear isotropic diffusion (NID) filter that automatically identifies and reduces local irregularities in the tilt projections. We illustrate the improvement in quality obtained using this approach for reconstructed tomograms generated from samples of malaria parasite-infected red blood cells. A quantitative and qualitative evaluation for our approach on both simulated and real data is provided.

  5. Pictorial review: electron beam computed tomography and multislice spiral computed tomography for cardiac imaging.

    PubMed

    Lembcke, Alexander; Hein, Patrick A; Dohmen, Pascal M; Klessen, Christian; Wiese, Till H; Hoffmann, Udo; Hamm, Bernd; Enzweiler, Christian N H

    2006-03-01

    Electron beam computed tomography (EBCT) revolutionized cardiac imaging by combining a constant high temporal resolution with prospective ECG triggering. For years, EBCT was the primary technique for some non-invasive diagnostic cardiac procedures such as calcium scoring and non-invasive angiography of the coronary arteries. Multislice spiral computed tomography (MSCT) on the other hand significantly advanced cardiac imaging through high volume coverage, improved spatial resolution and retrospective ECG gating. This pictorial review will illustrate the basic differences between both modalities with special emphasis to their image quality. Several experimental and clinical examples demonstrate the strengths and limitations of both imaging modalities in an intraindividual comparison for a broad range of diagnostic applications such as coronary artery calcium scoring, coronary angiography including stent visualization as well as functional assessment of the cardiac ventricles and valves. In general, our examples indicate that EBCT suffers from a number of shortcomings such as limited spatial resolution and a low contrast-to-noise ratio. Thus, EBCT should now only be used in selected cases where a constant high temporal resolution is a crucial issue, such as dynamic (cine) imaging. Due to isotropic submillimeter spatial resolution and retrospective data selection MSCT seems to be the non-invasive method of choice for cardiac imaging in general, and for assessment of the coronary arteries in particular. However, technical developments are still needed to further improve the temporal resolution in MSCT and to reduce the substantial radiation exposure. PMID:16427236

  6. A cylindrical specimen holder for electron cryo-tomography.

    PubMed

    Palmer, Colin M; Löwe, Jan

    2014-02-01

    The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the "missing wedge" problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future. PMID:24275523

  7. A cylindrical specimen holder for electron cryo-tomography

    PubMed Central

    Palmer, Colin M.; Löwe, Jan

    2014-01-01

    The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the “missing wedge” problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future. PMID:24275523

  8. Mapping Synapses by Conjugate Light-Electron Array Tomography

    PubMed Central

    Buchanan, JoAnn; Phend, Kristen D.; Micheva, Kristina D.; Weinberg, Richard J.; Smith, Stephen J

    2015-01-01

    Synapses of the mammalian CNS are diverse in size, structure, molecular composition, and function. Synapses in their myriad variations are fundamental to neural circuit development, homeostasis, plasticity, and memory storage. Unfortunately, quantitative analysis and mapping of the brain's heterogeneous synapse populations has been limited by the lack of adequate single-synapse measurement methods. Electron microscopy (EM) is the definitive means to recognize and measure individual synaptic contacts, but EM has only limited abilities to measure the molecular composition of synapses. This report describes conjugate array tomography (AT), a volumetric imaging method that integrates immunofluorescence and EM imaging modalities in voxel-conjugate fashion. We illustrate the use of conjugate AT to advance the proteometric measurement of EM-validated single-synapse analysis in a study of mouse cortex. PMID:25855189

  9. 3D Observation of GEMS by Electron Tomography

    NASA Technical Reports Server (NTRS)

    Matsuno, Junya; Miyake, Akira; Tsuchiyama, Akira; Nakamura-Messenger, Keiko; Messenger, Scott

    2014-01-01

    Amorphous silicates in chondritic porous interplanetary dust particles (CP-IDPs) coming from comets are dominated by glass with embedded metal and sulfides (GEMS). GEMS grains are submicron-sized rounded objects (typically 100-500) nm in diameter) with anaometer-sized (10-50 nm) Fe-Ni metal and sulfide grains embedded in an amorphous silicate matrix. Several formation processes for GEMS grains have been proposed so far, but these models are still being debated [2-5]. Bradley et al. proposed that GEMS grains are interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk and that they are amorphiation products of crystalline silicates in the interstellar medium by sputter-deposition of cosmic ray irradiation, similar to space weathering [2,4]. This consideration is based on the observation of nano-sized crystals (approximately 10 nm) called relict grains in GEMS grains and their shapes are pseudomorphs to the host GEMS grains. On the other hand, Keller and Messenger proposed that most GEMS formed in the protoplanetary disk as condensates from high temperature gas [3,5]. This model is based on the fact that most GEMS grains have solar isotopic compositions and have extremely heterogeneous and non-solar elemental compositions. Keller and Messenger (2011) also reported that amorphous silicates in GEMS grains are surrounded by sulfide grains, which formed as sulfidization of metallic iron grains located on the GEMS surface. The previous studies were performed with 2D observation by using transmission electron microscopy (TEM) or scanning TEM (STEM). In order to understand the structure of GEMS grains described above more clearly, we observed 3D structure of GEMS grains by electron tomography using a TEM/STEM (JEM-2100F, JEOL) at Kyoto University. Electron tomography gives not only 3D structures but also gives higher spatial resolution (approximately a few nm) than that in conventional 2D image, which is restricted by

  10. Robust registration of electron tomography projections without fiducial markers

    NASA Astrophysics Data System (ADS)

    Tran, Viet-Dung; Moreaud, Maxime; Thiébaut, Éric; Dénis, Loïc.; Becker, Jean-Marie

    2013-02-01

    A major issue in electron tomography is the misalignment of the projections contributing to the reconstruction. The current alignment techniques currently use fiducial markers such as gold particles. When the use of markers is not possible, the accurate alignment of the projections is a challenge. We describe a new method for the alignment of transmission electron microscopy (TEM) images series without the need of fiducial markers. The proposed approach is composed of two steps. The first step consists of an initial alignment process, which relies on the minimization of a cost function based on robust statistics measuring the similarity of a projection to its previous projections in the series. It reduces strong shifts resulting from the acquisition between successive projections. The second step aligns the projections finely. The issue is formalized as an inverse problem. The pre­ registered projections are used to initialize an iterative alignment-refinement process which alternates between (i) volume reconstructions and (ii) registrations of measured projections onto simulated projections computed from the volume reconstructed in (i). The accuracy of our method is very satisfying; we illustrate it on simulated data and real projections of different zeolite supports catalyst.

  11. Developments in cryo-electron tomography for in situ structural analysis.

    PubMed

    Dubrovsky, Anna; Sorrentino, Simona; Harapin, Jan; Sapra, K Tanuj; Medalia, Ohad

    2015-09-01

    Structural analysis of macromolecular assemblies and their remodeling during physiological processes is instrumental to defining the fundament of cellular and molecular biology. Recent advances in computational and analytical tools for cryo-electron tomography have enabled the study of macromolecular structures in their native environment, providing unprecedented insights into cell function. Moreover, the recent implementation of direct electron detectors has progressed cryo-electron tomography to a stage where it can now be applied to the reconstruction of macromolecular structures at high resolutions. Here, we discuss some of the recent technical developments in cryo-electron tomography to reveal structures of macromolecular complexes in their physiological medium, focusing mainly on eukaryotic cells.

  12. Compressed Sensing Electron tomography using adaptive dictionaries: a simulation study

    NASA Astrophysics Data System (ADS)

    AlAfeef, A.; Cockshott, P.; MacLaren, I.; McVitie, S.

    2014-06-01

    Electron tomography (ET) is an increasingly important technique for examining the three-dimensional morphologies of nanostructures. ET involves the acquisition of a set of 2D projection images to be reconstructed into a volumetric image by solving an inverse problem. However, due to limitations in the acquisition process this inverse problem is considered ill-posed (i.e., no unique solution exists). Furthermore reconstruction usually suffers from missing wedge artifacts (e.g., star, fan, blurring, and elongation artifacts). Compressed sensing (CS) has recently been applied to ET and showed promising results for reducing missing wedge artifacts caused by limited angle sampling. CS uses a nonlinear reconstruction algorithm that employs image sparsity as a priori knowledge to improve the accuracy of density reconstruction from a relatively small number of projections compared to other reconstruction techniques. However, The performance of CS recovery depends heavily on the degree of sparsity of the reconstructed image in the selected transform domain. Prespecified transformations such as spatial gradients provide sparse image representation, while synthesising the sparsifying transform based on the properties of the particular specimen may give even sparser results and can extend the application of CS to specimens that can not be sparsely represented with other transforms such as Total variation (TV). In this work, we show that CS reconstruction in ET can be significantly improved by tailoring the sparsity representation using a sparse dictionary learning principle.

  13. Noninvasive coronary artery angiography using electron beam computed tomography

    NASA Astrophysics Data System (ADS)

    Rumberger, John A.; Rensing, Benno J.; Reed, Judd E.; Ritman, Erik L.; Sheedy, Patrick F., II

    1996-04-01

    Electron beam computed tomography (EBCT), also known as ultrafast-CT or cine-CT, uses a unique scanning architecture which allows for multiple high spatial resolution electrocardiographic triggered images of the beating heart. A recent study has demonstrated the feasibility of qualitative comparisons between EBCT derived 3D coronary angiograms and invasive angiography. Stenoses of the proximal portions of the left anterior descending and right coronary arteries were readily identified, but description of atherosclerotic narrowing in the left circumflex artery (and distal epicardial disease) was not possible with any degree of confidence. Although these preliminary studies support the notion that this approach has potential, the images overall were suboptimal for clinical application as an adjunct to invasive angiography. Furthermore, these studies did not examine different methods of EBCT scan acquisition, tomographic slice thicknesses, extent of scan overlap, or other segmentation, thresholding, and interpolation algorithms. Our laboratory has initiated investigation of these aspects and limitations of EBCT coronary angiography. Specific areas of research include defining effects of cardiac orientation; defining the effects of tomographic slice thickness and intensity (gradient) versus positional (shaped based) interpolation; and defining applicability of imaging each of the major epicardial coronary arteries for quantitative definition of vessel size, cross-sectional area, taper, and discrete vessel narrowing.

  14. Electron Tomography Reveals the Steps in Filovirus Budding

    PubMed Central

    Welsch, Sonja; Kolesnikova, Larissa; Krähling, Verena; Riches, James D.; Becker, Stephan; Briggs, John A. G.

    2010-01-01

    The filoviruses, Marburg and Ebola, are non-segmented negative-strand RNA viruses causing severe hemorrhagic fever with high mortality rates in humans and nonhuman primates. The sequence of events that leads to release of filovirus particles from cells is poorly understood. Two contrasting mechanisms have been proposed, one proceeding via a “submarine-like” budding with the helical nucleocapsid emerging parallel to the plasma membrane, and the other via perpendicular “rocket-like” protrusion. Here we have infected cells with Marburg virus under BSL-4 containment conditions, and reconstructed the sequence of steps in the budding process in three dimensions using electron tomography of plastic-embedded cells. We find that highly infectious filamentous particles are released at early stages in infection. Budding proceeds via lateral association of intracellular nucleocapsid along its whole length with the plasma membrane, followed by rapid envelopment initiated at one end of the nucleocapsid, leading to a protruding intermediate. Scission results in local membrane instability at the rear of the virus. After prolonged infection, increased vesiculation of the plasma membrane correlates with changes in shape and infectivity of released viruses. Our observations demonstrate a cellular determinant of virus shape. They reconcile the contrasting models of filovirus budding and allow us to describe the sequence of events taking place during budding and release of Marburg virus. We propose that this represents a general sequence of events also followed by other filamentous and rod-shaped viruses. PMID:20442788

  15. Model based iterative reconstruction for Bright Field electron tomography

    NASA Astrophysics Data System (ADS)

    Venkatakrishnan, Singanallur V.; Drummy, Lawrence F.; De Graef, Marc; Simmons, Jeff P.; Bouman, Charles A.

    2013-02-01

    Bright Field (BF) electron tomography (ET) has been widely used in the life sciences to characterize biological specimens in 3D. While BF-ET is the dominant modality in the life sciences it has been generally avoided in the physical sciences due to anomalous measurements in the data due to a phenomenon called "Bragg scatter" - visible when crystalline samples are imaged. These measurements cause undesirable artifacts in the reconstruction when the typical algorithms such as Filtered Back Projection (FBP) and Simultaneous Iterative Reconstruction Technique (SIRT) are applied to the data. Model based iterative reconstruction (MBIR) provides a powerful framework for tomographic reconstruction that incorporates a model for data acquisition, noise in the measurement and a model for the object to obtain reconstructions that are qualitatively superior and quantitatively accurate. In this paper we present a novel MBIR algorithm for BF-ET which accounts for the presence of anomalous measurements from Bragg scatter in the data during the iterative reconstruction. Our method accounts for the anomalies by formulating the reconstruction as minimizing a cost function which rejects measurements that deviate significantly from the typical Beer's law model widely assumed for BF-ET. Results on simulated as well as real data show that our method can dramatically improve the reconstructions compared to FBP and MBIR without anomaly rejection, suppressing the artifacts due to the Bragg anomalies.

  16. STEM Tomography Imaging of Hypertrophied Golgi Stacks in Mucilage-Secreting Cells.

    PubMed

    Kang, Byung-Ho

    2016-01-01

    Because of the weak penetrating power of electrons, the signal-to-noise ratio of a transmission electron micrograph (TEM) worsens as section thickness increases. This problem is alleviated by the use of the scanning transmission electron microscopy (STEM). Tomography analyses using STEM of thick sections from yeast and mammalian cells are of higher quality than are bright-field (BF) images. In this study, we compared regular BF tomograms and STEM tomograms from 500-nm thick sections from hypertrophied Golgi stacks of alfalfa root cap cells. Due to their thickness and intense heavy metal staining, BF tomograms of the thick sections suffer from poor contrast and high noise levels. We were able to mitigate these drawbacks by using STEM tomography. When we performed STEM tomography of densely stained chloroplasts of Arabidopsis cotyledon, we observed similar improvements relative to BF tomograms. A longer time is required to collect a STEM tilt series than similar BF TEM images, and dynamic autofocusing required for STEM imaging often fails at high tilt angles. Despite these limitations, STEM tomography is a powerful method for analyzing structures of large or dense organelles of plant cells.

  17. STEM Tomography Imaging of Hypertrophied Golgi Stacks in Mucilage-Secreting Cells.

    PubMed

    Kang, Byung-Ho

    2016-01-01

    Because of the weak penetrating power of electrons, the signal-to-noise ratio of a transmission electron micrograph (TEM) worsens as section thickness increases. This problem is alleviated by the use of the scanning transmission electron microscopy (STEM). Tomography analyses using STEM of thick sections from yeast and mammalian cells are of higher quality than are bright-field (BF) images. In this study, we compared regular BF tomograms and STEM tomograms from 500-nm thick sections from hypertrophied Golgi stacks of alfalfa root cap cells. Due to their thickness and intense heavy metal staining, BF tomograms of the thick sections suffer from poor contrast and high noise levels. We were able to mitigate these drawbacks by using STEM tomography. When we performed STEM tomography of densely stained chloroplasts of Arabidopsis cotyledon, we observed similar improvements relative to BF tomograms. A longer time is required to collect a STEM tilt series than similar BF TEM images, and dynamic autofocusing required for STEM imaging often fails at high tilt angles. Despite these limitations, STEM tomography is a powerful method for analyzing structures of large or dense organelles of plant cells. PMID:27632001

  18. Advanced prior modeling for 3D bright field electron tomography

    NASA Astrophysics Data System (ADS)

    Sreehari, Suhas; Venkatakrishnan, S. V.; Drummy, Lawrence F.; Simmons, Jeffrey P.; Bouman, Charles A.

    2015-03-01

    Many important imaging problems in material science involve reconstruction of images containing repetitive non-local structures. Model-based iterative reconstruction (MBIR) could in principle exploit such redundancies through the selection of a log prior probability term. However, in practice, determining such a log prior term that accounts for the similarity between distant structures in the image is quite challenging. Much progress has been made in the development of denoising algorithms like non-local means and BM3D, and these are known to successfully capture non-local redundancies in images. But the fact that these denoising operations are not explicitly formulated as cost functions makes it unclear as to how to incorporate them in the MBIR framework. In this paper, we formulate a solution to bright field electron tomography by augmenting the existing bright field MBIR method to incorporate any non-local denoising operator as a prior model. We accomplish this using a framework we call plug-and-play priors that decouples the log likelihood and the log prior probability terms in the MBIR cost function. We specifically use 3D non-local means (NLM) as the prior model in the plug-and-play framework, and showcase high quality tomographic reconstructions of a simulated aluminum spheres dataset, and two real datasets of aluminum spheres and ferritin structures. We observe that streak and smear artifacts are visibly suppressed, and that edges are preserved. Also, we report lower RMSE values compared to the conventional MBIR reconstruction using qGGMRF as the prior model.

  19. Formation of bimetallic clusters in superfluid helium nanodroplets analysed by atomic resolution electron tomography

    PubMed Central

    Haberfehlner, Georg; Thaler, Philipp; Knez, Daniel; Volk, Alexander; Hofer, Ferdinand; Ernst, Wolfgang E.; Kothleitner, Gerald

    2015-01-01

    Structure, shape and composition are the basic parameters responsible for properties of nanoscale materials, distinguishing them from their bulk counterparts. To reveal these in three dimensions at the nanoscale, electron tomography is a powerful tool. Advancing electron tomography to atomic resolution in an aberration-corrected transmission electron microscope remains challenging and has been demonstrated only a few times using strong constraints or extensive filtering. Here we demonstrate atomic resolution electron tomography on silver/gold core/shell nanoclusters grown in superfluid helium nanodroplets. We reveal morphology and composition of a cluster identifying gold- and silver-rich regions in three dimensions and we estimate atomic positions without using any prior information and with minimal filtering. The ability to get full three-dimensional information down to the atomic scale allows understanding the growth and deposition process of the nanoclusters and demonstrates an approach that may be generally applicable to all types of nanoscale materials. PMID:26508471

  20. Developments in cryo-electron tomography for in situ structural analysis.

    PubMed

    Dubrovsky, Anna; Sorrentino, Simona; Harapin, Jan; Sapra, K Tanuj; Medalia, Ohad

    2015-09-01

    Structural analysis of macromolecular assemblies and their remodeling during physiological processes is instrumental to defining the fundament of cellular and molecular biology. Recent advances in computational and analytical tools for cryo-electron tomography have enabled the study of macromolecular structures in their native environment, providing unprecedented insights into cell function. Moreover, the recent implementation of direct electron detectors has progressed cryo-electron tomography to a stage where it can now be applied to the reconstruction of macromolecular structures at high resolutions. Here, we discuss some of the recent technical developments in cryo-electron tomography to reveal structures of macromolecular complexes in their physiological medium, focusing mainly on eukaryotic cells. PMID:25921875

  1. Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography.

    PubMed

    Nickell, Stephan; Hegerl, Reiner; Baumeister, Wolfgang; Rachel, Reinhard

    2003-01-01

    The hyperthermophilic archaeon Pyrodictium grows in the form of a macroscopically visible network. It consists of cells entrapped in an extracellular matrix of hollow tubules, the "cannulae." Here, we present the three-dimensional structure of a single cell in conjunction with two extracellular cannulae, as determined by cryo-electron microscopy. To achieve this, the information from two independent tilt series of the same specimen was combined, with the specimen rotated in the second series. In the three-dimensional tomographic reconstruction, we were able to trace the two cannulae in their full length, in particular, also inside the cell. One cannula enters the periplasmic space, while the other cannula contacts the surface of the cell, the S-layer. This indicates that the cannulae interconnect individual cells with each other on the level of their periplasmic space; we do not, however, have evidence that they enter the cytoplasm of the cells. The implications of these data for possible functions of the cannulae are discussed.

  2. Development of a novel straining holder for transmission electron microscopy compatible with single tilt-axis electron tomography.

    PubMed

    Sato, K; Miyazaki, H; Gondo, T; Miyazaki, S; Murayama, M; Hata, S

    2015-10-01

    We have developed a newly designed straining specimen holder for in situ transmission electron microscopy (TEM) compatible with high-angle single tilt-axis electron tomography. The holder can deform a TEM specimen under tensile stress with the strain rate between 1.5 × 10(-6) and 5.2 × 10(-3) s(-1). We have also confirmed that the maximum tilt angle of the specimen holder reaches ±60° with a rectangular shape aluminum specimen. The new specimen holder, termed as 'straining and tomography holder', will have wide range potential applications in materials science. PMID:25904643

  3. Electron tomography of HEK293T cells using scanning electron microscope-based scanning transmission electron microscopy.

    PubMed

    You, Yun-Wen; Chang, Hsun-Yun; Liao, Hua-Yang; Kao, Wei-Lun; Yen, Guo-Ji; Chang, Chi-Jen; Tsai, Meng-Hung; Shyue, Jing-Jong

    2012-10-01

    Based on a scanning electron microscope operated at 30 kV with a homemade specimen holder and a multiangle solid-state detector behind the sample, low-kV scanning transmission electron microscopy (STEM) is presented with subsequent electron tomography for three-dimensional (3D) volume structure. Because of the low acceleration voltage, the stronger electron-atom scattering leads to a stronger contrast in the resulting image than standard TEM, especially for light elements. Furthermore, the low-kV STEM yields less radiation damage to the specimen, hence the structure can be preserved. In this work, two-dimensional STEM images of a 1-μm-thick cell section with projection angles between ±50° were collected, and the 3D volume structure was reconstructed using the simultaneous iterative reconstructive technique algorithm with the TomoJ plugin for ImageJ, which are both public domain software. Furthermore, the cross-sectional structure was obtained with the Volume Viewer plugin in ImageJ. Although the tilting angle is constrained and limits the resulting structural resolution, slicing the reconstructed volume generated the depth profile of the thick specimen with sufficient resolution to examine cellular uptake of Au nanoparticles, and the final position of these nanoparticles inside the cell was imaged.

  4. TEM, HRTEM, electron holography and electron tomography studies of gamma' and gamma'' nanoparticles in Inconel 718 superalloy.

    PubMed

    Dubiel, B; Kruk, A; Stepniowska, E; Cempura, G; Geiger, D; Formanek, P; Hernandez, J; Midgley, P; Czyrska-Filemonowicz, A

    2009-11-01

    The aim of the study was the identification of gamma' and gamma'' strengthening precipitates in a commercial nickel-base superalloy Inconel 718 (Ni-19Fe-18Cr-5Nb-3Mo-1Ti-0.5Al-0.04C, wt %) using TEM dark-field, HRTEM, electron holography and electron tomography imaging. To identify gamma' and gamma'' nanoparticles unambiguously, a systematic analysis of experimental and theoretical diffraction patterns were performed. Using HRTEM method it was possible to analyse small areas of precipitates appearance. Electron holography and electron tomography techniques show new possibilities of visualization of gamma' and gamma'' nanoparticles. The analysis by means of different complementary TEM methods showed that gamma'' particles exhibit a shape of thin plates, while gamma' phase precipitates are almost spherical. PMID:19903242

  5. The emergence of electron tomography as an important tool for investigating cellular ultrastructure.

    PubMed

    McEwen, B F; Marko, M

    2001-05-01

    Electron tomography has emerged as the leading method for the study of three-dimensional (3D) ultrastructure in the 5-20-nm resolution range. It is ideally suited for studying cell organelles, subcellular assemblies and, in some cases, whole cells. Tomography occupies a place in 3D biological electron microscopy between the work now being done at near-atomic resolution on isolated macromolecules or 2D protein arrays and traditional serial-section reconstructions of whole cells and tissue specimens. Tomography complements serial-section reconstruction by providing higher resolution in the depth dimension, whereas serial-section reconstruction is better able to trace continuity over long distances throughout the depth of a cell. The two techniques can be combined with good results for favorable specimens. Tomography also complements 3D macromolecular studies by offering sufficient resolution to locate the macromolecular complexes in their cellular context. The technology has matured to the point at which application of electron tomography to specimens in plastic sections is routine, and new developments to overcome limitations due to beam exposure and specimen geometry promise to further improve its capabilities. In this review we give a brief description of the methodology and a summary of the new insights gained in a few representative applications.(J Histochem Cytochem 49:553-563, 2001)

  6. Telocytes and putative stem cells in the lungs: electron microscopy, electron tomography and laser scanning microscopy.

    PubMed

    Popescu, Laurentiu M; Gherghiceanu, Mihaela; Suciu, Laura C; Manole, Catalin G; Hinescu, Mihail E

    2011-09-01

    This study describes a novel type of interstitial (stromal) cell - telocytes (TCs) - in the human and mouse respiratory tree (terminal and respiratory bronchioles, as well as alveolar ducts). TCs have recently been described in pleura, epicardium, myocardium, endocardium, intestine, uterus, pancreas, mammary gland, etc. (see www.telocytes.com ). TCs are cells with specific prolongations called telopodes (Tp), frequently two to three per cell. Tp are very long prolongations (tens up to hundreds of μm) built of alternating thin segments known as podomers (≤ 200 nm, below the resolving power of light microscope) and dilated segments called podoms, which accommodate mitochondria, rough endoplasmic reticulum and caveolae. Tp ramify dichotomously, making a 3-dimensional network with complex homo- and heterocellular junctions. Confocal microscopy reveals that TCs are c-kit- and CD34-positive. Tp release shed vesicles or exosomes, sending macromolecular signals to neighboring cells and eventually modifying their transcriptional activity. At bronchoalveolar junctions, TCs have been observed in close association with putative stem cells (SCs) in the subepithelial stroma. SCs are recognized by their ultrastructure and Sca-1 positivity. Tp surround SCs, forming complex TC-SC niches (TC-SCNs). Electron tomography allows the identification of bridging nanostructures, which connect Tp with SCs. In conclusion, this study shows the presence of TCs in lungs and identifies a TC-SC tandem in subepithelial niches of the bronchiolar tree. In TC-SCNs, the synergy of TCs and SCs may be based on nanocontacts and shed vesicles.

  7. Annular dark-field scanning transmission electron microscopy (ADF-STEM) tomography of polymer systems.

    PubMed

    Lu, Kangbo; Sourty, Erwan; Loos, Joachim

    2010-08-01

    We have utilized bright-field conventional transmission electron microscopy tomography and annular dark-field scanning transmission electron microscopy (ADF-STEM) tomography to characterize a well-defined carbon black (CB)-filled polymer nanocomposite with known CB volume concentration. For both imaging methods, contrast can be generated between the CB and the surrounding polymer matrix. The involved contrast mechanisms, in particular for ADF-STEM, will be discussed in detail. The obtained volume reconstructions were analysed and the CB volume concentrations were carefully determined from the reconstructed data. For both imaging modes, the measured CB volume concentrations are substantially different and only quantification based on the ADF-STEM data revealed about the same value as the known CB loading. Moreover, when applying low-convergence angles for imaging ADF-STEM tomography, data can be obtained of micrometre-thick samples.

  8. Scanning precession electron tomography for three-dimensional nanoscale orientation imaging and crystallographic analysis.

    PubMed

    Eggeman, Alexander S; Krakow, Robert; Midgley, Paul A

    2015-01-01

    Three-dimensional (3D) reconstructions from electron tomography provide important morphological, compositional, optical and electro-magnetic information across a wide range of materials and devices. Precession electron diffraction, in combination with scanning transmission electron microscopy, can be used to elucidate the local orientation of crystalline materials. Here we show, using the example of a Ni-base superalloy, that combining these techniques and extending them to three dimensions, to produce scanning precession electron tomography, enables the 3D orientation of nanoscale sub-volumes to be determined and provides a one-to-one correspondence between 3D real space and 3D reciprocal space for almost any polycrystalline or multi-phase material. PMID:26028514

  9. Scanning precession electron tomography for three-dimensional nanoscale orientation imaging and crystallographic analysis

    PubMed Central

    Eggeman, Alexander S.; Krakow, Robert; Midgley, Paul A.

    2015-01-01

    Three-dimensional (3D) reconstructions from electron tomography provide important morphological, compositional, optical and electro-magnetic information across a wide range of materials and devices. Precession electron diffraction, in combination with scanning transmission electron microscopy, can be used to elucidate the local orientation of crystalline materials. Here we show, using the example of a Ni-base superalloy, that combining these techniques and extending them to three dimensions, to produce scanning precession electron tomography, enables the 3D orientation of nanoscale sub-volumes to be determined and provides a one-to-one correspondence between 3D real space and 3D reciprocal space for almost any polycrystalline or multi-phase material. PMID:26028514

  10. Probing the Macromolecular Organization of Cells by Electron Tomography

    PubMed Central

    Hoenger, Andreas; McIntosh, J. Richard

    2010-01-01

    Summary A major goal in cell biology is to understand the functional organization of macromolecular complexes in vivo. Electron microscopy is helping cell biologists to achieve this goal, thanks to its ability to resolve structural details in the nanometer range. While issues related to specimen preparation, imaging, and image interpretation make this approach to cell architecture difficult, recent improvements in methods, equipment, and software have facilitated the study of both important macromolecular complexes and comparatively large volumes from cellular specimens. Here, we describe recent progress in electron microscopy of cells and the ways in which the relevant methodologies are helping to elucidate cell architecture. PMID:19185480

  11. Whole-Cell Analysis of Low-Density Lipoprotein Uptake by Macrophages Using STEM Tomography

    PubMed Central

    Baudoin, Jean-Pierre; Jerome, W. Gray; Kübel, Christian; de Jonge, Niels

    2013-01-01

    Nanoparticles of heavy materials such as gold can be used as markers in quantitative electron microscopic studies of protein distributions in cells with nanometer spatial resolution. Studying nanoparticles within the context of cells is also relevant for nanotoxicological research. Here, we report a method to quantify the locations and the number of nanoparticles, and of clusters of nanoparticles inside whole eukaryotic cells in three dimensions using scanning transmission electron microscopy (STEM) tomography. Whole-mount fixed cellular samples were prepared, avoiding sectioning or slicing. The level of membrane staining was kept much lower than is common practice in transmission electron microscopy (TEM), such that the nanoparticles could be detected throughout the entire cellular thickness. Tilt-series were recorded with a limited tilt-range of 80° thereby preventing excessive beam broadening occurring at higher tilt angles. The 3D locations of the nanoparticles were nevertheless determined with high precision using computation. The obtained information differed from that obtained with conventional TEM tomography data since the nanoparticles were highlighted while only faint contrast was obtained on the cellular material. Similar as in fluorescence microscopy, a particular set of labels can be studied. This method was applied to study the fate of sequentially up-taken low-density lipoprotein (LDL) conjugated to gold nanoparticles in macrophages. Analysis of a 3D reconstruction revealed that newly up-taken LDL-gold was delivered to lysosomes containing previously up-taken LDL-gold thereby forming onion-like clusters. PMID:23383042

  12. High-pressure freezing for scanning transmission electron tomography analysis of cellular organelles.

    PubMed

    Walther, Paul; Schmid, Eberhard; Höhn, Katharina

    2013-01-01

    Using an electron microscope's scanning transmission mode (STEM) for collection of tomographic datasets is advantageous compared to bright field transmission electron microscopic (TEM). For image formation, inelastic scattering does not cause chromatic aberration, since in STEM mode no image forming lenses are used after the beam has passed the sample, in contrast to regular TEM. Therefore, thicker samples can be imaged. It has been experimentally demonstrated that STEM is superior to TEM and energy filtered TEM for tomography of samples as thick as 1 μm. Even when using the best electron microscope, adequate sample preparation is the key for interpretable results. We adapted protocols for high-pressure freezing of cultivated cells from a physiological state. In this chapter, we describe optimized high-pressure freezing and freeze substitution protocols for STEM tomography in order to obtain high membrane contrast.

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

    PubMed

    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

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

    PubMed

    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.

  15. Visualizing biointerfaces in three dimensions: electron tomography of the bone–hydroxyapatite interface

    PubMed Central

    Grandfield, K.; McNally, E. A.; Palmquist, A.; Botton, G. A.; Thomsen, P.; Engqvist, H.

    2010-01-01

    A positive interaction between human bone tissue and synthetics is crucial for the success of bone-regenerative materials. A greater understanding of the mechanisms governing bone-bonding is often gained via visualization of the bone–implant interface. Interfaces to bone have long been imaged with light, X-rays and electrons. Most of these techniques, however, only provide low-resolution or two-dimensional information. With the advances in modern day transmission electron microscopy, including new hardware and increased software computational speeds, the high-resolution visualization and analysis of three-dimensional structures is possible via electron tomography. We report, for the first time, a three-dimensional reconstruction of the interface between human bone and a hydroxyapatite implant using Z-contrast electron tomography. Viewing this structure in three dimensions enabled us to observe the nanometre differences in the orientation of hydroxyapatite crystals precipitated on the implant surface in vivo versus those in the collagen matrix of bone. Insight into the morphology of biointerfaces is considerably enhanced with three-dimensional techniques. In this regard, electron tomography may revolutionize the approach to high-resolution biointerface characterization. PMID:20534599

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

    NASA Astrophysics Data System (ADS)

    van Dyck, Dirk; Chen, Fu-Rong

    2012-06-01

    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.

  17. '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.

  18. Evaluation of denoising algorithms for biological electron tomography.

    PubMed

    Narasimha, Rajesh; Aganj, Iman; Bennett, Adam E; Borgnia, Mario J; Zabransky, Daniel; Sapiro, Guillermo; McLaughlin, Steven W; Milne, Jacqueline L S; Subramaniam, Sriram

    2008-10-01

    Tomograms of biological specimens derived using transmission electron microscopy can be intrinsically noisy due to the use of low electron doses, the presence of a "missing wedge" in most data collection schemes, and inaccuracies arising during 3D volume reconstruction. Before tomograms can be interpreted reliably, for example, by 3D segmentation, it is essential that the data be suitably denoised using procedures that can be individually optimized for specific data sets. Here, we implement a systematic procedure to compare various nonlinear denoising techniques on tomograms recorded at room temperature and at cryogenic temperatures, and establish quantitative criteria to select a denoising approach that is most relevant for a given tomogram. We demonstrate that using an appropriate denoising algorithm facilitates robust segmentation of tomograms of HIV-infected macrophages and Bdellovibrio bacteria obtained from specimens at room and cryogenic temperatures, respectively. We validate this strategy of automated segmentation of optimally denoised tomograms by comparing its performance with manual extraction of key features from the same tomograms.

  19. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

    PubMed Central

    Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

    2005-01-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  20. The Microstructure of Cellulose Nanocrystal Aerogels as Revealed by Transmission Electron Microscope Tomography.

    PubMed

    Buesch, Christian; Smith, Sean W; Eschbach, Peter; Conley, John F; Simonsen, John

    2016-09-12

    The microstructure of highly porous cellulose nanocrystal (CNC) aerogels is investigated via transmission electron microscope (TEM) tomography. The aerogels were fabricated by first supercritically drying a carboxylated CNC organogel and then coating via atomic layer deposition with a thin conformal layer of Al2O3 to protect the CNCs against prolonged electron beam exposure. A series of images was then acquired, reconstructed, and segmented in order to generate a three-dimensional (3D) model of the aerogel. The model agrees well with theory and macroscopic measurements, indicating that a thin conformal inorganic coating enables TEM tomography as an analysis tool for microstructure characterization of CNC aerogels. The 3D model also reveals that the aerogels consist of randomly orientated CNCs that attach to one another primarily in three ways: end to end contact, "T″ contact, and "X″ contact.

  1. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography.

    PubMed

    Nicastro, Daniela; McIntosh, J Richard; Baumeister, Wolfgang

    2005-11-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  2. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

  3. The Microstructure of Cellulose Nanocrystal Aerogels as Revealed by Transmission Electron Microscope Tomography.

    PubMed

    Buesch, Christian; Smith, Sean W; Eschbach, Peter; Conley, John F; Simonsen, John

    2016-09-12

    The microstructure of highly porous cellulose nanocrystal (CNC) aerogels is investigated via transmission electron microscope (TEM) tomography. The aerogels were fabricated by first supercritically drying a carboxylated CNC organogel and then coating via atomic layer deposition with a thin conformal layer of Al2O3 to protect the CNCs against prolonged electron beam exposure. A series of images was then acquired, reconstructed, and segmented in order to generate a three-dimensional (3D) model of the aerogel. The model agrees well with theory and macroscopic measurements, indicating that a thin conformal inorganic coating enables TEM tomography as an analysis tool for microstructure characterization of CNC aerogels. The 3D model also reveals that the aerogels consist of randomly orientated CNCs that attach to one another primarily in three ways: end to end contact, "T″ contact, and "X″ contact. PMID:27500897

  4. Studying synapses in human brain with array tomography and electron microscopy

    PubMed Central

    Kay, Kevin R.; Smith, Colin; Wright, Ann K.; Serrano-Pozo, Alberto; Pooler, Amy M.; Koffie, Robert; Bastin, Mark E.; Bak, Thomas H.; Abrahams, Sharon; Kopeikina, Katherine J.; McGuone, Declan; Frosch, Matthew P.; Gillingwater, Thomas H.; Hyman, Bradley T.; Spires-Jones, Tara L.

    2013-01-01

    Postmortem studies of synapses in human brain are problematic due to the axial resolution limit of light microscopy and the difficulty preserving and analyzing ultrastructure with electron microscopy. Array tomography overcomes these problems by embedding autopsy tissue in resin and cutting ribbons of ultrathin serial sections. Ribbons are imaged with immunofluorescence, allowing high-throughput imaging of tens of thousands of synapses to assess synapse density and protein composition. The protocol takes approximately 3 days per case, excluding image analysis, which is done at the end of the study. Parallel processing for transmission electron microscopy (TEM) using a protocol modified to preserve structure in human samples allows complimentary ultrastructural studies. Incorporation of array tomography and TEM into brain banking is a potent way of phenotyping synapses in well-characterized clinical cohorts to develop clinico-pathological correlations at the synapse level. This will be important for research in neurodegenerative disease, developmental diseases, and psychiatric illness. PMID:23787894

  5. Mapping fullerene crystallization in a photovoltaic blend: an electron tomography study

    NASA Astrophysics Data System (ADS)

    Bäcke, Olof; Lindqvist, Camilla; Diaz de Zerio Mendaza, Amaia; Gustafsson, Stefan; Wang, Ergang; Andersson, Mats R.; Müller, Christian; Olsson, Eva

    2015-04-01

    The formation of fullerene crystals represents a major degradation pathway of polymer/fullerene bulk-heterojunction thin films that inexorably deteriorates their photovoltaic performance. Currently no tools exist that reveal the origin of fullerene crystal formation vertically through the film. Here, we show that electron tomography can be used to study nucleation and growth of fullerene crystals. A model bulk-heterojunction blend based on a thiophene-quinoxaline copolymer and a fullerene derivative is examined after controlled annealing above the glass transition temperature. We image a number of fullerene nanocrystals, ranging in size from 70 to 400 nanometers, and observe that their center is located close to the free-surface of spin-coated films. The results show that the nucleation of fullerene crystals predominately occurs in the upper part of the films. Moreover, electron tomography reveals that the nucleation is preceded by more pronounced phase separation of the blend components.

  6. In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology.

    PubMed

    Asano, Shoh; Engel, Benjamin D; Baumeister, Wolfgang

    2016-01-29

    Cryo-electron tomography is a powerful technique that can faithfully image the native cellular environment at nanometer resolution. Unlike many other imaging approaches, cryo-electron tomography provides a label-free method of detecting biological structures, relying on the intrinsic contrast of frozen cellular material for direct identification of macromolecules. Recent advances in sample preparation, detector technology, and phase plate imaging have enabled the structural characterization of protein complexes within intact cells. Here, we review these technical developments and outline a detailed computational workflow for in situ structural analysis. Two recent studies are described to illustrate how this workflow can be adapted to examine both known and unknown cellular complexes. The stage is now set to realize the promise of visual proteomics--a complete structural description of the cell's native molecular landscape. PMID:26456135

  7. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography.

    PubMed

    Nicastro, Daniela; McIntosh, J Richard; Baumeister, Wolfgang

    2005-11-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ.

  8. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

  9. In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology.

    PubMed

    Asano, Shoh; Engel, Benjamin D; Baumeister, Wolfgang

    2016-01-29

    Cryo-electron tomography is a powerful technique that can faithfully image the native cellular environment at nanometer resolution. Unlike many other imaging approaches, cryo-electron tomography provides a label-free method of detecting biological structures, relying on the intrinsic contrast of frozen cellular material for direct identification of macromolecules. Recent advances in sample preparation, detector technology, and phase plate imaging have enabled the structural characterization of protein complexes within intact cells. Here, we review these technical developments and outline a detailed computational workflow for in situ structural analysis. Two recent studies are described to illustrate how this workflow can be adapted to examine both known and unknown cellular complexes. The stage is now set to realize the promise of visual proteomics--a complete structural description of the cell's native molecular landscape.

  10. An 8×8 Row-Column Summing Readout Electronics for Preclinical Positron Emission Tomography Scanners.

    PubMed

    Shih, Y C; Sun, F W; Macdonald, L R; Otis, B P; Miyaoka, R S; McDougald, W; Lewellen, T K

    2009-10-24

    This work presents a row/column summing readout electronics for an 8×8 silicon photomultiplier array. The summation circuit greatly reduces the number of electronic channels, which is desirable for pursuing higher resolution positron emission tomography scanners. By using a degenerated common source topology in the summation circuit, more fan-in is possible and therefore a greater reduction in the number of electronic channels can be achieved. The timing signal is retrieved from a common anode, which allows the use of a single fast-sampling analog to digital converter (ADC) for the timing channel and slower, lower power ADCs for the 64 spatial channels. Preliminary results of one row summation of the 8×8 readout electronics exhibited FWHM energy resolution of 17.8% and 18.3% with and without multiplexing, respectively. The measured timing resolution is 2.9ns FWHM.

  11. An 8×8 Row-Column Summing Readout Electronics for Preclinical Positron Emission Tomography Scanners

    PubMed Central

    Shih, Y. C.; Sun, F. W.; MacDonald, L. R.; Otis, B. P.; Miyaoka, R. S.; McDougald, W.; Lewellen, T. K.

    2010-01-01

    This work presents a row/column summing readout electronics for an 8×8 silicon photomultiplier array. The summation circuit greatly reduces the number of electronic channels, which is desirable for pursuing higher resolution positron emission tomography scanners. By using a degenerated common source topology in the summation circuit, more fan-in is possible and therefore a greater reduction in the number of electronic channels can be achieved. The timing signal is retrieved from a common anode, which allows the use of a single fast-sampling analog to digital converter (ADC) for the timing channel and slower, lower power ADCs for the 64 spatial channels. Preliminary results of one row summation of the 8×8 readout electronics exhibited FWHM energy resolution of 17.8% and 18.3% with and without multiplexing, respectively. The measured timing resolution is 2.9ns FWHM. PMID:20729983

  12. Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography.

    PubMed

    Schröder, Rasmus R

    2015-09-01

    Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy.(1) While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation - often developed in other fields of electron microscopy - may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.

  13. Electron Tomography of Nanoparticle Clusters: Implications for Atmospheric Lifetimes and Radiative Forcing of Soot

    NASA Technical Reports Server (NTRS)

    vanPoppel, Laura H.; Friedrich, Heiner; Spinsby, Jacob; Chung, Serena H.; Seinfeld, John H.; Buseck, Peter R.

    2005-01-01

    Nanoparticles are ubiquitous in nature. Their large surface areas and consequent chemical reactivity typically result in their aggregation into clusters. Their chemical and physical properties depend on cluster shapes, which are commonly complex and unknown. This is the first application of electron tomography with a transmission electron microscope to quantitatively determine the three-dimensional (3D) shapes, volumes, and surface areas of nanoparticle clusters. We use soot (black carbon, BC) nanoparticles as an example because it is a major contributor to environmental degradation and global climate change. To the extent that our samples are representative, we find that quantitative measurements of soot surface areas and volumes derived from electron tomograms differ from geometrically derived values by, respectively, almost one and two orders of magnitude. Global sensitivity studies suggest that the global burden and direct radiative forcing of fractal BC are only about 60% of the value if it is assumed that BC has a spherical shape.

  14. Analysis of the 3D distribution of stacked self-assembled quantum dots by electron tomography

    PubMed Central

    2012-01-01

    The 3D distribution of self-assembled stacked quantum dots (QDs) is a key parameter to obtain the highest performance in a variety of optoelectronic devices. In this work, we have measured this distribution in 3D using a combined procedure of needle-shaped specimen preparation and electron tomography. We show that conventional 2D measurements of the distribution of QDs are not reliable, and only 3D analysis allows an accurate correlation between the growth design and the structural characteristics. PMID:23249477

  15. Direct electronic linearization for camera-based spectral domain optical coherence tomography.

    PubMed

    Payne, Andrew; Podoleanu, Adrian Gh

    2012-06-15

    An electronic method of k-space linearization for an analog camera for use in optical coherence tomography is demonstrated. The method applies a chirp to the data transfer clock signal of the camera in order to temporally compensate for diffraction that is nonlinear in wavenumber. The optimum parameters are obtained experimentally and theoretically and are shown to be in good accordance. Close to maximum measurable axial range, by applying this method, the FWHM of the point spread function is reduced by a factor of 5.6 and sensitivity is increased by 9.8 dB. PMID:22739929

  16. Three-dimensional visualization of forming Hepatitis C virus-like particles by electron-tomography

    SciTech Connect

    Badia-Martinez, Daniel; Peralta, Bibiana; Andres, German; Guerra, Milagros; Gil-Carton, David; Abrescia, Nicola G.A.

    2012-09-01

    Hepatitis C virus infects almost 170 million people per year but its assembly pathway, architecture and the structures of its envelope proteins are poorly understood. Using electron tomography of plastic-embedded sections of insect cells, we have visualized the morphogenesis of recombinant Hepatitis C virus-like particles. Our data provide a three-dimensional sketch of viral assembly at the endoplasmic reticulum showing different budding stages and contiguity of buds. This latter phenomenon could play an important role during the assembly of wt-HCV and explain the size-heterogeneity of its particles.

  17. All-optical tomography of electron spins in (In,Ga)As quantum dots

    NASA Astrophysics Data System (ADS)

    Varwig, S.; René, A.; Economou, Sophia E.; Greilich, A.; Yakovlev, D. R.; Reuter, D.; Wieck, A. D.; Reinecke, T. L.; Bayer, M.

    2014-02-01

    We demonstrate the basic features of an all-optical spin tomography on picosecond time scale. The magnetization vector associated with a mode-locked electron spin ensemble in singly charged quantum dots is traced by ellipticity measurements using picosecond laser pulses. After optical orientation the spins precess about a perpendicular magnetic field. By comparing the dynamics of two interacting ensembles with the dynamics of a single ensemble we find buildup of a spin component along the magnetic field in the two-ensemble case. This component arises from a Heisenberg-like spin-spin interaction.

  18. Markov Random Field Based Automatic Image Alignment for ElectronTomography

    SciTech Connect

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

    2007-11-30

    Cryo electron tomography (cryo-ET) is the primary method for obtaining 3D reconstructions of intact bacteria, viruses, and complex molecular machines ([7],[2]). It first flash freezes a specimen in a thin layer of ice, and then rotates the ice sheet in a transmission electron microscope (TEM) recording images of different projections through the sample. The resulting images are aligned and then back projected to form the desired 3-D model. The typical resolution of biological electron microscope is on the order of 1 nm per pixel which means that small imprecision in the microscope's stage or lenses can cause large alignment errors. To enable a high precision alignment, biologists add a small number of spherical gold beads to the sample before it is frozen. These beads generate high contrast dots in the image that can be tracked across projections. Each gold bead can be seen as a marker with a fixed location in 3D, which provides the reference points to bring all the images to a common frame as in the classical structure from motion problem. A high accuracy alignment is critical to obtain a high resolution tomogram (usually on the order of 5-15nm resolution). While some methods try to automate the task of tracking markers and aligning the images ([8],[4]), they require user intervention if the SNR of the image becomes too low. Unfortunately, cryogenic electron tomography (or cryo-ET) often has poor SNR, since the samples are relatively thick (for TEM) and the restricted electron dose usually results in projections with SNR under 0 dB. This paper shows that formulating this problem as a most-likely estimation task yields an approach that is able to automatically align with high precision cryo-ET datasets using inference in graphical models. This approach has been packaged into a publicly available software called RAPTOR-Robust Alignment and Projection estimation for Tomographic Reconstruction.

  19. Electron holographic tomography for mapping the three-dimensional distribution of electrostatic potential in III-V semiconductor nanowires

    NASA Astrophysics Data System (ADS)

    Wolf, D.; Lichte, H.; Pozzi, G.; Prete, P.; Lovergine, N.

    2011-06-01

    Electron holographic tomography (EHT), the combination of off-axis electron holography with electron tomography, is a technique, which can be applied to the quantitative 3-dimensional (3D) mapping of electrostatic potential at the nanoscale. Here, we show the results obtained in the EHT investigation of GaAs and GaAs-AlGaAs core-shell nanowires grown by Au-catalysed metalorganic vapor phase epitaxy. The unique ability of EHT of disentangling the materials mean inner potential (MIP) from the specimen projected thickness allows reconstruction of the nanowire 3D morphology and inner compositional structure as well as the measurement of the MIP.

  20. Electron holographic tomography for mapping the three-dimensional distribution of electrostatic potential in III-V semiconductor nanowires

    SciTech Connect

    Wolf, D.; Lichte, H.; Pozzi, G.; Lovergine, N.

    2011-06-27

    Electron holographic tomography (EHT), the combination of off-axis electron holography with electron tomography, is a technique, which can be applied to the quantitative 3-dimensional (3D) mapping of electrostatic potential at the nanoscale. Here, we show the results obtained in the EHT investigation of GaAs and GaAs-AlGaAs core-shell nanowires grown by Au-catalysed metalorganic vapor phase epitaxy. The unique ability of EHT of disentangling the materials mean inner potential (MIP) from the specimen projected thickness allows reconstruction of the nanowire 3D morphology and inner compositional structure as well as the measurement of the MIP.

  1. A new apparatus for electron tomography in the scanning electron microscope

    SciTech Connect

    Morandi, V. Maccagnani, P.; Masini, L.; Migliori, A.; Ortolani, L.; Pezza, A.; Del Marro, M.; Pallocca, G.; Vinciguerra, P.; Rossi, M.; Ferroni, M.; Sberveglieri, G.; Vittori-Antisari, M.

    2015-06-23

    The three-dimensional reconstruction of a microscopic specimen has been obtained by applying the tomographic algorithm to a set of images acquired in a Scanning Electron Microscope. This result was achieved starting from a series of projections obtained by stepwise rotating the sample under the beam raster. The Scanning Electron Microscope was operated in the scanning-transmission imaging mode, where the intensity of the transmitted electron beam is a monotonic function of the local mass-density and thickness of the specimen. The detection strategy has been implemented and tailored in order to maintain the projection requirement over the large tilt range, as required by the tomographic workflow. A Si-based electron detector and an eucentric-rotation specimen holder have been specifically developed for the purpose.

  2. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  3. Intracellular trafficking of superparamagnetic iron oxide nanoparticles conjugated with TAT peptide: 3-dimensional electron tomography analysis

    SciTech Connect

    Nair, Baiju G.; Fukuda, Takahiro; Mizuki, Toru; Hanajiri, Tatsuro; Maekawa, Toru

    2012-05-18

    Highlights: Black-Right-Pointing-Pointer We study the intracellular localisation of TAT-SPIONs using 3-D electron tomography. Black-Right-Pointing-Pointer 3-D images of TAT-SPIONs in a cell are clearly shown. Black-Right-Pointing-Pointer Release of TAT-SPIONs from endocytic vesicles into the cytoplasm is clearly shown. -- Abstract: Internalisation of nanoparticles conjugated with cell penetrating peptides is a promising approach to various drug delivery applications. Cell penetrating peptides such as transactivating transcriptional activator (TAT) peptides derived from HIV-1 proteins are effective intracellular delivery vectors for a wide range of nanoparticles and pharmaceutical agents thanks to their amicable ability to enter cells and minimum cytotoxicity. Although different mechanisms of intracellular uptake and localisation have been proposed for TAT conjugated nanoparticles, it is necessary to visualise the particles on a 3-D plane in order to investigate the actual intracellular uptake and localisation. Here, we study the intracellular localisation and trafficking of TAT peptide conjugated superparamagnetic ion oxide nanoparticles (TAT-SPIONs) using 3-D electron tomography. 3-D tomograms clearly show the location of TAT-SPIONs in a cell and their slow release from the endocytic vesicles into the cytoplasm. The present methodology may well be utilised for further investigations of the behaviours of nanoparticles in cells and eventually for the development of nano drug delivery systems.

  4. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  5. 3D mapping of nanoscale electric potentials in semiconductor structures using electron-holographic tomography

    NASA Astrophysics Data System (ADS)

    Wolf, Daniel; Lubk, Axel; Prete, Paola; Lovergine, Nico; Lichte, Hannes

    2016-09-01

    Off-axis electron holography (EH) is a powerful method for mapping projected electric potentials, such as built-in potentials in semiconductor devices, in two dimensions (2D) at nanometer resolution. However, not well-defined thickness profiles, surface effects, and composition changes of the sample under investigation complicate the interpretation of the projected potentials. Here, we demonstrate how these problems can be overcome by combining EH with tomographic techniques, that is, electron holographic tomography (EHT), reconstructing electric potentials in 3D. We present EHT reconstructions of an n-type MOSFET including its dopant-related built-in potentials inside the device, as well as of a GaAs/AlGaAs core-multishell nanowire containing a 5 nm thick quantum well tube.

  6. Whole cell cryo-electron tomography suggests mitochondria divide by budding.

    PubMed

    Hu, Guo-Bin

    2014-08-01

    Eukaryotes rely on mitochondrial division to guarantee that each new generation of cells acquires an adequate number of mitochondria. Mitochondrial division has long been thought to occur by binary fission and, more recently, evidence has supported the idea that binary fission is mediated by dynamin-related protein (Drp1) and the endoplasmic reticulum. However, studies to date have depended on fluorescence microscopy and conventional electron microscopy. Here, we utilize whole cell cryo-electron tomography to visualize mitochondrial division in frozen hydrated intact HeLa cells. We observe a large number of relatively small mitochondria protruding from and connected to large mitochondria or mitochondrial networks. Therefore, this study provides evidence that mitochondria divide by budding. PMID:24870811

  7. Analytical electron tomography mapping of the SiCporeoxidation at the nanoscale

    NASA Astrophysics Data System (ADS)

    Florea, Ileana; Ersen, Ovidiu; Hirlimann, Charles; Roiban, Lucian; Deneuve, Adrien; Houllé, Matthieu; Janowska, Izabela; Nguyen, Patrick; Pham, Charlotte; Pham-Huu, Cuong

    2010-12-01

    Silicon carbide is a ceramic material that has been widely studied because of its potential applications, ranging from electronics to heterogeneous catalysis. Recently, a new type of SiC materials with a medium specific surface area and thermal conductivity, called β-SiC, has attracted overgrowing interest as a new class of catalyst support in several catalytic reactions. A primary electron tomography study, performed in usual mode, has revealed a dual surface structure defined by two types of porosities made of networks of connected channels with sizes larger than 50 nm and ink-bottled pores with sizes spanning from 4 to 50 nm. Depending on the solvent nature, metal nanoparticles could be selectively deposited inside one of the two porosities, a fact that illustrates a selective wetting titration of the two types of surfaces by different liquids. The explaining hypothesis that has been put forward was that this selectivity against solvents is related to the pore surface oxidation degree of the two types of pores. A new technique of analytical electron tomography, where the series of projections used to reconstruct the volume of an object is recorded in energy filtered mode (EFTEM), has been implemented to map the poreoxidation state and to correlate it with the morphology and the accessibility of the porous network. Applied, for the first time, at a nanoscale resolution, this technique allowed us to obtain 3D elemental maps of different elements present in the analysed porous grains, in particular oxygen; we found thus that the interconnected channelpores are more rapidly oxidized than the ink-bottled ones. Alternatively, our study highlights the great interest of this method that opens the way for obtaining precise information on the chemical composition of a 3D surface at a nanometer scale.Silicon carbide is a ceramic material that has been widely studied because of its potential applications, ranging from electronics to heterogeneous catalysis. Recently, a new

  8. Compressed sensing electron tomography of needle-shaped biological specimens--Potential for improved reconstruction fidelity with reduced dose.

    PubMed

    Saghi, Zineb; Divitini, Giorgio; Winter, Benjamin; Leary, Rowan; Spiecker, Erdmann; Ducati, Caterina; Midgley, Paul A

    2016-01-01

    Electron tomography is an invaluable method for 3D cellular imaging. The technique is, however, limited by the specimen geometry, with a loss of resolution due to a restricted tilt range, an increase in specimen thickness with tilt, and a resultant need for subjective and time-consuming manual segmentation. Here we show that 3D reconstructions of needle-shaped biological samples exhibit isotropic resolution, facilitating improved automated segmentation and feature detection. By using scanning transmission electron tomography, with small probe convergence angles, high spatial resolution is maintained over large depths of field and across the tilt range. Moreover, the application of compressed sensing methods to the needle data demonstrates how high fidelity reconstructions may be achieved with far fewer images (and thus greatly reduced dose) than needed by conventional methods. These findings open the door to high fidelity electron tomography over critically relevant length-scales, filling an important gap between existing 3D cellular imaging techniques.

  9. Compressed sensing electron tomography of needle-shaped biological specimens--Potential for improved reconstruction fidelity with reduced dose.

    PubMed

    Saghi, Zineb; Divitini, Giorgio; Winter, Benjamin; Leary, Rowan; Spiecker, Erdmann; Ducati, Caterina; Midgley, Paul A

    2016-01-01

    Electron tomography is an invaluable method for 3D cellular imaging. The technique is, however, limited by the specimen geometry, with a loss of resolution due to a restricted tilt range, an increase in specimen thickness with tilt, and a resultant need for subjective and time-consuming manual segmentation. Here we show that 3D reconstructions of needle-shaped biological samples exhibit isotropic resolution, facilitating improved automated segmentation and feature detection. By using scanning transmission electron tomography, with small probe convergence angles, high spatial resolution is maintained over large depths of field and across the tilt range. Moreover, the application of compressed sensing methods to the needle data demonstrates how high fidelity reconstructions may be achieved with far fewer images (and thus greatly reduced dose) than needed by conventional methods. These findings open the door to high fidelity electron tomography over critically relevant length-scales, filling an important gap between existing 3D cellular imaging techniques. PMID:26555323

  10. The internal architecture of leukocyte lipid body organelles captured by three-dimensional electron microscopy tomography.

    PubMed

    Melo, Rossana C N; Paganoti, Guillherme F; Dvorak, Ann M; Weller, Peter F

    2013-01-01

    Lipid bodies (LBs), also known as lipid droplets, are complex organelles of all eukaryotic cells linked to a variety of biological functions as well as to the development of human diseases. In cells from the immune system, such as eosinophils, neutrophils and macrophages, LBs are rapidly formed in the cytoplasm in response to inflammatory and infectious diseases and are sites of synthesis of eicosanoid lipid mediators. However, little is known about the structural organization of these organelles. It is unclear whether leukocyte LBs contain a hydrophobic core of neutral lipids as found in lipid droplets from adipocytes and how diverse proteins, including enzymes involved in eicosanoid formation, incorporate into LBs. Here, leukocyte LB ultrastructure was studied in detail by conventional transmission electron microscopy (TEM), immunogold EM and electron tomography. By careful analysis of the two-dimensional ultrastructure of LBs from human blood eosinophils under different conditions, we identified membranous structures within LBs in both resting and activated cells. Cyclooxygenase, a membrane inserted protein that catalyzes the first step in prostaglandin synthesis, was localized throughout the internum of LBs. We used fully automated dual-axis electron tomography to study the three-dimensional architecture of LBs in high resolution. By tracking 4 nm-thick serial digital sections we found that leukocyte LBs enclose an intricate system of membranes within their "cores". After computational reconstruction, we showed that these membranes are organized as a network of tubules which resemble the endoplasmic reticulum (ER). Our findings explain how membrane-bound proteins interact and are spatially arranged within LB "cores" and support a model for LB formation by incorporating cytoplasmic membranes of the ER, instead of the conventional view that LBs emerge from the ER leaflets. This is important to understand the functional capabilities of leukocyte LBs in health and

  11. Heterogeneities of the nanostructure of platinum/zeolite y catalysts revealed by electron tomography.

    PubMed

    Zečević, Jovana; van der Eerden, Ad M J; Friedrich, Heiner; de Jongh, Petra E; de Jong, Krijn P

    2013-04-23

    To develop structure-performance relationships for important catalysts, a detailed characterization of their morphology is essential. Using electron tomography, we determined in three dimensions the structure of Pt/zeolite Y bifunctional catalysts. Optimum experimental conditions enabled for the first time high-resolution 3D imaging of Pt particles as small as 1 nm located inside zeolite micropores. Semiautomated image analysis of 3D reconstructions provided an efficient study of numbers, size distributions, and interparticle distances of thousands of Pt particles within individual zeolite crystals. Upon extending this approach to a number of zeolite crystals of one batch of Pt/zeolite Y catalyst, heterogeneities were revealed. The Pt loading, an important parameter for catalyst performance, varied between zeolite crystals up to a factor of 35. This discovery calls for re-evaluation of catalyst preparation methods and suggests potential for lowering the nominal loading with noble metals.

  12. Electron beam computed tomography for assessment of patients presenting to the emergency department with chest pain.

    PubMed

    McCord, James; Amsterdam, Ezra A

    2004-12-01

    Electron beam computed tomography (EBCT) is a unique, noninvasive radiologic method capable of high-resolution imaging that is being increasingly used for evaluation of the cardiovascular system. Among its multiple applications, coronary artery calcium (CAC) imaging has attracted considerable attention because of the potential of this technique for early detection of coronary artery disease (CAD), the leading cause of mortality in our society. Although measurement of CAC has been primarily performed in the outpatient setting in both symptomatic and asymptomatic subjects, several studies have assessed the utility of the method to identify CAD in patients presenting to the emergency department with chest pain suggestive of myocardial ischemia but without objective evidence of the latter. This group comprises a majority of those presenting to the emergency department with chest pain, and their safe, accurate and cost-effective evaluation has been a continuing challenge. PMID:18340176

  13. Three-dimensional architecture of hair-cell linkages as revealedby electron-microscopic tomography

    SciTech Connect

    Auer, Manfred; Koster, Bram; Ziese, Ulrike; Bajaj, Chandrajit; Volkmann, Niels; Wang, Da Neng; Hudspeth, A. James

    2006-07-28

    The senses of hearing and balance rest upon mechanoelectrical transduction by the hair bundles of hair cells in the inner ear. Located at the apical cellular surface, each hair bundle comprises several tens of stereocilia and a single kinocilium that are interconnected by extracellular proteinaceous links. Using electron-microscopic tomography of bullfrog saccular sensory epithelia, we examined the three-dimensional structures of ankle or basal links, kinociliary links, and tip links. We observed clear differences in the dimensions and appearances of the three links. We found two distinct populations of tip links suggestive of the involvement of two proteins or splice variants. We noted auxiliary links connecting the upper portions of tip links to the taller stereocilia. Tip links and auxiliary links show a tendency to adopt a globular conformation when disconnected from the membrane surface.

  14. Direct visualization of dispersed lipid bicontinuous cubic phases by cryo-electron tomography.

    PubMed

    Demurtas, Davide; Guichard, Paul; Martiel, Isabelle; Mezzenga, Raffaele; Hébert, Cécile; Sagalowicz, Laurent

    2015-01-01

    Bulk and dispersed cubic liquid crystalline phases (cubosomes), present in the body and in living cell membranes, are believed to play an essential role in biological phenomena. Moreover, their biocompatibility is attractive for nutrient or drug delivery system applications. Here the three-dimensional organization of dispersed cubic lipid self-assembled phases is fully revealed by cryo-electron tomography and compared with simulated structures. It is demonstrated that the interior is constituted of a perfect bicontinuous cubic phase, while the outside shows interlamellar attachments, which represent a transition state between the liquid crystalline interior phase and the outside vesicular structure. Therefore, compositional gradients within cubosomes are inferred, with a lipid bilayer separating at least one water channel set from the external aqueous phase. This is crucial to understand and enhance controlled release of target molecules and calls for a revision of postulated transport mechanisms from cubosomes to the aqueous phase. PMID:26573367

  15. Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli

    SciTech Connect

    Liu Jun; Chen Chengyen; Shiomi, Daisuke; Niki, Hironori; Margolin, William

    2011-09-01

    Bacteriophage P1 has a contractile tail that targets the conserved lipopolysaccharide on the outer membrane surface of the host for initial adsorption. The mechanism by which P1 DNA enters the host cell is not well understood, mainly because the transient molecular interactions between bacteriophage and bacteria have been difficult to study by conventional approaches. Here, we engineered tiny E. coli host cells so that the initial stages of P1-host interactions could be captured in unprecedented detail by cryo-electron tomography. Analysis of three-dimensional reconstructions of frozen-hydrated specimens revealed three predominant configurations: an extended tail stage with DNA present in the phage head, a contracted tail stage with DNA, and a contracted tail stage without DNA. Comparative analysis of various conformations indicated that there is uniform penetration of the inner tail tube into the E. coli periplasm and a significant movement of the baseplate away from the outer membrane during tail contraction.

  16. Ultrastructure of compacted DNA in cyanobacteria by high-voltage cryo-electron tomography

    PubMed Central

    Murata, Kazuyoshi; Hagiwara, Sayuri; Kimori, Yoshitaka; Kaneko, Yasuko

    2016-01-01

    Some cyanobacteria exhibit compaction of DNA in synchrony with their circadian rhythms accompanying cell division. Since the structure is transient, it has not yet been described in detail. Here, we successfully visualize the ultrastructure of compacted DNA in the cyanobacterium Synechococcus elongatus PCC 7942 under rigorous synchronized cultivation by means of high-voltage cryo-electron tomography. In 3D reconstructions of rapidly frozen cells, the compacted DNA appears as an undulating rod resembling a eukaryotic condensed chromosome. The compacted DNA also includes many small and paired polyphosphate bodies (PPBs), some of which seem to maintain contact with DNA that appears to twist away from them, indicating that they may act as interactive suppliers and regulators of phosphate for DNA synthesis. These observations throw light on the duplication and segregation mechanisms of cyanobacterial DNA and point to an important role for PPBs. PMID:27731339

  17. Electron tomography of the nucleoid of Gemmata obscuriglobus reveals complex liquid crystalline cholesteric structure

    PubMed Central

    Yee, Benjamin; Sagulenko, Evgeny; Morgan, Garry P.; Webb, Richard I.; Fuerst, John A.

    2012-01-01

    The nucleoid of the planctomycete Gemmata obscuriglobus is unique within the Bacteria in being both highly condensed and enclosed by a double-membrane nuclear envelope, seemingly analogous to the nucleus of eukaryotes. Here we have applied electron tomography to study high-pressure frozen, cryosubstituted cells of G. obscuriglobus and found multiple nested orders of DNA organization within the condensed nucleoid structure. Detailed examination of the nucleoid revealed a series of nested arcs characteristic of liquid crystalline cholesteric DNA structure. The finest fibers were arranged in parallel concentrically in a double-twist organization. At the highest order of nucleoid organization, several of these structures come together to form the core of the G. obscuriglobus nucleoid. The complex structure of DNA within this nucleoid may have implications for understanding the evolutionary significance of compartmentalized planctomycete cells. PMID:22993511

  18. Analysis of Iron Meteorites Using Computed Tomography and Electron-probe Microanalysis

    NASA Technical Reports Server (NTRS)

    Carpenter, P. K.; Gillies, D. C.

    2005-01-01

    Computed tomography (CT) imaging and electron-probe microanalysis (EPMA) have been used to study samples of the Mundrabilla and Colomera iron meteorites in order to perform structural, textural, and mineralogical analysis. Both gamma-ray (Co-60 source, essentially monochromatic 1.25MeV avg.) and x-ray (420 KeV, continuous) sources have been used, with effective resolution of approximately 1 mm and 0.25 mm, respectively. The gamma-ray source provides approx. 15 cm penetration through steel and is used for larger samples, whereas the x-ray source provides superior resolution at reduced penetration but exhibits beam hardening artifacts. Here we present a combined approach where CT and EPMA imaging and microanalysis aid in the identification of structural and compositional features in iron meteorites.

  19. Direct visualization of dispersed lipid bicontinuous cubic phases by cryo-electron tomography

    NASA Astrophysics Data System (ADS)

    Demurtas, Davide; Guichard, Paul; Martiel, Isabelle; Mezzenga, Raffaele; Hébert, Cécile; Sagalowicz, Laurent

    2015-11-01

    Bulk and dispersed cubic liquid crystalline phases (cubosomes), present in the body and in living cell membranes, are believed to play an essential role in biological phenomena. Moreover, their biocompatibility is attractive for nutrient or drug delivery system applications. Here the three-dimensional organization of dispersed cubic lipid self-assembled phases is fully revealed by cryo-electron tomography and compared with simulated structures. It is demonstrated that the interior is constituted of a perfect bicontinuous cubic phase, while the outside shows interlamellar attachments, which represent a transition state between the liquid crystalline interior phase and the outside vesicular structure. Therefore, compositional gradients within cubosomes are inferred, with a lipid bilayer separating at least one water channel set from the external aqueous phase. This is crucial to understand and enhance controlled release of target molecules and calls for a revision of postulated transport mechanisms from cubosomes to the aqueous phase.

  20. Cryo electron tomography of herpes simplex virus during axonal transport and secondary envelopment in primary neurons.

    PubMed

    Ibiricu, Iosune; Huiskonen, Juha T; Döhner, Katinka; Bradke, Frank; Sodeik, Beate; Grünewald, Kay

    2011-12-01

    During herpes simplex virus 1 (HSV1) egress in neurons, viral particles travel from the neuronal cell body along the axon towards the synapse. Whether HSV1 particles are transported as enveloped virions as proposed by the 'married' model or as non-enveloped capsids suggested by the 'separate' model is controversial. Specific viral proteins may form a recruitment platform for microtubule motors that catalyze such transport. However, their subviral location has remained elusive. Here we established a system to analyze herpesvirus egress by cryo electron tomography. At 16 h post infection, we observed intra-axonal transport of progeny HSV1 viral particles in dissociated hippocampal neurons by live-cell fluorescence microscopy. Cryo electron tomography of frozen-hydrated neurons revealed that most egressing capsids were transported independently of the viral envelope. Unexpectedly, we found not only DNA-containing capsids (cytosolic C-capsids), but also capsids lacking DNA (cytosolic A-/B-capsids) in mid-axon regions. Subvolume averaging revealed lower amounts of tegument on cytosolic A-/B-capsids than on C-capsids. Nevertheless, all capsid types underwent active axonal transport. Therefore, even few tegument proteins on the capsid vertices seemed to suffice for transport. Secondary envelopment of capsids was observed at axon terminals. On their luminal face, the enveloping vesicles were studded with typical glycoprotein-like spikes. Furthermore, we noted an accretion of tegument density at the concave cytosolic face of the vesicle membrane in close proximity to the capsids. Three-dimensional analysis revealed that these assembly sites lacked cytoskeletal elements, but that filamentous actin surrounded them and formed an assembly compartment. Our data support the 'separate model' for HSV1 egress, i.e. progeny herpes viruses being transported along axons as subassemblies and not as complete virions within transport vesicles. PMID:22194682

  1. Three dimensional accurate morphology measurements of polystyrene standard particles on silicon substrate by electron tomography.

    PubMed

    Hayashida, Misa; Kumagai, Kazuhiro; Malac, Marek

    2015-12-01

    Polystyrene latex (PSL) nanoparticle (NP) sample is one of the most widely used standard materials. It is used for calibration of particle counters and particle size measurement tools. It has been reported that the measured NP sizes by various methods, such as Differential Mobility Analysis, dynamic light scattering (DLS), optical microscopy (OM), scanning electron microscopy (SEM) and atomic force microscopy (AFM), differ from each other. Deformation of PSL NPs on mica substrate has been reported in AFM measurements: the lateral width of PSL NPs is smaller than their vertical height. To provide a reliable calibration standard, the deformation must be measured by a method that can reliably visualize the entire three dimensional (3D) shape of the PSL NPs. Here we present a method for detailed measurement of PSL NP 3D shape by means of electron tomography in a transmission electron microscope. The observed shape of the PSL NPs with 100 nm and 50 nm diameter were not spherical, but squished in direction perpendicular to the support substrate by about 7.4% and 12.1%, respectively. The high difference in surface energy of the PSL NPs and that of substrate together with their low Young modulus appear to explain the squishing of the NPs without presence of water film.

  2. 3D Reconstruction of the Glycocalyx Structure in Mammalian Capillaries using Electron Tomography

    PubMed Central

    Arkill, KP; Neal, CR; Mantell, JM; Michel, CC; Qvortrup, K; Bates, DO; Knupp, C; Squire, JM

    2013-01-01

    Visualising the molecular strands making up the glycocalyx in the lumen of small blood vessels has proved to be difficult using conventional transmission electron microscopy techniques. Images obtained from tissue stained in a variety of ways have revealed a regularity in the organisation of the proteoglycan components of the glycocalyx layer (fundamental spacing about 20 nm), but require a large sample number. Attempts to visualise the glycocalyx face-on (i.e. in a direction perpendicular to the endothelial cell layer in the lumen and directly applicable for permeability modelling) has had limited success (e.g. freeze fracture). A new approach is therefore needed. Here we demonstrate the effectiveness of using the relatively novel electron microscopy technique of 3D electron tomography on two differently stained preparations to reveal details of the architecture of the glycocalyx just above the endothelial cell layer. One preparation uses the novel staining technique using Lanthanum Dysprosium Glycosamino Glycan adhesion (the LaDy GAGa method). PMID:22324320

  3. Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography

    SciTech Connect

    Norlen, Lars . E-mail: lars.norlen@ki.se; Masich, Sergej; Goldie, Kenneth N.; Hoenger, Andreas

    2007-06-10

    Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly {alpha}-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

  4. Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.

    PubMed

    Galaz-Montoya, Jesús G; Hecksel, Corey W; Baldwin, Philip R; Wang, Eryu; Weaver, Scott C; Schmid, Michael F; Ludtke, Steven J; Chiu, Wah

    2016-06-01

    Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions. PMID:27016284

  5. Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.

    PubMed

    Galaz-Montoya, Jesús G; Hecksel, Corey W; Baldwin, Philip R; Wang, Eryu; Weaver, Scott C; Schmid, Michael F; Ludtke, Steven J; Chiu, Wah

    2016-06-01

    Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions.

  6. Cellular uptake mechanisms of functionalised multi-walled carbon nanotubes by 3D electron tomography imaging

    NASA Astrophysics Data System (ADS)

    Al-Jamal, Khuloud T.; Nerl, Hannah; Müller, Karin H.; Ali-Boucetta, Hanene; Li, Shouping; Haynes, Peter D.; Jinschek, Joerg R.; Prato, Maurizio; Bianco, Alberto; Kostarelos, Kostas; Porter, Alexandra E.

    2011-06-01

    Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed that MWNT-NH3+ were internalised in both phagocytic and non-phagocytic cells by any one of three mechanisms: (a) individually via membrane wrapping; (b) individually by direct membrane translocation; and (c) in clusters within vesicular compartments. At early time points following intracellular translocation, we noticed accumulation of nanotube material within various intracellular compartments, while a long-term (14-day) study using primary human macrophages revealed that MWNT-NH3+ were able to escape vesicular (phagosome) entrapment by translocating directly into the cytoplasm.Carbon nanotubes (CNTs) are being investigated for a variety of biomedical applications. Despite numerous studies, the pathways by which carbon nanotubes enter cells and their subsequent intracellular trafficking and distribution remain poorly determined. Here, we use 3-D electron tomography techniques that offer optimum enhancement of contrast between carbon nanotubes and the plasma membrane to investigate the mechanisms involved in the cellular uptake of shortened, functionalised multi-walled carbon nanotubes (MWNT-NH3+). Both human lung epithelial (A549) cells, that are almost incapable of phagocytosis and primary macrophages, capable of extremely efficient phagocytosis, were used. We observed

  7. Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography

    SciTech Connect

    Liberton, Michelle; Austin II, Jotham R; Berg, R. Howard; Pakrasi, Himadri B

    2011-04-01

    Cyanobacteria, descendants of the endosymbiont that gave rise to modern-day chloroplasts, are vital contributors to global biological energy conversion processes. A thorough understanding of the physiology of cyanobacteria requires detailed knowledge of these organisms at the level of cellular architecture and organization. In these prokaryotes, the large membrane protein complexes of the photosynthetic and respiratory electron transport chains function in the intracellular thylakoid membranes. Like plants, the architecture of the thylakoid membranes in cyanobacteria has direct impact on cellular bioenergetics, protein transport, and molecular trafficking. However, whole-cell thylakoid organization in cyanobacteria is not well understood. Here we present, by using electron tomography, an in-depth analysis of the architecture of the thylakoid membranes in a unicellular cyanobacterium, Cyanothece sp. ATCC 51142. Based on the results of three-dimensional tomographic reconstructions of near-entire cells, we determined that the thylakoids in Cyanothece 51142 form a dense and complex network that extends throughout the entire cell. This thylakoid membrane network is formed from the branching and splitting of membranes and encloses a single lumenal space. The entire thylakoid network spirals as a peripheral ring of membranes around the cell, an organization that has not previously been described in a cyanobacterium. Within the thylakoid membrane network are areas of quasi-helical arrangement with similarities to the thylakoid membrane system in chloroplasts. This cyanobacterial thylakoid arrangement is an efficient means of packing a large volume of membranes in the cell while optimizing intracellular transport and trafficking.

  8. Unique Thylakoid Membrane Architecture of a Unicellular N2-Fixing Cyanobacterium Revealed by Electron Tomography

    SciTech Connect

    Liberton, Michelle L.; Austin, Jotham R.; Berg, R. H.; Pakrasi, Himadri B.

    2011-04-01

    Cyanobacteria, descendants of the endosymbiont that gave rise to modern-day chloroplasts, are vital contributors to global biological energy conversion processes. A thorough understanding of the physiology of cyanobacteria requires detailed knowledge of these organisms at the level of cellular architecture and organization. In these prokaryotes, the large membrane protein complexes of the photosynthetic and respiratory electron transport chains function in the intracellular thylakoid membranes. Like plants, the architecture of the thylakoid membranes in cyanobacteria has direct impact on cellular bioenergetics, protein transport, and molecular trafficking. However, whole-cell thylakoid organization in cyanobacteria is not well understood. Here we present, by using electron tomography, an in-depth analysis of the architecture of the thylakoid membranes in a unicellular cyanobacterium, Cyanothece sp. ATCC 51142. Based on the results of three-dimensional tomographic reconstructions of near-entire cells, we determined that the thylakoids in Cyanothece 51142 form a dense and complex network that extends throughout the entire cell. This thylakoid membrane network is formed from the branching and splitting of membranes and encloses a single lumenal space. The entire thylakoid network spirals as a peripheral ring of membranes around the cell, an organization that has not previously been described in a cyanobacterium. Within the thylakoid membrane network are areas of quasi-helical arrangement with similarities to the thylakoid membrane system in chloroplasts. This cyanobacterial thylakoid arrangement is an efficient means of packing a large volume of membranes in the cell while optimizing intracellular transport and trafficking.

  9. FPGA-Based Front-End Electronics for Positron Emission Tomography

    PubMed Central

    Haselman, Michael; DeWitt, Don; McDougald, Wendy; Lewellen, Thomas K.; Miyaoka, Robert; Hauck, Scott

    2010-01-01

    Modern Field Programmable Gate Arrays (FPGAs) are capable of performing complex discrete signal processing algorithms with clock rates above 100MHz. This combined with FPGA’s low expense, ease of use, and selected dedicated hardware make them an ideal technology for a data acquisition system for positron emission tomography (PET) scanners. Our laboratory is producing a high-resolution, small-animal PET scanner that utilizes FPGAs as the core of the front-end electronics. For this next generation scanner, functions that are typically performed in dedicated circuits, or offline, are being migrated to the FPGA. This will not only simplify the electronics, but the features of modern FPGAs can be utilizes to add significant signal processing power to produce higher resolution images. In this paper two such processes, sub-clock rate pulse timing and event localization, will be discussed in detail. We show that timing performed in the FPGA can achieve a resolution that is suitable for small-animal scanners, and will outperform the analog version given a low enough sampling period for the ADC. We will also show that the position of events in the scanner can be determined in real time using a statistical positioning based algorithm. PMID:21961085

  10. Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION.

    PubMed

    Bharat, Tanmay A M; Scheres, Sjors H W

    2016-11-01

    Electron cryo-tomography (cryo-ET) is a technique that is used to produce 3D pictures (tomograms) of complex objects such as asymmetric viruses, cellular organelles or whole cells from a series of tilted electron cryo-microscopy (cryo-EM) images. Averaging of macromolecular complexes found within tomograms is known as subtomogram averaging, and this technique allows structure determination of macromolecular complexes in situ. Subtomogram averaging is also gaining in popularity for the calculation of initial models for single-particle analysis. We describe herein a protocol for subtomogram averaging from cryo-ET data using the RELION software (http://www2.mrc-lmb.cam.ac.uk/relion). RELION was originally developed for cryo-EM single-particle analysis, and the subtomogram averaging approach presented in this protocol has been implemented in the existing workflow for single-particle analysis so that users may conveniently tap into existing capabilities of the RELION software. We describe how to calculate 3D models for the contrast transfer function (CTF) that describe the transfer of information in the imaging process, and we illustrate the results of classification and subtomogram averaging refinement for cryo-ET data of purified hepatitis B capsid particles and Saccharomyces cerevisiae 80S ribosomes. Using the steps described in this protocol, along with the troubleshooting and optimization guidelines, high-resolution maps can be obtained in which secondary structure elements are resolved subtomogram. PMID:27685097

  11. Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION.

    PubMed

    Bharat, Tanmay A M; Scheres, Sjors H W

    2016-11-01

    Electron cryo-tomography (cryo-ET) is a technique that is used to produce 3D pictures (tomograms) of complex objects such as asymmetric viruses, cellular organelles or whole cells from a series of tilted electron cryo-microscopy (cryo-EM) images. Averaging of macromolecular complexes found within tomograms is known as subtomogram averaging, and this technique allows structure determination of macromolecular complexes in situ. Subtomogram averaging is also gaining in popularity for the calculation of initial models for single-particle analysis. We describe herein a protocol for subtomogram averaging from cryo-ET data using the RELION software (http://www2.mrc-lmb.cam.ac.uk/relion). RELION was originally developed for cryo-EM single-particle analysis, and the subtomogram averaging approach presented in this protocol has been implemented in the existing workflow for single-particle analysis so that users may conveniently tap into existing capabilities of the RELION software. We describe how to calculate 3D models for the contrast transfer function (CTF) that describe the transfer of information in the imaging process, and we illustrate the results of classification and subtomogram averaging refinement for cryo-ET data of purified hepatitis B capsid particles and Saccharomyces cerevisiae 80S ribosomes. Using the steps described in this protocol, along with the troubleshooting and optimization guidelines, high-resolution maps can be obtained in which secondary structure elements are resolved subtomogram.

  12. Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

    PubMed

    Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

    2002-01-01

    A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

  13. 3D image analysis of plants using electron tomography and micro-CT.

    PubMed

    Mineyuki, Yoshinobu

    2014-11-01

    Precise control of the cell division plane is a prerequisite for plant development. The division site (the position of the division plane insertion) in plant cells is the site along which the cell plate margin joins the parental cell walls. How this division site is determined and established during cell division is an essential question in plant morphogenesis. Herein we demonstrate how computer tomography techniques can aid in understanding nano-machines involved in determination of the division site and in analysing air space development after cytokinesis. The preprophase band (PPB) is a cytokinetic nano-machine used to determine the plant division site. The PPB appears as a broad microtubule (MT) band in the G2 phase and the MT band narrows during the prophase to establish the specialized belt zone in the cell cortex (cortical division zone, [CDZ]). The MT band disappears at prometaphase, but some memories remain in the CDZ throughout the process of cell division, and this is the site of attachment of the newly formed cell plate. We have examined PPB development of high-pressure frozen onion cotyledon epidermis using dual-axis electron tomography. MTs as well as actin microfilaments (MFs) and membrane systems can be preserved well by high-pressure freezing [1]. Since detection of ∼100 vesicles and ∼40 MT ends was possible in a tomogram of the PPB surface (0.25 mm × 0.25 mm) obtained from 250-nm-thick tangential sections of epidermal cells, we were able to quantitatively analyze the frequencies of various types of vesicles and MT ends in the PPB [2]. The results clearly showed that endocytosis is active [2,3] and MTs are very dynamic in the late PPB. Light microscopic studies with fluorescent probes have demonstrated that actins are among the main components of PPB. Electron tomography analysis showed that one actin configuration in the PPB is a relatively short single MFs running parallel to the plasma membrane. The actin MFs connecting two adjacent MTs

  14. Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure

    PubMed Central

    Shawkey, Matthew D.; Saranathan, Vinodkumar; Pálsdóttir, Hildur; Crum, John; Ellisman, Mark H.; Auer, Manfred; Prum, Richard O.

    2009-01-01

    Organismal colour can be created by selective absorption of light by pigments or light scattering by photonic nanostructures. Photonic nanostructures may vary in refractive index over one, two or three dimensions and may be periodic over large spatial scales or amorphous with short-range order. Theoretical optical analysis of three-dimensional amorphous nanostructures has been challenging because these structures are difficult to describe accurately from conventional two-dimensional electron microscopy alone. Intermediate voltage electron microscopy (IVEM) with tomographic reconstruction adds three-dimensional data by using a high-power electron beam to penetrate and image sections of material sufficiently thick to contain a significant portion of the structure. Here, we use IVEM tomography to characterize a non-iridescent, three-dimensional biophotonic nanostructure: the spongy medullary layer from eastern bluebird Sialia sialis feather barbs. Tomography and three-dimensional Fourier analysis reveal that it is an amorphous, interconnected bicontinuous matrix that is appropriately ordered at local spatial scales in all three dimensions to coherently scatter light. The predicted reflectance spectra from the three-dimensional Fourier analysis are more precise than those predicted by previous two-dimensional Fourier analysis of transmission electron microscopy sections. These results highlight the usefulness, and obstacles, of tomography in the description and analysis of three-dimensional photonic structures. PMID:19158016

  15. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography.

    PubMed

    Zhang, Lei; Lei, Dongsheng; Smith, Jessica M; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A Paul; Ren, Gang

    2016-03-30

    DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ∼2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

  16. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

    PubMed Central

    Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

    2016-01-01

    DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ∼2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics. PMID:27025159

  17. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

    NASA Astrophysics Data System (ADS)

    Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

    2016-03-01

    DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

  18. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography.

    PubMed

    Zhang, Lei; Lei, Dongsheng; Smith, Jessica M; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A Paul; Ren, Gang

    2016-01-01

    DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ∼2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics. PMID:27025159

  19. Three-dimensional coordinates of individual atoms in materials revealed by electron tomography.

    PubMed

    Xu, Rui; Chen, Chien-Chun; Wu, Li; Scott, M C; Theis, W; Ophus, Colin; Bartels, Matthias; Yang, Yongsoo; Ramezani-Dakhel, Hadi; Sawaya, Michael R; Heinz, Hendrik; Marks, Laurence D; Ercius, Peter; Miao, Jianwei

    2015-11-01

    Crystallography, the primary method for determining the 3D atomic positions in crystals, has been fundamental to the development of many fields of science. However, the atomic positions obtained from crystallography represent a global average of many unit cells in a crystal. Here, we report, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material by electron tomography with a precision of ∼19 pm, where the crystallinity of the material is not assumed. From the coordinates of these individual atoms, we measure the atomic displacement field and the full strain tensor with a 3D resolution of ∼1 nm(3) and a precision of ∼10(-3), which are further verified by density functional theory calculations and molecular dynamics simulations. The ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity is expected to find important applications in materials science, nanoscience, physics, chemistry and biology.

  20. Membrane contact sites between apicoplast and ER in Toxoplasma gondii revealed by electron tomography.

    PubMed

    Tomova, Cveta; Humbel, Bruno M; Geerts, Willie J C; Entzeroth, Rolf; Holthuis, Joost C M; Verkleij, Arie J

    2009-10-01

    Toxoplasma gondii is an obligate intracellular parasite from the phylum Apicomplexa. A hallmark of these protozoans is the presence of a unique apical complex of organelles that includes the apicoplast, a plastid acquired by secondary endosymbiosis. The apicoplast is indispensible for parasite viability. It harbours a fatty acid biosynthesis type II (FAS II) pathway and plays a key role in the parasite lipid metabolism. Possibly, the apicoplast provides components for the establishment and the maturation of the parasitophorous vacuole, ensuring the successful infection of the host cell. This implies the presence of a transport mechanism for fast and accurate allocation of lipids between the apicoplast and other membrane-bound compartments in the parasite cell. Using a combination of high-pressure freezing, freeze-substitution and electron tomography, we analysed the ultrastructural organization of the apicoplast of T. gondii in relation with the endoplasmic reticulum (ER). This allowed us to clearly show the presence of four continuous membranes surrounding the apicoplast. We present, for the first time, the existence of membrane contact sites between the apicoplast outermost membrane and the ER. We describe the morphological characteristics of these structures and discuss their potential significance for the subcellular distribution of lipids in the parasite. PMID:19602198

  1. Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography.

    PubMed

    Engel, Benjamin D; Schaffer, Miroslava; Kuhn Cuellar, Luis; Villa, Elizabeth; Plitzko, Jürgen M; Baumeister, Wolfgang

    2015-01-13

    Chloroplast function is orchestrated by the organelle's intricate architecture. By combining cryo-focused ion beam milling of vitreous Chlamydomonas cells with cryo-electron tomography, we acquired three-dimensional structures of the chloroplast in its native state within the cell. Chloroplast envelope inner membrane invaginations were frequently found in close association with thylakoid tips, and the tips of multiple thylakoid stacks converged at dynamic sites on the chloroplast envelope, implicating lipid transport in thylakoid biogenesis. Subtomogram averaging and nearest neighbor analysis revealed that RuBisCO complexes were hexagonally packed within the pyrenoid, with ~15 nm between their centers. Thylakoid stacks and the pyrenoid were connected by cylindrical pyrenoid tubules, physically bridging the sites of light-dependent photosynthesis and light-independent carbon fixation. Multiple parallel minitubules were bundled within each pyrenoid tubule, possibly serving as conduits for the targeted one-dimensional diffusion of small molecules such as ATP and sugars between the chloroplast stroma and the pyrenoid matrix.

  2. Direct Visualization of HIV-1 with Correlative Live-Cell Microscopy and Cryo-Electron Tomography

    PubMed Central

    Jun, Sangmi; Ke, Danxia; Debiec, Karl; Zhao, Gongpu; Meng, Xin; Ambrose, Zandrea; Gibson, Gregory A.; Watkins, Simon C.; Zhang, Peijun

    2011-01-01

    SUMMARY Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-native state, and therefore has the potential to help elucidate early events of HIV-1 infection in host cells. However, direct observation of structural details of infecting HIV-1 has not been realized due to technological challenges in working with rare and dynamic HIV-1 particles in human cells. Here, we report structural analysis of HIV-1 and host-cell interactions by developing a correlative high-speed 3D live-cell imaging and cryoET method. Using this methodology, we showed, for the first time under near-native conditions, that intact hyperstable mutant HIV-1 cores are released into the cytoplasm of host-cells. We further obtained direct evidence to suggest that a hyperstable mutant capsid, E45A, delayed capsid disassembly compared to the wild-type capsid. Together, these results demonstrate the advantage of our correlative live-cell and cryoET approach to image dynamic processes, such as viral infection. PMID:22078557

  3. Three-dimensional coordinates of individual atoms in materials revealed by electron tomography

    NASA Astrophysics Data System (ADS)

    Xu, Rui; Chen, Chien-Chun; Wu, Li; Scott, M. C.; Theis, W.; Ophus, Colin; Bartels, Matthias; Yang, Yongsoo; Ramezani-Dakhel, Hadi; Sawaya, Michael R.; Heinz, Hendrik; Marks, Laurence D.; Ercius, Peter; Miao, Jianwei

    2015-11-01

    Crystallography, the primary method for determining the 3D atomic positions in crystals, has been fundamental to the development of many fields of science. However, the atomic positions obtained from crystallography represent a global average of many unit cells in a crystal. Here, we report, for the first time, the determination of the 3D coordinates of thousands of individual atoms and a point defect in a material by electron tomography with a precision of ~19 pm, where the crystallinity of the material is not assumed. From the coordinates of these individual atoms, we measure the atomic displacement field and the full strain tensor with a 3D resolution of ~1 nm3 and a precision of ~10-3, which are further verified by density functional theory calculations and molecular dynamics simulations. The ability to precisely localize the 3D coordinates of individual atoms in materials without assuming crystallinity is expected to find important applications in materials science, nanoscience, physics, chemistry and biology.

  4. Molecular architecture of axonemal microtubule doublets revealed by cryo-electron tomography.

    PubMed

    Sui, Haixin; Downing, Kenneth H

    2006-07-27

    The axoneme, which forms the core of eukaryotic flagella and cilia, is one of the largest macromolecular machines, with a structure that is largely conserved from protists to mammals. Microtubule doublets are structural components of axonemes that contain a number of proteins besides tubulin, and are usually found in arrays of nine doublets arranged around two singlet microtubules. Coordinated sliding of adjacent doublets, which involves a host of other proteins in the axoneme, produces periodic beating movements of the axoneme. We have obtained a three-dimensional density map of intact microtubule doublets using cryo-electron tomography and image averaging. Our map, with a resolution of about 3 nm, provides insights into locations of particular proteins within the doublets and the structural features of the doublets that define their mechanical properties. We identify likely candidates for several of these non-tubulin components of the doublets. This work offers insight on how tubulin protofilaments and accessory proteins attach together to form the doublets and provides a structural basis for understanding doublet function in axonemes. PMID:16738547

  5. System for quantitative analysis of coronary calcification via electron-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Reed, Judd E.; Rumberger, John A.; Davitt, Patrick J.; Kaufman, R. B.; Sheedy, Patrick F., II

    1994-05-01

    Electron beam computed tomography (EBCT) has provided a new tool for identification and possible quantification of coronary arterial plaque calcium. EBCT is the only imaging modality currently available which generates images of the spatial, temporal, and contrast resolution required for the identification of small foci of calcium and the potential for accurate quantification of calcium. Meanwhile, interest in quantification of coronary arterial calcium via EBCT and its correlation with severity of coronary atherosclerosis is increasing. Data remain inconclusive, but it appears that the reproducibility of quantitative grading of the extent of calcification by EBCT may be limited, in part, by the arbitrary nature of the scoring algorithm employed within the analysis tools currently provided by the EBCT manufacturer. It has not been possible to objectively determine optimum values for minimum plaque area and brightness threshold or to quantitatively determine whether single optimal values even exist. Also, although the current system tabulates the score, area, and mean attenuation for each plaque, the locations of the plaques are not reported.

  6. Anchoring structure of the calvarial periosteum revealed by focused ion beam/scanning electron microscope tomography

    PubMed Central

    Hirashima, Shingo; Ohta, Keisuke; Kanazawa, Tomonoshin; Uemura, Kei-ichiro; Togo, Akinobu; Yoshitomi, Munetake; Okayama, Satoko; Kusukawa, Jingo; Nakamura, Kei-ichiro

    2015-01-01

    An important consideration in regeneration therapy is the fact that the tissue surrounding an organ supports its function. Understanding the structure of the periosteum can contribute to more effective bone regeneration therapy. As a cellular source, the periosteum also assists bone growth and fracture healing; this further necessitates its direct contact with the bone. However, its anchoring strength appears to be inexplicably stronger than expected. In this study, we used focused ion beam/scanning electron microscope tomography to investigate ultrathin serial sections as well as the three dimensional ultrastructure of the periosteum to clarify the architecture of its anchoring strength, as such assessments are challenging using conventional methods. We discovered perforating fibres that arise from the bone surface at 30 degree angles. Additionally, the fibres across the osteoblast layer were frequently interconnected to form a net-like structure. Fibroblast processes were observed extending into the perforating fibres; their morphologies were distinct from those of typical fibroblasts. Thus, our study revealed novel ultrastructures of the periosteum that support anchorage and serve as a cellular source as well as a mechanical stress transmitter. PMID:26627533

  7. Molecular architecture of axonemal microtubule doublets revealedby cryo-electron tomography

    SciTech Connect

    Sui, Haixin; Downing, Kenneth H.

    2006-05-22

    The axoneme, which forms the core of eukaryotic flagella and cilia, is one of the largest macromolecular machines with a structure that is largely conserved from protists to mammals. Microtubule doublets are structural components of axonemes containing a number of proteins besides tubulin, and are usually found in arrays of nine doublets arranged around two singlet microtubules. Coordinated sliding of adjacent doublets, which involves a host of other proteins in the axoneme, produces periodic beating movements of the axoneme. We have obtained a 3D density map of intact microtubule doublets using cryo-electron tomography and image averaging. Our map, with a resolution of about 3 nm, provides insights into locations of particular proteins within the doublets and the structural features of the doublets that define their mechanical properties. We identify likely candidates for several of these non-tubulin components of the doublets. This work offers novel insight on how tubulin protofilaments and accessory proteins attach together to form the doublets and provides a structural basis for understanding doublet function in axonemes.

  8. 3D Magnetic Induction Maps of Nanoscale Materials Revealed by Electron Holographic Tomography

    PubMed Central

    2015-01-01

    The investigation of three-dimensional (3D) ferromagnetic nanoscale materials constitutes one of the key research areas of the current magnetism roadmap and carries great potential to impact areas such as data storage, sensing, and biomagnetism. The properties of such nanostructures are closely connected with their 3D magnetic nanostructure, making their determination highly valuable. Up to now, quantitative 3D maps providing both the internal magnetic and electric configuration of the same specimen with high spatial resolution are missing. Here, we demonstrate the quantitative 3D reconstruction of the dominant axial component of the magnetic induction and electrostatic potential within a cobalt nanowire (NW) of 100 nm in diameter with spatial resolution below 10 nm by applying electron holographic tomography. The tomogram was obtained using a dedicated TEM sample holder for acquisition, in combination with advanced alignment and tomographic reconstruction routines. The powerful approach presented here is widely applicable to a broad range of 3D magnetic nanostructures and may trigger the progress of novel spintronic nonplanar nanodevices. PMID:27182110

  9. Examination of Scanning Electron Microscope and Computed Tomography Images of PICA

    NASA Technical Reports Server (NTRS)

    Lawson, John W.; Stackpoole, Margaret M.; Shklover, Valery

    2010-01-01

    Micrographs of PICA (Phenolic Impregnated Carbon Ablator) taken using a Scanning Electron Microscope (SEM) and 3D images taken with a Computed Tomography (CT) system are examined. PICA is a carbon fiber based composite (Fiberform ) with a phenolic polymer matrix. The micrographs are taken at different surface depths and at different magnifications in a sample after arc jet testing and show different levels of oxidative removal of the charred matrix (Figs 1 though 13). CT scans, courtesy of Xradia, Inc. of Concord CA, were captured for samples of virgin PICA, charred PICA and raw Fiberform (Fig. 14). We use these images to calculate the thermal conductivity (TC) of these materials using correlation function (CF) methods. CF methods give a mathematical description of how one material is embedded in another and is thus ideally suited for modeling composites like PICA. We will evaluate how the TC of the materials changes as a function of surface depth. This work is in collaboration with ETH-Zurich, which has expertise in high temperature materials and TC modeling (including CF methods).

  10. Direct visualization of vaults within intact cells by electron cryo-tomography

    PubMed Central

    Woodward, Cora L.; Mendonça, Luiza M.

    2016-01-01

    The vault complex is the largest cellular ribonucleoprotein complex ever characterized and is present across diverse Eukarya. Despite significant information regarding the structure, composition and evolutionary conservation of the vault, little is know about the complex’s actual biological function. To determine if intracellular vaults are morphologically similar to previously studied purified and recombinant vaults, we have used electron cryo-tomography to characterize the vault complexes found in the thin edges of primary human cells growing in tissue culture. Our studies confirm that intracellular vaults are similar in overall size and shape to purified and recombinant vaults previously analyzed. Results from subtomogram averaging indicate that densities within the vault lumen are not ordered, but randomly distributed. We also observe that vaults located in the extreme periphery of the cytoplasm predominately associate with granule-like structures and actin. Our ultrastructure studies augment existing biochemical, structural and genetic information on the vault, and provide important intracellular context for the ongoing efforts to understand the biological function of the native cytoplasmic vault. PMID:25864047

  11. Molecular architecture of axonemal microtubule doublets revealed by cryo-electron tomography.

    PubMed

    Sui, Haixin; Downing, Kenneth H

    2006-07-27

    The axoneme, which forms the core of eukaryotic flagella and cilia, is one of the largest macromolecular machines, with a structure that is largely conserved from protists to mammals. Microtubule doublets are structural components of axonemes that contain a number of proteins besides tubulin, and are usually found in arrays of nine doublets arranged around two singlet microtubules. Coordinated sliding of adjacent doublets, which involves a host of other proteins in the axoneme, produces periodic beating movements of the axoneme. We have obtained a three-dimensional density map of intact microtubule doublets using cryo-electron tomography and image averaging. Our map, with a resolution of about 3 nm, provides insights into locations of particular proteins within the doublets and the structural features of the doublets that define their mechanical properties. We identify likely candidates for several of these non-tubulin components of the doublets. This work offers insight on how tubulin protofilaments and accessory proteins attach together to form the doublets and provides a structural basis for understanding doublet function in axonemes.

  12. Compensation of Missing Wedge Effects with Sequential Statistical Reconstruction in Electron Tomography

    PubMed Central

    Tuna, Uygar; Peltonen, Sari; Moriya, Toshio; Soonsawad, Pan; Marjomäki, Varpu; Cheng, R. Holland; Ruotsalainen, Ulla

    2014-01-01

    Electron tomography (ET) of biological samples is used to study the organization and the structure of the whole cell and subcellular complexes in great detail. However, projections cannot be acquired over full tilt angle range with biological samples in electron microscopy. ET image reconstruction can be considered an ill-posed problem because of this missing information. This results in artifacts, seen as the loss of three-dimensional (3D) resolution in the reconstructed images. The goal of this study was to achieve isotropic resolution with a statistical reconstruction method, sequential maximum a posteriori expectation maximization (sMAP-EM), using no prior morphological knowledge about the specimen. The missing wedge effects on sMAP-EM were examined with a synthetic cell phantom to assess the effects of noise. An experimental dataset of a multivesicular body was evaluated with a number of gold particles. An ellipsoid fitting based method was developed to realize the quantitative measures elongation and contrast in an automated, objective, and reliable way. The method statistically evaluates the sub-volumes containing gold particles randomly located in various parts of the whole volume, thus giving information about the robustness of the volume reconstruction. The quantitative results were also compared with reconstructions made with widely-used weighted backprojection and simultaneous iterative reconstruction technique methods. The results showed that the proposed sMAP-EM method significantly suppresses the effects of the missing information producing isotropic resolution. Furthermore, this method improves the contrast ratio, enhancing the applicability of further automatic and semi-automatic analysis. These improvements in ET reconstruction by sMAP-EM enable analysis of subcellular structures with higher three-dimensional resolution and contrast than conventional methods. PMID:25279759

  13. Sub-micron resolution high-speed spectral domain optical coherence tomography in quality inspection for printed electronics

    NASA Astrophysics Data System (ADS)

    Czajkowski, J.; Lauri, J.; Sliz, R.; Fält, P.; Fabritius, T.; Myllylä, R.; Cense, B.

    2012-04-01

    We present the use of sub-micron resolution optical coherence tomography (OCT) in quality inspection for printed electronics. The device used in the study is based on a supercontinuum light source, Michelson interferometer and high-speed spectrometer. The spectrometer in the presented spectral-domain optical coherence tomography setup (SD-OCT) is centered at 600 nm and covers a 400 nm wide spectral region ranging from 400 nm to 800 nm. Spectra were acquired at a continuous rate of 140,000 per second. The full width at half maximum of the point spread function obtained from a Parylene C sample was 0:98 m. In addition to Parylene C layers, the applicability of sub-micron SD-OCT in printed electronics was studied using PET and epoxy covered solar cell, a printed RFID antenna and a screen-printed battery electrode. A commercial SD-OCT system was used for reference measurements.

  14. Automatic detection of mitochondria from electron microscope tomography images: a curve fitting approach

    NASA Astrophysics Data System (ADS)

    Tasel, Serdar F.; Hassanpour, Reza; Mumcuoglu, Erkan U.; Perkins, Guy C.; Martone, Maryann

    2014-03-01

    Mitochondria are sub-cellular components which are mainly responsible for synthesis of adenosine tri-phosphate (ATP) and involved in the regulation of several cellular activities such as apoptosis. The relation between some common diseases of aging and morphological structure of mitochondria is gaining strength by an increasing number of studies. Electron microscope tomography (EMT) provides high-resolution images of the 3D structure and internal arrangement of mitochondria. Studies that aim to reveal the correlation between mitochondrial structure and its function require the aid of special software tools for manual segmentation of mitochondria from EMT images. Automated detection and segmentation of mitochondria is a challenging problem due to the variety of mitochondrial structures, the presence of noise, artifacts and other sub-cellular structures. Segmentation methods reported in the literature require human interaction to initialize the algorithms. In our previous study, we focused on 2D detection and segmentation of mitochondria using an ellipse detection method. In this study, we propose a new approach for automatic detection of mitochondria from EMT images. First, a preprocessing step was applied in order to reduce the effect of nonmitochondrial sub-cellular structures. Then, a curve fitting approach was presented using a Hessian-based ridge detector to extract membrane-like structures and a curve-growing scheme. Finally, an automatic algorithm was employed to detect mitochondria which are represented by a subset of the detected curves. The results show that the proposed method is more robust in detection of mitochondria in consecutive EMT slices as compared with our previous automatic method.

  15. Three-Dimensional Morphological Analysis of ALH84001 Magnetite Using Electron Tomography

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie L.; Clemett, Simon J.; Shimmin, Joel; Morphew, Mary; McIntosh, J. Richard; Bazylinski, Dennis A.; Kirschvink, Joseph L.; Wentworth, Susan J.; McKay, David S.; Vali, Hojatollah

    2003-01-01

    We report here the crystal morphologies of MV-1 and ALH84001 magnetites as calculated by back-projection using electron tomography. In the present study, we used a 300 keV TEM with a field emission gun (Tecnai F-30 from FEI Inc.), equipped with a 2048 x 2048 pixel CCD camera from Gatan Inc. to image magnetite crystals over tilt ranges of approx. +/- 72 deg in 2 deg tilt intervals. The images were aligned for back-projection, either manually, or through the use of fiducial 5 nm Au spheres affixed to the specimen prior to microscopy. Three-dimensional (3-D) reconstructions were computed using weighted back-projection of the tilted views. The tomograms were viewed and analyzed as a series of slices 1.0 nm thick, taken parallel to the specimen-supporting grid, using the IMOD software package. The shape of each magnetite crystal was determined by defining the external contour of a given magnetite in each slice and assembling a stack of these contours in 3-D. To aid in visualization, the stacked contour array was reduced to an optimal mesh by Delaunay triangulation. The surface normal to each of the triangles in the mesh was calculated and the triangle faces colored according to the orientation of that surface normal relative to the principal crystallographic axis of magnetite. Green surfaces correspond to {111} orientations, blue surfaces to {100} orientations, and red surfaces to {110} orientations. Triangles whose surface normal did not correspond to one of the principal axes were colored gray. Within the experimental and numerical uncertainties of the deconvolution, the tomographic reconstruction of both MV-1 and ALH84001 magnetites are equivalent and correspond to a truncated hexa-octahedral morphology.

  16. Health behavior modification after electron beam computed tomography and physician consultation.

    PubMed

    Schwartz, Jennifer; Allison, Mathew; Wright, C Michael

    2011-04-01

    This study aimed to determine whether participants reported altering health behaviors (physical activity, diet, and alcohol consumption) after seeing results from an electron-beam computed tomography (EBCT) scan for coronary artery calcium and reviewing these results with a physician. Clinicians attempt to motivate patients to control cardiovascular risk factors by adopting healthy behaviors and reducing harmful actions. Asymptomatic patients (N = 510) were evaluated by EBCT for the extent of coronary artery calcium. Information pertaining to demographics, health history, and lifestyle/health behaviors was obtained from each participant at the time of the EBCT scan. Patients were given their numerical calcium score, shown images of their coronary arteries, and counseled by a physician for lifestyle and medical risk modification based on their coronary artery calcium score. Approximately 6 years after the scan, participants completed a follow-up questionnaire related to lifestyle modifications. In multivariable analysis, the presence and extent of coronary artery calcium was significantly associated with beneficial health behavior modifications. Specifically, the greater a patient's coronary artery calcium score, the more likely they were to report increasing exercise (odds ratio = 1.34, P = 0.02), changing diet (odds ratio = 1.40, P < 0.01), and changing alcohol intake (odds ratio = 1.46, P = 0.05). This study suggests that seeing and being counseled on the presence and extent of coronary artery calcium is significantly associated with behavior change. PMID:20857186

  17. Visualization of the Herpes Simplex Virus Portal in situ by Cryo-electron Tomography

    PubMed Central

    Cardone, Giovanni; Winkler, Dennis C.; Trus, Benes L.; Cheng, Naiqian; Heuser, John E.; Newcomb, William W.; Brown, Jay C.; Steven, Alasdair C.

    2007-01-01

    Herpes simplex virus type 1 (HSV-1), the prototypical herpesvirus, has an icosahedral nucleocapsid surrounded by a proteinaceous tegument and a lipoprotein envelope. As in tailed bacteriophages, the icosahedral symmetry of the capsid is broken at one of the twelve vertices, which is occupied by a dodecameric ring of portal protein, UL6, instead of a pentamer of the capsid protein, UL19. The portal ring serves as a conduit for DNA entering and exiting the capsid. From a cryo-EM reconstruction of capsids immuno-gold-labeled with anti-UL6 antibodies, we confirmed that UL6 resides at a vertex. To visualize the portal in the context of the assembled capsid, we used cryo-electron tomography to determine the three-dimensional structures of individual A-capsids (empty, mature capsids). The similarity in size and overall shape of the portal and a UL19 pentamer - both are cylinders of ~ 800 kDa - combined with residual noise in the tomograms, prevented us from identifying the portal vertices directly; however, this was accomplished by a computational classification procedure. Averaging the portal-containing subtomograms produced a structure that tallies with the isolated portal, as previously reconstructed by cryo-EM. The portal is mounted on the outer surface of the capsid floor layer, with its narrow end pointing outwards. This disposition differs from that of known phage portals in that the bulk of its mass lies outside, not inside, the floor. This distinction may be indicative of functional divergence at the level of portal-related functions other than its role as a DNA channel. PMID:17188319

  18. Structural evolution and strain induced mixing in Cu–Co composites studied by transmission electron microscopy and atom probe tomography

    SciTech Connect

    Bachmaier, A.; Aboulfadl, H.; Pfaff, M.; Mücklich, F.; Motz, C.

    2015-02-15

    A Cu–Co composite material is chosen as a model system to study structural evolution and phase formations during severe plastic deformation. The evolving microstructures as a function of the applied strain were characterized at the micro-, nano-, and atomic scale-levels by combining scanning electron microscopy and transmission electron microscopy including energy-filtered transmission electron microscopy and electron energy-loss spectroscopy. The amount of intermixing between the two phases at different strains was examined at the atomic scale using atom probe tomography as complimentary method. It is shown that Co particles are dissolved in the Cu matrix during severe plastic deformation to a remarkable extent and their size, number, and volume fraction were quantitatively determined during the deformation process. From the results, it can be concluded that supersaturated solid solutions up to 26 at.% Co in a fcc Cu–26 at.% Co alloy are obtained during deformation. However, the distribution of Co was found to be inhomogeneous even at the highest degree of investigated strain. - Highlights: • Structural evolution in a deformed Cu–Co composite is studied on all length scales. • Amount of intermixing is examined by atom-probe tomography. • Supersaturated solid solutions up to 26 at.% Co in Cu are observed.

  19. Regional pulmonary blood flow measurement in humans with electron-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Holt, William W.; Konhilas, John; Wolfkiel, Christopher J.

    1995-05-01

    Electron beam computed tomography (EBCT) is a potentially useful modality to quantitate regional pulmonary flow (RPF) with minimal invasiveness, in part because it has good spatial and temporal resolution. The present studies used a single compartment model of indicator transport and EBCT to measure regional tissue flow in the lungs of human subjects. The model postulates that flow is proportional to maximal enhancement and assumes complete tissue accumulation of indicator before significant indicator washout (WO). EBCT flow studies were retrospectively analyzed with respect to RPF in 10 adult patients who had undergone clinically indicated or research cardiovascular studies. Time density curves from the left atrial (LA) cavity and one-third segments of left (LL) and right (RL) lungs (A: anterior, M: middle, and P: posterior segments) were used to calculate RPF. Washout was determined as the percent of the LA curve at the time of peak parenchymal opacification using gamma curve fits to both tissue data and the LA curve data. Mean +/- standard deviation RPF in ml/min/ml was 0.8 +/- 0.4, 1.1 +/- 0.4, and 1.3 +/- 0.4 for A, M, and P respectively for one-third regions in the left lung. Similar results were found in the right lung. No difference in RPF was found when images were measured either by including the largest of visible parenchymal vessels or when such vessels were excluded. Flow in A of LL and RL was less than that in M or P. Average WO was about 10%, with a range of 0-41% of the LA curve area. There was no significant difference between one-third segment WO using pairwise comparison on the left and right sides when tested separately. RPF values were greater in the posterior vs anterior regions of these supine patients. In conclusion, EBCT can detect gravity related flow differences in the human lung. EBCT has potential for clinical assessment of absolute regional pulmonary flow determination in animals and man.

  20. Regional pulmonary blood flow measurement in humans with electron beam computed tomography

    SciTech Connect

    Holt, W.W.; Konhilas, J.; Wolfkiel, C.

    1995-12-31

    Electron beam computed tomography (EBCT) is a potentially useful modality to quantitate regional pulmonary flow (RPF) with minimal invasiveness, in part because it has good spatial and temporal resolution. The present studies used a single compartment model of indicator transport and EBCT to measure regional tissue flow in the lungs of human subjects. The model postulates that flow is proportional to maximal enhancement and assumes complete tissue accumulation of indicator before significant indicator washout (WO). EBCT flow studies were retrospectively analyzed with respect to regional pulmonary flow (RPF) in 10 adult patients who had undergone clinically indicated or research cardiovascular studies. Time density curves from the left atrial (LA) cavity and one-third segments of left (LL) and right (RL) lungs (A: anterior, M: middle and P: posterior segments) were used to calculate RPF. Washout was determined as the percent of the LA curve at the time of peak parenchymal opacification using gamma curve fits to both tissue data and the LA curve data. Mean {+-} standard deviation RPF in ml/min/ml was 0.8 {+-} 0.4, 1.1 {+-} 0.4 and 1.3 {+-} 0.4 for A, M and P respectively for one-third regions in the left lung. Similar results were found in the right lung. No difference in RPF was found when images were measured either by including the largest of visible parenchymal vessels or when such vessels were excluded. Flow in A of LL and RL was less than that in M or P. Average WO was about 10%, with a range of 0--41% of the LA curve area. There was no significant difference between one-third segment WO using pairwise comparison on the left and right sides when tested separately. RPF values were greater in the posterior vs anterior regions of these supine patients. In conclusion, EBCT can detect gravity related flow differences in the human lung. EBCT has potential for clinical assessment of absolute regional pulmonary flow determination in animals and man.

  1. Electron beam diagnostic system using computed tomography and an annular sensor

    DOEpatents

    Elmer, John W.; Teruya, Alan T.

    2014-07-29

    A system for analyzing an electron beam including a circular electron beam diagnostic sensor adapted to receive the electron beam, the circular electron beam diagnostic sensor having a central axis; an annular sensor structure operatively connected to the circular electron beam diagnostic sensor, wherein the sensor structure receives the electron beam; a system for sweeping the electron beam radially outward from the central axis of the circular electron beam diagnostic sensor to the annular sensor structure wherein the electron beam is intercepted by the annular sensor structure; and a device for measuring the electron beam that is intercepted by the annular sensor structure.

  2. Electron beam diagnostic system using computed tomography and an annular sensor

    DOEpatents

    Elmer, John W.; Teruya, Alan T.

    2015-08-11

    A system for analyzing an electron beam including a circular electron beam diagnostic sensor adapted to receive the electron beam, the circular electron beam diagnostic sensor having a central axis; an annular sensor structure operatively connected to the circular electron beam diagnostic sensor, wherein the sensor structure receives the electron beam; a system for sweeping the electron beam radially outward from the central axis of the circular electron beam diagnostic sensor to the annular sensor structure wherein the electron beam is intercepted by the annular sensor structure; and a device for measuring the electron beam that is intercepted by the annular sensor structure.

  3. Atom probe tomography and transmission electron microscopy characterisation of precipitation in an Al-Cu-Li-Mg-Ag alloy.

    PubMed

    Gault, B; de Geuser, F; Bourgeois, L; Gabble, B M; Ringer, S P; Muddle, B C

    2011-05-01

    State-of-the art atom probe tomography (APT) combined with transmission electron microscopy (TEM) were used to investigate the microstructure at different stages of the ageing process of an alloy of composition (at%) Al-1.68%Cu-4.62%Li-0.33%Mg-0.1%Ag. These alloys were shown to exhibit a complex microstructure of T(1) plates and several metastable phases, including θ' and S. We will highlight the early stages of clustering, precipitate interactions and possible solute segregation at the matrix/precipitate interfaces and detail the chemical composition of the different phases.

  4. Characterizing the Three-Dimensional Structure of Block Copolymers via Sequential Infiltration Synthesis and Scanning Transmission Electron Tomography.

    PubMed

    Segal-Peretz, Tamar; Winterstein, Jonathan; Doxastakis, Manolis; Ramírez-Hernández, Abelardo; Biswas, Mahua; Ren, Jiaxing; Suh, Hyo Seon; Darling, Seth B; Liddle, J Alexander; Elam, Jeffrey W; de Pablo, Juan J; Zaluzec, Nestor J; Nealey, Paul F

    2015-05-26

    Understanding and controlling the three-dimensional structure of block copolymer (BCP) thin films is critical for utilizing these materials for sub-20 nm nanopatterning in semiconductor devices, as well as in membranes and solar cell applications. Combining an atomic layer deposition (ALD)-based technique for enhancing the contrast of BCPs in transmission electron microscopy (TEM) together with scanning TEM (STEM) tomography reveals and characterizes the three-dimensional structures of poly(styrene-block-methyl methacrylate) (PS-b-PMMA) thin films with great clarity. Sequential infiltration synthesis (SIS), a block-selective technique for growing inorganic materials in BCPs films in an ALD tool and an emerging technique for enhancing the etch contrast of BCPs, was harnessed to significantly enhance the high-angle scattering from the polar domains of BCP films in the TEM. The power of combining SIS and STEM tomography for three-dimensional (3D) characterization of BCP films was demonstrated with the following cases: self-assembled cylindrical, lamellar, and spherical PS-b-PMMA thin films. In all cases, STEM tomography has revealed 3D structures that were hidden underneath the surface, including (1) the 3D structure of defects in cylindrical and lamellar phases, (2) the nonperpendicular 3D surface of grain boundaries in the cylindrical phase, and (3) the 3D arrangement of spheres in body-centered-cubic (BCC) and hexagonal-closed-pack (HCP) morphologies in the spherical phase. The 3D data of the spherical morphologies was compared to coarse-grained simulations and assisted in validating the simulations' parameters. STEM tomography of SIS-treated BCP films enables the characterization of the exact structure used for pattern transfer and can lead to a better understating of the physics that is utilized in BCP lithography.

  5. A study of 3D structure of nighttime electron density enhancement in the mid-latitude ionosphere by GPS tomography

    NASA Astrophysics Data System (ADS)

    Chen, C.; Saito, A.

    2011-12-01

    The mid-latitude summer nighttime anomaly (MSNA) is a feature that the nighttime electron density larger than that in the daytime mid-latitude ionosphere. This anomaly was first detected in the southern hemisphere five decades ago and observed in the northern hemisphere recently by ionosondes and satellites. Previous studies presented the electron density structure of MSNA by using COSMIC occultation data and found that MSNA is clearly seen around 300 km altitude during local summer. However, due to lack of observation, the day-to-day variation of MSNA was not investigated. A GPS tomography method by SPEL of Kyoto University using the total electron content (TEC) data measured by the ground-based GPS receiver network is employed in this study. The wide coverage and continuous observation of GPS receivers are suitable for investigating the spatial and day-to-day variations of ionospheric electron densities. The algorithm of the GPS tomography developed by SPEL of Kyoto University use a constraint condition that the gradient of election density tends to be smooth in the horizontal direction and steep in the vicinity of the F2 peak, instead of inputting the initial conditions. Therefore, the algorithm is independent of any ionospheric and plasmaspheric electron density distribution models. The dense ground-based GPS receiver network around European region is used to study the three dimensional (3D) structure of MSNA with GPS tomography. Results show that the MSNA usually appear around the geomagnetic mid-latitude region during local summer nighttime. The feature of MSNA is most obvious at the ionospheric F2-peak altitudes. The result also shows a day-to-day variation in the formation of MSNA, in terms of the occurrence time, intensity, and spatial extent. The tomographic results are compared with the ionosondes, satellites, and radar measurements. A theoretical model simulation, SAMI2, is also used to further discuss the mechanism of MSNA. The comparison with other

  6. Atom probe tomography and transmission electron microscopy of a Mg-doped AlGaN/GaN superlattice.

    PubMed

    Bennett, S E; Ulfig, R M; Clifton, P H; Kappers, M J; Barnard, J S; Humphreys, C J; Oliver, R A

    2011-02-01

    The electronic characteristics of semiconductor-based devices are greatly affected by the local dopant atom distribution. In Mg-doped GaN, the clustering of dopants at structural defects has been widely reported, and can significantly affect p-type conductivity. We have studied a Mg-doped AlGaN/GaN superlattice using transmission electron microscopy (TEM) and atom probe tomography (APT). Pyramidal inversion domains were observed in the TEM and the compositional variations of the dopant atoms associated with those defects have been studied using APT. Rarely has APT been used to assess the compositional variations present due to structural defects in semiconductors. Here, TEM and APT are used in a complementary fashion, and the strengths and weaknesses of the two techniques are compared.

  7. 3D visualization of TiO2 nanocrystals in mesoporous nanocomposite using energy filtered transmission electron microscopy tomography.

    PubMed

    Gondo, Takashi; Kasama, Takeshi; Kaneko, Kenji

    2014-11-01

    IntroductionMesoporous silica, SBA-15, is one of the best candidate for the supporting material of catalytic nanoparticles because of its relative large and controllable pore size and large specific surface area [1]. So far, various nanoparticles, such as Au, Pt and Pd, have been introduced into the pore for catalytic application [2]. The size of nanoparticles supported inside SBA-15 is restricted by that of the pore, and they are usually ranging from 2 nm and 50 nm in space.It is necessary to anchor the nanoparticles within pores to avoid segregation / sintering of them. However, it is difficult to anchor them within pores in the case of use of deposition-precipitation method due to extreme low iso-electric point (IEP) of silica (∼2). Therefore, TiO2 nanocrystals (IEP 6-8) were then introduced to anchor AuNPs [3].In this study, EFTEM tomography was applied to examine the effectiveness of TiO2 for AuNPs. Materials and methodAu/TiO2-SBA-15 was embedded into epoxy resin for electron microscopy and microtomed to about 30 nm thickness. EFTEM-tomography was operated at 120 kV and using Ti-L ionization edge via three-window method. Prior to EFTEM, STEM-HAADF tomography was also carried out for visualizing AuNPs and for comparison. Result and discussionFigure 1 shows 3D-volume of AuNPs and TiO2 nanocrystals from EFTEM-tomography. TiO2 nanocrystals in the porous material were successfully visualized using EFTEM -tomography, and local relationship between AuNPs and TiO2 nanocrystals were revealed. A large number of TiO2 nanocrystals were randomly distributed in the SBA-15. It was found that most AuNPs were directly on the exposed TiO2 nanocrystals. It implies that TiO2 nanocrystals were exposed on the surface of the pore and anchored AuNPs inside the pores.jmicro;63/suppl_1/i27/DFU081F1F1DFU081F1Fig. 1.3D volume of AuNPs and TiO2 nanocrystals.

  8. Directly correlated transmission electron microscopy and atom probe tomography of grain boundary oxidation in a Ni-Al binary alloy exposed to high-temperature water

    SciTech Connect

    Schreiber, Daniel K.; Olszta, Matthew J.; Bruemmer, Stephen M.

    2013-06-14

    Intergranular oxidation of a Ni-4Al alloy exposed to hydrogenated, high-temperature water was characterized using directly correlated transmission electron microscopy and atom probe tomography. These combined analyses revealed that discrete, well-separated oxides (NiAl2O4) precipitated along grain boundaries in the metal. Aluminum was depleted from the grain boundary between oxides and also from one side of the boundary as a result of grain boundary migration. The discrete oxide morphology, disconnected from the continuous surface oxidation, suggests intergranular solid-state internal oxidation of Al. Keywords: oxidation; grain boundaries; nickel alloys; atom probe tomography; transmission electron microscopy (TEM)

  9. Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography

    PubMed Central

    Chang, Juan; Liu, Xiangan; Rochat, Ryan H.; Baker, Matthew L.; Chiu, Wah

    2014-01-01

    The past few decades have seen tremendous advances in single particle electron cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of non-icosahedrally arranged proteins in viruses by employing either single particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course has been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic and biochemical states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures “in situ”. Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future. PMID:22297510

  10. Structural evolution and strain induced mixing in Cu–Co composites studied by transmission electron microscopy and atom probe tomography

    PubMed Central

    Bachmaier, A.; Aboulfadl, H.; Pfaff, M.; Mücklich, F.; Motz, C.

    2015-01-01

    A Cu–Co composite material is chosen as a model system to study structural evolution and phase formations during severe plastic deformation. The evolving microstructures as a function of the applied strain were characterized at the micro-, nano-, and atomic scale-levels by combining scanning electron microscopy and transmission electron microscopy including energy-filtered transmission electron microscopy and electron energy-loss spectroscopy. The amount of intermixing between the two phases at different strains was examined at the atomic scale using atom probe tomography as complimentary method. It is shown that Co particles are dissolved in the Cu matrix during severe plastic deformation to a remarkable extent and their size, number, and volume fraction were quantitatively determined during the deformation process. From the results, it can be concluded that supersaturated solid solutions up to 26 at.% Co in a fcc Cu–26 at.% Co alloy are obtained during deformation. However, the distribution of Co was found to be inhomogeneous even at the highest degree of investigated strain. PMID:26523113

  11. Skeletal Muscle Triad Junction Ultrastructure by Focused-Ion-Beam Milling of Muscle and Cryo-Electron Tomography.

    PubMed

    Wagenknecht, Terence; Hsieh, Chyongere; Marko, Michael

    2015-01-01

    Cryo-electron tomography (cryo-ET) has emerged as perhaps the only practical technique for revealing nanometer-level three-dimensional structural details of subcellular macromolecular complexes in their native context, inside the cell. As currently practiced, the specimen should be 0.1-0.2 microns in thickness to achieve optimal resolution. Thus, application of cryo-ET to intact frozen (vitreous) tissues, such as skeletal muscle, requires that they be sectioned. Cryo-ultramicrotomy is notoriously difficult and artifact-prone when applied to frozen cells and tissue, but a new technique, focused ion beam milling (cryo-FIB), shows great promise for "thinning" frozen biological specimens. Here we describe our initial results in applying cryo-FIB and cryo-ET to triad junctions of skeletal muscle.

  12. Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus, a globally important marine cyanobacterium.

    PubMed

    Ting, Claire S; Hsieh, Chyongere; Sundararaman, Sesh; Mannella, Carmen; Marko, Michael

    2007-06-01

    In an age of comparative microbial genomics, knowledge of the near-native architecture of microorganisms is essential for achieving an integrative understanding of physiology and function. We characterized and compared the three-dimensional architecture of the ecologically important cyanobacterium Prochlorococcus in a near-native state using cryo-electron tomography and found that closely related strains have diverged substantially in cellular organization and structure. By visualizing native, hydrated structures within cells, we discovered that the MED4 strain, which possesses one of the smallest genomes (1.66 Mbp) of any known photosynthetic organism, has evolved a comparatively streamlined cellular architecture. This strain possesses a smaller cell volume, an attenuated cell wall, and less extensive intracytoplasmic (photosynthetic) membrane system compared to the more deeply branched MIT9313 strain. Comparative genomic analyses indicate that differences have evolved in key structural genes, including those encoding enzymes involved in cell wall peptidoglycan biosynthesis. Although both strains possess carboxysomes that are polygonal and cluster in the central cytoplasm, the carboxysomes of MED4 are smaller. A streamlined cellular structure could be advantageous to microorganisms thriving in the low-nutrient conditions characteristic of large regions of the open ocean and thus have consequences for ecological niche differentiation. Through cryo-electron tomography we visualized, for the first time, the three-dimensional structure of the extensive network of photosynthetic lamellae within Prochlorococcus and the potential pathways for intracellular and intermembrane movement of molecules. Comparative information on the near-native structure of microorganisms is an important and necessary component of exploring microbial diversity and understanding its consequences for function and ecology. PMID:17449628

  13. High-voltage electron microscopy tomography and structome analysis of unique spiral bacteria from the deep sea.

    PubMed

    Yamaguchi, Masashi; Yamada, Hiroyuki; Higuchi, Kimitaka; Yamamoto, Yuta; Arai, Shigeo; Murata, Kazuyoshi; Mori, Yuko; Furukawa, Hiromitsu; Uddin, Mohammad Shorif; Chibana, Hiroji

    2016-08-01

    Structome analysis is a useful tool for identification of unknown microorganisms that cannot be cultured. In 2012, we discovered a unique deep-sea microorganism with a cell structure intermediate between those of prokaryotes and eukaryotes and described its features using freeze-substitution electron microscopy and structome analysis (quantitative and three-dimensional structural analysis of a whole cell at the electron microscopic level). We named it Myojin parakaryote Here we describe, using serial ultrathin sectioning and high-voltage electron microscopy tomography of freeze-substituted specimens, the structome analysis and 3D reconstruction of another unique spiral bacteria, found in the deep sea off the coast of Japan. The bacteria, which is named as 'Myojin spiral bacteria' after the discovery location and their morphology, had a total length of 1.768 ± 0.478 µm and a total diameter of 0.445 ± 0.050 µm, and showed either clockwise or counter-clockwise spiral. The cells had a cell surface membrane, thick fibrous layer, ribosomes and inner fibrous structures (most likely DNA). They had no flagella. The bacteria had 322 ± 119 ribosomes per cell. This ribosome number is only 1.2% of that of Escherichia coli and 19.3% of Mycobacterium tuberculosis and may reflect a very slow growth rate of this organism in the deep sea. PMID:27230559

  14. High-voltage electron microscopy tomography and structome analysis of unique spiral bacteria from the deep sea.

    PubMed

    Yamaguchi, Masashi; Yamada, Hiroyuki; Higuchi, Kimitaka; Yamamoto, Yuta; Arai, Shigeo; Murata, Kazuyoshi; Mori, Yuko; Furukawa, Hiromitsu; Uddin, Mohammad Shorif; Chibana, Hiroji

    2016-08-01

    Structome analysis is a useful tool for identification of unknown microorganisms that cannot be cultured. In 2012, we discovered a unique deep-sea microorganism with a cell structure intermediate between those of prokaryotes and eukaryotes and described its features using freeze-substitution electron microscopy and structome analysis (quantitative and three-dimensional structural analysis of a whole cell at the electron microscopic level). We named it Myojin parakaryote Here we describe, using serial ultrathin sectioning and high-voltage electron microscopy tomography of freeze-substituted specimens, the structome analysis and 3D reconstruction of another unique spiral bacteria, found in the deep sea off the coast of Japan. The bacteria, which is named as 'Myojin spiral bacteria' after the discovery location and their morphology, had a total length of 1.768 ± 0.478 µm and a total diameter of 0.445 ± 0.050 µm, and showed either clockwise or counter-clockwise spiral. The cells had a cell surface membrane, thick fibrous layer, ribosomes and inner fibrous structures (most likely DNA). They had no flagella. The bacteria had 322 ± 119 ribosomes per cell. This ribosome number is only 1.2% of that of Escherichia coli and 19.3% of Mycobacterium tuberculosis and may reflect a very slow growth rate of this organism in the deep sea.

  15. Preparation of Primary Neurons for Visualizing Neurites in a Frozen-hydrated State Using Cryo-Electron Tomography

    PubMed Central

    Shahmoradian, Sarah H.; Galiano, Mauricio R.; Wu, Chengbiao; Chen, Shurui; Rasband, Matthew N.; Mobley, William C.; Chiu, Wah

    2014-01-01

    Neurites, both dendrites and axons, are neuronal cellular processes that enable the conduction of electrical impulses between neurons. Defining the structure of neurites is critical to understanding how these processes move materials and signals that support synaptic communication. Electron microscopy (EM) has been traditionally used to assess the ultrastructural features within neurites; however, the exposure to organic solvent during dehydration and resin embedding can distort structures. An important unmet goal is the formulation of procedures that allow for structural evaluations not impacted by such artifacts. Here, we have established a detailed and reproducible protocol for growing and flash-freezing whole neurites of different primary neurons on electron microscopy grids followed by their examination with cryo-electron tomography (cryo-ET). This technique allows for 3-D visualization of frozen, hydrated neurites at nanometer resolution, facilitating assessment of their morphological differences. Our protocol yields an unprecedented view of dorsal root ganglion (DRG) neurites, and a visualization of hippocampal neurites in their near-native state. As such, these methods create a foundation for future studies on neurites of both normal neurons and those impacted by neurological disorders. PMID:24561719

  16. Electron tomography and cryo-SEM characterization reveals novel ultrastructural features of host-parasite interaction during Chlamydia abortus infection.

    PubMed

    Wilkat, M; Herdoiza, E; Forsbach-Birk, V; Walther, P; Essig, A

    2014-08-01

    Chlamydia (C.) abortus is a widely spread pathogen among ruminants that can be transmitted to women during pregnancy leading to severe systemic infection with consecutive abortion. As a member of the Chlamydiaceae, C. abortus shares the characteristic feature of an obligate intracellular biphasic developmental cycle with two morphological forms including elementary bodies (EBs) and reticulate bodies (RBs). In contrast to other chlamydial species, C. abortus ultrastructure has not been investigated yet. To do so, samples were fixed by high-pressure freezing and processed by different electron microscopic methods. Freeze-substituted samples were analysed by transmission electron microscopy, scanning transmission electron microscopical tomography and immuno-electron microscopy, and freeze-fractured samples were analysed by cryo-scanning electron microscopy. Here, we present three ultrastructural features of C. abortus that have not been reported up to now. Firstly, the morphological evidence that C. abortus is equipped with the type three secretion system. Secondly, the accumulation and even coating of whole inclusion bodies by membrane complexes consisting of multiple closely adjacent membranes which seems to be a C. abortus specific feature. Thirdly, the formation of small vesicles in the periplasmic space of RBs in the second half of the developmental cycle. Concerning the time point of their formation and the fact that they harbour chlamydial components, these vesicles might be morphological correlates of an intermediate step during the process of redifferentiation of RBs into EBs. As this feature has also been shown for C. trachomatis and C. pneumoniae, it might be a common characteristic of the family of Chlamydiaceae.

  17. Native immunogold labeling of cell surface proteins and viral glycoproteins for cryo-electron microscopy and cryo-electron tomography applications.

    PubMed

    Yi, Hong; Strauss, Joshua D; Ke, Zunlong; Alonas, Eric; Dillard, Rebecca S; Hampton, Cheri M; Lamb, Kristen M; Hammonds, Jason E; Santangelo, Philip J; Spearman, Paul W; Wright, Elizabeth R

    2015-10-01

    Numerous methods have been developed for immunogold labeling of thick, cryo-preserved biological specimens. However, most of the methods are permutations of chemical fixation and sample sectioning, which select and isolate the immunolabeled region of interest. We describe a method for combining immunogold labeling with cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) of the surface proteins of intact mammalian cells or the surface glycoproteins of assembling and budding viruses in the context of virus-infected mammalian cells cultured on EM grids. In this method, the cells were maintained in culture media at physiologically relevant temperatures while sequentially incubated with the primary and secondary antibodies. Subsequently, the immunogold-labeled specimens were vitrified and observed under cryo-conditions in the transmission electron microscope. Cryo-EM and cryo-ET examination of the immunogold-labeled cells revealed the association of immunogold particles with the target antigens. Additionally, the cellular structure was unaltered by pre-immunolabeling chemical fixation and retained well-preserved plasma membranes, cytoskeletal elements, and macromolecular complexes. We think this technique will be of interest to cell biologists for cryo-EM and conventional studies of native cells and pathogen-infected cells.

  18. Native Immunogold Labeling of Cell Surface Proteins and Viral Glycoproteins for Cryo-Electron Microscopy and Cryo-Electron Tomography Applications

    PubMed Central

    Yi, Hong; Strauss, Joshua D.; Ke, Zunlong; Alonas, Eric; Dillard, Rebecca S.; Hampton, Cheri M.; Lamb, Kristen M.; Hammonds, Jason E.; Santangelo, Philip J.; Spearman, Paul W.

    2015-01-01

    Numerous methods have been developed for immunogold labeling of thick, cryo-preserved biological specimens. However, most of the methods are permutations of chemical fixation and sample sectioning, which select and isolate the immunolabeled region of interest. We describe a method for combining immunogold labeling with cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) of the surface proteins of intact mammalian cells or the surface glycoproteins of assembling and budding viruses in the context of virus-infected mammalian cells cultured on EM grids. In this method, the cells were maintained in culture media at physiologically relevant temperatures while sequentially incubated with the primary and secondary antibodies. Subsequently, the immunogold-labeled specimens were vitrified and observed under cryo-conditions in the transmission electron microscope. Cryo-EM and cryo-ET examination of the immunogold-labeled cells revealed the association of immunogold particles with the target antigens. Additionally, the cellular structure was unaltered by pre-immunolabeling chemical fixation and retained well-preserved plasma membranes, cytoskeletal elements, and macromolecular complexes. We think this technique will be of interest to cell biologists for cryo-EM and conventional studies of native cells and pathogen-infected cells. PMID:26069287

  19. Gold nanoparticles generated in ethosome bilayers, as revealed by cryo-electron-tomography.

    PubMed

    de la Presa, Patricia; Rueda, Tatiana; del Puerto Morales, María; Javier Chichón, F; Arranz, Rocío; Valpuesta, José María; Hernando, Antonio

    2009-03-12

    Gold nanoparticles have been synthesized inside ethosomes, vesicles composed of phospholipid, ethanol, and water, which could be very efficient not only in delivery probes to the skin but also as diagnostic and therapeutic multimodal agents. High efficiency encapsulation of gold nanoparticles is achieved by a simple strategy: the nanoparticles synthesis occurs simultaneously with the ethosomes formation in the absence of any undesirable reducing agents. A three-dimensional reconstruction of a gold-embedded ethosome generated by cryoelectron tomography reveals that the gold particle is localized inside the lipid bilayer, leaving the ethosome surface and core free for further functionalization. The resulting gold nanoparticles are homogeneous in size and shape and, depending on synthesis temperature, the size ranges from 10 to 20 nm, as revealed by TEM. The ethosome-nanoparticles hybrids' size has been investigated by means of dynamic light scattering and has been found to vary with temperature and gold salt concentration from 700 to 400 nm. Gold nanoparticles-encapsulated ethosomes offer a versatile platform for the enhancement of pharmacological efficacy in transdermal and dermal delivery systems.

  20. Gold nanoparticles generated in ethosome bilayers, as revealed by cryo-electron-tomography.

    PubMed

    de la Presa, Patricia; Rueda, Tatiana; del Puerto Morales, María; Javier Chichón, F; Arranz, Rocío; Valpuesta, José María; Hernando, Antonio

    2009-03-12

    Gold nanoparticles have been synthesized inside ethosomes, vesicles composed of phospholipid, ethanol, and water, which could be very efficient not only in delivery probes to the skin but also as diagnostic and therapeutic multimodal agents. High efficiency encapsulation of gold nanoparticles is achieved by a simple strategy: the nanoparticles synthesis occurs simultaneously with the ethosomes formation in the absence of any undesirable reducing agents. A three-dimensional reconstruction of a gold-embedded ethosome generated by cryoelectron tomography reveals that the gold particle is localized inside the lipid bilayer, leaving the ethosome surface and core free for further functionalization. The resulting gold nanoparticles are homogeneous in size and shape and, depending on synthesis temperature, the size ranges from 10 to 20 nm, as revealed by TEM. The ethosome-nanoparticles hybrids' size has been investigated by means of dynamic light scattering and has been found to vary with temperature and gold salt concentration from 700 to 400 nm. Gold nanoparticles-encapsulated ethosomes offer a versatile platform for the enhancement of pharmacological efficacy in transdermal and dermal delivery systems. PMID:19708264

  1. Removing high contrast artifacts via digital inpainting in cryo-electron tomography: an application of compressed sensing.

    PubMed

    Song, Kahye; Comolli, Luis R; Horowitz, Mark

    2012-05-01

    To cope with poor quality in cryo-electron tomography images, electron-dense markers, such as colloidal goldbeads, are often used to assist image registration and analysis algorithms. However, these markers can create artifacts that occlude a specimen due to their high contrast, which can also cause failure of some image processing algorithms. One way of reducing these artifacts is to replace high contrast objects with pixel densities that blend into the surroundings in the projection domain before volume reconstruction. In this paper, we propose digital inpainting via compressed sensing (CS) as a new method to achieve this goal. We show that cryo-ET projections are sparse in the discrete cosine transform (DCT) domain, and, by finding the sparsest DCT domain decompositions given uncorrupted pixels, we can fill in the missing pixel values that are occluded by high contrast objects without discontinuities. Our method reduces visual artifacts both in projections and in tomograms better than conventional algorithms, such as polynomial interpolation and random noise inpainting.

  2. Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography1[S

    PubMed Central

    Yu, Yadong; Kuang, Yu-Lin; Lei, Dongsheng; Zhai, Xiaobo; Zhang, Meng; Krauss, Ronald M.; Ren, Gang

    2016-01-01

    Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis. PMID:27538822

  3. Analysis of β-tricalcium phosphate granules prepared with different formulations by nano-computed tomography and scanning electron microscopy.

    PubMed

    Terranova, Lisa; Libouban, Hélène; Mallet, Romain; Chappard, Daniel

    2015-12-01

    Among biomaterials used for filling bone defects, beta-tricalcium phosphate (β-TCP) is suitable in non-bearing bones, particularly in dental implantology, oral and maxillofacial surgery. When β-TCP granules are placed in a bone defect, they occupy the void 3D volume. Little is known about the 3D arrangement of the granules, which depends on the nature and size of the granules. The aim of this study was to examine the 3D architecture of porous β-TCP granules. Granules were prepared with different concentrations of β-TCP powder in slurry (10, 11, 15, 18, 21, and 25 g of β-TCP powder in distilled water). Granules were prepared by the polyurethane foam method. They were analyzed by nano-computed tomography (nanoCT) and compared with scanning electron microscopy (SEM). Commercial granules of hydroxyapatite-β-TCP prepared by the same methodology were also used. The outer and inner architectures of the granules were shown by nanoCT which evidenced macroporosity, internal porosity and microporosity between the sintered grains. Macroporosity was reduced at high concentration and conversely, numerous concave surfaces were observed. Internal porosity, related to the sublimation of the polyurethane foam, was present in all the granules. Microporosity at the grain joints was evidenced by SEM and on 2D nanoCT sections. Granules presented a heterogeneous aspect due to the different mineralization degree of the sintered powder grains in the β-TCP granules; the difference between hydroxyapatite and β-TCP was also evidenced. NanoCT is an interesting method to analyze the fine morphology of biomaterials with a resolution close to synchrotron and better than microcomputed tomography. PMID:25899237

  4. MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography

    PubMed Central

    Cheng, Anchi; Henderson, Richard; Mastronarde, David; Ludtke, Steven J.; Schoenmakers, Remco H.M.; Short, Judith; Marabini, Roberto; Dallakyan, Sargis; Agard, David; Winn, Martyn

    2015-01-01

    The MRC binary file format is widely used in the three-dimensional electron microscopy field for storing image and volume data. Files contain a header which describes the kind of data held, together with other important metadata. In response to advances in electron microscopy techniques, a number of variants to the file format have emerged which contain useful additional data, but which limit interoperability between different software packages. Following extensive discussions, the authors, who represent leading software packages in the field, propose a set of extensions to the MRC format standard designed to accommodate these variants, while restoring interoperability. The MRC format is equivalent to the map format used in the CCP4 suite for macromolecular crystallography, and the proposal also maintains interoperability with crystallography software. This Technical Note describes the proposed extensions, and serves as a reference for the standard. PMID:25882513

  5. Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope.

    PubMed

    Ferroni, Matteo; Signoroni, Alberto; Sanzogni, Andrea; Masini, Luca; Migliori, Andrea; Ortolani, Luca; Pezza, Alessandro; Morandi, Vittorio

    2016-01-01

    The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections. PMID:27646194

  6. Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope

    NASA Astrophysics Data System (ADS)

    Ferroni, Matteo; Signoroni, Alberto; Sanzogni, Andrea; Masini, Luca; Migliori, Andrea; Ortolani, Luca; Pezza, Alessandro; Morandi, Vittorio

    2016-09-01

    The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections.

  7. MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography.

    PubMed

    Cheng, Anchi; Henderson, Richard; Mastronarde, David; Ludtke, Steven J; Schoenmakers, Remco H M; Short, Judith; Marabini, Roberto; Dallakyan, Sargis; Agard, David; Winn, Martyn

    2015-11-01

    The MRC binary file format is widely used in the three-dimensional electron microscopy field for storing image and volume data. Files contain a header which describes the kind of data held, together with other important metadata. In response to advances in electron microscopy techniques, a number of variants to the file format have emerged which contain useful additional data, but which limit interoperability between different software packages. Following extensive discussions, the authors, who represent leading software packages in the field, propose a set of extensions to the MRC format standard designed to accommodate these variants, while restoring interoperability. The MRC format is equivalent to the map format used in the CCP4 suite for macromolecular crystallography, and the proposal also maintains interoperability with crystallography software. This Technical Note describes the proposed extensions, and serves as a reference for the standard. PMID:25882513

  8. Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope

    PubMed Central

    Ferroni, Matteo; Signoroni, Alberto; Sanzogni, Andrea; Masini, Luca; Migliori, Andrea; Ortolani, Luca; Pezza, Alessandro; Morandi, Vittorio

    2016-01-01

    The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections. PMID:27646194

  9. Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope.

    PubMed

    Ferroni, Matteo; Signoroni, Alberto; Sanzogni, Andrea; Masini, Luca; Migliori, Andrea; Ortolani, Luca; Pezza, Alessandro; Morandi, Vittorio

    2016-09-20

    The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections.

  10. Electron tomography of insect flight muscle in rigor and AMPPNP at 23 degrees C.

    PubMed

    Schmitz, H; Reedy, M C; Reedy, M K; Tregear, R T; Winkler, H; Taylor, K A

    1996-11-29

    Treatment of rigor fibers of insect flight muscle (IFM) with AMPPNP at 23 degrees C causes a 70% drop in tension with little change in stiffness. In order to visualize the changes in crossbridge conformation and distribution that give rise to the mechanical response, we have produced three-dimensional reconstructions by tomography of both rigor and AMPPNP-treated muscle that do not average the repeating motifs of crossbridges, and thereby retain information on variability of crossbridge structure and distribution. Tomograms can be averaged when display of only the regular features is wanted. Tomograms of rigor IFM show double-headed lead and single-headed rear crossbridges. Tomograms of IFM treated with AMPPNP at 23 degrees C reveal many double-headed and some single-headed "lead" bridges but few crossbridges corresponding to the rear bridges of rigor. Instead, new non-rigor forms of variably angled crossbridges are found bound to actin sites not labeled with myosin heads in rigor. This indicates that the rear bridges of rigor have redistributed during the transition from rigor to the AMPPNP state, which could explain the maintenance of rigor stiffness despite the loss of tension. Comparison of in situ crossbridges in tomograms of rigor with atomic model of acto-S1, the complex formed by myosin subfragment 1 and actin, reveals that the regulatory domain of S1 would require significant bending and realignment to fit into both types of rigor crossbridges. The modifications are particularly significant for the rear bridges and suggest that differential strain in the regulatory domain of rear bridges may be the basis for their detachment and redistribution upon binding AMPPNP. Similar comparison using lead-type crossbridges in AMPPNP reveals departures from the rigor acto-S1 atomic model that include azimuthal straightening and a slight M-ward bending in the regulatory domain. Both the motor and regulatory domains of the new non-rigor crossbridges differ from those in

  11. 3D Reconstruction of VZV Infected Cell Nuclei and PML Nuclear Cages by Serial Section Array Scanning Electron Microscopy and Electron Tomography

    PubMed Central

    Reichelt, Mike; Joubert, Lydia; Perrino, John; Koh, Ai Leen; Phanwar, Ibanri; Arvin, Ann M.

    2012-01-01

    Varicella-zoster virus (VZV) is a human alphaherpesvirus that causes varicella (chickenpox) and herpes zoster (shingles). Like all herpesviruses, the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in the cytoplasm. Our recent work showed that VZV nucleocapsids are sequestered in nuclear cages formed from promyelocytic leukemia protein (PML) in vitro and in human dorsal root ganglia and skin xenografts in vivo. We sought a method to determine the three-dimensional (3D) distribution of nucleocapsids in the nuclei of herpesvirus-infected cells as well as the 3D shape, volume and ultrastructure of these unique PML subnuclear domains. Here we report the development of a novel 3D imaging and reconstruction strategy that we term Serial Section Array-Scanning Electron Microscopy (SSA-SEM) and its application to the analysis of VZV-infected cells and these nuclear PML cages. We show that SSA-SEM permits large volume imaging and 3D reconstruction at a resolution sufficient to localize, count and distinguish different types of VZV nucleocapsids and to visualize complete PML cages. This method allowed a quantitative determination of how many nucleocapsids can be sequestered within individual PML cages (sequestration capacity), what proportion of nucleocapsids are entrapped in single nuclei (sequestration efficiency) and revealed the ultrastructural detail of the PML cages. More than 98% of all nucleocapsids in reconstructed nuclear volumes were contained in PML cages and single PML cages sequestered up to 2,780 nucleocapsids, which were shown by electron tomography to be embedded and cross-linked by an filamentous electron-dense meshwork within these unique subnuclear domains. This SSA-SEM analysis extends our recent characterization of PML cages and provides a proof of concept for this new strategy to investigate events during virion assembly at the single cell

  12. Computed tomography of cryogenic cells

    SciTech Connect

    Schneider, Gerd; Anderson, E.; Vogt, S.; Knochel, C.; Weiss, D.; LeGros, M.; Larabell, C.

    2001-08-30

    Due to the short wavelengths of X-rays and low numerical aperture of the Fresnel zone plates used as X-ray objectives, the depth of field is several microns. Within the focal depth, imaging a thick specimen is to a good approximation equivalent to projecting the specimen absorption. Therefore, computed tomography based on a tilt series of X-ray microscopic images can be used to reconstruct the local linear absorption coefficient and image the three-dimensional specimen structure. To preserve the structural integrity of biological objects during image acquisition, microscopy is performed at cryogenic temperatures. Tomography based on X-ray microscopic images was applied to study the distribution of male specific lethal 1 (MSL-1), a nuclear protein involved in dosage compensation in Drosophila melanogaster, which ensures that males with single X chromosome have the same amount of most X-linked gene products as females with two X chromosomes. Tomographic reconstructions of X-ray microscopic images were used to compute the local three-dimensional linear absorption coefficient revealing the arrangement of internal structures of Drosophila melanogaster cells. Combined with labelling techniques, nanotomography is a new technique to study the 3D distribution of selected proteins inside whole cells. We want to improve this technique with respect to resolution and specimen preparation. The resolution in the reconstruction can be significantly improved by reducing the angular step size to collect more viewing angles, which requires an automated data acquisition. In addition, fast-freezing with liquid ethane instead of cryogenic He gas will be applied to improve the vitrification of the hydrated samples. We also plan to apply cryo X-ray nanotomography in order to study different types of cells and their nuclear protein distributions.

  13. 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

  14. Three-dimensional imaging of copper pillars using x-ray tomography within a scanning electron microscope: A simulation study based on synchrotron data

    SciTech Connect

    Martin, N.; Bertheau, J.; Charbonnier, J.; Hugonnard, P.; Lorut, F.; Bleuet, P.; Tabary, J.; Laloum, D.

    2013-02-15

    While microelectronic devices are frequently characterized with surface-sensitive techniques having nanometer resolution, interconnections used in 3D integration require 3D imaging with high penetration depth and deep sub-micrometer spatial resolution. X-ray tomography is well adapted to this situation. In this context, the purpose of this study is to assess a versatile and turn-key tomographic system allowing for 3D x-ray nanotomography of copper pillars. The tomography tool uses the thin electron beam of a scanning electron microscope (SEM) to provoke x-ray emission from specific metallic targets. Then, radiographs are recorded while the sample rotates in a conventional cone beam tomography scheme that ends up with 3D reconstructions of the pillar. Starting from copper pillars data, collected at the European Synchrotron Radiation Facility, we build a 3D numerical model of a copper pillar, paying particular attention to intermetallics. This model is then used to simulate physical radiographs of the pillar using the geometry of the SEM-hosted x-ray tomography system. Eventually, data are reconstructed and it is shown that the system makes it possible the quantification of 3D intermetallics volume in copper pillars. The paper also includes a prospective discussion about resolution issues.

  15. Ultrastructure Features and Three-Dimensional Transmission Electron Tomography of Dhub Lizard (Uromastyx Aegyptia) Cornea and Its Adaptation to a Desert Environment.

    PubMed

    Akhtar, Saeed; Alkhalaf, Mousa; Khan, Adnan A; Almubrad, Turki M

    2016-08-01

    We report ultrastructural features and transmission electron tomography of the dhub lizard (Uromastyx aegyptia) cornea and its adaptation to hot and dry environments. Six corneas of dhub lizards were fixed in 2.5% glutaraldehyde and processed for electron microscopy and tomography. The ultrathin sections were observed with a JEOL 1400 transmission electron microscope. The cornea of the dhub lizard is very thin (~28-30 µm). The epithelium constitutes ~14% of the cornea, whereas the stroma constitutes 80% of the cornea. The middle stromal lamellae are significantly thicker than anterior and posterior stromal lamellae. Collagen fibril (CF) diameters in the anterior stroma are variable in size (25-75 nm). Proteoglycans (PGs) are very large in the middle and posterior stroma, whereas they are small in the anterior stroma. Three-dimensional electron tomography was carried out to understand the structure and arrangement of the PG and CFs. The presence of large PGs in the posterior and middle stroma might help the animal retain a large amount of water to protect it from dryness. The dhub corneal structure is equipped to adapt to the dry and hot desert environment. PMID:27619263

  16. Structure refinement using precession electron diffraction tomography and dynamical diffraction: tests on experimental data.

    PubMed

    Palatinus, Lukáš; Corrêa, Cinthia Antunes; Steciuk, Gwladys; Jacob, Damien; Roussel, Pascal; Boullay, Philippe; Klementová, Mariana; Gemmi, Mauro; Kopeček, Jaromír; Domeneghetti, M Chiara; Cámara, Fernando; Petříček, Václav

    2015-12-01

    The recently published method for the structure refinement from three-dimensional precession electron diffraction data using dynamical diffraction theory [Palatinus et al. (2015). Acta Cryst. A71, 235-244] has been applied to a set of experimental data sets from five different samples - Ni2Si, PrVO3, kaolinite, orthopyroxene and mayenite. The data were measured on different instruments and with variable precession angles. For each sample a reliable reference structure was available. A large series of tests revealed that the method provides structure models with an average error in atomic positions typically between 0.01 and 0.02 Å. The obtained structure models are significantly more accurate than models obtained by refinement using kinematical approximation for the calculation of model intensities. The method also allows a reliable determination of site occupancies and determination of absolute structure. Based on the extensive tests, an optimal set of the parameters for the method is proposed.

  17. 3D electron tomography of pretreated biomass informs atomic modeling of cellulose microfibrils.

    PubMed

    Ciesielski, Peter N; Matthews, James F; Tucker, Melvin P; Beckham, Gregg T; Crowley, Michael F; Himmel, Michael E; Donohoe, Bryon S

    2013-09-24

    Fundamental insights into the macromolecular architecture of plant cell walls will elucidate new structure-property relationships and facilitate optimization of catalytic processes that produce fuels and chemicals from biomass. Here we introduce computational methodology to extract nanoscale geometry of cellulose microfibrils within thermochemically treated biomass directly from electron tomographic data sets. We quantitatively compare the cell wall nanostructure in corn stover following two leading pretreatment strategies: dilute acid with iron sulfate co-catalyst and ammonia fiber expansion (AFEX). Computational analysis of the tomographic data is used to extract mathematical descriptions for longitudinal axes of cellulose microfibrils from which we calculate their nanoscale curvature. These nanostructural measurements are used to inform the construction of atomistic models that exhibit features of cellulose within real, process-relevant biomass. By computational evaluation of these atomic models, we propose relationships between the crystal structure of cellulose Iβ and the nanoscale geometry of cellulose microfibrils. PMID:23988022

  18. Electronic stopping power calculation for water under the Lindhard formalism for application in proton computed tomography

    NASA Astrophysics Data System (ADS)

    Guerrero, A. F.; Mesa, J.

    2016-07-01

    Because of the behavior that charged particles have when they interact with biological material, proton therapy is shaping the future of radiation therapy in cancer treatment. The planning of radiation therapy is made up of several stages. The first one is the diagnostic image, in which you have an idea of the density, size and type of tumor being treated; to understand this it is important to know how the particles beam interacts with the tissue. In this work, by using de Lindhard formalism and the Y.R. Waghmare model for the charge distribution of the proton, the electronic stopping power (SP) for a proton beam interacting with a liquid water target in the range of proton energies 101 eV - 1010 eV taking into account all the charge states is calculated.

  19. Theory of bright-field scanning transmission electron microscopy for tomography

    SciTech Connect

    Levine, Zachary H.

    2005-02-01

    Radiation transport theory is applied to electron microscopy of samples composed of one or more materials. The theory, originally due to Goudsmit and Saunderson, assumes only elastic scattering and an amorphous medium dominated by atomic interactions. For samples composed of a single material, the theory yields reasonable parameter-free agreement with experimental data taken from the literature for the multiple scattering of 300-keV electrons through aluminum foils up to 25 {mu}m thick. For thin films, the theory gives a validity condition for Beer's law. For thick films, a variant of Moliere's theory [V. G. Moliere, Z. Naturforschg. 3a, 78 (1948)] of multiple scattering leads to a form for the bright-field signal for foils in the multiple-scattering regime. The signal varies as [t ln(e{sup 1-2{gamma}}t/{tau})]{sup -1} where t is the path length of the beam, {tau} is the mean free path for elastic scattering, and {gamma} is Euler's constant. The Goudsmit-Saunderson solution interpolates numerically between these two limits. For samples with multiple materials, elemental sensitivity is developed through the angular dependence of the scattering. From the elastic scattering cross sections of the first 92 elements, a singular-value decomposition of a vector space spanned by the elastic scattering cross sections minus a delta function shows that there is a dominant common mode, with composition-dependent corrections of about 2%. A mathematically correct reconstruction procedure beyond 2% accuracy requires the acquisition of the bright-field signal as a function of the scattering angle. Tomographic reconstructions are carried out for three singular vectors of a sample problem with four elements Cr, Cu, Zr, and Te. The three reconstructions are presented jointly as a color image; all four elements are clearly identifiable throughout the image.

  20. Cellular Architecture of Treponema pallidum: Novel Flagellum, Periplasmic Cone, and Cell Envelope as Revealed by Cryo-Electron Tomography

    PubMed Central

    Liu, Jun; Howell, Jerrilyn K.; Bradley, Sherille D.; Zheng, Yesha; Zhou, Z. Hong; Norris, Steven J.

    2010-01-01

    High resolution cryo-electron tomography (cryo-ET) was utilized to visualize Treponema pallidum, the causative agent of syphilis, at the molecular level. Three-dimensional (3-D) reconstructions from 304 infectious organisms revealed unprecedented cellular structures of this unusual member in the spirochetal family. High resolution cryo-ET reconstructions provided the detailed structures of the cell envelope, which is significantly different from that of gram-negative bacteria. The 4 nm lipid bilayer of both outer and cytoplasmic membranes resolved in 3-D reconstructions, providing an important marker for interpreting membrane-associated structures. Abundant lipoproteins cover the outer leaflet of the cytoplasmic membrane, in contrast to the rare outer membrane proteins visible by scanning probe microscopy. High resolution cryo-ET images also provided the first observation of T. pallidum chemoreceptor arrays, as well as structural details of the periplasmically located, cone-shaped structure at both ends of bacterium. Furthermore, 3-D subvolume averages of the periplasmic flagellar motors and filaments from living organisms revealed the novel flagellar architectures that may facilitate their rotation within the confining periplasmic space. Together, our findings provide the most detailed structural understanding of the periplasmic flagella and the surrounding cell envelope, which enable this enigmatic bacterium to efficiently penetrate tissue and escape host immune responses. PMID:20850455

  1. Three-dimensional cellular architecture of the flagellar pocket and associated cytoskeleton in trypanosomes revealed by electron microscope tomography

    PubMed Central

    Lacomble, Sylvain; Vaughan, Sue; Gadelha, Catarina; Morphew, Mary K.; Shaw, Michael K.; McIntosh, J. Richard; Gull, Keith

    2009-01-01

    Summary This study uses electron tomography linked to a variety of other EM methods to provide an integrated view of the flagellar pocket and basal body area of the African trypanosome procyclic trypomastigote. We reveal the pocket as an asymmetric membranous `balloon' with two boundary structures. One of these – the collar – defines the flagellum exit point. The other defines the entry point of the flagellum into the pocket and consists of both an internal transitional fibre array and an external membrane collarette. A novel set of nine radial fibres is described in the basal body proximal zone. The pocket asymmetry is invariably correlated with the position of the probasal body and Golgi. The neck region, just distal to the flagellum exit site, is a specialised area of membrane associated with the start of the flagellum attachment zone and signifies the point where a special set of four microtubules, nucleated close to the basal bodies, joins the subpellicular array. The neck region is also associated with the single Golgi apparatus of the cell. The flagellar exit point interrupts the subpellicular microtubule array with discrete endings of microtubules at the posterior side. Overall, our studies reveal a highly organised, yet dynamic, area of cytoplasm and will be informative in understanding its function. PMID:19299460

  2. Laboratory-based cryogenic soft x-ray tomography with correlative cryo-light and electron microscopy.

    PubMed

    Carlson, David B; Gelb, Jeff; Palshin, Vadim; Evans, James E

    2013-02-01

    Here we present a novel laboratory-based cryogenic soft X-ray microscope for whole cell tomography of frozen hydrated samples. We demonstrate the capabilities of this compact cryogenic microscope by visualizing internal subcellular structures of Saccharomyces cerevisiae cells. The microscope is shown to achieve better than 50 nm half-pitch spatial resolution with a Siemens star test sample. For whole biological cells, the microscope can image specimens up to 5 μm thick. Structures as small as 90 nm can be detected in tomographic reconstructions following a low cumulative radiation dose of only 7.2 MGy. Furthermore, the design of the specimen chamber utilizes a standard sample support that permits multimodal correlative imaging of the exact same unstained yeast cell via cryo-fluorescence light microscopy, cryo-soft X-ray microscopy, and cryo-transmission electron microscopy. This completely laboratory-based cryogenic soft X-ray microscope will enable greater access to three-dimensional ultrastructure determination of biological whole cells without chemical fixation or physical sectioning.

  3. Electron tomography and simulation of baculovirus actin comet tails support a tethered filament model of pathogen propulsion.

    PubMed

    Mueller, Jan; Pfanzelter, Julia; Winkler, Christoph; Narita, Akihiro; Le Clainche, Christophe; Nemethova, Maria; Carlier, Marie-France; Maeda, Yuichiro; Welch, Matthew D; Ohkawa, Taro; Schmeiser, Christian; Resch, Guenter P; Small, J Victor

    2014-01-01

    Several pathogens induce propulsive actin comet tails in cells they invade to disseminate their infection. They achieve this by recruiting factors for actin nucleation, the Arp2/3 complex, and polymerization regulators from the host cytoplasm. Owing to limited information on the structural organization of actin comets and in particular the spatial arrangement of filaments engaged in propulsion, the underlying mechanism of pathogen movement is currently speculative and controversial. Using electron tomography we have resolved the three-dimensional architecture of actin comet tails propelling baculovirus, the smallest pathogen yet known to hijack the actin motile machinery. Comet tail geometry was also mimicked in mixtures of virus capsids with purified actin and a minimal inventory of actin regulators. We demonstrate that propulsion is based on the assembly of a fishbone-like array of actin filaments organized in subsets linked by branch junctions, with an average of four filaments pushing the virus at any one time. Using an energy-minimizing function we have simulated the structure of actin comet tails as well as the tracks adopted by baculovirus in infected cells in vivo. The results from the simulations rule out gel squeezing models of propulsion and support those in which actin filaments are continuously tethered during branch nucleation and polymerization. Since Listeria monocytogenes, Shigella flexneri, and Vaccinia virus among other pathogens use the same common toolbox of components as baculovirus to move, we suggest they share the same principles of actin organization and mode of propulsion. PMID:24453943

  4. Study of vertical Si/SiO2 interface using laser-assisted atom probe tomography and transmission electron microscopy.

    PubMed

    Lee, J H; Lee, B H; Kim, Y T; Kim, J J; Lee, S Y; Lee, K P; Park, C G

    2014-03-01

    Laser-assisted atom probe tomography has opened the way to three-dimensional visualization of nanostructures. However, many questions related to the laser-matter interaction remain unresolved. We demonstrate that the interface reaction can be activated by laser-assisted field evaporation and affects the quantification of the interfacial composition. At a vertical interface between Si and SiO2, a SiO2 molecule tends to combine with a Si atom and evaporate as a SiO molecule, reducing the evaporation field. The features of the reaction depend on the direction of the laser illumination and the inner structure of tip. A high concentration of SiO is observed at a vertical interface between Si and SiO2 when the Si column is positioned at the center of the tip, whereas no significant SiO is detected when the SiO2 layer is at the center. The difference in the interfacial compositions of two samples was due to preferential evaporation of the Si layer. This was explained using transmission electron microscopy observations before and after atom probe experiments.

  5. Microstructural investigation of magnetic CoFe2O4 nanowires inside carbon nanotubes by electron tomography.

    PubMed

    Ersen, Ovidiu; Bégin, Sylvie; Houllé, Matthieu; Amadou, Julien; Janowska, Izabela; Grenèche, Jean-Marc; Crucifix, Corinne; Pham-Huu, Cuong

    2008-04-01

    Magnetic nanowires of CoFe 2O4 were casted inside the channel of multiwall carbon nanotubes by mild chemical synthesis. A detailed investigation of these nanowires was performed using mainly the electron tomography technique; this study provides a complete characterization of their microstructure in terms of the spatial organization and the size distribution of individual particles forming the nanowire as well as its residual porosity. In particular, we have shown that the size of the CoFe 2O4 monocrystalline particles is closely dependent on the location of the particle within the nanotube, i.e., small particles close to the tube tip (5 nm) and bigger particles inside the tube channel (15 nm). As the theoretical critical size for superparamagnetic relaxation in CoFe 2O4 is estimated within the range of 4-9 nm, the size distribution obtained by 3D-TEM agrees with the Mossbauer study that suggests the presence of two different magnetic components inside the nanowire. We have shown also that, by using this preparation method and for this internal diameter of nanotube, the CoFe 2O4 nanowire exhibits a continuous structure along the tube, has a residual porosity of 38%, and can fill the tube at only 50%, parameters which influence in a significant manner the magnetic behavior of this system. PMID:18336009

  6. Acute coronary artery dilation due to Kawasaki disease and subsequent late calcification as detected by electron beam computed tomography.

    PubMed

    Kaichi, S; Tsuda, E; Fujita, H; Kurosaki, K; Tanaka, R; Naito, H; Echigo, S

    2008-05-01

    We wanted to clarify the relationships between the degree of acute coronary artery dilation caused by Kawasaki disease and subsequent late calcification. Electron beam computed tomography (EBCT) was used to study 79 patients who had previously undergone selective coronary angiograms less than 100 days after the onset of Kawasaki disease. The EBCT was performed using an Imatron C-150 with a 100-ms exposure time and consecutive images at 6-mm intervals. The interval from the onset of Kawasaki disease to EBCT ranged from 2 to 242 months (median, 103 months). The maximum diameters of the right coronary, the left anterior descending, and the left circumflex arteries, as well as the bifurcation of the left coronary artery were measured in the initial coronary angiograms. A total of 250 branches, including 53 left coronary arteries, were measured, and the relationship between the degree of the initial coronary artery dilation and subsequent calcification in the branches and left coronary artery was analyzed. The coronary arterial diameter of all branches that eventually calcified was 6 mm or greater. The incidence of calcification in branches measuring 6 mm or greater on the initial coronary angiogram was 12% at 5 years, 44% at 10 years, and 94% at 20 years (n = 141). Dilation greater than 6 mm is associated with a high probability of late calcification. PMID:18043859

  7. Coronary electron beam computed tomography in 13 patients with systemic lupus erythematosus and two or more cardiovascular risk factors.

    PubMed

    Von Feldt, Joan M; Eisner, Elana R; Sawaires, Amal

    2002-12-01

    Cardiovascular and cerebrovascular events, the third leading cause of death in patients with systemic lupus erythematosus (SLE), are disproportionately common by age and gender. Risk factors for atherosclerotic cardiovascular disease (ASCVD) cannot reliably predict subsets of patients at risk for events. Coronary electron beam computed tomography (EBCT), a noninvasive imaging technique that quantifies ASCVD by measuring calcium deposition in the walls of coronary arteries, has been demonstrated to be a marker of ASCVD in traditional populations. A pilot group of 13 SLE patients (ages, 33-48 years) with two or more traditional risk factors for cardiovascular disease were studied by EBCT. Five of these SLE patients had calcification scores in the 70th percentile or higher, as compared with age-matched women without known coronary artery disease, and three had scores in the 90th percentile. Four of these five patients had antiphospholipid antibodies currently or in the past. These data suggest that EBCT may be able to detect premature ASCVD in SLE patients and may be a useful noninvasive tool as more attention is directed to ASCVD as a major complication of SLE. PMID:17041400

  8. Laboratory-Based Cryogenic Soft X-ray Tomography with Correlative Cryo-Light and Electron Microscopy

    SciTech Connect

    Carlson, David B.; Gelb, Jeff; Palshin, Vadim; Evans, James E.

    2013-02-01

    Here we present a novel laboratory-based cryogenic soft X-ray microscope for whole cell tomography of frozen hydrated samples. We demonstrate the capabilities of this compact cryogenic microscope by visualizing internal sub-cellular structures of Saccharomyces cerevisiae cells. The microscope is shown to achieve better than 50 nm spatial resolution with a Siemens star test sample. For whole biological cells, the microscope can image specimens up to 5 micrometers thick. Structures as small as 90 nm can be detected in tomographic reconstructions at roughly 70 nm spatial resolution following a low cumulative radiation dose of only 7.2 MGy. Furthermore, the design of the specimen chamber utilizes a standard sample support that permits multimodal correlative imaging of the exact same unstained yeast cell via cryo-fluorescence light microscopy, cryo-soft x-ray microscopy and cryo-transmission electron microscopy. This completely laboratory-based cryogenic soft x-ray microscope will therefore enable greater access to three-dimensional ultrastructure determination of biological whole cells without chemical fixation or physical sectioning.

  9. Cellular architecture of Treponema pallidum: novel flagellum, periplasmic cone, and cell envelope as revealed by cryo electron tomography.

    PubMed

    Liu, Jun; Howell, Jerrilyn K; Bradley, Sherille D; Zheng, Yesha; Zhou, Z Hong; Norris, Steven J

    2010-11-01

    High-resolution cryo electron tomography (cryo-ET) was utilized to visualize Treponema pallidum, the causative agent of syphilis, at the molecular level. Three-dimensional (3D) reconstructions from 304 infectious organisms revealed unprecedented cellular structures of this unusual member of the spirochetal family. High-resolution cryo-ET reconstructions provided detailed structures of the cell envelope, which is significantly different from that of Gram-negative bacteria. The 4-nm lipid bilayer of both outer membrane and cytoplasmic membrane resolved in 3D reconstructions, providing an important marker for interpreting membrane-associated structures. Abundant lipoproteins cover the outer leaflet of the cytoplasmic membrane, in contrast to the rare outer membrane proteins visible by scanning probe microscopy. High-resolution cryo-ET images also provided the first observation of T. pallidum chemoreceptor arrays, as well as structural details of the periplasmically located cone-shaped structure at both ends of the bacterium. Furthermore, 3D subvolume averages of periplasmic flagellar motors and flagellar filaments from living organisms revealed the novel flagellar architectures that may facilitate their rotation within the confining periplasmic space. Our findings provide the most detailed structural understanding of periplasmic flagella and the surrounding cell envelope, which enable this enigmatic bacterium to efficiently penetrate tissue and to escape host immune responses.

  10. Electron Tomography Analysis of Tick-Borne Encephalitis Virus Infection in Human Neurons

    PubMed Central

    Bílý, Tomáš; Palus, Martin; Eyer, Luděk; Elsterová, Jana; Vancová, Marie; Růžek, Daniel

    2015-01-01

    Tick-borne encephalitis virus (TBEV) causes serious, potentially fatal neurological infections that affect humans in endemic regions of Europe and Asia. Neurons are the primary target for TBEV infection in the central nervous system. However, knowledge about this viral infection and virus-induced neuronal injury is fragmental. Here, we directly examined the pathology that occurs after TBEV infection in human primary neurons. We exploited the advantages of advanced high-pressure freezing and freeze-substitution techniques to achieve optimal preservation of infected cell architecture. Electron tomographic (ET) reconstructions elucidated high-resolution 3D images of the proliferating endoplasmic reticulum, and individual tubule-like structures of different diameters in the endoplasmic reticulum cisternae of single cells. ET revealed direct connections between the tubule-like structures and viral particles in the endoplasmic reticulum. Furthermore, ET showed connections between cellular microtubules and vacuoles that harbored the TBEV virions in neuronal extensions. This study was the first to characterize the 3D topographical organization of membranous whorls and autophagic vacuoles in TBEV-infected human neurons. The functional importance of autophagy during TBEV replication was studied in human neuroblastoma cells; stimulation of autophagy resulted in significantly increased dose-dependent TBEV production, whereas the inhibition of autophagy showed a profound, dose-dependent decrease of the yield of infectious virus. PMID:26073783

  11. Electron Tomography Analysis of Tick-Borne Encephalitis Virus Infection in Human Neurons.

    PubMed

    Bílý, Tomáš; Palus, Martin; Eyer, Luděk; Elsterová, Jana; Vancová, Marie; Růžek, Daniel

    2015-01-01

    Tick-borne encephalitis virus (TBEV) causes serious, potentially fatal neurological infections that affect humans in endemic regions of Europe and Asia. Neurons are the primary target for TBEV infection in the central nervous system. However, knowledge about this viral infection and virus-induced neuronal injury is fragmental. Here, we directly examined the pathology that occurs after TBEV infection in human primary neurons. We exploited the advantages of advanced high-pressure freezing and freeze-substitution techniques to achieve optimal preservation of infected cell architecture. Electron tomographic (ET) reconstructions elucidated high-resolution 3D images of the proliferating endoplasmic reticulum, and individual tubule-like structures of different diameters in the endoplasmic reticulum cisternae of single cells. ET revealed direct connections between the tubule-like structures and viral particles in the endoplasmic reticulum. Furthermore, ET showed connections between cellular microtubules and vacuoles that harbored the TBEV virions in neuronal extensions. This study was the first to characterize the 3D topographical organization of membranous whorls and autophagic vacuoles in TBEV-infected human neurons. The functional importance of autophagy during TBEV replication was studied in human neuroblastoma cells; stimulation of autophagy resulted in significantly increased dose-dependent TBEV production, whereas the inhibition of autophagy showed a profound, dose-dependent decrease of the yield of infectious virus. PMID:26073783

  12. Microstructural characterization of the cycling behavior of electrodeposited manganese oxide supercapacitors using 3D electron tomography

    NASA Astrophysics Data System (ADS)

    Dalili, N.; Clark, M. P.; Davari, E.; Ivey, D. G.

    2016-10-01

    Manganese oxide has been investigated extensively as an electrochemical capacitor or supercapacitor electrode material. Manganese oxide is inexpensive to fabricate and exhibits relatively high capacitance values, i.e., in excess of 200 F g-1 in many cases; the actual value depends very much on the fabrication method and test conditions. The cycling behavior of Mn oxide, fabricated using anodic electrodeposition, is investigated using slice and view techniques, via a dual scanning electron microscope (SEM) and focused ion beam (FIB) instrument to generate three-dimensional (3D) images, coupled with electrochemical characterization. The initial as-fabricated electrode has a rod-like appearance, with a fine-scale, sheet-like morphology within the rods. The rod-like structure remains after cycling, but there are significant morphological changes. These include partial dissolution of Mn oxide followed by redeposition of Mn oxide in regions close to the substrate. The redeposited material has a finer morphology than the original as-fabricated Mn oxide. The Mn oxide coverage is also better near the substrate. These effects result in an increase in the specific capacitance.

  13. Characterization of herpes simplex virus type 1 L-particle assembly and egress in hippocampal neurones by electron cryo-tomography

    PubMed Central

    Ibiricu, Iosune; Maurer, Ulrike E; Grünewald, Kay

    2013-01-01

    Visualizing virus–host interactions in situ inside infected cells by electron cryo-tomography provides unperturbed snapshots of the infection process. Here we focus on the assembly and egress pathway of herpesviruses. Cells infected with herpes simplex virus 1 produce and release not only infective virions but also non-infectious light particles (L-particles). L-particles are devoid of viral capsids and genomes. In this study, we analysed L-particle assembly and egress pathways in cultured dissociated hippocampus neurones by electron cryo-tomography. Virion and L-particle formation occurred in close proximity, suggesting shared assembly and exit pathways. Clathrin-like coats were occasionally associated with L-particle and virion assembly sites. Further, we compared the three-dimensional ultrastructure of intracellular and extracellular L-particles and quantified their diameters and the abundance of inclusion bodies contained. PMID:23253400

  14. Exploring the benefits of electron tomography to characterize the precise morphology of core-shell Au@Ag nanoparticles and its implications on their plasmonic properties.

    PubMed

    Hernández-Garrido, J C; Moreno, M S; Ducati, C; Pérez, L A; Midgley, P A; Coronado, E A

    2014-11-01

    In the design and engineering of functional core-shell nanostructures, material characterization at small length scales remains one of the major challenges. Here we show how electron tomography in high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) mode can be applied successfully to perform nano-metrological characterization of Au@Ag core-shell nanostructures. This work stresses the benefits of HAADF-STEM tomography and its use as a novel and rigorous tool for understanding the physical-chemical properties of complex 3D core-shell nanostructures. The reconstructed Au@Ag core-shell architecture was used as an input for discrete dipole approximation (DDA)-based electrodynamics simulations of the optical properties of the nanostructures. The implications of localized surface plasmon spectroscopy as well as Raman-enhanced spectroscopy are analysed.

  15. Electron Tomography of Cryofixed, Isometrically Contracting Insect Flight Muscle Reveals Novel Actin-Myosin Interactions

    SciTech Connect

    Wu, Shenping; Liu, Jun; Reedy, Mary C.; Tregear, Richard T.; Winkler, Hanspeter; Franzini-Armstrong, Clara; Sasaki, Hiroyuki; Lucaveche, Carmen; Goldman, Yale E.; Reedy, Michael K.; Taylor, Kenneth A.

    2010-10-22

    Isometric muscle contraction, where force is generated without muscle shortening, is a molecular traffic jam in which the number of actin-attached motors is maximized and all states of motor action are trapped with consequently high heterogeneity. This heterogeneity is a major limitation to deciphering myosin conformational changes in situ. We used multivariate data analysis to group repeat segments in electron tomograms of isometrically contracting insect flight muscle, mechanically monitored, rapidly frozen, freeze substituted, and thin sectioned. Improved resolution reveals the helical arrangement of F-actin subunits in the thin filament enabling an atomic model to be built into the thin filament density independent of the myosin. Actin-myosin attachments can now be assigned as weak or strong by their motor domain orientation relative to actin. Myosin attachments were quantified everywhere along the thin filament including troponin. Strong binding myosin attachments are found on only four F-actin subunits, the 'target zone', situated exactly midway between successive troponin complexes. They show an axial lever arm range of 77{sup o}/12.9 nm. The lever arm azimuthal range of strong binding attachments has a highly skewed, 127{sup o} range compared with X-ray crystallographic structures. Two types of weak actin attachments are described. One type, found exclusively in the target zone, appears to represent pre-working-stroke intermediates. The other, which contacts tropomyosin rather than actin, is positioned M-ward of the target zone, i.e. the position toward which thin filaments slide during shortening. We present a model for the weak to strong transition in the myosin ATPase cycle that incorporates azimuthal movements of the motor domain on actin. Stress/strain in the S2 domain may explain azimuthal lever arm changes in the strong binding attachments. The results support previous conclusions that the weak attachments preceding force generation are very

  16. A model based iterative reconstruction algorithm for high angle annular dark field-scanning transmission electron microscope (HAADF-STEM) tomography.

    PubMed

    Venkatakrishnan, S V; Drummy, Lawrence F; Jackson, Michael A; De Graef, Marc; Simmons, Jeff; Bouman, Charles A

    2013-11-01

    High angle annular dark field (HAADF)-scanning transmission electron microscope (STEM) data is increasingly being used in the physical sciences to research materials in 3D because it reduces the effects of Bragg diffraction seen in bright field TEM data. Typically, tomographic reconstructions are performed by directly applying either filtered back projection (FBP) or the simultaneous iterative reconstruction technique (SIRT) to the data. Since HAADF-STEM tomography is a limited angle tomography modality with low signal to noise ratio, these methods can result in significant artifacts in the reconstructed volume. In this paper, we develop a model based iterative reconstruction algorithm for HAADF-STEM tomography. We combine a model for image formation in HAADF-STEM tomography along with a prior model to formulate the tomographic reconstruction as a maximum a posteriori probability (MAP) estimation problem. Our formulation also accounts for certain missing measurements by treating them as nuisance parameters in the MAP estimation framework. We adapt the iterative coordinate descent algorithm to develop an efficient method to minimize the corresponding MAP cost function. Reconstructions of simulated as well as experimental data sets show results that are superior to FBP and SIRT reconstructions, significantly suppressing artifacts and enhancing contrast. PMID:23955748

  17. Understanding of the field evaporation of surface modified oxide materials through transmission electron microscopy and atom probe tomography

    NASA Astrophysics Data System (ADS)

    Seol, Jae-Bok; Kwak, Chang-Min; Kim, Y.-T.; Park, Chan-Gyung

    2016-04-01

    Understanding of triggering the field evaporation of surface ions on the non-conductive materials enables improvement in the mass resolution in laser-pulsed atom probe tomography. This study addresses the influence of surface modification through metallic-capped layers, such as Co, Ni, and Ag, with surrounding bulk MgO tips on the physical mechanisms responsible for field evaporation and on the mass resolving power compared to uncapped bulk MgO. In particular, the field evaporation on the surface regions of Ag-capped bulk MgO tips during analysis was extensively observed by transmission electron microscopy to confirm the overall evaporation sequences occurring at the tip surface. We found that the introduction of such capping layers, especially for Ag-capping, controls both symmetric tip geometry at the surface of the specimens and the mass resolving power of ion species consisting of MgO materials. This implies the improvements in the symmetries of local field distributions and the isotropy of thermal heating across the tip surface. It reveals that Ag-capping with high thermal diffusivity promotes the compositional uniformities between the laser illumination side and the opposite side for MgO samples as well as the reduced fraction of multiple events for oxygen ions between both sides. Moreover, a variation in the thickness of the Ag-capping layer is an additional factor governing a thermal-assisted mechanism of MgO evaporation. Based on our findings, homogeneous thermal heat transfer for MgO emission along the tip axis by Ag-capping layers may be significant in potential methods for improvement.

  18. Effect of patient visualization of coronary calcium by electron beam computed tomography on changes in beneficial lifestyle behaviors.

    PubMed

    Orakzai, Raza H; Nasir, Khurram; Orakzai, Sarwar H; Kalia, Nove; Gopal, Ambarish; Musunuru, Kiran; Blumenthal, Roger S; Budoff, Mathew J

    2008-04-01

    Despite convincing data demonstrating the benefits of aspirin (ASA), exercise, and dietary changes for both primary and secondary prevention of coronary heart disease, they remain underused. In this study, we assess whether higher coronary artery calcium (CAC) scores determined by electron beam computed tomography (EBCT) are associated with beneficial lifestyle behaviors in asymptomatic individuals. A total of 980 asymptomatic patients referred for EBCT risk assessment by their primary physician were sent a survey questioning them about health behaviors. We evaluated long-term ASA utilization, exercise, and dietary changes based on CAC using multivariable analysis. The study population consisted of 980 individuals (78% men, mean age 60 +/- 8 years) who were followed for a mean of 3 +/- 2 years after an initial EBCT scan. Overall, ASA initiation was lowest (29%) among those with CAC = 0, and gradually increased with higher CAC scores (1 to 99, 55%; 100 to 399, 61%; > or =400, 63%; p <0.001 for trend). Similarly, dietary changes and exercise were lowest (33% and 44%, respectively) among those with CAC = 0 and gradually increased with higher CAC scores (1 to 99, 40%; 100 to 399, 58%; > or =400, 56%; p <0.001 for trend for dietary changes; and 1 to 99, 62%; 100 to 399, 63%; > or =400, 67%; p <0.001 for trend for exercise). In multivariable analysis, greater baseline CAC was strongly associated with initiation of ASA therapy, dietary changes, and increased exercise. In conclusion, in addition to risk stratification of asymptomatic individuals, determination of CAC may also improve utilization of ASA therapy and behavioral modification. PMID:18359321

  19. Three-Dimensional Analysis of Syncytial-Type Cell Plates during Endosperm Cellularization Visualized by High Resolution Electron Tomography W⃞

    PubMed Central

    Otegui, Marisa S.; Mastronarde, David N.; Kang, Byung-Ho; Bednarek, Sebastian Y.; Staehelin, L. Andrew

    2001-01-01

    The three-dimensional architecture of syncytial-type cell plates in the endosperm of Arabidopsis has been analyzed at ∼6-nm resolution by means of dual-axis high-voltage electron tomography of high-pressure frozen/freeze-substituted samples. Mini-phragmoplasts consisting of microtubule clusters assemble between sister and nonsister nuclei. Most Golgi-derived vesicles appear connected to these microtubules by two molecules that resemble kinesin-like motor proteins. These vesicles fuse with each other to form hourglass-shaped intermediates, which become wide (∼45 nm in diameter) tubules, the building blocks of wide tubular networks. New mini-phragmoplasts also are generated de novo around the margins of expanding wide tubular networks, giving rise to new foci of cell plate growth, which later become integrated into the main cell plate. Spiral-shaped rings of the dynamin-like protein ADL1A constrict but do not fission the wide tubules at irregular intervals. These rings appear to maintain the tubular geometry of the network. The wide tubular network matures into a convoluted fenestrated sheet in a process that involves increases of 45 and 130% in relative membrane surface area and volume, respectively. The proportionally larger increase in volume appears to reflect callose synthesis. Upon fusion with the parental plasma membrane, the convoluted fenestrated sheet is transformed into a planar fenestrated sheet. This transformation involves clathrin-coated vesicles that reduce the relative membrane surface area and volume by ∼70%. A ribosome-excluding matrix encompasses the cell plate membranes from the fusion of the first vesicles until the onset of the planar fenestrated sheet formation. We postulate that this matrix contains the molecules that mediate cell plate assembly. PMID:11549762

  20. Breast Patient Setup Error Assessment: Comparison of Electronic Portal Image Devices and Cone-Beam Computed Tomography Matching Results

    SciTech Connect

    Topolnjak, Rajko; Sonke, Jan-Jakob; Nijkamp, Jasper; Rasch, Coen; Minkema, Danny; Remeijer, Peter; Vliet-Vroegindeweij, Corine van

    2010-11-15

    Purpose: To quantify the differences in setup errors measured with the cone-beam computed tomography (CBCT) and electronic portal image devices (EPID) in breast cancer patients. Methods and Materials: Repeat CBCT scan were acquired for routine offline setup verification in 20 breast cancer patients. During the CBCT imaging fractions, EPID images of the treatment beams were recorded. Registrations of the bony anatomy for CBCT to planning CT and EPID to digitally reconstructed-radiographs (DRRs) were compared. In addition, similar measurements of an anthropomorphic thorax phantom were acquired. Bland-Altman and linear regression analysis were performed for clinical and phantom registrations. Systematic and random setup errors were quantified for CBCT and EPID-driven correction protocols in the EPID coordinate system (U, V), with V parallel to the cranial-caudal axis and U perpendicular to V and the central beam axis. Results: Bland-Altman analysis of clinical EPID and CBCT registrations yielded 4 to 6-mm limits of agreement, indicating that both methods were not compatible. The EPID-based setup errors were smaller than the CBCT-based setup errors. Phantom measurements showed that CBCT accurately measures setup error whereas EPID underestimates setup errors in the cranial-caudal direction. In the clinical measurements, the residual bony anatomy setup errors after offline CBCT-based corrections were {Sigma}{sub U} = 1.4 mm, {Sigma}{sub V} = 1.7 mm, and {sigma}{sub U} = 2.6 mm, {sigma}{sub V} = 3.1 mm. Residual setup errors of EPID driven corrections corrected for underestimation were estimated at {Sigma}{sub U} = 2.2mm, {Sigma}{sub V} = 3.3 mm, and {sigma}{sub U} = 2.9 mm, {sigma}{sub V} = 2.9 mm. Conclusion: EPID registration underestimated the actual bony anatomy setup error in breast cancer patients by 20% to 50%. Using CBCT decreased setup uncertainties significantly.

  1. Structural analysis of the PSD-95 cluster by electron tomography and CEMOVIS: a proposal for the application of the genetically encoded metallothionein tag.

    PubMed

    Hirabayashi, Ai; Fukunaga, Yuko; Miyazawa, Atsuo

    2014-06-01

    Postsynaptic density-95 (PSD-95) accumulates at excitatory postsynapses and plays important roles in the clustering and anchoring of numerous proteins at the PSD. However, a detailed ultrastructural analysis of clusters exclusively consisting of PSD-95 has never been performed. Here, we employed a genetically encoded tag, three tandem repeats of metallothionein (3MT), to study the structure of PSD-95 clusters in cells by electron tomography and cryo-electron microscopy of vitreous sections. We also performed conventional transmission electron microscopy (TEM). Cultured hippocampal neurons expressing a fusion protein of PSD-95 coupled to 3MT (PDS-95-3MT) were incubated with CdCl2 to result in the formation of Cd-bound PSD-95-3MT. Two types of electron-dense deposits composed of Cd-bound PSD-95-3MT were observed in these cells by TEM, as reported previously. Electron tomography revealed the presence of membrane-shaped structures representing PSD-95 clusters at the PSD and an ellipsoidal structure located in the non-synaptic cytoplasm. By TEM, the PSD-95 clusters appeared to be composed of a number of dense cores. In frozen hydrated sections, these dense cores were also found beneath the postsynaptic membrane. Taken together, our findings suggest that dense cores of PSD-95 aggregate to form the larger clusters present in the PSD and the non-synaptic cytoplasm.

  2. Ultra-structural study of insulin granules in pancreatic β-cells of db/db mouse by scanning transmission electron microscopy tomography.

    PubMed

    Xue, Yanhong; Zhao, Wei; Du, Wen; Zhang, Xiang; Ji, Gang; Ying, Wang; Xu, Tao

    2012-07-01

    Insulin granule trafficking is a key step in the secretion of glucose-stimulated insulin from pancreatic β-cells. The main feature of type 2 diabetes (T2D) is the failure of pancreatic β-cells to secrete sufficient amounts of insulin to maintain normal blood glucose levels. In this work, we developed and applied tomography based on scanning transmission electron microscopy (STEM) to image intact insulin granules in the β-cells of mouse pancreatic islets. Using three-dimensional (3D) reconstruction, we found decreases in both the number and the grey level of insulin granules in db/db mouse pancreatic β-cells. Moreover, insulin granules were closer to the plasma membrane in diabetic β-cells than in control cells. Thus, 3D ultra-structural tomography may provide new insights into the pathology of insulin secretion in T2D.

  3. Correlative Tomography

    PubMed Central

    Burnett, T. L.; McDonald, S. A.; Gholinia, A.; Geurts, R.; Janus, M.; Slater, T.; Haigh, S. J.; Ornek, C.; Almuaili, F.; Engelberg, D. L.; Thompson, G. E.; Withers, P. J.

    2014-01-01

    Increasingly researchers are looking to bring together perspectives across multiple scales, or to combine insights from different techniques, for the same region of interest. To this end, correlative microscopy has already yielded substantial new insights in two dimensions (2D). Here we develop correlative tomography where the correlative task is somewhat more challenging because the volume of interest is typically hidden beneath the sample surface. We have threaded together x-ray computed tomography, serial section FIB-SEM tomography, electron backscatter diffraction and finally TEM elemental analysis all for the same 3D region. This has allowed observation of the competition between pitting corrosion and intergranular corrosion at multiple scales revealing the structural hierarchy, crystallography and chemistry of veiled corrosion pits in stainless steel. With automated correlative workflows and co-visualization of the multi-scale or multi-modal datasets the technique promises to provide insights across biological, geological and materials science that are impossible using either individual or multiple uncorrelated techniques. PMID:24736640

  4. Correlative Tomography

    NASA Astrophysics Data System (ADS)

    Burnett, T. L.; McDonald, S. A.; Gholinia, A.; Geurts, R.; Janus, M.; Slater, T.; Haigh, S. J.; Ornek, C.; Almuaili, F.; Engelberg, D. L.; Thompson, G. E.; Withers, P. J.

    2014-04-01

    Increasingly researchers are looking to bring together perspectives across multiple scales, or to combine insights from different techniques, for the same region of interest. To this end, correlative microscopy has already yielded substantial new insights in two dimensions (2D). Here we develop correlative tomography where the correlative task is somewhat more challenging because the volume of interest is typically hidden beneath the sample surface. We have threaded together x-ray computed tomography, serial section FIB-SEM tomography, electron backscatter diffraction and finally TEM elemental analysis all for the same 3D region. This has allowed observation of the competition between pitting corrosion and intergranular corrosion at multiple scales revealing the structural hierarchy, crystallography and chemistry of veiled corrosion pits in stainless steel. With automated correlative workflows and co-visualization of the multi-scale or multi-modal datasets the technique promises to provide insights across biological, geological and materials science that are impossible using either individual or multiple uncorrelated techniques.

  5. Dosimetric characterization and application of an imaging beam line with a carbon electron target for megavoltage cone beam computed tomography.

    PubMed

    Flynn, Ryan T; Hartmann, Julia; Bani-Hashemi, Ali; Nixon, Earl; Alfredo, R; Siochi, C; Pennington, Edward C; Bayouth, John E

    2009-06-01

    Imaging dose from megavoltage cone beam computed tomography (MVCBCT) can be significantly reduced without loss of image quality by using an imaging beam line (IBL), with no flattening filter and a carbon, rather than tungsten, electron target. The IBL produces a greater keV-range x-ray fluence than the treatment beam line (TBL), which results in a more optimal detector response. The IBL imaging dose is not necessarily negligible, however. In this work an IBL was dosimetrically modeled with the Philips Pinnacle3 treatment planning system (TPS), verified experimentally, and applied to clinical cases. The IBL acquisition dose for a 200 degrees gantry rotation was verified in a customized acrylic cylindrical phantom at multiple imaging field sizes with 196 ion chamber measurements. Agreement between the measured and calculated IBL dose was quantified with the 3D gamma index. Representative IBL and TBL imaging dose distributions were calculated for head and neck and prostate patients and included in treatment plans using the imaging dose incorporation (IDI) method. Surface dose was measured for the TBL and IBL for four head and neck cancer patients with MOSFETs. The IBL model, when compared to the percentage depth dose and profile measurements, had 97% passing gamma indices for dosimetric and distance acceptance criteria of 3%, 3 mm, and 100% passed for 5.2%, 5.2 mm. For the ion chamber measurements of phantom image acquisition dose, the IBL model had 93% passing gamma indices for acceptance criteria of 3%, 3 mm, and 100% passed for 4%, 4 mm. Differences between the IBL- and TBL-based IMRT treatment plans created with the IDI method were dosimetrically insignificant for both the prostate and head and neck cases. For IBL and TBL beams with monitor unit values that would result in the delivery of the same dose to the depth of maximum dose under standard calibration conditions, the IBL imaging surface dose was higher than the TBL imaging surface dose by an average of 18

  6. Digital retrospective motion-mode display and processing of electron beam cine-computed tomography and other cross-sectional cardiac imaging techniques

    NASA Astrophysics Data System (ADS)

    Reed, Judd E.; Rumberger, John A.; Buithieu, Jean; Behrenbeck, Thomas; Breen, Jerome F.; Sheedy, Patrick F., II

    1995-05-01

    Electron beam computed tomography is unparalleled in its ability to consistently produce high quality dynamic images of the human heart. Its use in quantification of left ventricular dynamics is well established in both clinical and research applications. However, the image analysis tools supplied with the scanners offer a limited number of analysis options. They are based on embedded computer systems which have not been significantly upgraded since the scanner was introduced over a decade ago in spite of the explosive improvements in available computer power which have occured during this period. To address these shortcomings, a workstation-based ventricular analysis system has been developed at our institution. This system, which has been in use for over five years, is based on current workstation technology and therefore has benefited from the periodic upgrades in processor performance available to these systems. The dynamic image segmentation component of this system is an interactively supervised, semi-automatic surface identification and tracking system. It characterizes the endocardial and epicardial surfaces of the left ventricle as two concentric 4D hyper-space polyhedrons. Each of these polyhedrons have nearly ten thousand vertices which are deposited into a relational database. The right ventricle is also processed in a similar manner. This database is queried by other custom components which extract ventricular function parameters such as regional ejection fraction and wall stress. The interactive tool which supervises dynamic image segmentation has been enhanced with a temporal domain display. The operator interactively chooses the spatial location of the endpoints of a line segment while the corresponding space/time image is displayed. These images, with content resembling M-Mode echocardiography, benefit form electron beam computed tomography's high spatial and contrast resolution. The segmented surfaces are displayed along with the imagery. These

  7. Effects of coordinate system choice on measured regional myocardial function in short-axis cine electron-beam tomography

    NASA Astrophysics Data System (ADS)

    Reed, Judd E.; Rumberger, John A.; Buithieu, Jean; Behrenbeck, Thomas; Breen, Jerome F.; Sheedy, Patrick F., II

    1995-05-01

    Following myocardial infarction, the size of the infarcted region and the systolic functioning of the noninfarcted region are commonly assessed by various cross- sectional imaging techniques. A series of images representing successive phases of the cardiac cycle can be acquired by several imaging modalities including electron beam computed tomography, magnetic resonance imaging, and echocardiography. For the assessment of patterns of ventricular contraction, images are commonly acquired of ventricular cross-sections normal to the 'long' axis of the heart and parallel to the mitral valve plane. The endocardial and epicardial surfaces of the myocardium are identified. Then the ventricle is divided into sectors and the volumes of blood and myocardium within each sector at multiple phases of the cardiac cycle are measured. Regional function parameters are derived from these measurements. This generally mandates the use of a polar or cylindrical coordinate system. Various algorithms have been used to select the origin of this coordinate system. These include the centroid of the endocardial surface, the epicardial surface, or of a polygon whose vertices lie midway between the epicardial and endocardial surfaces of the myocardium (centerline method). Another algorithm has been developed in our laboratory. This uses the centroid (or center of mass) of the myocardium exclusive of the ventricular cavity. Each of these choices for origin of coordinate system can be derived from the end- diastolic image or from the end-systolic image. Alternately, new coordinate systems can be selected for each phase of the cardiac cycle. These are referred to as 'floating' coordinate systems. A series of computer models have been developed in our laboratory to study the effects of each of these choices on the regional function parameters of normal ventricles and how these choices effect the quantification of regional abnormalities after myocardial infarction. The most sophisticated of these

  8. Novel characteristics of normal supraspinatus insertion in rats: an ultrastructural analysis using three-dimensional reconstruction using focused ion beam/scanning electron microscope tomography

    PubMed Central

    Kanazawa, Tomonoshin; Gotoh, Masafumi; Ohta, Keisuke; Shiba, Naoto; Nakamura, Kei-ichiro

    2014-01-01

    Summary Background: the histological architecture of the insertion after a rotator cuff repair is completely different from that of normal tendon-bone insertions. Analysis of normal insertions by electron microscopy may enhance the understanding of the pathophysiology of tendon-to-bone healing after rotator cuff repair. The present study examined the normal supraspinatus insertion in rats using a new three-dimensional (3D) electron microscopic method, focused ion beam/scanning electron microscope (FIB/SEM) tomography. Methods: normal supraspinatus insertion of adult Sprague-Dawley rats was analyzed. FIB/SEM tomography was performed on the entire insertion. The obtained serial images were reconstructed, and the 3D cellular morphology and organization of collagen bundles was observed. Results: the cellular shapes between the tendon-cartilage interface were successfully reconstructed. The cells in the cartilage region were spherical without any cellular processes, while the cells in the intermediate region had some cellular processes oriented longitudinally along the collagen bundles. In addition, these 2 regions were smoothly transferred under ultrastructural resolution. Conclusions: structures at the normal insertion gradually changed from the fibrous cartilage to the tendon midsubstance, which may contribute to the biomechanical strength of the site. These novel cell characteristics may provide necessary knowledge for better regeneration of tendon-to-bone insertions after rotator cuff repair. PMID:25332933

  9. 3D Visualization of the Iron Oxidation State in FeO/Fe3O4 Core-Shell Nanocubes from Electron Energy Loss Tomography.

    PubMed

    Torruella, Pau; Arenal, Raúl; de la Peña, Francisco; Saghi, Zineb; Yedra, Lluís; Eljarrat, Alberto; López-Conesa, Lluís; Estrader, Marta; López-Ortega, Alberto; Salazar-Alvarez, Germán; Nogués, Josep; Ducati, Caterina; Midgley, Paul A; Peiró, Francesca; Estradé, Sonia

    2016-08-10

    The physicochemical properties used in numerous advanced nanostructured devices are directly controlled by the oxidation states of their constituents. In this work we combine electron energy-loss spectroscopy, blind source separation, and computed tomography to reconstruct in three dimensions the distribution of Fe(2+) and Fe(3+) ions in a FeO/Fe3O4 core/shell cube-shaped nanoparticle with nanometric resolution. The results highlight the sharpness of the interface between both oxides and provide an average shell thickness, core volume, and average cube edge length measurements in agreement with the magnetic characterization of the sample. PMID:27383904

  10. 3D Visualization of the Iron Oxidation State in FeO/Fe3O4 Core-Shell Nanocubes from Electron Energy Loss Tomography.

    PubMed

    Torruella, Pau; Arenal, Raúl; de la Peña, Francisco; Saghi, Zineb; Yedra, Lluís; Eljarrat, Alberto; López-Conesa, Lluís; Estrader, Marta; López-Ortega, Alberto; Salazar-Alvarez, Germán; Nogués, Josep; Ducati, Caterina; Midgley, Paul A; Peiró, Francesca; Estradé, Sonia

    2016-08-10

    The physicochemical properties used in numerous advanced nanostructured devices are directly controlled by the oxidation states of their constituents. In this work we combine electron energy-loss spectroscopy, blind source separation, and computed tomography to reconstruct in three dimensions the distribution of Fe(2+) and Fe(3+) ions in a FeO/Fe3O4 core/shell cube-shaped nanoparticle with nanometric resolution. The results highlight the sharpness of the interface between both oxides and provide an average shell thickness, core volume, and average cube edge length measurements in agreement with the magnetic characterization of the sample.

  11. Argon broad ion beam tomography in a cryogenic scanning electron microscope: a novel tool for the investigation of representative microstructures in sedimentary rocks containing pore fluid.

    PubMed

    Desbois, G; Urai, J L; Pérez-Willard, F; Radi, Z; Offern, S; Burkart, I; Kukla, P A; Wollenberg, U

    2013-03-01

    The contribution describes the implementation of a broad ion beam (BIB) polisher into a scanning electron microscope (SEM) functioning at cryogenic temperature (cryo). The whole system (BIB-cryo-SEM) provides a first generation of a novel multibeam electron microscope that combines broad ion beam with cryogenic facilities in a conventional SEM to produce large, high-quality cross-sections (up to 2 mm(2)) at cryogenic temperature to be imaged at the state-of-the-art SEM resolution. Cryogenic method allows detecting fluids in their natural environment and preserves samples against desiccation and dehydration, which may damage natural microstructures. The investigation of microstructures in the third dimension is enabled by serial cross-sectioning, providing broad ion beam tomography with slices down to 350 nm thick. The functionalities of the BIB-cryo-SEM are demonstrated by the investigation of rock salts (synthetic coarse-grained sodium chloride synthesized from halite-brine mush cold pressed at 150 MPa and 4.5 GPa, and natural rock salt mylonite from a salt glacier at Qom Kuh, central Iran). In addition, results from BIB-cryo-SEM on a gas shale and Boom Clay are also presented to show that the instrument is suitable for a large range of sedimentary rocks. For the first time, pore and grain fabrics of preserved host and reservoir rocks can be investigated at nm-scale range over a representative elementary area. In comparison with the complementary and overlapping performances of the BIB-SEM method with focused ion beam-SEM and X-ray tomography methods, the BIB cross-sectioning enables detailed insights about morphologies of pores at greater resolution than X-ray tomography and allows the production of large representative surfaces suitable for FIB-SEM investigations of a specific representative site within the BIB cross-section.

  12. Argon broad ion beam tomography in a cryogenic scanning electron microscope: a novel tool for the investigation of representative microstructures in sedimentary rocks containing pore fluid.

    PubMed

    Desbois, G; Urai, J L; Pérez-Willard, F; Radi, Z; Offern, S; Burkart, I; Kukla, P A; Wollenberg, U

    2013-03-01

    The contribution describes the implementation of a broad ion beam (BIB) polisher into a scanning electron microscope (SEM) functioning at cryogenic temperature (cryo). The whole system (BIB-cryo-SEM) provides a first generation of a novel multibeam electron microscope that combines broad ion beam with cryogenic facilities in a conventional SEM to produce large, high-quality cross-sections (up to 2 mm(2)) at cryogenic temperature to be imaged at the state-of-the-art SEM resolution. Cryogenic method allows detecting fluids in their natural environment and preserves samples against desiccation and dehydration, which may damage natural microstructures. The investigation of microstructures in the third dimension is enabled by serial cross-sectioning, providing broad ion beam tomography with slices down to 350 nm thick. The functionalities of the BIB-cryo-SEM are demonstrated by the investigation of rock salts (synthetic coarse-grained sodium chloride synthesized from halite-brine mush cold pressed at 150 MPa and 4.5 GPa, and natural rock salt mylonite from a salt glacier at Qom Kuh, central Iran). In addition, results from BIB-cryo-SEM on a gas shale and Boom Clay are also presented to show that the instrument is suitable for a large range of sedimentary rocks. For the first time, pore and grain fabrics of preserved host and reservoir rocks can be investigated at nm-scale range over a representative elementary area. In comparison with the complementary and overlapping performances of the BIB-SEM method with focused ion beam-SEM and X-ray tomography methods, the BIB cross-sectioning enables detailed insights about morphologies of pores at greater resolution than X-ray tomography and allows the production of large representative surfaces suitable for FIB-SEM investigations of a specific representative site within the BIB cross-section. PMID:23323728

  13. Direct atomic-scale imaging of hydrogen and oxygen interstitials in pure niobium using atom-probe tomography and aberration-corrected scanning transmission electron microscopy.

    PubMed

    Kim, Yoon-Jun; Tao, Runzhe; Klie, Robert F; Seidman, David N

    2013-01-22

    Imaging the three-dimensional atomic-scale structure of complex interfaces has been the goal of many recent studies, due to its importance to technologically relevant areas. Combining atom-probe tomography and aberration-corrected scanning transmission electron microscopy (STEM), we present an atomic-scale study of ultrathin (~5 nm) native oxide layers on niobium (Nb) and the formation of ordered niobium hydride phases near the oxide/Nb interface. Nb, an elemental type-II superconductor with the highest critical temperature (T(c) = 9.2 K), is the preferred material for superconducting radio frequency (SRF) cavities in next-generation particle accelerators. Nb exhibits high solubilities for oxygen and hydrogen, especially within the RF-field penetration depth, which is believed to result in SRF quality factor losses. STEM imaging and electron energy-loss spectroscopy followed by ultraviolet laser-assisted local-electrode atom-probe tomography on the same needle-like sample reveals the NbO(2), Nb(2)O(5), NbO, Nb stacking sequence; annular bright-field imaging is used to visualize directly hydrogen atoms in bulk β-NbH.

  14. Electron tomography of (In,Ga)N insertions in GaN nanocolumns grown on semi-polar (112{sup -}2) GaN templates

    SciTech Connect

    Niehle, M. Trampert, A.; Albert, S.; Bengoechea-Encabo, A.; Calleja, E.

    2015-03-01

    We present results of scanning transmission electron tomography on GaN/(In,Ga)N/GaN nanocolumns (NCs) that grew uniformly inclined towards the patterned, semi-polar GaN(112{sup -}2) substrate surface by molecular beam epitaxy. For the practical realization of the tomographic experiment, the nanocolumn axis has been aligned parallel to the rotation axis of the electron microscope goniometer. The tomographic reconstruction allows for the determination of the three-dimensional indium distribution inside the nanocolumns. This distribution is strongly interrelated with the nanocolumn morphology and faceting. The (In,Ga)N layer thickness and the indium concentration differ between crystallographically equivalent and non-equivalent facets. The largest thickness and the highest indium concentration are found at the nanocolumn apex parallel to the basal planes.

  15. Structure resolution by electron diffraction tomography of the complex layered iron-rich Fe-2234-type Sr5Fe6O15.4

    NASA Astrophysics Data System (ADS)

    Lepoittevin, Christophe

    2016-10-01

    The crystal structure of the strontium ferrite Sr5Fe6O15.4, was solved by direct methods on electron diffraction tomography data acquired on a transmission electron microscope. The refined cell parameters are a=27.4047(3) Å, b=5.48590(7) Å and c=42.7442(4) Å in Fm2m symmetry. Its structure is built up from the intergrowth sequence between a quadruple perovskite-type layer with a complex rock-salt (RS)-type block. In the latter iron atoms are found in two different environments : tetragonal pyramid and tetrahedron. The structural model was refined by Rietveld method based on the powder X-ray diffraction pattern.

  16. Characterization of electrical properties in axial Si-Ge nanowire heterojunctions using off-axis electron holography and atom-probe tomography

    NASA Astrophysics Data System (ADS)

    Gan, Zhaofeng; Perea, Daniel E.; Yoo, Jinkyoung; He, Yang; Colby, Robert J.; Barker, Josh E.; Gu, Meng; Mao, Scott X.; Wang, Chongmin; Picraux, S. T.; Smith, David J.; McCartney, Martha R.

    2016-09-01

    Nanowires (NWs) consisting of P-doped Si/B-doped Ge axial heterojunctions were grown via vapor-liquid-solid synthesis using a combination of Au and AuGa catalyst particles. Off-axis electron holography (EH) was used to measure the electrostatic potential profile across the junction resulting from electrically active dopants, and atom-probe tomography (APT) was used to map total dopant concentration profiles. A comparison of the electrostatic potential profile measured from EH with simulations that were based on the APT results indicates that Ga atoms unintentionally introduced during AuGa catalyst growth were mostly electronically inactive. This finding was also corroborated by in situ electron-holography biasing experiments. Electronic band structure simulations guided by the experimental results helped to provide a much better explanation of the NW electrical behavior. Overall, this work demonstrates that the combination of EH, APT, in situ biasing, and simulations allows a more complete understanding of NW electrical properties to be developed.

  17. Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic Resolution Electron Microscopy and Field Evaporation Simulation

    SciTech Connect

    Devaraj, Arun; Colby, Robert J.; Vurpillot, F.; Thevuthasan, Suntharampillai

    2014-03-26

    Metal-dielectric composite materials, specifically metal nanoparticles supported on or embedded in metal oxides, are widely used in catalysis. The accurate optimization of such nanostructures warrants the need for detailed three-dimensional characterization. Atom probe tomography is uniquely capable of generating sub-nanometer structural and compositional data with part-per-million mass sensitivity, but there are reconstruction artifacts for composites containing materials with strongly differing fields of evaporation, as for oxide-supported metal nanoparticles. By correlating atom probe tomography with scanning transmission electron microscopy for Au nanoparticles embedded in an MgO support, deviations from an ideal topography during evaporation are demonstrated directly, and correlated with compositional errors in the reconstructed data. Finite element simulations of the field evaporation process confirm that protruding Au nanoparticles will evolve on the tip surface, and that evaporation field variations lead to an inaccurate assessment of the local composition, effectively lowering the spatial resolution of the final reconstructed dataset. Cross-correlating the experimental data with simulations results in a more detailed understanding of local evaporation aberrations during APT analysis of metal-oxide composites, paving the way towards a more accurate three-dimensional characterization of this technologically important class of materials.

  18. Electron Tomography of Cryo-Immobilized Plant Tissue: A Novel Approach to Studying 3D Macromolecular Architecture of Mature Plant Cell Walls In Situ

    PubMed Central

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G.; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H.; Auer, Manfred

    2014-01-01

    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

  19. Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ.

    PubMed

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H; Auer, Manfred

    2014-01-01

    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼ 2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

  20. Experimental study of heavy-ion computed tomography using a scintillation screen and an electron-multiplying charged coupled device camera for human head imaging

    NASA Astrophysics Data System (ADS)

    Muraishi, Hiroshi; Hara, Hidetake; Abe, Shinji; Yokose, Mamoru; Watanabe, Takara; Takeda, Tohoru; Koba, Yusuke; Fukuda, Shigekazu

    2016-03-01

    We have developed a heavy-ion computed tomography (IonCT) system using a scintillation screen and an electron-multiplying charged coupled device (EMCCD) camera that can measure a large object such as a human head. In this study, objective with the development of the system was to investigate the possibility of applying this system to heavy-ion treatment planning from the point of view of spatial resolution in a reconstructed image. Experiments were carried out on a rotation phantom using 12C accelerated up to 430 MeV/u by the Heavy-Ion Medical Accelerator in Chiba (HIMAC) at the National Institute of Radiological Sciences (NIRS). We demonstrated that the reconstructed image of an object with a water equivalent thickness (WET) of approximately 18 cm was successfully achieved with the spatial resolution of 1 mm, which would make this IonCT system worth applying to the heavy-ion treatment planning for head and neck cancers.

  1. The mechanism of DNA ejection in the Bacillus anthracis spore-binding phage 8a revealed by cryo-electron tomography

    PubMed Central

    Fu, Xiaofeng; Walter, Michael H.; Paredes, Angel; Morais, Marc C.; Liu, Jun

    2013-01-01

    The structure of the Bacillus anthracis spore-binding phage 8a was determined by cryo-electron tomography. The phage capsid forms a T=16 icosahedron attached to a contractile tail via a head–tail connector protein. The tail consists of a six-start helical sheath surrounding a central tail tube, and a structurally novel baseplate at the distal end of the tail that recognizes and attaches to host cells. The parameters of the icosahedral capsid lattice and the helical tail sheath suggest protein folds for the capsid and tail-sheath proteins, respectively, and indicate evolutionary relationships to other dsDNA viruses. Analysis of 2518 intact phage particles show four distinct conformations that likely correspond to four sequential states of the DNA ejection process during infection. Comparison of the four observed conformations suggests a mechanism for DNA ejection, including the molecular basis underlying coordination of tail sheath contraction and genome release from the capsid. PMID:22018785

  2. Influence of the Electronic Structure and Optical Properties of CeO2 and UO2 for Characterization with UV-Laser Assisted Atom Probe Tomography

    SciTech Connect

    Billy Valderrama; H.B. Henderson; C. Yablinsky; J. Gan; T.R. Allen; M.V. Manuel

    2015-09-01

    Oxide materials are used in numerous applications such as thermal barrier coatings, nuclear fuels, and electrical conductors and sensors, all applications where nanometer-scale stoichiometric changes can affect functional properties. Atom probe tomography can be used to characterize the precise chemical distribution of individual species and spatially quantify the oxygen to metal ratio at the nanometer scale. However, atom probe analysis of oxides can be accompanied by measurement artifacts caused by laser-material interactions. In this investigation, two technologically relevant oxide materials with the same crystal structure and an anion to cation ratio of 2.00, pure cerium oxide (CeO2) and uranium oxide (UO2) are studied. It was determined that electronic structure, optical properties, heat transfer properties, and oxide stability strongly affect their evaporation behavior, thus altering their measured stoichiometry, with thermal conductance and thermodynamic stability being strong factors.

  3. The mechanism of DNA ejection in the Bacillus anthracis spore-binding phage 8a revealed by cryo-electron tomography

    SciTech Connect

    Fu, Xiaofeng; Walter, Michael H.; Paredes, Angel; Morais, Marc C.; Liu, Jun

    2011-12-20

    The structure of the Bacillus anthracis spore-binding phage 8a was determined by cryo-electron tomography. The phage capsid forms a T = 16 icosahedron attached to a contractile tail via a head-tail connector protein. The tail consists of a six-start helical sheath surrounding a central tail tube, and a structurally novel baseplate at the distal end of the tail that recognizes and attaches to host cells. The parameters of the icosahedral capsid lattice and the helical tail sheath suggest protein folds for the capsid and tail-sheath proteins, respectively, and indicate evolutionary relationships to other dsDNA viruses. Analysis of 2518 intact phage particles show four distinct conformations that likely correspond to four sequential states of the DNA ejection process during infection. Comparison of the four observed conformations suggests a mechanism for DNA ejection, including the molecular basis underlying coordination of tail sheath contraction and genome release from the capsid.

  4. Atomic arrangement at ZnTe/CdSe interfaces determined by high resolution scanning transmission electron microscopy and atom probe tomography

    SciTech Connect

    Bonef, Bastien; Rouvière, Jean-Luc; Jouneau, Pierre-Henri; Bellet-Amalric, Edith; Gérard, Lionel; Mariette, Henri; André, Régis; Bougerol, Catherine; Grenier, Adeline

    2015-02-02

    High resolution scanning transmission electron microscopy and atom probe tomography experiments reveal the presence of an intermediate layer at the interface between two binary compounds with no common atom, namely, ZnTe and CdSe for samples grown by Molecular Beam Epitaxy under standard conditions. This thin transition layer, of the order of 1 to 3 atomic planes, contains typically one monolayer of ZnSe. Even if it occurs at each interface, the direct interface, i.e., ZnTe on CdSe, is sharper than the reverse one, where the ZnSe layer is likely surrounded by alloyed layers. On the other hand, a CdTe-like interface was never observed. This interface knowledge is crucial to properly design superlattices for optoelectronic applications and to master band-gap engineering.

  5. High-resolution three-dimensional scanning transmission electron microscopy characterization of oxide-nitride-oxide layer interfaces in Si-based semiconductors using computed tomography.

    PubMed

    Sadayama, Shoji; Sekiguchi, Hiromi; Bright, Alexander; Suzuki, Naohisa; Yamada, Kazuhiro; Kaneko, Kenji

    2011-01-01

    Oxide-nitride-oxide (ONO) layer structures are widely used for charge storage in flash memory devices. The ONO layer interfaces should be as flat as possible, so measurement of the nanoscale roughness of those interfaces is needed. In this study, quantification of an ONO film from a commercially available flash memory device was carried out with a pillar-shaped specimen using scanning transmission electron microscopy (STEM) and computed tomography. The ONO area contained only low Z- and low STEM-contrast materials, which makes high-quality reconstruction difficult. The optimum three-dimensional reconstruction was achieved with an STEM annular dark-field detector inner collection angle of 32 mrad, a sample tilt range from -78° to +78° and 25 iterations for the simultaneous iterative reconstruction technique.

  6. Solution synthesis of a new thermoelectric Zn(1+x)Sb nanophase and its structure determination using automated electron diffraction tomography.

    PubMed

    Birkel, Christina S; Mugnaioli, Enrico; Gorelik, Tatiana; Kolb, Ute; Panthöfer, Martin; Tremel, Wolfgang

    2010-07-21

    Engineering materials with specific physical properties have recently focused on the effect of nanoscopic inhomogeneities at the 10 nm scale. Such features are expected to scatter medium- and long-wavelength phonons thereby lowering the thermal conductivity of the system. Low thermal conductivity is a prerequisite for effective thermoelectric materials, and the challenge is to limit the transport of heat by phonons, without simultaneously decreasing charge transport. A solution-phase technique was devised for synthesis of thermoelectric "Zn(4)Sb(3)" nanocrystals as a precursor for phase segregation into ZnSb and a new Zn-Sb intermetallic phase, Zn(1+delta)Sb, in a peritectoid reaction. Our approach uses activated metal nanoparticles as precursors for the synthesis of this intermetallic compound. The small particle size of the reactants ensures minimum diffusion paths, low activation barriers, and low reaction temperatures, thereby eliminating solid-solid diffusion as the rate-limiting step in conventional bulk-scale solid-state synthesis. Both phases were identified and structurally characterized by automated electron diffraction tomography combined with precession electron diffraction. An ab initio structure solution based on electron diffraction data revealed two different phases. The new pseudo-hexagonal phase, Zn(1+delta)Sb, was identified and classified within the structural diversity of the Zn-Sb phase diagram.

  7. Working Length Determination Using Cone-Beam Computed Tomography, Periapical Radiography and Electronic Apex Locator in Teeth with Apical Periodontitis: A Clinical Study

    PubMed Central

    de Morais, André Luiz Gomide; de Alencar, Ana Helena Gonçalves; Estrela, Cyntia Rodrigues de Araújo; Decurcio, Daniel Almeida; Estrela, Carlos

    2016-01-01

    Introduction: The purpose of this clinical study was to compare the accuracy of working length (WL) determination using cone-beam computed tomography (CBCT), conventional periapical radiographies and electronic apex locator. Methods and Materials: This study was conducted during root canal treatment of 19 patients with a total of 30 single-rooted teeth diagnosed with apical periodontitis. After taking the initial parallel periapical radiographies, the initial file was advanced into the canal until the WL was detected by the apex locator. Subsequently, the WL was measured and WL radiographies were taken with the file set in the canal. Afterwards, CBCT images were acquired. These three measurements were tabulated and compared and the data were analyzed using the Friedman test. The level of significance was set at 0.05. Results: The mean values for WL determination by electronic apex locator, periapical radiograph and CBCT images were 22.25, 22.43 and 22.65, respectively which was not statistically significant (P>0.05). Conclusion: Working length determination using CBCT images was precise when compared to radiographic method and electronic apex locator. PMID:27471524

  8. The Electron Density Features Revealed by the GNSS-Based Radio Tomography in the Different Latitudinal and Longitudinal Sectors of the Ionosphere

    NASA Astrophysics Data System (ADS)

    Andreeva, Elena; Tereshchenko, Evgeniy; Nazarenko, Marina; Nesterov, Ivan; Kozharin, Maksim; Padokhin, Artem; Tumanova, Yulia

    2016-04-01

    The ionospheric radio tomography is an efficient method for electron density imaging in the different geographical regions of the world under different space weather conditions. The input for the satellite-based ionospheric radio tomography is provided by the signals that are transmitted from the navigational satellites and recorded by the chains or networks of ground receivers. The low-orbiting (LO) radio tomography employs the 150/400 MHz radio transmissions from the Earth's orbiters (like the Russian Tsikada/Parus and American Transit) flying at a height of ~1000 km above the Earth in the nearly polar orbits. The phases of the signals from a moving satellite which are recorded by the chains of ground receivers oriented along the satellite path form the families of linear integrals of electron density along the satellite-receiver rays that are used as the input data for LORT. The LO tomographic inversion of these data by phase difference method yields the 2D distributions of the ionospheric plasma in the vertical plane containing the receiving chain and the satellite path. LORT provides vertical resolution of 20-30 km and horizontal resolution of 30-40 km. The high-orbiting (HO) radio tomography employs the radio transmissions from the GPS/GLONASS satellites and enables 4D imaging of the ionosphere (3 spatial coordinates and time). HORT has a much wider spatial coverage (almost worldwide) and provides continuous time series of the reconstructions. However, the spatial resolution of HORT is lower (~100 km horizontally with a time step 60-20 min). In the regions with dense receiving networks (Europe, USA, Alaska, Japan), the resolution can be increased to 30-50 km with a time interval of 30-10 min. To date, the extensive RT data collected from the existing RT chains and networks enable a thorough analysis of both the regular and sporadic ionospheric features which are observed systematically or appear spontaneously, whose origin is fairly well understood or

  9. Electron tomography provides a direct link between the Payne effect and the inter-particle spacing of rubber composites

    PubMed Central

    Staniewicz, Lech; Vaudey, Thomas; Degrandcourt, Christophe; Couty, Marc; Gaboriaud, Fabien; Midgley, Paul

    2014-01-01

    Rubber-filler composites are a key component in the manufacture of tyres. The filler provides mechanical reinforcement and additional wear resistance to the rubber, but it in turn introduces non-linear mechanical behaviour to the material which most likely arises from interactions between the filler particles, mediated by the rubber matrix. While various studies have been made on the bulk mechanical properties and of the filler network structure (both imaging and by simulations), there presently does not exist any work directly linking filler particle spacing and mechanical properties. Here we show that using STEM tomography, aided by a machine learning image analysis procedure, to measure silica particle spacings provides a direct link between the inter-particle spacing and the reduction in shear modulus as a function of strain (the Payne effect), measured using dynamic mechanical analysis. Simulations of filler network formation using attractive, repulsive and non-interacting potentials were processed using the same method and compared with the experimental data, with the net result being that an attractive inter-particle potential is the most accurate way of modelling styrene-butadiene rubber-silica composite formation. PMID:25487130

  10. Electron tomography provides a direct link between the Payne effect and the inter-particle spacing of rubber composites.

    PubMed

    Staniewicz, Lech; Vaudey, Thomas; Degrandcourt, Christophe; Couty, Marc; Gaboriaud, Fabien; Midgley, Paul

    2014-01-01

    Rubber-filler composites are a key component in the manufacture of tyres. The filler provides mechanical reinforcement and additional wear resistance to the rubber, but it in turn introduces non-linear mechanical behaviour to the material which most likely arises from interactions between the filler particles, mediated by the rubber matrix. While various studies have been made on the bulk mechanical properties and of the filler network structure (both imaging and by simulations), there presently does not exist any work directly linking filler particle spacing and mechanical properties. Here we show that using STEM tomography, aided by a machine learning image analysis procedure, to measure silica particle spacings provides a direct link between the inter-particle spacing and the reduction in shear modulus as a function of strain (the Payne effect), measured using dynamic mechanical analysis. Simulations of filler network formation using attractive, repulsive and non-interacting potentials were processed using the same method and compared with the experimental data, with the net result being that an attractive inter-particle potential is the most accurate way of modelling styrene-butadiene rubber-silica composite formation. PMID:25487130

  11. In Depth Analyses of LEDs by a Combination of X-ray Computed Tomography (CT) and Light Microscopy (LM) Correlated with Scanning Electron Microscopy (SEM).

    PubMed

    Meyer, Jörg; Thomas, Christian; Tappe, Frank; Ogbazghi, Tekie

    2016-01-01

    In failure analysis, device characterization and reverse engineering of light emitting diodes (LEDs), and similar electronic components of micro-characterization, plays an important role. Commonly, different techniques like X-ray computed tomography (CT), light microscopy (LM) and scanning electron microscopy (SEM) are used separately. Similarly, the results have to be treated for each technique independently. Here a comprehensive study is shown which demonstrates the potentials leveraged by linking CT, LM and SEM. In depth characterization is performed on a white emitting LED, which can be operated throughout all characterization steps. Major advantages are: planned preparation of defined cross sections, correlation of optical properties to structural and compositional information, as well as reliable identification of different functional regions. This results from the breadth of information available from identical regions of interest (ROIs): polarization contrast, bright and dark-field LM images, as well as optical images of the LED cross section in operation. This is supplemented by SEM imaging techniques and micro-analysis using energy dispersive X-ray spectroscopy. PMID:27341190

  12. Peptide-Conjugation Induced Conformational Changes in Human IgG1 Observed by Optimized Negative-Staining and Individual-Particle Electron Tomography

    PubMed Central

    Tong, Huimin; Zhang, Lei; Kaspar, Allan; Rames, Matthew J.; Huang, Liqing; Woodnutt, Gary; Ren, Gang

    2013-01-01

    Peptides show much promise as potent and selective drug candidates. Fusing peptides to a scaffold monoclonal antibody produces a conjugated antibody which has the advantages of peptide activity yet also has the pharmacokinetics determined by the scaffold antibody. However, the conjugated antibody often has poor binding affinity to antigens that may be related to unknown structural changes. The study of the conformational change is difficult by conventional techniques because structural fluctuation under equilibrium results in multiple structures co-existing. Here, we employed our two recently developed electron microscopy (EM) techniques: optimized negative-staining (OpNS) EM and individual-particle electron tomography (IPET). Two-dimensional (2D) image analyses and three-dimensional (3D) maps have shown that the domains of antibodies present an elongated peptide-conjugated conformational change, suggesting that our EM techniques may be novel tools to monitor the structural conformation changes in heterogeneous and dynamic macromolecules, such as drug delivery vehicles after pharmacological synthesis and development. PMID:23346347

  13. Microaspiration for high-pressure freezing: a new method for ultrastructural preservation of fragile and sparse tissues for TEM and electron tomography

    SciTech Connect

    Auer, Manfred; Triffo, W.J.; Palsdottir, H.; McDonald, K.L.; Inman, J.L.; Bissell, M.J.; Raphael, R.M.; Auer, M.; Lee, J.K.

    2008-02-13

    High-pressure freezing is the preferred method to prepare thick biological specimens for ultrastructural studies. However, the advantages obtained by this method often prove unattainable for samples that are difficult to handle during the freezing and substitution protocols. Delicate and sparse samples are difficult to manipulate and maintain intact throughout the sequence of freezing, infiltration, embedding, and final orientation for sectioning and subsequent TEM imaging. An established approach to surmount these difficulties is the use of cellulose microdialysis tubing to transport the sample. With an inner diameter of 200 micrometers, the tubing protects small and fragile samples within the thickness constraints of high-pressure freezing, and the tube ends can be sealed to avoid loss of sample. Importantly, the transparency of the tubing allows optical study of the specimen at different steps in the process. Here, we describe the use of a micromanipulator and microinjection apparatus to handle and position delicate specimens within the tubing. We report two biologically significant examples that benefit from this approach, 3D cultures of mammary epithelial cells and cochlear outer hair cells. We illustrate the potential for correlative light and electron microscopy as well as electron tomography.

  14. In Depth Analyses of LEDs by a Combination of X-ray Computed Tomography (CT) and Light Microscopy (LM) Correlated with Scanning Electron Microscopy (SEM).

    PubMed

    Meyer, Jörg; Thomas, Christian; Tappe, Frank; Ogbazghi, Tekie

    2016-06-16

    In failure analysis, device characterization and reverse engineering of light emitting diodes (LEDs), and similar electronic components of micro-characterization, plays an important role. Commonly, different techniques like X-ray computed tomography (CT), light microscopy (LM) and scanning electron microscopy (SEM) are used separately. Similarly, the results have to be treated for each technique independently. Here a comprehensive study is shown which demonstrates the potentials leveraged by linking CT, LM and SEM. In depth characterization is performed on a white emitting LED, which can be operated throughout all characterization steps. Major advantages are: planned preparation of defined cross sections, correlation of optical properties to structural and compositional information, as well as reliable identification of different functional regions. This results from the breadth of information available from identical regions of interest (ROIs): polarization contrast, bright and dark-field LM images, as well as optical images of the LED cross section in operation. This is supplemented by SEM imaging techniques and micro-analysis using energy dispersive X-ray spectroscopy.

  15. Extracellular vesicles of calcifying turkey leg tendon characterized by immunocytochemistry and high voltage electron microscopic tomography and 3-D graphic image reconstruction

    NASA Technical Reports Server (NTRS)

    Landis, W. J.; Hodgens, K. J.; McKee, M. D.; Nanci, A.; Song, M. J.; Kiyonaga, S.; Arena, J.; McEwen, B.

    1992-01-01

    To gain insight into the structure and possible function of extracellular vesicles in certain calcifying vertebrate tissues, normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo, have been studied in two separate investigations, one concerning the electron microscopic immunolocalization of the 66 kDa phosphoprotein, osteopontin, and the other detailing the organization and distribution of mineral crystals associated with the vesicles as determined by high voltage microscopic tomography and 3-D graphic image reconstruction. Immunolabeling shows that osteopontin is related to extracellular vesicles of the tendon in the sense that its initial presence appears coincident with the development of mineral associated with the vesicle loci. By high voltage electron microscopy and 3-D imaging techniques, mineral crystals are found to consist of small irregularly shaped particles somewhat randomly oriented throughout individual vesicles sites. Their appearance is different from that found for the mineral observed within calcifying tendon collagen, and their 3-D disposition is not regularly ordered. Possible spatial and temporal relationships of vesicles, osteopontin, mineral, and collagen are being examined further by these approaches.

  16. Electron energy-loss spectroscopic tomography of FexCo(3-x)O4 impregnated Co3O4 mesoporous particles: unraveling the chemical information in three dimensions.

    PubMed

    Yedra, L; Eljarrat, A; Arenal, R; López-Conesa, L; Pellicer, E; López-Ortega, A; Estrader, M; Sort, J; Baró, M D; Estradé, S; Peiró, F

    2016-08-01

    Electron energy-loss spectroscopy-spectrum image (EELS-SI) tomography is a powerful tool to investigate the three dimensional chemical configuration in nanostructures. Here, we demonstrate, for the first time, the possibility to characterize the spatial distribution of Fe and Co cations in a complex FexCo(3-x)O4/Co3O4 ordered mesoporous system. This hybrid material is relevant because of the ferrimagnetic/antiferromagnetic coupling and high surface area. We unambiguously prove that the EELS-SI tomography shows a sufficiently high resolution to simultaneously unravel the pore structure and the chemical signal. PMID:27314942

  17. Computed Tomography

    NASA Astrophysics Data System (ADS)

    Castellano, Isabel; Geleijns, Jacob

    After its clinical introduction in 1973, computed tomography developed from an x-ray modality for axial imaging in neuroradiology into a versatile three dimensional imaging modality for a wide range of applications in for example oncology, vascular radiology, cardiology, traumatology and even in interventional radiology. Computed tomography is applied for diagnosis, follow-up studies and screening of healthy subpopulations with specific risk factors. This chapter provides a general introduction in computed tomography, covering a short history of computed tomography, technology, image quality, dosimetry, room shielding, quality control and quality criteria.

  18. Holography and tomography

    SciTech Connect

    Howells, M.

    1997-02-01

    This session includes a collection of outlines of pertinent information, diagrams, graphs, electron micrographs, and color photographs pertaining to historical aspects and recent advances in the development of X-ray Gabor Holography. Many of the photographs feature or pertain to instrumentation used in holography, tomography, and cryo-holography.

  19. Nanoscale three-dimensional reconstruction of elastic and inelastic mean free path lengths by electron holographic tomography

    SciTech Connect

    Lubk, A.; Wolf, D.; Kern, F.; Röder, F.; Lichte, H.; Prete, P.; Lovergine, N.

    2014-10-27

    Electron holography at medium resolution simultaneously probes projected electrostatic and magnetostatic potentials as well as elastic and inelastic attenuation coefficients with a spatial resolution of a few nanometers. In this work, we derive how the elastic and inelastic attenuation can be disentangled. Using that result, we perform the first three dimensional tomographic reconstruction of potential and (in)elastic attenuation in parallel. The technique can be applied to distinguish between functional potentials and composition changes in nanostructures, as demonstrated using the example of a GaAs—Al{sub 0.33}Ga{sub 0.67}As core-shell nanowire.

  20. Visco-plasticity of polycrystalline olivine at high pressure and 900°C: fresh outcomes from high resolution EBSD and electron tomography

    NASA Astrophysics Data System (ADS)

    Demouchy, S. A.; Mussi, A.; Barou, F.; Tommasi, A.; Cordier, P.

    2013-12-01

    The rheology of olivine-rich rocks at lithospheric temperatures (<1000°C) remains poorly constrained, in contrast to the extensive experimental dataset on creep of olivine single crystals and aggregates at high temperature (T > 1200°C). Consequently, we have performed tri-axial compression experiments (in a Paterson's press) on two fine-grained polycrystalline olivine (San Carlos olivine) specimens at 900°C, under a confining pressure of 300 MPa. Two dense samples were deformed at constant strain rates of 1.0 × 10-5 s-1 and 3.4 × 10-5 s-1. Mechanical curves show continuous hardening, with a decrease of hardening rate with increasing strain. Both samples failed just before 10% of finite strain and yield final differential stresses of 930 and 1076 MPa. Recovered samples were characterized by scanning electron microscopy (SEM), electron backscatter diffraction (EBSD) and transmission electron microscopy (TEM). High resolution EBSD maps (step size 0.15 and 0.2 microns) permit to quantify accurately the microstructure (grain size, shape, aspect ratio, and angle distribution of the grain ellipse relative to the compression axis). Weak crystallographic preferred orientations (CPO) developed in the deformed olivine aggregates, where [010] axes are mostly parallel to the compression axis; [100] and [001] axes are more dispersed, but tend to be oriented at high angle to the compression axis. Misorientations across grain boundaries and sub-grain boundaries were analyzed as well, evidencing common subgrain boundaries parallel to (100) and rotations dominantly around [001], that is an ';ideal' tilt boundary of the [100](010) system. Furthermore, transmission electron microscopy, involving electron tomography of dislocations has identified dislocations with [100] and [001] Burgers vectors gliding on multiple planes, evidence for cross-slip, and dislocation entanglements. These data permit to better constrain the active deformation mechanisms and slip systems involved in the

  1. Atom Probe Tomography 2012

    NASA Astrophysics Data System (ADS)

    Kelly, Thomas F.; Larson, David J.

    2012-08-01

    In the world of tomographic imaging, atom probe tomography (APT) occupies the high-spatial-resolution end of the spectrum. It is highly complementary to electron tomography and is applicable to a wide range of materials. The current state of APT is reviewed. Emphasis is placed on applications and data analysis as they apply to many fields of research and development including metals, semiconductors, ceramics, and organic materials. We also provide a brief review of the history and the instrumentation associated with APT and an assessment of the existing challenges in the field.

  2. Biodegradable radiopaque microspheres for the evaluation of regional pulmonary blood flow distribution using electron-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Workman, Michael J.; Tajik, Jehangir K.; Robinson, Miguel T.; Hoffman, Eric A.

    1994-05-01

    Accurate measurement of regional pulmonary blood flow distribution is of interest both as a research and diagnostic tool. Measurements of regional pulmonary perfusion via x-ray CT offer the possibility of detecting perfusion deficits due to pulmonary embolus while maintaining a high degree of anatomic detail. Use of bolus injection of conventional radiopaque contrast with associated short mean transit times (5 - 7 seconds), requires a high degree of temporal resolution offered clinically only by electron beam x-ray CT (Imatron). The present study was intended to characterize biodegradable radiopaque microspheres as an alternative contrast agent which would allow for measurement of regional pulmonary blood flow with scanning times associated with conventional or spiral thin slice, volumetric x-ray CT protocols. To test this, a dog was scanned at 6 slice levels and 13 time points with image acquisition gated to the cardiac cycle. Lung volumes were maintained at functional residual capacity.

  3. A Study of the Oxidation Behaviour of Pile Grade A (PGA) Nuclear Graphite Using Thermogravimetric Analysis (TGA), Scanning Electron Microscopy (SEM) and X-Ray Tomography (XRT).

    PubMed

    Payne, Liam; Heard, Peter J; Scott, Thomas B

    2015-01-01

    Pile grade A (PGA) graphite was used as a material for moderating and reflecting neutrons in the UK's first generation Magnox nuclear power reactors. As all but one of these reactors are now shut down there is a need to understand the residual state of the material prior to decommissioning of the cores, in particular the location and concentration of key radio-contaminants such as 14C. The oxidation behaviour of unirradiated PGA graphite was studied, in the temperature range 600-1050°C, in air and nitrogen using thermogravimetric analysis, scanning electron microscopy and X-ray tomography to investigate the possibility of using thermal degradation techniques to examine 14C distribution within irradiated material. The thermal decomposition of PGA graphite was observed to follow the three oxidation regimes historically identified by previous workers with limited, uniform oxidation at temperatures below 600°C and substantial, external oxidation at higher temperatures. This work demonstrates that the different oxidation regimes of PGA graphite could be developed into a methodology to characterise the distribution and concentration of 14C in irradiated graphite by thermal treatment.

  4. A Study of the Oxidation Behaviour of Pile Grade A (PGA) Nuclear Graphite Using Thermogravimetric Analysis (TGA), Scanning Electron Microscopy (SEM) and X-Ray Tomography (XRT)

    PubMed Central

    Payne, Liam; Heard, Peter J.; Scott, Thomas B.

    2015-01-01

    Pile grade A (PGA) graphite was used as a material for moderating and reflecting neutrons in the UK’s first generation Magnox nuclear power reactors. As all but one of these reactors are now shut down there is a need to understand the residual state of the material prior to decommissioning of the cores, in particular the location and concentration of key radio-contaminants such as 14C. The oxidation behaviour of unirradiated PGA graphite was studied, in the temperature range 600–1050°C, in air and nitrogen using thermogravimetric analysis, scanning electron microscopy and X-ray tomography to investigate the possibility of using thermal degradation techniques to examine 14C distribution within irradiated material. The thermal decomposition of PGA graphite was observed to follow the three oxidation regimes historically identified by previous workers with limited, uniform oxidation at temperatures below 600°C and substantial, external oxidation at higher temperatures. This work demonstrates that the different oxidation regimes of PGA graphite could be developed into a methodology to characterise the distribution and concentration of 14C in irradiated graphite by thermal treatment. PMID:26575374

  5. A Study of the Oxidation Behaviour of Pile Grade A (PGA) Nuclear Graphite Using Thermogravimetric Analysis (TGA), Scanning Electron Microscopy (SEM) and X-Ray Tomography (XRT).

    PubMed

    Payne, Liam; Heard, Peter J; Scott, Thomas B

    2015-01-01

    Pile grade A (PGA) graphite was used as a material for moderating and reflecting neutrons in the UK's first generation Magnox nuclear power reactors. As all but one of these reactors are now shut down there is a need to understand the residual state of the material prior to decommissioning of the cores, in particular the location and concentration of key radio-contaminants such as 14C. The oxidation behaviour of unirradiated PGA graphite was studied, in the temperature range 600-1050°C, in air and nitrogen using thermogravimetric analysis, scanning electron microscopy and X-ray tomography to investigate the possibility of using thermal degradation techniques to examine 14C distribution within irradiated material. The thermal decomposition of PGA graphite was observed to follow the three oxidation regimes historically identified by previous workers with limited, uniform oxidation at temperatures below 600°C and substantial, external oxidation at higher temperatures. This work demonstrates that the different oxidation regimes of PGA graphite could be developed into a methodology to characterise the distribution and concentration of 14C in irradiated graphite by thermal treatment. PMID:26575374

  6. Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study.

    PubMed

    Afonina, Zhanna A; Myasnikov, Alexander G; Shirokov, Vladimir A; Klaholz, Bruno P; Spirin, Alexander S

    2014-08-01

    The polyribosomes newly formed on recombinant GFP-encoding mRNAs in a wheat germ cell-free translation system were analyzed using cryo-electron tomography, with sub-tomogram averaging of polysomal ribosomes and reconstruction of 3D structures of individual polyribosomes. The achieved level of resolution in the reconstructed polyribosomes allowed deducing the mRNA path by connecting adjacent exit and entry sites at the ribosomes inside each polyribosome. In this way, the circularity of a significant fraction (about 50%) of translating polyribosomes was proved in the case of the capped poly(A)-tailed mRNA, in agreement with the existing paradigm of the circularization via interaction of cap-bound initiation factor eIF4F with poly(A)-binding protein. However, translation of the capped mRNA construct without poly(A) tail, but with unspecific 3'-UTR derived from non-coding plasmid sequence, also led to the formation of circular polyribosomes in similar proportion (40%). Moreover, the polyribosomes formed on the uncapped non-polyadenylated mRNA with non-synergistic 5'- and 3'-UTRs proved to be circular as well, and appeared in the same proportion as in the previous cases. Thus, the formation of circular polyribosomes was found to be virtually independent of the presence of cap structure and poly(A) tail in mRNA, in contrast to the longstanding paradigm in the field.

  7. Analysis of a New High-Toughness Ultra-high-Strength Martensitic Steel by Transmission Electron Microscopy and Atom Probe Tomography

    NASA Astrophysics Data System (ADS)

    Hartshorne, Matthew I.; McCormick, Caroline; Schmidt, Michael; Novotny, Paul; Isheim, Dieter; Seidman, David N.; Taheri, Mitra L.

    2016-04-01

    The microstructure of a new martensitic high-strength steel (Fe-0.40C-3.81Ni-1.31Cr-1.50Si-0.75Mn-0.52Mo-0.51Cu-0.30V) with high fracture toughness is characterized by transmission electron microscopy and atom probe tomography (APT). MC, M6C, and M23C6 precipitates form inside the martensitic lath matrix. The fracture toughness is insensitive to the dissolution of M23C6 precipitates at austenitizing temperatures above 1164 K (891 °C). APT reveals that solute segregation at the prior austenite grain boundaries (PAGB) is not uniform, with C, Mo, Si, Ni, and/or P enrichment varying at different areas of the PAGB. Si depletion is detected in the same area as the highest C enrichment. Carbon also segregates at lath boundaries. Segregation of C indicates the presence of retained austenite films at both PAGB and lath boundaries. Regions enriched in C up to 10 pct were found within the laths; however, no regions were enriched to the level expected of cementite or ɛ-carbide. The observed C distribution and high fracture toughness indicates that the tempering behavior is significantly different than that observed in 300M steel. The effect of Si, Ni, and Cu on the formation and stabilization of the regions of C enrichment and retained austenite require further study, as it may be key to the increased toughness.

  8. The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon

    PubMed Central

    1994-01-01

    The three dimensional (3D) structure of chromatin fibers in sections of nuclei has been determined using electron tomography. Low temperature embedding and nucleic acid-specific staining allowed individual nucleosomes to be clearly seen, and the tomographic data collection parameters provided a reconstruction resolution of 2.5 nm. Chromatin fibers have complex 3D trajectories, with smoothly bending regions interspersed with abrupt changes in direction, and U turns. Nucleosomes are located predominantly at the fiber periphery, and linker DNA tends to project toward the fiber interior. Within the fibers, a unifying structural motif is a two nucleosome-wide ribbon that is variably bent and twisted, and in which there is little face-to-face contact between nucleosomes. It is suggested that this asymmetric 3D zig-zag of nucleosomes and linker DNA represents a basic principle of chromatin folding that is determined by the properties of the nucleosome-linker unit. This concept of chromatin fiber architecture is contrasted with helical models in which specific nucleosome-nucleosome contacts play a major role in generating a symmetrical higher order structure. The transcriptional control implications of a more open and irregular chromatin structure are discussed. PMID:8138564

  9. Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic-Resolution Electron Microscopy and Field Evaporation Simulation.

    PubMed

    Devaraj, Arun; Colby, Robert; Vurpillot, François; Thevuthasan, Suntharampillai

    2014-04-17

    Oxide-supported metal nanoparticles are widely used in heterogeneous catalysis. The increasingly detailed design of such catalysts necessitates three-dimensional characterization with high spatial resolution and elemental selectivity. Laser-assisted atom probe tomography (APT) is uniquely suited to the task but faces challenges with the evaporation of metal/insulator systems. Correlation of APT with aberration-corrected scanning transmission electron microscopy (STEM), for Au nanoparticles embedded in MgO, reveals preferential evaporation of the MgO and an inaccurate assessment of nanoparticle composition. Finite element field evaporation modeling is used to illustrate the evolution of the evaporation front. Nanoparticle composition is most accurately predicted when the MgO is treated as having a locally variable evaporation field, indicating the importance of considering laser-oxide interactions and the evaporation of various molecular oxide ions. These results demonstrate the viability of APT for analysis of oxide-supported metal nanoparticles, highlighting the need for developing a theoretical framework for the evaporation of heterogeneous materials.

  10. Electron

    NASA Astrophysics Data System (ADS)

    Springford, Michael

    1997-03-01

    1. J. J. Thomson and the discovery of the electron A. B. P. Pippard; 2. The isolated electron W. N. Cottingham; 3. The relativistic electron D. I. Olive; 4. The electron glue B. L. Gyorffy; 5. The electron fluid P. Coleman; 6. The magnetic electron G. G. Lonzarich; 7. The paired electron A. J. Leggett; 8. The heavy electron M. Springford; 9. The coherent electron Y. Imry and M. Peskin; 10. The composite electron R. Nicholas; 11. The electron in the cosmos M. S. Longair.

  11. Electron

    NASA Astrophysics Data System (ADS)

    Springford, Michael

    2008-12-01

    1. J. J. Thomson and the discovery of the electron A. B. P. Pippard; 2. The isolated electron W. N. Cottingham; 3. The relativistic electron D. I. Olive; 4. The electron glue B. L. Gyorffy; 5. The electron fluid P. Coleman; 6. The magnetic electron G. G. Lonzarich; 7. The paired electron A. J. Leggett; 8. The heavy electron M. Springford; 9. The coherent electron Y. Imry and M. Peskin; 10. The composite electron R. Nicholas; 11. The electron in the cosmos M. S. Longair.

  12. Cryo-electron tomography of plunge-frozen whole bacteria and vitreous sections to analyze the recently described bacterial cytoplasmic structure, the Stack.

    PubMed

    Delgado, Lidia; Martínez, Gema; López-Iglesias, Carmen; Mercadé, Elena

    2015-03-01

    Cryo-electron tomography (CET) of plunge-frozen whole bacteria and vitreous sections (CETOVIS) were used to revise and expand the structural knowledge of the "Stack", a recently described cytoplasmic structure in the Antarctic bacterium Pseudomonas deceptionensis M1(T). The advantages of both techniques can be complementarily combined to obtain more reliable insights into cells and their components with three-dimensional imaging at different resolutions. Cryo-electron microscopy (Cryo-EM) and CET of frozen-hydrated P. deceptionensis M1(T) cells confirmed that Stacks are found at different locations within the cell cytoplasm, in variable number, separately or grouped together, very close to the plasma membrane (PM) and oriented at different angles (from 35° to 90°) to the PM, thus establishing that they were not artifacts of the previous sample preparation methods. CET of plunge-frozen whole bacteria and vitreous sections verified that each Stack consisted of a pile of oval disc-like subunits, each disc being surrounded by a lipid bilayer membrane and separated from each other by a constant distance with a mean value of 5.2±1.3nm. FM4-64 staining and confocal microscopy corroborated the lipid nature of the membrane of the Stacked discs. Stacks did not appear to be invaginations of the PM because no continuity between both membranes was visible when whole bacteria were analyzed. We are still far from deciphering the function of these new structures, but a first experimental attempt links the Stacks with a given phase of the cell replication process.

  13. In vivo virus structures: Simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography

    PubMed Central

    Wang, Kang; Fu, Chi-yu; Khayat, Reza; Johnson, John E.

    2011-01-01

    Sulfolobus Turreted Icosahedral Virus (STIV) experiences an extra-cellular environment of near boiling acid (80 C, pH 3) and particles purified under these conditions were previously analyzed by cryo electron microscopy and image reconstruction. Here we describe cryo-tomograms of Solfolobus cells infected with STIV and the maximum likelihood algorithm employed to compute reconstructions of virions within the cell. Virions in four different tomograms were independently reconstructed with an average of 91 particles per tomogram and their structures compared with each other and with the higher resolution single-particle reconstruction from purified virions. The algorithm described here automatically classified and oriented two different particle types within each cell and generated reconstructions of full and empty particles. Because the particles are randomly oriented within the cell, the reconstructions do not suffer from the missing wedge of data absent from the reciprocal-space tomogram. The fact that the particles have icosahedral symmetry is used to dramatically improve the signal to noise ratio in the reconstructions. The reconstructions have approximately 60Å resolution (based on Fourier Shell Correlation analysis among reconstructions computed by the algorithm described here from four different tomograms). PMID:21396453

  14. Respirator triggering of electron beam computed tomography (EBCT): evaluation of dynamic changes during mechanical expiration in the traumatized patient

    NASA Astrophysics Data System (ADS)

    Recheis, Wolfgang A.; Kleinsasser, Axel; Hatschenberger, Robert; Knapp, Rudolf; zur Nedden, Dieter; Hoermann, Christoph

    1999-05-01

    The purpose of this project is to evaluate the dynamic changes during expiration at different levels of positive end- expiratory pressure (PEEP) in the ventilated patient. We wanted to discriminate between normal lung function and acute respiratory distress syndrome (ARDS). After approval by the local Ethic Committee we studied two ventilated patients: (1) with normal lung function; (2) ARDS). We used the 50 ms scan mode of the EBCT. The beam was positioned 1 cm above the diaphragm. The table position remained unchanged. An electronic trigger was developed, that utilizes the respirators synchronizing signal to start the EBCT at the onset of expiration. During controlled mechanical expiration at two levels of PEEP (0 and 15 cm H2O), pulmonary aeration was rated as: well-aerated (-900HU/-500HU), poorly- aerated (-500HU/-100HU) and non-aerated (-100HU/+100HU). Pathological and normal lung function showed different dynamic changes (FIG.4-12). The different PEEP levels resulted in a significant change of pulmonary aeration in the same patient. Although we studied only a very limited number of patients, respirator triggered EBCT may be accurate in discriminating pathological changes due to the abnormal lung function in the mechanically ventilated patient.

  15. Determination of the Three-Dimensional Morphology of ALH84001 and Biogenic MV-1 Magnetite: Comparison of Results from Electron Tomography and Classical Transmission Electron Microscopy

    NASA Technical Reports Server (NTRS)

    Thomas-Keprta, Kathie L.; Clemett, Simon J.; Schwartz, Cindy; Morphew, Mary; McIntosh, J. Richard; Bazylinski, Dennis A.; Kirschvink, Joseph L.; Wentworth, Susan J.; McKay, David S.; Vali, Hojatollah

    2004-01-01

    Dated at approximately 3.9 billion years of age, carbonate disks, found within fractures of the host rock of Martian meteorite ALH84001, have been interpreted as secondary minerals that formed at low temperature in an aqueous medium. Heterogeneously distributed within these disks are magnetite nanocrystals that are of Martian origin. Approximately one quarter of these magnetites have morphological and chemical similarities to magnetite particles produced by magnetotactic bacteria strain MV-1, which are ubiquitous in aquatic habitats on Earth. Moreover, these types of magnetite particles are not known or expected to be produced by abiotic means either through geological processes or synthetically in the laboratory. The remaining three quarters of the ALH84001 magnetites are likely products of multiple processes including, but not limited to, precipitation from a hydrothermal fluid, thermal decomposition of the carbonate matrix in which they are embedded, and extracellular formation by dissimilatory Fe-reducing bacteria. We have proposed that the origins of magnetites in ALH84001 can be best explained as the products of multiple processes, one of which is biological. Recently the three-dimensional (3-D) external morphology of the purported biogenic fraction of the ALH84001 magnetites has been the subject of considerable debate. We report here the 3-D geometry of biogenic magnetite crystals extracted from MV-1 and of those extracted from ALH84001 carbonate disks using a combination of high resolution classical and tomographic transmission electron microscopy (TEM). We focus on answering the following questions: (1) which technique provides adequate information to deduce the 3-D external crystal morphology?; and, (2) what is the precise 3-D geometry of the ALH84001 and MV-1 magnetites?

  16. Analysis of Schwalbe’s Line (Limbal Smooth Zone) by Scanning Electron Microscopy and Optical Coherence Tomography in Human Eye Bank Eyes

    PubMed Central

    Breazzano, Mark P; Fikhman, Michael; Abraham, Jerrold L; Barker-Griffith, Ann E

    2013-01-01

    Purpose Implantation of intraocular devices may become critical as they decrease in size in the future. Therefore, it is desirable to evaluate the relationship between radial location and Schwalbe’s line (smooth zone) by examining its width with scanning electron microscopy (SEM) and to correlate this with observations by optical coherence tomography (OCT). Methods Full corneoscleral rings were obtained from twenty-six formalin-fixed human phakic donor eyes. SEM of each eye yielded a complete montage of the smooth zone, from which the area was measured, and width was determined in each quadrant. In three different eyes, time domain anterior segment OCT (Visante, Carl Zeiss Meditec Inc., Dublin, CA, USA) and spectral domain OCT (Cirrus 4.0, Carl Zeiss Meditec Inc., Dublin, CA, USA) were used to further characterize Schwalbe’s line. Results The overall smooth zone width was 79±22 µm, (n=15) ranging from 43 to 115 µm. The superior quadrant (103±8 µm, n=19), demonstrated significantly wider smooth zone than both the nasal (71±5 µm, n=19, P<0.001), and inferior (64±5 µm, n=18, P<0.0001) quadrants but not the temporal quadrant (81±7 µm, n=17, P>0.05). SEM findings of the smooth zone were correlated with visualization of Schwalbe’s line by Cirrus and Visante OCT imaging. Conclusion The smooth zone appears widest superiorly and thinnest inferonasally, suggesting that as glaucoma surgical devices become smaller, their placement could be argeted clinically by using OCT with preference to the superior quadrant, to minimize damage to the corneal endothelium. PMID:23825707

  17. Effect of acid etching on marginal adaptation of mineral trioxide aggregate to apical dentin: microcomputed tomography and scanning electron microscopy analysis.

    PubMed

    Al-Fouzan, Khalid; Al-Garawi, Ziad; Al-Hezaimi, Khalid; Javed, Fawad; Al-Shalan, Thakib; Rotstein, Ilan

    2012-12-01

    The present investigation assessed the effect of acid etching on marginal adaptation of white- and gray-colored mineral trioxide aggregate (MTA) to apical dentin using microcomputed tomography (micro-CT) and scanning electron microscopy (SEM). Sixty-four extracted single-rooted human maxillary teeth were used. Following root-end resection and apical preparation, the teeth were equally divided into four groups according to the following root end filling materials: (i) white-colored MTA (WMTA), (ii) etched WMTA (EWMTA), (iii) gray-colored MTA (GMTA) and (iv) etched GMTA (EGMTA). After 48 h, the interface between root-end filling materials and the dentinal walls was assessed using micro-CT and SEM. Data were statistically analyzed using the Kruskal-Wallis and Dunn tests. Micro-CT analysis revealed gap volumes between the apical cavity dentin walls and EGMTA, GMTA, EWMTA and WMTA of (0.007 1±0.004) mm(3), (0.053±0.002) mm(3), (0.003 6±0.001) mm(3) and (0.005 9±0.002) mm(3) respectively. SEM analysis revealed gap sizes for EGMTA, WMTA, EWMTA and GMTA to be (492.3±13.8) µm, (594.5±17.12) µm, (543.1±15.33) µm and (910.7±26.2) µm respectively. A significant difference in gap size between root end preparations filled with GMTA and EGMTA was found (P<0.05). No significance difference in gap size between WMTA and EWMTA were found in either SEM or micro-CT analysis. In conclusion, pre-etching of apical dentin can provide a better seal for GMTA but not for WMTA. PMID:23306857

  18. The progress of coronary heart disease in Type 2 diabetes as measured by coronary calcium score from electron beam computed tomography (EBCT): the PREDICT study.

    PubMed

    Elkeles, Robert S; Godsland, Ian F; Rubens, Michael B; Feher, Michael D; Nugara, Fiona; Flather, Marcus D

    2008-04-01

    Coronary calcification score (CACS) measured by electron beam tomography is well established in the evaluation of cardiovascular risk in general populations. The PREDICT study aims to evaluate prediction of cardiovascular events by CACS in Type 2 diabetic subjects without previous clinical cardiovascular disease. In the present PREDICT sub-study, the rate of progression of CACS and factors influencing this rate were assessed. CACS was measured at baseline and after a mean interval of 4.0 (range of 2.1-5.0) years in the 202 PREDICT participants who agreed to have a second scan. Participants also had a range of conventional and novel biochemical risk factors measured at baseline. Progression of calcification was apparent in 170 (84%), while in 32 (16%) there was regression or no progression. Those showing progression had a significantly more adverse risk factor profile. Rate of change in CACS was strongly related to baseline CACS (p<0.0001). Rate of change also correlated with, waist:hip ratio (p=0.004), male gender (p=0.009), age (p=0.04), use of antihypertensive drugs (p=0.03) and statins (p=0.05) and, independently of baseline CACS, systolic blood pressure (p=0.0006), waist circumference (p=0.001) and urine albumin:creatine ratio (p=0.04). Most subjects with Type 2 diabetes showed progression of CACS. The absence of a relationship between progression and lipid risk factors and the positive relationship with statin and antihypertensive drug use may reflect earlier risk factor exposure. Independent relationships between progression and established calcification, blood pressure, central adiposity and urine albumin:creatinine ratio suggest areas for risk factor modification that could be especially relevant in Type 2 diabetes. PMID:17920067

  19. The Detectability and Localization Accuracy of Implanted Fiducial Markers Determined on In-Room Computerized Tomography (CT) and Electronic Portal Images (EPI)

    SciTech Connect

    Owen, Rebecca Kron, Tomas; Foroudi, Farshad; Cox, Jennifer; Zhu Li; Cramb, Jim; Sparks, Laura; Duchesne, Gillian

    2008-10-01

    Many different methods of image guidance are available for radiotherapy treatment (IGRT). The aims of the study were (1) to determine the optimal diameter of gold markers for IGRT to the prostate; (2) to compare, using the Siemens Primatom, the relative merits of in-room computerized tomography (CT) and electronic portal image (EPI) for locating the marker seeds. Gold markers of differing widths were embedded in 2 phantoms (perspex slabs and anthropomorphic). Images were acquired with an amorphous silicon flat panel detector (Siemens Optivue 500) and with the in-room CT scanner (Siemens Somatom Balance). The EPIs were reviewed independently by 6 operators to determine which diameter marker could be best visualized. The optimal marker technique was determined by comparing the investigators' observed marker co-ordinates with the known locations within the phantom. The visibility of all markers on anterior-posterior EPIs was 100%. On the lateral EPI, of a possible 180 visualizations of 1.2-, 1.0-, and 0.8-mm diameter markers, 176 (97.8%), 151 (83.9%), and 132 (73.3%), respectively, were successful. On EPI, the average deviation of fiducial markers from the known position was less than 0.5 mm in any direction. On CT, the largest deviation (2.17 mm) of markers from the known coordinate position was in the superior-inferior direction, reflecting the 3.0-mm slice thickness used. EPI accurately located internal markers in all dimensions. The availability of 'gold standard' CT imagery at the treatment unit does not improve how accurately the position of markers in a phantom can be defined compared with EPI. However, CT imagery does provide important soft tissue information, the benefits of which are being investigated further.

  20. Intact Flagellar Motor of Borrelia burgdorferi Revealed by Cryo-Electron Tomography: Evidence for Stator Ring Curvature and Rotor/C-Ring Assembly Flexion▿ †

    PubMed Central

    Liu, Jun; Lin, Tao; Botkin, Douglas J.; McCrum, Erin; Winkler, Hanspeter; Norris, Steven J.

    2009-01-01

    The bacterial flagellar motor is a remarkable nanomachine that provides motility through flagellar rotation. Prior structural studies have revealed the stunning complexity of the purified rotor and C-ring assemblies from flagellar motors. In this study, we used high-throughput cryo-electron tomography and image analysis of intact Borrelia burgdorferi to produce a three-dimensional (3-D) model of the in situ flagellar motor without imposing rotational symmetry. Structural details of B. burgdorferi, including a layer of outer surface proteins, were clearly visible in the resulting 3-D reconstructions. By averaging the 3-D images of ∼1,280 flagellar motors, a ∼3.5-nm-resolution model of the stator and rotor structures was obtained. flgI transposon mutants lacked a torus-shaped structure attached to the flagellar rod, establishing the structural location of the spirochetal P ring. Treatment of intact organisms with the nonionic detergent NP-40 resulted in dissolution of the outermost portion of the motor structure and the C ring, providing insight into the in situ arrangement of the stator and rotor structures. Structural elements associated with the stator followed the curvature of the cytoplasmic membrane. The rotor and the C ring also exhibited angular flexion, resulting in a slight narrowing of both structures in the direction perpendicular to the cell axis. These results indicate an inherent flexibility in the rotor-stator interaction. The FliG switching and energizing component likely provides much of the flexibility needed to maintain the interaction between the curved stator and the relatively symmetrical rotor/C-ring assembly during flagellar rotation. PMID:19429612

  1. Pseudolocal tomography

    DOEpatents

    Katsevich, A.J.; Ramm, A.G.

    1996-07-23

    Local tomographic data is used to determine the location and value of a discontinuity between a first internal density of an object and a second density of a region within the object. A beam of radiation is directed in a predetermined pattern through the region of the object containing the discontinuity. Relative attenuation data of the beam is determined within the predetermined pattern having a first data component that includes attenuation data through the region. The relative attenuation data is input to a pseudo-local tomography function, where the difference between the internal density and the pseudo-local tomography function is computed across the discontinuity. The pseudo-local tomography function outputs the location of the discontinuity and the difference in density between the first density and the second density. 7 figs.

  2. Pseudolocal tomography

    DOEpatents

    Katsevich, Alexander J.; Ramm, Alexander G.

    1996-01-01

    Local tomographic data is used to determine the location and value of a discontinuity between a first internal density of an object and a second density of a region within the object. A beam of radiation is directed in a predetermined pattern through the region of the object containing the discontinuity. Relative attenuation data of the beam is determined within the predetermined pattern having a first data component that includes attenuation data through the region. The relative attenuation data is input to a pseudo-local tomography function, where the difference between the internal density and the pseudo-local tomography function is computed across the discontinuity. The pseudo-local tomography function outputs the location of the discontinuity and the difference in density between the first density and the second density.

  3. Electron tomography of IFT particles.

    PubMed

    Pigino, Gaia; Cantele, Francesca; Vannuccini, Elisa; Lanzavecchia, Salvatore; Paccagnini, Eugenio; Lupetti, Pietro

    2013-01-01

    Cilia and flagella play very important roles in eukaryotic cells, ranging from cell motility to chemo- and mechanosensation with active involvement in embryonic development and control of cell division. Cilia and flagella are highly dynamic organelles undergoing constant turnover at their tip, where multiprotein precursors synthesized in the cell cytoplasm are assembled, turnover products are released and carried back for recycling. Such bidirectional trafficking is maintained by an ATP-dependent active transport that is carried out by intraflagellar transport (IFT) particles. Despite our knowledge of the cell biology, the genomic, and the biochemistry of IFT, high-resolution 3D models for IFT are still missing. To date, the only information on the 3D structure of IFT come from our analysis of full-length flagella from the biflagellate green alga Chlamydomonas reinhardtii: the model organism where IFT was discovered and first characterized. In this chapter, we describe and discuss the strategy we implemented to produce the first 3D models of in situ IFT trains in flat-embedded flagella. We provide detailed information about the acquisition of tomographic images, the simultaneous alignment of the double-tilt tomographic series, and the analysis of the tomograms by subtomogram averaging for the generation of detailed 3D models of IFT particles. PMID:23498748

  4. Electron tomography of IFT particles.

    PubMed

    Pigino, Gaia; Cantele, Francesca; Vannuccini, Elisa; Lanzavecchia, Salvatore; Paccagnini, Eugenio; Lupetti, Pietro

    2013-01-01

    Cilia and flagella play very important roles in eukaryotic cells, ranging from cell motility to chemo- and mechanosensation with active involvement in embryonic development and control of cell division. Cilia and flagella are highly dynamic organelles undergoing constant turnover at their tip, where multiprotein precursors synthesized in the cell cytoplasm are assembled, turnover products are released and carried back for recycling. Such bidirectional trafficking is maintained by an ATP-dependent active transport that is carried out by intraflagellar transport (IFT) particles. Despite our knowledge of the cell biology, the genomic, and the biochemistry of IFT, high-resolution 3D models for IFT are still missing. To date, the only information on the 3D structure of IFT come from our analysis of full-length flagella from the biflagellate green alga Chlamydomonas reinhardtii: the model organism where IFT was discovered and first characterized. In this chapter, we describe and discuss the strategy we implemented to produce the first 3D models of in situ IFT trains in flat-embedded flagella. We provide detailed information about the acquisition of tomographic images, the simultaneous alignment of the double-tilt tomographic series, and the analysis of the tomograms by subtomogram averaging for the generation of detailed 3D models of IFT particles.

  5. Seismic Tomography.

    ERIC Educational Resources Information Center

    Anderson, Don L.; Dziewonski, Adam M.

    1984-01-01

    Describes how seismic tomography is used to analyze the waves produced by earthquakes. The information obtained from the procedure can then be used to map the earth's mantle in three dimensions. The resulting maps are then studied to determine such information as the convective flow that propels the crustal plates. (JN)

  6. NOTE: Cone beam computerized tomography: the effect of calibration of the Hounsfield unit number to electron density on dose calculation accuracy for adaptive radiation therapy

    NASA Astrophysics Data System (ADS)

    Hatton, Joan; McCurdy, Boyd; Greer, Peter B.

    2009-08-01

    The availability of cone beam computerized tomography (CBCT) images at the time of treatment has opened possibilities for dose calculations representing the delivered dose for adaptive radiation therapy. A significant component in the accuracy of dose calculation is the calibration of the Hounsfield unit (HU) number to electron density (ED). The aim of this work is to assess the impact of HU to ED calibration phantom insert composition and phantom volume on dose calculation accuracy for CBCT. CBCT HU to ED calibration curves for different commercial phantoms were measured and compared. The effect of the scattering volume of the phantom on the HU to ED calibration was examined as a function of phantom length and radial diameter. The resulting calibration curves were used at the treatment planning system to calculate doses for geometrically simple phantoms and a pelvic anatomical phantom to compare against measured doses. Three-dimensional dose distributions for the pelvis phantom were calculated using the HU to ED curves and compared using Chi comparisons. The HU to ED calibration curves for the commercial phantoms diverge at densities greater than that of water, depending on the elemental composition of the phantom insert. The effect of adding scatter material longitudinally, increasing the phantom length from 5 cm to 26 cm, was found to be up to 260 HU numbers for the high-density insert. The change in the HU value, by increasing the diameter of the phantom from 18 to 40 cm, was found to be up to 1200 HU for the high-density insert. The effect of phantom diameter on the HU to ED curve can lead to dose differences for 6 MV and 18 MV x-rays under bone inhomogeneities of up to 20% in extreme cases. These results show significant dosimetric differences when using a calibration phantom with materials which are not tissue equivalent. More importantly, the amount of scattering material used with the HU to ED calibration phantom has a significant effect on the dosimetric

  7. Nondestructive computed tomography for pit inspections

    SciTech Connect

    Martz, H.; Logan, C.; Haskins, J.; Johansson, E.; Perkins, D.; Hernandez, J.M.; Schneberk, D.; Dolan, K.

    1997-02-07

    Objective is to develop new approaches to electronically capture digital radiography and computed tomography images at high x-ray energies to satisfy spatial and contrast requirements for inspection of high-density weapons components.

  8. The cell surface glycoprotein layer of the extreme halophile Halobacterium salinarum and its relation to Haloferax volcanii: cryo-electron tomography of freeze-substituted cells and projection studies of negatively stained envelopes.

    PubMed

    Trachtenberg, S; Pinnick, B; Kessel, M

    2000-05-01

    We have studied the surface layer (S-layer) of Halobacterium salinarum (formerly Halobacterium halobium), an extreme halophile requiring high concentrations of sodium, by electron microscopy of (a) isolated, negatively stained, flattened envelopes and (b) cryo-fixation of intact cells in their high-salt growth medium followed by freeze substitution and tomography of thin sections. From the negatively stained isolated envelopes we have calculated a two-dimensional, projection map that is strikingly similar to that of Haloferax volcanii, an extreme halophile requiring high concentrations of magnesium; both projection maps show the hexagonal arrangement of the morphological units with an identical center-to-center spacing of 150 A; each of the morphological units of the two species has six subunits with a similar density distribution and apparent domain organization. In contrast to the two-dimensional map, the tomographic reconstruction of Halob. salinarum does not agree in a straightforward way with the three-dimensional, electron crystallographic map of negatively stained Halof. volcanii envelopes, although the main features of the lattice and the morphological units are evident. The tomographic reconstruction of sections from epoxy-embedded material suffers from directional compression due to sectioning stress and continuous dimensional changes and mass loss due to electron irradiation. This communication consists, therefore, of three parts: (a) a comparison of the projection maps of negatively stained envelopes of Halof. volcanii and Halob. salinarum; (b) a comparison of the three-dimensional maps obtained by electron crystallography (Halof. volcanii) and low-dose cryo-tomography (Halob. salinarum); and (c) a methodological study of mass loss and dimensional changes of plastic-embedded material under low-dose conditions at room and liquid nitrogen temperatures.

  9. Optical Coherence Tomography

    MedlinePlus

    ... Cardiac Magnetic Resonance Imaging (MRI and MRA) Computed Tomography (CT) Scan Diagnostic Tests and Procedures Echocardiography Electrocardiogram ... Ultrasound Nuclear Stress Test Nuclear Ventriculography Positron Emission Tomography (PET) Stress ... Optical Coherence Tomography | ...

  10. Three-dimensional architecture of murine rod outer segments determined by cryoelectron tomography

    PubMed Central

    Nickell, Stephan; Park, Paul S.-H.; Baumeister, Wolfgang; Palczewski, Krzysztof

    2007-01-01

    The rod outer segment (ROS) of photoreceptor cells houses all components necessary for phototransduction, a set of biochemical reactions that amplify and propagate a light signal. Theoretical approaches to quantify this process require precise information about the physical boundaries of the ROS. Dimensions of internal structures within the ROS of mammalian species have yet to be determined with the precision required for quantitative considerations. Cryoelectron tomography was utilized to obtain reliable three-dimensional morphological information about this important structure from murine retina. Vitrification of samples permitted imaging of the ROS in a minimally perturbed manner and the preservation of substructures. Tomograms revealed the characteristic highly organized arrangement of disc membranes stacked on top of one another with a surrounding plasma membrane. Distances among the various membrane components of the ROS were measured to define the space available for phototransduction to occur. Reconstruction of segments of the ROS from single-axis tilt series images provided a glimpse into the three-dimensional architecture of this highly differentiated neuron. The reconstructions revealed spacers that likely maintain the proper distance between adjacent discs and between discs and the plasma membrane. Spacers were found distributed throughout the discs, including regions that are distant from the rim region of discs. PMID:17535966

  11. Three-dimensional architecture of murine rod outer segments determined by cryoelectron tomography.

    PubMed

    Nickell, Stephan; Park, Paul S-H; Baumeister, Wolfgang; Palczewski, Krzysztof

    2007-06-01

    The rod outer segment (ROS) of photoreceptor cells houses all components necessary for phototransduction, a set of biochemical reactions that amplify and propagate a light signal. Theoretical approaches to quantify this process require precise information about the physical boundaries of the ROS. Dimensions of internal structures within the ROS of mammalian species have yet to be determined with the precision required for quantitative considerations. Cryoelectron tomography was utilized to obtain reliable three-dimensional morphological information about this important structure from murine retina. Vitrification of samples permitted imaging of the ROS in a minimally perturbed manner and the preservation of substructures. Tomograms revealed the characteristic highly organized arrangement of disc membranes stacked on top of one another with a surrounding plasma membrane. Distances among the various membrane components of the ROS were measured to define the space available for phototransduction to occur. Reconstruction of segments of the ROS from single-axis tilt series images provided a glimpse into the three-dimensional architecture of this highly differentiated neuron. The reconstructions revealed spacers that likely maintain the proper distance between adjacent discs and between discs and the plasma membrane. Spacers were found distributed throughout the discs, including regions that are distant from the rim region of discs.

  12. Correction of absorption-edge artifacts in polychromatic X-ray tomography in a scanning electron microscope for 3D microelectronics

    SciTech Connect

    Laloum, D.; Printemps, T.; Bleuet, P.; Lorut, F.

    2015-01-15

    X-ray tomography is widely used in materials science. However, X-ray scanners are often based on polychromatic radiation that creates artifacts such as dark streaks. We show this artifact is not always due to beam hardening. It may appear when scanning samples with high-Z elements inside a low-Z matrix because of the high-Z element absorption edge: X-rays whose energy is above this edge are strongly absorbed, violating the exponential decay assumption for reconstruction algorithms and generating dark streaks. A method is proposed to limit the absorption edge effect and is applied on a microelectronic case to suppress dark streaks between interconnections.

  13. Understanding the micro structure of Berea Sandstone by the simultaneous use of micro-computed tomography (micro-CT) and focused ion beam-scanning electron microscopy (FIB-SEM).

    PubMed

    Bera, Bijoyendra; Mitra, Sushanta K; Vick, Douglas

    2011-07-01

    Berea sandstone is the building block for reservoirs containing precious hydrocarbon fuel. In this study, we comprehensively reveal the microstructure of Berea sandstone, which is often treated as a porous material with interconnected micro-pores of 2-5 μm. This has been possible due to the combined application of micro-computed tomography (CT) and focused ion beam (FIB)-scanning electron microscopy (SEM) on a Berea sample. While the use of micro-CT images are common for geological materials, the clubbing and comparison of tomography on Berea with state-of-the-art microstructure imaging techniques like FIB-SEM reveals some unforeseen features of Berea microstructure. In particular, for the first time FIB-SEM has been used to understand the micro-structure of reservoir rock material like Berea sandstone. By using these characterization tools, we are able to show that the micro-pores (less than 30 μm) are absent below the solid material matrix, and that it has small interconnected pores (30-40 μm) and large crater-like voids (100-250 μm) throughout the bulk material. Three-dimensional pore space reconstructions have been prepared from the CT images. Accordingly, characterization of Berea sandstone specimen is performed by calculation of pore-structure volumes and determination of porosity values.

  14. Correlation of microphotoluminescence spectroscopy, scanning transmission electron microscopy, and atom probe tomography on a single nano-object containing an InGaN/GaN multiquantum well system.

    PubMed

    Rigutti, Lorenzo; Blum, Ivan; Shinde, Deodatta; Hernández-Maldonado, David; Lefebvre, Williams; Houard, Jonathan; Vurpillot, François; Vella, Angela; Tchernycheva, Maria; Durand, Christophe; Eymery, Joël; Deconihout, Bernard

    2014-01-01

    A single nanoscale object containing a set of InGaN/GaN nonpolar multiple-quantum wells has been analyzed by microphotoluminescence spectroscopy (μPL), high-resolution scanning transmission electron microscopy (HR-STEM) and atom probe tomography (APT). The correlated measurements constitute a rich and coherent set of data supporting the interpretation that the observed μPL narrow emission lines, polarized perpendicularly to the crystal c-axis and with energies in the interval 2.9-3.3 eV, are related to exciton states localized in potential minima induced by the irregular 3D In distribution within the quantum well (QW) planes. This novel method opens up interesting perspectives, as it will be possible to apply it on a wide class of quantum confining emitters and nano-objects.

  15. Photoacoustic Tomography

    NASA Astrophysics Data System (ADS)

    Wang, Lihong V.

    Photoacoustic tomography (PAT) refers to imaging that is based on the photoacoustic effect. Although the photoacoustic effect as a physical phenomenon was first reported on by Alexander Graham Bell in 1880 [1], PAT as an imaging technology was developed only after the advent of ultrasonic transducers, computers, and lasers [2-31]. A review on biomedical photoacoustics is available [32]. The motivation for PAT is to combine optical-absorption contrast with ultrasonic spatial resolution for deep imaging in the optical quasi-diffusive or diffusive regime. In PAT, the tissue is irradiated by usually a short-pulsed laser beam to achieve a thermal and acoustic impulse response (Fig. 19.1). Locally absorbed light is converted into heat, which is further converted to a pressure rise via thermo-elastic expansion. The initial pressure rise - determined by the local optical absorption coefficient (μ â ), fluence (ψ) and other thermal and mechanical properties - propagates as an ultrasonic wave, which is referred to as a photoacoustic wave.

  16. High resolution IVEM tomography of biological specimens

    SciTech Connect

    Sedat, J.W.; Agard, D.A.

    1997-02-01

    Electron tomography is a powerful tool for elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. The introduction of intermediate voltage electron microscopes further extended the technique by providing the means to examine very large and non-symmetrical subcellular organelles, at resolutions beyond what would be possible using light microscopy. Recent studies using electron tomography on a variety of cellular organelles and assemblies such as centrosomes, kinetochores, and chromatin have clearly demonstrated the power of this technique for obtaining 3D structural information on non-symmetric cell components. When combined with biochemical and molecular observations, these 3D reconstructions have provided significant new insights into biological function.

  17. Tomography and High-Resolution Electron Microscopy Study of Surfaces and Porosity in a Plate-Like γ-Al2O3

    SciTech Connect

    Kovarik, Libor; Genc, Arda; Wang, Chong M.; Qiu, Annie; Peden, Charles HF; Szanyi, Janos; Kwak, Ja Hun

    2012-12-10

    Morphological and surface characteristics of gamma-Al2O3 are topics of high relevance in the field of catalysis. Using tomography and high-resolution S/TEM imaging, we have studied the surface characteristics of a model gamma-Al2O3 synthesized in the shape of platelets and macroscopically defined by (110)Al2O3 and (111)Al2O3 surface facets. We show that the dominant (110)Al2O3 surface of the synthesized gamma-Al2O3 is not atomically flat but undergoes a significant reconstruction, forming nanoscale (111)Al2O3 terraces. In addition to high resolution imaging, tomographic analysis was carried out, enabling an examination of the pores/voids, which were found to be mostly enclosed within the bulk and inaccessible to gasses or metals. Tomographic analysis shows that the surfaces of the pores are defined exclusively by (100)Al2O3 and (111)Al2O3 facets. The importance of these findings is discussed in the context of relative surface energies of low index surfaces and ethanol desorption characteristics.

  18. Computed Tomography (CT) - Spine

    MedlinePlus

    ... News Physician Resources Professions Site Index A-Z Computed Tomography (CT) - Spine Computed tomography (CT) of the spine is a diagnostic imaging ... Spine? What is CT Scanning of the Spine? Computed tomography, more commonly known as a CT or CAT ...

  19. Interventional video tomography

    NASA Astrophysics Data System (ADS)

    Truppe, Michael J.; Pongracz, Ferenc; Ploder, Oliver; Wagner, Arne; Ewers, Rolf

    1995-05-01

    Interventional Video Tomography (IVT) is a new imaging modality for Image Directed Surgery to visualize in real-time intraoperatively the spatial position of surgical instruments relative to the patient's anatomy. The video imaging detector is based on a special camera equipped with an optical viewing and lighting system and electronic 3D sensors. When combined with an endoscope it is used for examining the inside of cavities or hollow organs of the body from many different angles. The surface topography of objects is reconstructed from a sequence of monocular video or endoscopic images. To increase accuracy and speed of the reconstruction the relative movement between objects and endoscope is continuously tracked by electronic sensors. The IVT image sequence represents a 4D data set in stereotactic space and contains image, surface topography and motion data. In ENT surgery an IVT image sequence of the planned and so far accessible surgical path is acquired prior to surgery. To simulate the surgical procedure the cross sectional imaging data is superimposed with the digitally stored IVT image sequence. During surgery the video sequence component of the IVT simulation is substituted by the live video source. The IVT technology makes obsolete the use of 3D digitizing probes for the patient image coordinate transformation. The image fusion of medical imaging data with live video sources is the first practical use of augmented reality in medicine. During surgery a head-up display is used to overlay real-time reformatted cross sectional imaging data with the live video image.

  20. EDITORIAL: Industrial Process Tomography

    NASA Astrophysics Data System (ADS)

    Anton Johansen, Geir; Wang, Mi

    2008-09-01

    There has been tremendous development within measurement science and technology over the past couple of decades. New sensor technologies and compact versatile signal recovery electronics are continuously expanding the limits of what can be measured and the accuracy with which this can be done. Miniaturization of sensors and the use of nanotechnology push these limits further. Also, thanks to powerful and cost-effective computer systems, sophisticated measurement and reconstruction algorithms previously only accessible in advanced laboratories are now available for in situ online measurement systems. The process industries increasingly require more process-related information, motivated by key issues such as improved process control, process utilization and process yields, ultimately driven by cost-effectiveness, quality assurance, environmental and safety demands. Industrial process tomography methods have taken advantage of the general progress in measurement science, and aim at providing more information, both quantitatively and qualitatively, on multiphase systems and their dynamics. The typical approach for such systems has been to carry out one local or bulk measurement and assume that this is representative of the whole system. In some cases, this is sufficient. However, there are many complex systems where the component distribution varies continuously and often unpredictably in space and time. The foundation of industrial tomography is to conduct several measurements around the periphery of a multiphase process, and use these measurements to unravel the cross-sectional distribution of the process components in time and space. This information is used in the design and optimization of industrial processes and process equipment, and also to improve the accuracy of multiphase system measurements in general. In this issue we are proud to present a selection of the 145 papers presented at the 5th World Congress on Industrial Process Tomography in Bergen

  1. Turbocharging Quantum Tomography

    SciTech Connect

    Blume-Kohout, Robin J.; Gamble, John King; Nielsen, Erik; Maunz, Peter Lukas Wilhelm; Scholten, Travis L.; Rudinger, Kenneth Michael

    2015-01-01

    Quantum tomography is used to characterize quantum operations implemented in quantum information processing (QIP) hardware. Traditionally, state tomography has been used to characterize the quantum state prepared in an initialization procedure, while quantum process tomography is used to characterize dynamical operations on a QIP system. As such, tomography is critical to the development of QIP hardware (since it is necessary both for debugging and validating as-built devices, and its results are used to influence the next generation of devices). But tomography suffers from several critical drawbacks. In this report, we present new research that resolves several of these flaws. We describe a new form of tomography called gate set tomography (GST), which unifies state and process tomography, avoids prior methods critical reliance on precalibrated operations that are not generally available, and can achieve unprecedented accuracies. We report on theory and experimental development of adaptive tomography protocols that achieve far higher fidelity in state reconstruction than non-adaptive methods. Finally, we present a new theoretical and experimental analysis of process tomography on multispin systems, and demonstrate how to more effectively detect and characterize quantum noise using carefully tailored ensembles of input states.

  2. Micro-computed tomography and scanning electron microscopy comparisons of two nickel-titanium rotary root canal instruments used with reciprocating motion.

    PubMed

    Kim, Hee-Chul; Hwang, You-Jeong; Jung, Da-Woon; You, Sung-Yeop; Kim, Hyeon-Cheol; Lee, WooCheol

    2013-01-01

    The single-file root canal instrumentation technique using reciprocating motion has been gaining concern. Therefore, the purpose of this study was to compare the shaping ability of single ProTaper F2 file and WaveOne Primary file when they were used in the curved root canal with reciprocation motion and to investigate the durability of the file after use with a scanning electron microscopy (SEM). Changes in structure model index (SMI), root canal volume, curvature, surface area, and degree of transportation were measured from the cross-sectional images of the prepared canals using the micro-CT system with an isotropic resolution of 16 μm. Results showed that there were no differences in the changes of root canal volume, surface area, and SMI between the two file groups after the preparation (p > 0.05). The ProTaper group showed a curvature straightening value of 25.45 ± 12.51%, while the WaveOne group showed 27.30 ± 10.91%, and there was no statistically significant difference (p > 0.05). The transportation values between the two groups showed no significant differences (p > 0.05). SEM revealed that 60% of ProTaper files showed initiation of microcracks on the surface while those were detected on the only one WaveOne file. The single-file technique using either WaveOne Primary or ProTaper F2 can be safely used under each reciprocating motion without creating an increased apical transportation in curved canals. However, the metallurgic property resists cyclic fatigue was more favorable with WaveOne under the scanning evaluation.

  3. MO-A-BRD-07: Feasibility of X-Ray Acoustic Computed Tomography as a Tool for Calibration and In Vivo Dosimetry of Radiotherapy Electron and Photon Beams

    SciTech Connect

    Hickling, S; Hobson, M; El Naqa, I

    2014-06-15

    Purpose: This work simulates radiation-induced acoustic waves to assess the feasibility of x-ray acoustic computed tomography (XACT) as a dosimeter. XACT exploits the phenomenon that acoustic waves with amplitude proportional to the dose deposited are induced following a radiation pulse. After detecting these acoustic waves with an ultrasound transducer, an image of the dose distribution can be reconstructed in realtime. Methods: Monte Carlo was used to simulate the dose distribution for monoenergetic 6 MeV photon and 9 MeV electron beams incident on a water tank. The dose distribution for a prostate patient planned with a photon 4-field box technique was calculated using clinical treatment planning software. All three dose distributions were converted into initial pressure distributions, and transportation of the induced acoustic waves was simulated using an open-source toolkit. Ideal transducers were placed around the circumference of the target to detect the acoustic waves, and a time reversal reconstruction algorithm was used to obtain an XACT image of the dose for each radiation pulse. Results: For the photon water tank relative dosimetry case, it was found that the normalized acoustic signal amplitude agreed with the normalized dose at depths from 0 cm to 10 cm, with an average percent difference of 0.5%. For the reconstructed in-plane dose distribution of an electron water tank irradiation, all pixels passed a 3%–3 mm 2D gamma test. The reconstructed prostate dose distribution closely resembled the plan, with 89% of pixels passing a 3%–3 mm 2D gamma test. For all situations, the amplitude of the induced acoustic waves ranged from 0.01 Pa to 1 Pa. Conclusion: Based on the amplitude of the radiation-induced acoustic waves and accuracy of the reconstructed dose distributions, XACT is a feasible technique for dosimetry in both calibration and in vivo environments for photon and electron beams and merits further investigation. Funding from NSERC, CIHR and Mc

  4. Advanced Instrumentation for Positron Emission Tomography [PET

    DOE R&D Accomplishments Database

    Derenzo, S. E.; Budinger, T. F.

    1985-04-01

    This paper summarizes the physical processes and medical science goals that underlay modern instrumentation design for Positron Emission Tomography. The paper discusses design factors such as detector material, crystalphototube coupling, shielding geometry, sampling motion, electronics design, time-of-flight, and the interrelationships with quantitative accuracy, spatial resolution, temporal resolution, maximum data rates, and cost.

  5. In situ localization of N and C termini of subunits of the flagellar nexin-dynein regulatory complex (N-DRC) using SNAP tag and cryo-electron tomography.

    PubMed

    Song, Kangkang; Awata, Junya; Tritschler, Douglas; Bower, Raqual; Witman, George B; Porter, Mary E; Nicastro, Daniela

    2015-02-27

    Cryo-electron tomography (cryo-ET) has reached nanoscale resolution for in situ three-dimensional imaging of macromolecular complexes and organelles. Yet its current resolution is not sufficient to precisely localize or identify most proteins in situ; for example, the location and arrangement of components of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility that is conserved from algae to humans, have remained elusive despite many cryo-ET studies of cilia and flagella. Here, we developed an in situ localization method that combines cryo-ET/subtomogram averaging with the clonable SNAP tag, a widely used cell biological probe to visualize fusion proteins by fluorescence microscopy. Using this hybrid approach, we precisely determined the locations of the N and C termini of DRC3 and the C terminus of DRC4 within the three-dimensional structure of the N-DRC in Chlamydomonas flagella. Our data demonstrate that fusion of SNAP with target proteins allowed for protein localization with high efficiency and fidelity using SNAP-linked gold nanoparticles, without disrupting the native assembly, structure, or function of the flagella. After cryo-ET and subtomogram averaging, we localized DRC3 to the L1 projection of the nexin linker, which interacts directly with a dynein motor, whereas DRC4 was observed to stretch along the N-DRC base plate to the nexin linker. Application of the technique developed here to the N-DRC revealed new insights into the organization and regulatory mechanism of this complex, and provides a valuable tool for the structural dissection of macromolecular complexes in situ.

  6. Dual seven pinhole tomography

    SciTech Connect

    Bizais, Y.; Zubal, I.G.; Rowe, R.W.; Bennett, G.W.; Brill, A.B.

    1982-01-01

    Emission tomography using two orthogonal sets of projections through seven pinhole collimators is considered. This paper describes the acquisition system, the reconstruction algorithm, presents results obtained in phantom studies, and discusses the advantages and disadvantages of this method over conventional Seven Pinhole Tomography.

  7. Computed body tomography.

    PubMed

    Alfidi, R J; Haaga, J R

    1976-12-01

    Only the surface of the diagnostic possibilities inherent in CT imaging has been scratched. Solic organ pathology is readily visible in most instances by computed tomography. With further extension of present knowledge and development of newer contrast agents, the ability of computed body tomography to image a wide range of diseases appears almost limitless.

  8. Three-dimensional scanning transmission electron microscopy of biological specimens.

    PubMed

    de Jonge, Niels; Sougrat, Rachid; Northan, Brian M; Pennycook, Stephen J

    2010-02-01

    A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset.

  9. Three-dimensional scanning transmission electron microscopy of biological specimens

    SciTech Connect

    De Jonge, Niels; Sougrat, Rachid; Northan, Brian; Pennycook, Stephen J

    2010-01-01

    A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2 - 3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original data set. The precision of the height determination was 0.2 nm. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy (TEM). However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved data set.

  10. Biomass accessibility analysis using electron tomography

    DOE PAGESBeta

    Hinkle, Jacob D.; Ciesielski, Peter N.; Gruchalla, Kenny; Munch, Kristin R.; Donohoe, Bryon S.

    2015-12-25

    Substrate accessibility to catalysts has been a dominant theme in theories of biomass deconstruction. Furthermore, current methods of quantifying accessibility do not elucidate mechanisms for increased accessibility due to changes in microstructure following pretreatment.

  11. Geophysical wave tomography

    NASA Astrophysics Data System (ADS)

    Zhou, Chaoguang

    2000-11-01

    This study is concerned with geophysical wave tomography techniques that include advanced diffraction tomography, traveltime calculation techniques and simultaneous attenuation and velocity tomography approaches. We propose the source independent approximation, the Modified Quasi-Linear approximation and develop a fast and accurate diffraction tomography algorithm that uses this approximation. Since the Modified Quasi-Linear approximation accounts for the scattering fields within scatterers, this tomography algorithm produces better image quality than conventional Born approximation tomography algorithm does with or without the presence of multiple scatterers and can be used to reconstruct images of high contrast objects. Since iteration is not required, this algorithm is efficient. We improve the finite difference traveltime calculation algorithm proposed by Vidale (1990). The bucket theory is utilized in order to enhance the sorting efficiency, which accounts for about ten percent computing time improvement for large velocity models. Snell's law is employed to solve the causality problem analytically, which enables the modified algorithm to compute traveltimes accurately and rapidly for high velocity contrast media. We also develop two simultaneous attenuation and velocity tomography approaches, which use traveltimes and amplitude spectra of the observed data, and discuss some of their applications. One approach is processing geophysical data that come from one single survey and the other deals with the repeated survey cases. These approaches are nonlinear and therefore more accurate than linear tomography. A linear system for wave propagation and constant-Q media are assumed in order to develop the tomography algorithms. These approaches not only produce attenuation and velocity images at the same time but also can be used to infer the physical rock properties, such as the dielectric permittivity, the electric conductivity, and the porosity. A crosshole radar

  12. Computed Tomography (CT) -- Head

    MedlinePlus

    ... further information please consult the ACR Manual on Contrast Media and its references. The risk of serious allergic ... Angiography (CTA) Stroke Brain Tumors Computer Tomography (CT) Safety During Pregnancy Head and Neck Cancer X-ray, ...

  13. Computed Tomography (CT) -- Sinuses

    MedlinePlus

    ... further information please consult the ACR Manual on Contrast Media and its references. The risk of serious allergic ... X-ray, Interventional Radiology and Nuclear Medicine Radiation Safety Images related to Computed Tomography (CT) - Sinuses About ...

  14. Mesoscale ionospheric tomography at the Auroral region

    NASA Astrophysics Data System (ADS)

    Luntama, J.; Kokkatil, G. V.

    2008-12-01

    FMI (Finnish Meteorological Institute) has used observations from the dense GNSS network in Finland for high resolution regional ionospheric tomography. The observation system used in this work is the VRS (Virtual Reference Station) network in Finland operated by Geotrim Ltd. This network contains 86 GNSS ground stations providing two frequency GPS and GLONASS observations with the sampling rate of 1 Hz. The network covers the whole Finland and the sampling of the ionosphere is very good for observing mesoscale ionospheric structures at the Auroral region. The ionospheric tomography software used by FMI is the MIDAS (Multi-Instrument Data Analysis System) algorithm developed and implemented by the University of Bath (Mitchell and Spencer, 2003). MIDAS is a 3-D extension of the 2-D tomography algorithm originally presented by Fremouw et al. (1992). The research at FMI is based on ground based GNSS data collected in December 2006. The impacts of the two geomagnetic storms during the month are clearly visible in the retrieved electron density and TEC maps and they can be correlated with the magnetic field disturbances measured by the IMAGE magnetometer network. This is the first time that mesoscale structures in the ionospheric plasma can be detected from ground based GNSS observations at the Auroral region. The continuous high rate observation data from the Geotrim network allows monitoring of the temporal evolution of these structures throughout the storms. Validation of the high resolution electron density and TEC maps is a challenge as independent reference observations with a similar resolution are not available. FMI has compared the 3-D electron density maps against the 2-D electron density plots retrieved from the observations from the Ionospheric Tomography Chain operated by the Sodankylä Geophysical Observatory (SGO). Additional validation has been performed with intercomparisons with observations from the ground based magnetometer and auroral camera network

  15. Practical Bayesian tomography

    NASA Astrophysics Data System (ADS)

    Granade, Christopher; Combes, Joshua; Cory, D. G.

    2016-03-01

    In recent years, Bayesian methods have been proposed as a solution to a wide range of issues in quantum state and process tomography. State-of-the-art Bayesian tomography solutions suffer from three problems: numerical intractability, a lack of informative prior distributions, and an inability to track time-dependent processes. Here, we address all three problems. First, we use modern statistical methods, as pioneered by Huszár and Houlsby (2012 Phys. Rev. A 85 052120) and by Ferrie (2014 New J. Phys. 16 093035), to make Bayesian tomography numerically tractable. Our approach allows for practical computation of Bayesian point and region estimators for quantum states and channels. Second, we propose the first priors on quantum states and channels that allow for including useful experimental insight. Finally, we develop a method that allows tracking of time-dependent states and estimates the drift and diffusion processes affecting a state. We provide source code and animated visual examples for our methods.

  16. Efficient quantum state tomography.

    PubMed

    Cramer, Marcus; Plenio, Martin B; Flammia, Steven T; Somma, Rolando; Gross, David; Bartlett, Stephen D; Landon-Cardinal, Olivier; Poulin, David; Liu, Yi-Kai

    2010-01-01

    Quantum state tomography--deducing quantum states from measured data--is the gold standard for verification and benchmarking of quantum devices. It has been realized in systems with few components, but for larger systems it becomes unfeasible because the number of measurements and the amount of computation required to process them grows exponentially in the system size. Here, we present two tomography schemes that scale much more favourably than direct tomography with system size. One of them requires unitary operations on a constant number of subsystems, whereas the other requires only local measurements together with more elaborate post-processing. Both rely only on a linear number of experimental operations and post-processing that is polynomial in the system size. These schemes can be applied to a wide range of quantum states, in particular those that are well approximated by matrix product states. The accuracy of the reconstructed states can be rigorously certified without any a priori assumptions.

  17. Orbital tomography for highly symmetric adsorbate systems

    NASA Astrophysics Data System (ADS)

    Stadtmüller, B.; Willenbockel, M.; Reinisch, E. M.; Ules, T.; Bocquet, F. C.; Soubatch, S.; Puschnig, P.; Koller, G.; Ramsey, M. G.; Tautz, F. S.; Kumpf, C.

    2012-10-01

    Orbital tomography is a new and very powerful tool to analyze the angular distribution of a photoemission spectroscopy experiment. It was successfully used for organic adsorbate systems to identify (and consequently deconvolute) the contributions of specific molecular orbitals to the photoemission data. The technique was so far limited to surfaces with low symmetry like fcc(110) oriented surfaces, owing to the small number of rotational domains that occur on such surfaces. In this letter we overcome this limitation and present an orbital tomography study of a 3,4,9,10-perylene-tetra-carboxylic-dianhydride (PTCDA) monolayer film adsorbed on Ag(111). Although this system exhibits twelve differently oriented molecules, the angular resolved photoemission data still allow a meaningful analysis of the different local density of states and reveal different electronic structures for symmetrically inequivalent molecules. We also discuss the precision of the orbital tomography technique in terms of counting statistics and linear regression fitting algorithm. Our results demonstrate that orbital tomography is not limited to low-symmetry surfaces, a finding which makes a broad field of complex adsorbate systems accessible to this powerful technique.

  18. Waste inspection tomography (WIT)

    SciTech Connect

    Bernardi, R.T.

    1996-12-31

    WIT is a self-sufficient mobile semitrailer for nondestructive evaluation and nondestructive assay of nuclear waste drums using x-ray and gamma-ray tomography. The recently completed Phase I included the design, fabrication, and initial testing of all WIT subsystems installed on-board the trailer. Initial test results include 2 MeV digital radiography, computed tomography, Anger camera imaging, single photon emission computed tomography, gamma-ray spectroscopy, collimated gamma scanning, and active and passive computed tomography using a 1.4 mCi source of {sup 166}Ho. These techniques were initially demonstrated on a 55-gallon phantom drum with 3 simulated waste matrices of combustibles, heterogeneous metals, and cement using check sources of gamma active isotopes such as {sup 137}Cs and {sup 133}Ba with 9-250 {mu}Ci activities. Waste matrix identification, isotopic identification, and attenuation-corrected gamma activity determination were demonstrated nondestructively and noninvasively in Phase I. Currently ongoing Phase II involves DOE site field test demonstrations at LLNL, RFETS, and INEL with real nuclear waste drums. Current WIT experience includes 55 gallon drums of cement, graphite, sludge, glass, metals, and combustibles. Thus far WIT has inspected drums with 0-20 gms of {sup 239}Pu.

  19. Dental Optical Coherence Tomography

    PubMed Central

    Hsieh, Yao-Sheng; Ho, Yi-Ching; Lee, Shyh-Yuan; Chuang, Ching-Cheng; Tsai, Jui-che; Lin, Kun-Feng; Sun, Chia-Wei

    2013-01-01

    This review paper describes the applications of dental optical coherence tomography (OCT) in oral tissue images, caries, periodontal disease and oral cancer. The background of OCT, including basic theory, system setup, light sources, spatial resolution and system limitations, is provided. The comparisons between OCT and other clinical oral diagnostic methods are also discussed. PMID:23857261

  20. Neural networks for calibration tomography

    NASA Technical Reports Server (NTRS)

    Decker, Arthur

    1993-01-01

    Artificial neural networks are suitable for performing pattern-to-pattern calibrations. These calibrations are potentially useful for facilities operations in aeronautics, the control of optical alignment, and the like. Computed tomography is compared with neural net calibration tomography for estimating density from its x-ray transform. X-ray transforms are measured, for example, in diffuse-illumination, holographic interferometry of fluids. Computed tomography and neural net calibration tomography are shown to have comparable performance for a 10 degree viewing cone and 29 interferograms within that cone. The system of tomography discussed is proposed as a relevant test of neural networks and other parallel processors intended for using flow visualization data.

  1. The meaning of interior tomography.

    PubMed

    Wang, Ge; Yu, Hengyong

    2013-08-21

    The classic imaging geometry for computed tomography is for the collection of un-truncated projections and the reconstruction of a global image, with the Fourier transform as the theoretical foundation that is intrinsically non-local. Recently, interior tomography research has led to theoretically exact relationships between localities in the projection and image spaces and practically promising reconstruction algorithms. Initially, interior tomography was developed for x-ray computed tomography. Then, it was elevated to have the status of a general imaging principle. Finally, a novel framework known as 'omni-tomography' is being developed for a grand fusion of multiple imaging modalities, allowing tomographic synchrony of diversified features.

  2. Ultrafast limited-angle-type x-ray tomography

    SciTech Connect

    Bieberle, M.; Fischer, F.; Schleicher, E.; Hampel, U.; Koch, D.; Aktay, K. S. d. C.; Menz, H.-J.; Mayer, H.-G.

    2007-09-17

    The authors present an ultrafast electron beam x-ray computed tomography technique usable for imaging of fast processes, such as multiphase flows or moving parts in technical or biological objects. The setup consists of an electron beam unit with fast deflection capability and an ultrafast multielement x-ray detector and achieves 10 000 frames/s image rate. Since full sampling of the Radon space requires an angular overlap of source path and detector which strongly decreases axial resolution, the authors devised a limited-angle-type tomography. As a demonstration they visualized the movement of particles and gas bubbles rising in a stagnant liquid.

  3. Atom probe tomography of lithium-doped network glasses.

    PubMed

    Greiwe, Gerd-Hendrik; Balogh, Zoltan; Schmitz, Guido

    2014-06-01

    Li-doped silicate and borate glasses are electronically insulating, but provide considerable ionic conductivity. Under measurement conditions of laser-assisted atom probe tomography, mobile Li ions are redistributed in response to high electric fields. In consequence, the direct interpretation of measured composition profiles is prevented. It is demonstrated that composition profiles are nevertheless well understood by a complex model taking into account the electronic structure of dielectric materials, ionic mobility and field screening. Quantitative data on band bending and field penetration during measurement are derived which are important in understanding laser-assisted atom probe tomography of dielectric materials.

  4. FIB-SEM cathodoluminescence tomography: practical and theoretical considerations.

    PubMed

    De Winter, D A M; Lebbink, M N; Wiggers De Vries, D F; Post, J A; Drury, M R

    2011-09-01

    Focused ion beam-scanning electron microscope (FIB-SEM) tomography is a powerful application in obtaining three-dimensional (3D) information. The FIB creates a cross section and subsequently removes thin slices. The SEM takes images using secondary or backscattered electrons, or maps every slice using X-rays and/or electron backscatter diffraction patterns. The objective of this study is to assess the possibilities of combining FIB-SEM tomography with cathodoluminescence (CL) imaging. The intensity of CL emission is related to variations in defect or impurity concentrations. A potential problem with FIB-SEM CL tomography is that ion milling may change the defect state of the material and the CL emission. In addition the conventional tilted sample geometry used in FIB-SEM tomography is not compatible with conventional CL detectors. Here we examine the influence of the FIB on CL emission in natural diamond and the feasibility of FIB-SEM CL tomography. A systematic investigation establishes that the ion beam influences CL emission of diamond, with a dependency on both the ion beam and electron beam acceleration voltage. CL emission in natural diamond is enhanced particularly at low ion beam and electron beam voltages. This enhancement of the CL emission can be partly explained by an increase in surface defects induced by ion milling. CL emission enhancement could be used to improve the CL image quality. To conduct FIB-SEM CL tomography, a recently developed novel specimen geometry is adopted to enable sequential ion milling and CL imaging on an untilted sample. We show that CL imaging can be manually combined with FIB-SEM tomography with a modified protocol for 3D microstructure reconstruction. In principle, automated FIB-SEM CL tomography should be feasible, provided that dedicated CL detectors are developed that allow subsequent milling and CL imaging without manual intervention, as the current CL detector needs to be manually retracted before a slice can be milled

  5. Electron Cryotomography

    PubMed Central

    Tocheva, Elitza I.; Li, Zhuo; Jensen, Grant J.

    2010-01-01

    Electron cryotomography (ECT) is an emerging technology that allows thin samples such as macromolecular complexes and small bacterial cells to be imaged in 3-D in a nearly native state to “molecular” (∼4 nm) resolution. As such, ECT is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. This article describes the technique and summarizes its contributions to bacterial cell biology. For comparable recent reviews, see (Subramaniam 2005; Jensen and Briegel 2007; Murphy and Jensen 2007; Li and Jensen 2009). For reviews on the history, technical details, and broader application of electron tomography in general, see for example (Subramaniam and Milne 2004; Lucić et al. 2005; Leis et al. 2008; Midgley and Dunin-Borkowski 2009). PMID:20516135

  6. EDITORIAL: Industrial Process Tomography

    NASA Astrophysics Data System (ADS)

    West, Robert M.

    2004-07-01

    Industrial process tomography remains a multidisciplinary field with considerable interest for many varied participants. Indeed this adds greatly to its appeal. It is a pleasure and a privilege to once again act as guest editor for a special feature issue of Measurement Science and Technology on industrial process tomography, the last being in December 2002. Those involved in the subject appreciate the efforts of Measurement Science and Technology in producing another issue and I thank the journal on their behalf. It can be seen that there are considerable differences in the composition of material covered in this issue compared with previous publications. The dominance of electrical impedance and electrical capacitance techniques is reduced and there is increased emphasis on general utility of tomographic methods. This is encompassed in the papers of Hoyle and Jia (visualization) and Dierick et al (Octopus). Electrical capacitance tomography has been a core modality for industrial applications. This issue includes new work in two very interesting aspects of image reconstruction: pattern matching (Takei and Saito) and simulated annealing (Ortiz-Aleman et al). It is important to take advantage of knowledge of the process such as the presence of only two components, and then to have robust reconstruction methods provided by pattern matching and by simulated annealing. Although crude reconstruction methods such as approximation by linear back projection were utilized for initial work on electrical impedance tomography, the techniques published here are much more advanced. The paper by Kim et al includes modelling of a two-component system permitting an adaption-related approach; the paper by Tossavainen et al models free surface boundaries to enable the estimation of shapes of objects within the target. There are clear improvements on the previous crude and blurred reconstructions where boundaries were merely inferred rather than estimated as in these new developments

  7. Development of a proton Computed Tomography detector system

    NASA Astrophysics Data System (ADS)

    Naimuddin, Md.; Coutrakon, G.; Blazey, G.; Boi, S.; Dyshkant, A.; Erdelyi, B.; Hedin, D.; Johnson, E.; Krider, J.; Rukalin, V.; Uzunyan, S. A.; Zutshi, V.; Fordt, R.; Sellberg, G.; Rauch, J. E.; Roman, M.; Rubinov, P.; Wilson, P.

    2016-02-01

    Computer tomography is one of the most promising new methods to image abnormal tissues inside the human body. Tomography is also used to position the patient accurately before radiation therapy. Hadron therapy for treating cancer has become one of the most advantegeous and safe options. In order to fully utilize the advantages of hadron therapy, there is a necessity of performing radiography with hadrons as well. In this paper we present the development of a proton computed tomography system. Our second-generation proton tomography system consists of two upstream and two downstream trackers made up of fibers as active material and a range detector consisting of plastic scintillators. We present details of the detector system, readout electronics, and data acquisition system as well as the commissioning of the entire system. We also present preliminary results from the test beam of the range detector.

  8. Polarised light sheet tomography.

    PubMed

    Reidt, Sascha L; O'Brien, Daniel J; Wood, Kenneth; MacDonald, Michael P

    2016-05-16

    The various benefits of light sheet microscopy have made it a widely used modality for capturing three-dimensional images. It is mostly used for fluorescence imaging, but recently another technique called light sheet tomography solely relying on scattering was presented. The method was successfully applied to imaging of plant roots in transparent soil, but is limited when it comes to more turbid samples. This study presents a polarised light sheet tomography system and its advantages when imaging in highly scattering turbid media. The experimental configuration is guided by Monte Carlo radiation transfer methods, which model the propagation of a polarised light sheet in the sample. Images of both reflecting and absorbing phantoms in a complex collagenous matrix were acquired, and the results for different polarisation configurations are compared. Focus scanning methods were then used to reduce noise and produce three-dimensional reconstructions of absorbing targets.

  9. Controllable tomography phase microscopy

    NASA Astrophysics Data System (ADS)

    Xiu, Peng; Zhou, Xin; Kuang, Cuifang; Xu, Yingke; Liu, Xu

    2015-03-01

    Tomography phase microscopy (TPM) is a new microscopic method that can quantitatively yield the volumetric 3D distribution of a sample's refractive index (RI), which is significant for cell biology research. In this paper, a controllable TPM system is introduced. In this system a circulatory phase-shifting method and piezoelectric ceramic are used which enable the TPM system to record the 3D RI distribution at a more controllable speed, from 1 to 40 fps, than in the other TPM systems reported. The resolution of the RI distribution obtained by this controllable TPM is much better than that in images recorded by phase contrast microscopy and interference tomography microscopy. The realization of controllable TPM not only allows for the application of TPM to the measurement of kinds of RI sample, but also contributes to academic and technological support for the practical use of TPM.

  10. Computed tomography in neurocysticercosis.

    PubMed Central

    Minguetti, G; Ferreira, M V

    1983-01-01

    Neurocysticercosis is a major public health problem in developing countries. Before computed tomography became available its diagnosis was very restricted and the conventional diagnostic methods were unreliable. It also was frequently necessary to submit patients to costly and dangerous surgical procedures to confirm the precise nature of the disease. One hundred and seventy-one patients with neurocysticercosis were evaluated by computed tomography. The diagnostic findings of the different types of lesions produced by the larva of the parasite (Taenia solium) in the central nervous system, and the advantages of CT in the diagnosis of this clinical entity are described, as well as the main signs and symptoms of the patients referred for examination. The effect of corticosteroids in the acute stages of the disease and the changes they provoke in the CT images are described. Images PMID:6644318

  11. Polarised light sheet tomography.

    PubMed

    Reidt, Sascha L; O'Brien, Daniel J; Wood, Kenneth; MacDonald, Michael P

    2016-05-16

    The various benefits of light sheet microscopy have made it a widely used modality for capturing three-dimensional images. It is mostly used for fluorescence imaging, but recently another technique called light sheet tomography solely relying on scattering was presented. The method was successfully applied to imaging of plant roots in transparent soil, but is limited when it comes to more turbid samples. This study presents a polarised light sheet tomography system and its advantages when imaging in highly scattering turbid media. The experimental configuration is guided by Monte Carlo radiation transfer methods, which model the propagation of a polarised light sheet in the sample. Images of both reflecting and absorbing phantoms in a complex collagenous matrix were acquired, and the results for different polarisation configurations are compared. Focus scanning methods were then used to reduce noise and produce three-dimensional reconstructions of absorbing targets. PMID:27409945

  12. Using computerized tomography to determine ionospheric structures. Part 1, Notivation and basic approaches

    SciTech Connect

    Vittitoe, C.N.

    1993-08-01

    Properties of the ionosphere are reviewed along with its correlations with other geophysical phenomena and with applications of ionospheric studies to communication, navigation, and surveillance systems. Computer tomography is identified as a method to determine the detailed, three-dimensional distribution of electron density within the ionosphere. Several tomography methods are described, with a basic approach illustrated by an example. Limitations are identified.

  13. Computed tomography status

    SciTech Connect

    Hansche, B.D.

    1983-01-01

    Computed tomography (CT) is a relatively new radiographic technique which has become widely used in the medical field, where it is better known as computerized axial tomographic (CAT) scanning. This technique is also being adopted by the industrial radiographic community, although the greater range of densities, variation in samples sizes, plus possible requirement for finer resolution make it difficult to duplicate the excellent results that the medical scanners have achieved.

  14. Experimental adaptive Bayesian tomography

    NASA Astrophysics Data System (ADS)

    Kravtsov, K. S.; Straupe, S. S.; Radchenko, I. V.; Houlsby, N. M. T.; Huszár, F.; Kulik, S. P.

    2013-06-01

    We report an experimental realization of an adaptive quantum state tomography protocol. Our method takes advantage of a Bayesian approach to statistical inference and is naturally tailored for adaptive strategies. For pure states, we observe close to N-1 scaling of infidelity with overall number of registered events, while the best nonadaptive protocols allow for N-1/2 scaling only. Experiments are performed for polarization qubits, but the approach is readily adapted to any dimension.

  15. Computed Tomography Status

    DOE R&D Accomplishments Database

    Hansche, B. D.

    1983-01-01

    Computed tomography (CT) is a relatively new radiographic technique which has become widely used in the medical field, where it is better known as computerized axial tomographic (CAT) scanning. This technique is also being adopted by the industrial radiographic community, although the greater range of densities, variation in samples sizes, plus possible requirement for finer resolution make it difficult to duplicate the excellent results that the medical scanners have achieved.

  16. Tutorial on photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Zhou, Yong; Yao, Junjie; Wang, Lihong V.

    2016-06-01

    Photoacoustic tomography (PAT) has become one of the fastest growing fields in biomedical optics. Unlike pure optical imaging, such as confocal microscopy and two-photon microscopy, PAT employs acoustic detection to image optical absorption contrast with high-resolution deep into scattering tissue. So far, PAT has been widely used for multiscale anatomical, functional, and molecular imaging of biological tissues. We focus on PAT's basic principles, major implementations, imaging contrasts, and recent applications.

  17. Compton tomography system

    DOEpatents

    Grubsky, Victor; Romanoov, Volodymyr; Shoemaker, Keith; Patton, Edward Matthew; Jannson, Tomasz

    2016-02-02

    A Compton tomography system comprises an x-ray source configured to produce a planar x-ray beam. The beam irradiates a slice of an object to be imaged, producing Compton-scattered x-rays. The Compton-scattered x-rays are imaged by an x-ray camera. Translation of the object with respect to the source and camera or vice versa allows three-dimensional object imaging.

  18. Polychromatic diffraction contrast tomography

    SciTech Connect

    King, A.; Reischig, P.; Adrien, J.; Peetermans, S.; Ludwig, W.

    2014-11-15

    This tutorial review introduces the use of polychromatic radiation for 3D grain mapping using X-ray diffraction contrast tomography. The objective is to produce a 3D map of the grain shapes and orientations within a bulk, millimeter-sized polycrystalline sample. The use of polychromatic radiation enables the standard synchrotron X-ray technique to be applied in a wider range of contexts: 1) Using laboratory X-ray sources allows a much wider application of the diffraction contrast tomography technique. 2) Neutron sources allow large samples, or samples containing high Z elements to be studied. 3) Applied to synchrotron sources, smaller samples may be treated, or faster measurements may be possible. Challenges and particularities in the data acquisition and processing, and the limitations of the different variants, are discussed. - Highlights: • We present a tutorial review of polychromatic diffraction contrast tomography techniques. • The use of polychromatic radiation allows the standard synchrotron DCT technique to be extended to a range of other sources. • The characteristics and limitations of all variants of the techniques are derived, discussed and compared. • Examples using laboratory X-ray and cold neutron radiation are presented. • Suggestions for the future development of these techniques are presented.

  19. Ocean acoustic reverberation tomography.

    PubMed

    Dunn, Robert A

    2015-12-01

    Seismic wide-angle imaging using ship-towed acoustic sources and networks of ocean bottom seismographs is a common technique for exploring earth structure beneath the oceans. In these studies, the recorded data are dominated by acoustic waves propagating as reverberations in the water column. For surveys with a small receiver spacing (e.g., <10 km), the acoustic wave field densely samples properties of the water column over the width of the receiver array. A method, referred to as ocean acoustic reverberation tomography, is developed that uses the travel times of direct and reflected waves to image ocean acoustic structure. Reverberation tomography offers an alternative approach for determining the structure of the oceans and advancing the understanding of ocean heat content and mixing processes. The technique has the potential for revealing small-scale ocean thermal structure over the entire vertical height of the water column and along long survey profiles or across three-dimensional volumes of the ocean. For realistic experimental geometries and data noise levels, the method can produce images of ocean sound speed on a smaller scale than traditional acoustic tomography. PMID:26723303

  20. Ocean acoustic reverberation tomography.

    PubMed

    Dunn, Robert A

    2015-12-01

    Seismic wide-angle imaging using ship-towed acoustic sources and networks of ocean bottom seismographs is a common technique for exploring earth structure beneath the oceans. In these studies, the recorded data are dominated by acoustic waves propagating as reverberations in the water column. For surveys with a small receiver spacing (e.g., <10 km), the acoustic wave field densely samples properties of the water column over the width of the receiver array. A method, referred to as ocean acoustic reverberation tomography, is developed that uses the travel times of direct and reflected waves to image ocean acoustic structure. Reverberation tomography offers an alternative approach for determining the structure of the oceans and advancing the understanding of ocean heat content and mixing processes. The technique has the potential for revealing small-scale ocean thermal structure over the entire vertical height of the water column and along long survey profiles or across three-dimensional volumes of the ocean. For realistic experimental geometries and data noise levels, the method can produce images of ocean sound speed on a smaller scale than traditional acoustic tomography.

  1. Ultrasonic Lamb wave tomography

    NASA Astrophysics Data System (ADS)

    Leonard, Kevin R.; Malyarenko, Eugene V.; Hinders, Mark K.

    2002-12-01

    Nondestructive evaluation (NDE) of aerospace structures using traditional methods is a complex, time-consuming process critical to maintaining mission readiness and flight safety. Limited access to corrosion-prone structure and the restricted applicability of available NDE techniques for the detection of hidden corrosion or other damage often compound the challenge. In this paper we discuss our recent work using ultrasonic Lamb wave tomography to address this pressing NDE technology need. Lamb waves are ultrasonic guided waves, which allow large sections of aircraft structures to be rapidly inspected for structural flaws such as disbonds, corrosion and delaminations. Because the velocity of Lamb waves depends on thickness, for example, the travel times of the fundamental Lamb modes can be converted into a thickness map of the inspection region. However, extracting quantitative information from Lamb wave data has always involved highly trained personnel with a detailed knowledge of mechanical waveguide physics. Our work focuses on tomographic reconstruction to produce quantitative maps that can be easily interpreted by technicians or fed directly into structural integrity and lifetime prediction codes. Laboratory measurements discussed here demonstrate that Lamb wave tomography using a square perimeter array of transducers with algebraic reconstruction tomography is appropriate for detecting flaws in aircraft materials. The speed and fidelity of the reconstruction algorithms as well as practical considerations for person-portable array-based systems are discussed in this paper.

  2. Enhanced local tomography

    DOEpatents

    Katsevich, Alexander J.; Ramm, Alexander G.

    1996-01-01

    Local tomography is enhanced to determine the location and value of a discontinuity between a first internal density of an object and a second density of a region within the object. A beam of radiation is directed in a predetermined pattern through the region of the object containing the discontinuity. Relative attenuation data of the beam is determined within the predetermined pattern having a first data component that includes attenuation data through the region. In a first method for evaluating the value of the discontinuity, the relative attenuation data is inputted to a local tomography function .function..sub..LAMBDA. to define the location S of the density discontinuity. The asymptotic behavior of .function..sub..LAMBDA. is determined in a neighborhood of S, and the value for the discontinuity is estimated from the asymptotic behavior of .function..sub..LAMBDA.. In a second method for evaluating the value of the discontinuity, a gradient value for a mollified local tomography function .gradient..function..sub..LAMBDA..epsilon. (x.sub.ij) is determined along the discontinuity; and the value of the jump of the density across the discontinuity curve (or surface) S is estimated from the gradient values.

  3. Generalized local emission tomography

    DOEpatents

    Katsevich, Alexander J.

    1998-01-01

    Emission tomography enables locations and values of internal isotope density distributions to be determined from radiation emitted from the whole object. In the method for locating the values of discontinuities, the intensities of radiation emitted from either the whole object or a region of the object containing the discontinuities are inputted to a local tomography function .function..sub..LAMBDA..sup.(.PHI.) to define the location S of the isotope density discontinuity. The asymptotic behavior of .function..sub..LAMBDA..sup.(.PHI.) is determined in a neighborhood of S, and the value for the discontinuity is estimated from the asymptotic behavior of .function..sub..LAMBDA..sup.(.PHI.) knowing pointwise values of the attenuation coefficient within the object. In the method for determining the location of the discontinuity, the intensities of radiation emitted from an object are inputted to a local tomography function .function..sub..LAMBDA..sup.(.PHI.) to define the location S of the density discontinuity and the location .GAMMA. of the attenuation coefficient discontinuity. Pointwise values of the attenuation coefficient within the object need not be known in this case.

  4. New trend in electron holography

    NASA Astrophysics Data System (ADS)

    Tanigaki, Toshiaki; Harada, Ken; Murakami, Yasukazu; Niitsu, Kodai; Akashi, Tetsuya; Takahashi, Yoshio; Sugawara, Akira; Shindo, Daisuke

    2016-06-01

    Electron holography using a coherent electron wave is a promising technique for high-resolution visualization of electromagnetic fields in and around objects. The capability of electron holography has been enhanced by the development of new technologies and has thus become an even more powerful tool for exploring scientific frontiers. This review introduces these technologies including split-illumination electron holography and vector-field electron tomography. Split-illumination electron holography, which uses separated coherent waves, overcomes the limits imposed by the lateral coherence requirement for electron waves in electron holography. Areas that are difficult to observe using conventional electron holography are now observable. Exemplified applications include observing a singular magnetic domain wall in electrical steel sheets, local magnetizations at anti-phase boundaries, and electrostatic potentials in metal-oxide-semiconductor field-effect transistors. Vector-field electron tomography can be used to visualize magnetic vectors in three dimensions. Two components of the vectors are reconstructed using dual-axis tomography, and the remaining one is calculated using div B   =  0. A high-voltage electron microscope can be used to achieve precise magnetic reconstruction. For example, magnetic vortices have been visualized using a 1 MV holography electron microscope.

  5. FIB-SEM tomography in biology.

    PubMed

    Kizilyaprak, Caroline; Bittermann, Anne Greet; Daraspe, Jean; Humbel, Bruno M

    2014-01-01

    Three-dimensional information is much easier to understand than a set of two-dimensional images. Therefore a layman is thrilled by the pseudo-3D image taken in a scanning electron microscope (SEM) while, when seeing a transmission electron micrograph, his imagination is challenged. First approaches to gain insight in the third dimension were to make serial microtome sections of a region of interest (ROI) and then building a model of the object. Serial microtome sectioning is a tedious and skill-demanding work and therefore seldom done. In the last two decades with the increase of computer power, sophisticated display options, and the development of new instruments, an SEM with a built-in microtome as well as a focused ion beam scanning electron microscope (FIB-SEM), serial sectioning, and 3D analysis has become far easier and faster.Due to the relief like topology of the microtome trimmed block face of resin-embedded tissue, the ROI can be searched in the secondary electron mode, and at the selected spot, the ROI is prepared with the ion beam for 3D analysis. For FIB-SEM tomography, a thin slice is removed with the ion beam and the newly exposed face is imaged with the electron beam, usually by recording the backscattered electrons. The process, also called "slice and view," is repeated until the desired volume is imaged.As FIB-SEM allows 3D imaging of biological fine structure at high resolution of only small volumes, it is crucial to perform slice and view at carefully selected spots. Finding the region of interest is therefore a prerequisite for meaningful imaging. Thin layer plastification of biofilms offers direct access to the original sample surface and allows the selection of an ROI for site-specific FIB-SEM tomography just by its pronounced topographic features.

  6. 360-degree quantum tomography of a qudit

    NASA Astrophysics Data System (ADS)

    Baldwin, Charles; Kalev, Amir; Martinez, Hector; Lysne, Nathan; Jessen, Poul; Deutsch, Ivan

    2015-05-01

    Quantum information processing consists of three components each with a respective tomography technique: preparation/state, evolution/process, and measurement/detector. Previous works have diagnosed a single component individually yielding an estimated density matrix, process-matrix, or POVM, which is compared to a corresponding target. However, all three types of tomography are interrelated, and accounting for only one implies that the estimator produced suffers from systematic errors. Other techniques exist to quantify the average error rates of a single part, e.g. randomized benchmarking, but fail to give information on the type of error. One goal of quantum tomography is to produce a reliable estimate to diagnose sources of errors. To study this we model a cold-atom testbed-the coupled electron-nuclear spins of the 16-dimensional ground manifold of Cs, initialized by optical pumping, controlled by magnetic and optical fields, and measured by Stern-Gerlach analysis. In a complete 360-degree cycle we can use known states as leverage to correct errors in POVMs, and in turn correct errors in processes, which allows us to improve state preparation, etc. This protocol allows us to produce reliable estimates while diagnosing sources of errors that one can work to correct.

  7. Ionospheric tomography using the FORTE satellite

    SciTech Connect

    Murphy, T.C.

    1993-08-01

    The possibility of obtaining ionospheric profile data via tomographic techniques has elicited considerable interest in recent years. The input data for the method is a set of total electron content measurements along intersecting lines of sight which form a grid. This can conveniently be provided by a fast-moving satellite with a VHF beacon which will generate the multiple paths needed for effective tomography. Los Alamos and Sandia National Laboratories will launch and operate the FORTE satellite for the US Department of Energy, with launch scheduled in 1995. FORTE will provide such a beacon. Additionally, wideband VHF receivers aboard the satellite will allow corraborative measurements of ionospheric profile parameters in some cases.

  8. Shielding for thermoacoustic tomography with RF excitation

    NASA Astrophysics Data System (ADS)

    Mitchell, M.; Becker, G.; Dey, P.; Generotzky, J.; Patch, S. K.

    2008-02-01

    Radiofrequency (RF) pulses used to generate thermoacoustic computerized tomography (TCT) signal couple directly into the pulser-receiver and oscilloscope, swamping true TCT signal. We use a standard RF enclosure housing both RF amplifier and object being imaged. This is similar to RF shielding of magnetic resonance imaging (MRI) suites and protects electronics outside from stray RF. Unlike MRI, TCT receivers are ultrasound transducers, which must also be shielded from RF. A transducer housing that simultaneously shields RF and permits acoustic transmission was developed specifically for TCT. We compare TCT signals measured with and without RF shielding.

  9. Compressive Phase Contrast Tomography

    SciTech Connect

    Maia, Filipe; MacDowell, Alastair; Marchesini, Stefano; Padmore, Howard A.; Parkinson, Dula Y.; Pien, Jack; Schirotzek, Andre; Yang, Chao

    2010-09-01

    When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. Interference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher contrast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).

  10. Positron Emission Tomography (PET)

    SciTech Connect

    Welch, M.J.

    1990-01-01

    Positron emission tomography (PET) assesses biochemical processes in the living subject, producing images of function rather than form. Using PET, physicians are able to obtain not the anatomical information provided by other medical imaging techniques, but pictures of physiological activity. In metaphoric terms, traditional imaging methods supply a map of the body's roadways, its, anatomy; PET shows the traffic along those paths, its biochemistry. This document discusses the principles of PET, the radiopharmaceuticals in PET, PET research, clinical applications of PET, the cost of PET, training of individuals for PET, the role of the United States Department of Energy in PET, and the futures of PET. 22 figs.

  11. Atom probe tomography

    SciTech Connect

    Miller, M.K.; Forbes, R.G.

    2009-06-15

    This introductory tutorial describes the technique of atom probe tomography for materials characterization at the atomic level. The evolution of the technique from the initial atom probe field ion microscope to today's state-of-the-art three dimensional atom probe is outlined. An introduction is presented on the basic physics behind the technique, the operation of the instrument, and the reconstruction of the three-dimensional data. The common methods for analyzing the three-dimensional atom probe data, including atom maps, isoconcentration surfaces, proximity histograms, maximum separation methods, and concentration frequency distributions, are described.

  12. Tomography finds waste sites

    NASA Astrophysics Data System (ADS)

    Bush, Susan M.

    Geophysical diffraction tomography (GDT), a remote sensing method, is being developed for hazardous waste site characterization by researchers at Oak Ridge National Laboratory, Tenn., with the support of the U.S. Army Toxic and Hazardous Materials Agency, Aberdeen Proving Ground, Md.More accurate assessment of hazardous sites translates into more efficient and less costly cleanup efforts by defining parameters such as waste site boundaries, geophysical site characteristics, buried container leakage, and hazardous material migration. Remote sensing devices eliminate the potential for environmental damage, safety hazards, or high costs associated with intrusive site characterization techniques.

  13. Laser Doppler projection tomography.

    PubMed

    Zeng, Yaguang; Xiong, Ke; Lu, Xuanlong; Feng, Guanping; Han, Dingan; Wu, Jing

    2014-02-15

    We propose a laser Doppler projection tomography (LDPT) method to obtain visualization of three-dimensional (3D) flowing structures. With LDPT, the flowing signal is extracted by a modified laser Doppler method, and the 3D flowing image is reconstructed by the filtered backprojection algorithm. Phantom experiments are performed to demonstrate that LDPT is able to obtain 3D flowing structure with higher signal-to-noise ratio and spatial resolution. Our experiment results display its potentially useful application to develop 3D label-free optical angiography for the circulation system of live small animal models or microfluidic experiments.

  14. Radial reflection diffraction tomography

    DOEpatents

    Lehman, Sean K.

    2012-12-18

    A wave-based tomographic imaging method and apparatus based upon one or more rotating radially outward oriented transmitting and receiving elements have been developed for non-destructive evaluation. At successive angular locations at a fixed radius, a predetermined transmitting element can launch a primary field and one or more predetermined receiving elements can collect the backscattered field in a "pitch/catch" operation. A Hilbert space inverse wave (HSIW) algorithm can construct images of the received scattered energy waves using operating modes chosen for a particular application. Applications include, improved intravascular imaging, bore hole tomography, and non-destructive evaluation (NDE) of parts having existing access holes.

  15. Towards Global Adjoint Tomography

    NASA Astrophysics Data System (ADS)

    Bozdag, E.; Zhu, H.; Peter, D. B.; Tromp, J.

    2012-12-01

    Seismic tomography is at a stage where we can harness entire seismograms using the opportunities offered by advances in numerical wave propagation solvers and high-performance computing. Adjoint methods provide an efficient way for incorporating full nonlinearity of wave propagation and 3D Fréchet kernels in iterative seismic inversions which have so far given promising results at continental and regional scales. Our goal is to take adjoint tomography forward to image the entire planet. Using an iterative conjugate gradient scheme, we initially set the aim to obtain a global crustal and mantle model with confined transverse isotropy in the upper mantle. We have started with around 255 global CMT events having moment magnitudes between 5.8 and 7, and used GSN stations as well as some local networks such as USArray, European stations etc. Prior to the structure inversion, we reinvert global CMT solutions by computing Green functions in our 3D reference model to take into account effects of crustal variations on source parameters. Using the advantages of numerical simulations, our strategy is to invert crustal and mantle structure together to avoid any bias introduced into upper-mantle images due to "crustal corrections", which are commonly used in classical tomography. 3D simulations dramatically increase the usable amount of data so that, with the current earthquake-station setup, we perform each iteration with more than two million measurements. Multi-resolution smoothing based on ray density is applied to the gradient to better deal with the imperfect source-station distribution on the globe and extract more information underneath regions with dense ray coverage and vice versa. Similar to frequency domain approach, we reduce nonlinearities by starting from long periods and gradually increase the frequency content of data after successive model updates. To simplify the problem, we primarily focus on the elastic structure and therefore our measurements are based on

  16. Positron Emission Tomography (PET)

    DOE R&D Accomplishments Database

    Welch, M. J.

    1990-01-01

    Positron emission tomography (PET) assesses biochemical processes in the living subject, producing images of function rather than form. Using PET, physicians are able to obtain not the anatomical information provided by other medical imaging techniques, but pictures of physiological activity. In metaphoric terms, traditional imaging methods supply a map of the body's roadways, its, anatomy; PET shows the traffic along those paths, its biochemistry. This document discusses the principles of PET, the radiopharmaceuticals in PET, PET research, clinical applications of PET, the cost of PET, training of individuals for PET, the role of the United States Department of Energy in PET, and the futures of PET.

  17. Tomography and optical properties of silver nano-inukshuk

    SciTech Connect

    Ghosh, Tanmay; Das, Pabitra; Ghosh, Tapas; Satpati, Biswarup

    2015-06-24

    Following a simple dip-and-rinse galvanic displacement reaction silver nano-inukshuks were prepared directly on germanium surfaces. Morphology, 3-dimensional (3D) structure, chemical composition and optical properties of the silver nanostructurs were investigated using scanning electron microscopy (SEM), scanning transmission electron microscopy (STEM), energy-dispersive X-ray spectroscopy (EDX), and cathodoluminescence (CL) spectroscopy. Exact 3D morphology was reconstructed in the by tomography mode of TEM.

  18. Stripe sensor tomography.

    PubMed

    Barbic, Mladen; Vltava, Lvcian; Barrett, Christopher P; Emery, Teresa H; Scherer, Axel

    2008-03-01

    We introduce a general concept of tomographic imaging for the case of an imaging sensor that has a stripelike shape. We first show that there is no difference, in principle, between two-dimensional tomography using conventional electromagnetic or particle radiation and tomography where a stripe sensor is mechanically scanned over a sample at a sequence of different angles. For a single stripe detector imaging, linear motion and angular rotation are required. We experimentally demonstrate single stripe sensor imaging principle using an elongated inductive coil detector. By utilizing an array of parallel stripe sensors that can be individually addressed, two-dimensional imaging can be performed with rotation only, eliminating the requirement for linear motion, as we also experimentally demonstrate with parallel coil array. We conclude that imaging with a stripe-type sensor of particular width and thickness (where the width is much larger than the thickness) is resolution limited only by the thickness (smaller parameter) of the sensor. We give examples of multiple sensor families where this imaging technique may be beneficial such as magnetoresistive, inductive, superconducting quantum interference device, and Hall effect sensors, and, in particular, discuss the possibilities of the technique in the field of magnetic resonance imaging.

  19. Waste inspection tomography (WIT)

    SciTech Connect

    Bernardi, R.T.

    1995-10-01

    Waste Inspection Tomography (WIT) provides mobile semi-trailer mounted nondestructive examination (NDE) and assay (NDA) for nuclear waste drum characterization. WIT uses various computed tomography (CT) methods for both NDE and NDA of nuclear waste drums. Low level waste (LLW), transuranic (TRU), and mixed radioactive waste can be inspected and characterized without opening the drums. With externally transmitted x-ray NDE techniques, WIT has the ability to identify high density waste materials like heavy metals, define drum contents in two- and three-dimensional space, quantify free liquid volumes through density and x-ray attenuation coefficient discrimination, and measure drum wall thickness. With waste emitting gamma-ray NDA techniques, WIT can locate gamma emitting radioactive sources in two- and three-dimensional space, identify gamma emitting, isotopic species, identify the external activity levels of emitting gamma-ray sources, correct for waste matrix attenuation, provide internal activity approximations, and provide the data needed for waste classification as LLW or TRU.

  20. Positron Emission Tomography.

    PubMed

    Lameka, Katherine; Farwell, Michael D; Ichise, Masanori

    2016-01-01

    Positron emission tomography (PET) is a minimally invasive imaging procedure with a wide range of clinical and research applications. PET allows for the three-dimensional mapping of administered positron-emitting radiopharmaceuticals such as (18)F-fluorodeoxyglucose (for imaging glucose metabolism). PET enables the study of biologic function in both health and disease, in contrast to magnetic resonance imaging (MRI) and computed tomography (CT), that are more suited to study a body's morphologic changes, although functional MRI can also be used to study certain brain functions by measuring blood flow changes during task performance. This chapter first provides an overview of the basic physics principles and instrumentation behind PET methodology, with an introduction to the merits of merging functional PET imaging with anatomic CT or MRI imaging. We then focus on clinical neurologic disorders, and reference research on relevant PET radiopharmaceuticals when applicable. We then provide an overview of PET scan interpretation and findings in several specific neurologic disorders such as dementias, epilepsy, movement disorders, infection, cerebrovascular disorders, and brain tumors. PMID:27432667

  1. Internal tide oceanic tomography

    NASA Astrophysics Data System (ADS)

    Zhao, Zhongxiang

    2016-09-01

    A concept of internal tide oceanic tomography (ITOT) is proposed to monitor ocean warming on a global scale. ITOT is similar to acoustic tomography, but that work waves are internal tides. ITOT detects ocean temperature changes by precisely measuring travel time changes of long-range propagating internal tides. The underlying principle is that upper ocean warming strengthens ocean stratification and thus increases the propagation speed of internal tides. This concept is inspired by recent advances in observing internal tides by satellite altimetry. In particular, a plane wave fit method can separately resolve multiple internal tidal waves and thus accurately determines the phase of each wave. Two examples are presented to demonstrate the feasibility and usefulness of ITOT. In the eastern tropical Pacific, the yearly time series of travel time changes of the M2 internal tide is closely correlated with the El Niño-Southern Oscillation index. In the North Atlantic, significant interannual variations and bidecadal trends are observed and consistent with the changes in ocean heat content measured by Argo floats. ITOT offers a long-term, cost-effective, environmentally friendly technique for monitoring global ocean warming. Future work is needed to quantify the accuracy of this technique.

  2. Computed Tomography Measuring Inside Machines

    NASA Technical Reports Server (NTRS)

    Wozniak, James F.; Scudder, Henry J.; Anders, Jeffrey E.

    1995-01-01

    Computed tomography applied to obtain approximate measurements of radial distances from centerline of turbopump to leading edges of diffuser vanes in turbopump. Use of computed tomography has significance beyond turbopump application: example of general concept of measuring internal dimensions of assembly of parts without having to perform time-consuming task of taking assembly apart and measuring internal parts on coordinate-measuring machine.

  3. 4-D Photoacoustic Tomography

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  4. Global Adjoint Tomography

    NASA Astrophysics Data System (ADS)

    Bozdag, Ebru; Lefebvre, Matthieu; Lei, Wenjie; Peter, Daniel; Smith, James; Komatitsch, Dimitri; Tromp, Jeroen

    2015-04-01

    We will present our initial results of global adjoint tomography based on 3D seismic wave simulations which is one of the most challenging examples in seismology in terms of intense computational requirements and vast amount of high-quality seismic data that can potentially be assimilated in inversions. Using a spectral-element method, we incorporate full 3D wave propagation in seismic tomography by running synthetic seismograms and adjoint simulations to compute exact sensitivity kernels in realistic 3D background models. We run our global simulations on the Oak Ridge National Laboratory's Cray XK7 "Titan" system taking advantage of the GPU version of the SPECFEM3D_GLOBE package. We have started iterations with initially selected 253 earthquakes within the magnitude range of 5.5 < Mw < 7.0 and numerical simulations having resolution down to ~27 s to invert for a transversely isotropic crust and mantle model using a non-linear conjugate gradient algorithm. The measurements are currently based on frequency-dependent traveltime misfits. We use both minor- and major-arc body and surface waves by running 200 min simulations where inversions are performed with more than 2.6 million measurements. Our initial results after 12 iterations already indicate several prominent features such as enhanced slab (e.g., Hellenic, Japan, Bismarck, Sandwich), plume/hotspot (e.g., the Pacific superplume, Caroline, Yellowstone, Hawaii) images, etc. To improve the resolution and ray coverage, particularly in the lower mantle, our aim is to increase the resolution of numerical simulations first going down to ~17 s and then to ~9 s to incorporate high-frequency body waves in inversions. While keeping track of the progress and illumination of features in our models with a limited data set, we work towards to assimilate all available data in inversions from all seismic networks and earthquakes in the global CMT catalogue.

  5. Mapping distributed brain function and networks with diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Eggebrecht, Adam T.; Ferradal, Silvina L.; Robichaux-Viehoever, Amy; Hassanpour, Mahlega S.; Dehghani, Hamid; Snyder, Abraham Z.; Hershey, Tamara; Culver, Joseph P.

    2014-06-01

    Mapping of human brain function has revolutionized systems neuroscience. However, traditional functional neuroimaging by positron emission tomography or functional magnetic resonance imaging cannot be used when applications require portability, or are contraindicated because of ionizing radiation (positron emission tomography) or implanted metal (functional magnetic resonance imaging). Optical neuroimaging offers a non-invasive alternative that is radiation free and compatible with implanted metal and electronic devices (for example, pacemakers). However, optical imaging technology has heretofore lacked the combination of spatial resolution and wide field of view sufficient to map distributed brain functions. Here, we present a high-density diffuse optical tomography imaging array that can map higher-order, distributed brain function. The system was tested by imaging four hierarchical language tasks and multiple resting-state networks including the dorsal attention and default mode networks. Finally, we imaged brain function in patients with Parkinson's disease and implanted deep brain stimulators that preclude functional magnetic resonance imaging.

  6. Quantum-polarization state tomography

    NASA Astrophysics Data System (ADS)

    Bayraktar, Ömer; Swillo, Marcin; Canalias, Carlota; Björk, Gunnar

    2016-08-01

    We propose and demonstrate a method for quantum-state tomography of qudits encoded in the quantum polarization of N -photon states. This is achieved by distributing N photons nondeterministically into three paths and their subsequent projection, which for N =1 is equivalent to measuring the Stokes (or Pauli) operators. The statistics of the recorded N -fold coincidences determines the unknown N -photon polarization state uniquely. The proposed, fixed setup manifestly rules out any systematic measurement errors due to moving components and allows for simple switching between tomography of different states, which makes it ideal for adaptive tomography schemes.

  7. Computed tomography of the body

    SciTech Connect

    Lee, J.K.T.; Stanley, R.J.

    1982-01-01

    By the end of the fourth year of clinical use, the number of articles dealing with computed body tomography (CT) had increased exponentially. Over 100 articles were published during this review period. This chapter examines new application of CT in the neck, musculoskeletal system and the breast. The chapter begins with an examination of the technical aspects of the operation and performance of CT scanners during this review period. The anatomy of various regions of the body, such as neck, chest, liver and biliary system, genitourinary tract, and pelvis are examined. Brief discussions of pediatric computed tomography, computed tomography-guided biopsy, and radiation therapy are presented. (KRM)

  8. What is Computed Tomography?

    MedlinePlus

    ... CT Imaging System back to top Advances in Technology and Clinical Practice Today most CT systems are ... in relatively less time. Another advancement in the technology is electron beam CT, also known as EBCT. ...

  9. Super-sensing through industrial process tomography

    PubMed Central

    2016-01-01

    In this introduction article, we present a brief overview of industrial process tomography. This will start by linking between the concept of industrial process tomography and super-sensing. This will follow with a brief introduction to various process tomography systems and in particular electrical tomography methods. This article is part of the themed issue ‘Supersensing through industrial process tomography’. PMID:27185965

  10. Missing wedge computed tomography by iterative algorithm DIRECTT.

    PubMed

    Kupsch, Andreas; Lange, Axel; Hentschel, Manfred P; Lück, Sebastian; Schmidt, Volker; Grothausmann, Roman; Hilger, André; Manke, Ingo

    2015-01-01

    A strategy to mitigate typical reconstruction artefacts in missing wedge computed tomography is presented. These artefacts appear as elongations of reconstructed details along the mean direction (i.e. the symmetry centre of the projections). Although absent in standard computed tomography applications, they are most prominent in advanced electron tomography and also in special topics of X-ray and neutron tomography under restricted geometric boundary conditions. We investigate the performance of the DIRECTT (Direct Iterative Reconstruction of Computed Tomography Trajectories) algorithm to reduce the directional artefacts in standard procedures. In order to be sensitive to the anisotropic nature of missing wedge artefacts, we investigate isotropic substructures of metal foam as well as circular disc models. Comparison is drawn to filtered backprojection and algebraic techniques. Reference is made to reconstructions of complete data sets. For the purpose of assessing the reconstruction quality, Fourier transforms are employed to visualize the missing wedge directly. Deficient reconstructions of disc models are evaluated by a length-weighted kernel density estimation, which yields the probabilities of boundary orientations. The DIRECTT results are assessed at different signal-to-noise ratios by means of local and integral evaluation parameters. PMID:26367127

  11. Computed tomography of the prostate.

    PubMed

    Van Engelshoven, J M; Kreel, L

    1979-02-01

    The conventional anatomy of the prostate is reviewed and the computed tomography (CT) anatomy described and illustrated. The results of 55 "normal" cases were analyzed for size and relationship to the symphysis pubis, retropubic space, and bladder, as shown on CT sections correlating the features with age and possible urinary symptoms. Attention is also drawn to the differences between phleboliths and prostatic calcification. Computed tomography is an effective method of demonstrating the prostate and surrounding structures and of assessing prostatic enlargement.

  12. Solar tomography adaptive optics.

    PubMed

    Ren, Deqing; Zhu, Yongtian; Zhang, Xi; Dou, Jiangpei; Zhao, Gang

    2014-03-10

    Conventional solar adaptive optics uses one deformable mirror (DM) and one guide star for wave-front sensing, which seriously limits high-resolution imaging over a large field of view (FOV). Recent progress toward multiconjugate adaptive optics indicates that atmosphere turbulence induced wave-front distortion at different altitudes can be reconstructed by using multiple guide stars. To maximize the performance over a large FOV, we propose a solar tomography adaptive optics (TAO) system that uses tomographic wave-front information and uses one DM. We show that by fully taking advantage of the knowledge of three-dimensional wave-front distribution, a classical solar adaptive optics with one DM can provide an extra performance gain for high-resolution imaging over a large FOV in the near infrared. The TAO will allow existing one-deformable-mirror solar adaptive optics to deliver better performance over a large FOV for high-resolution magnetic field investigation, where solar activities occur in a two-dimensional field up to 60'', and where the near infrared is superior to the visible in terms of magnetic field sensitivity.

  13. Multiphoton tomography of astronauts

    NASA Astrophysics Data System (ADS)

    König, Karsten; Weinigel, Martin; Pietruszka, Anna; Bückle, Rainer; Gerlach, Nicole; Heinrich, Ulrike

    2015-03-01

    Weightlessness may impair the astronaut's health conditions. Skin impairments belong to the most frequent health problems during space missions. Within the Skin B project, skin physiological changes during long duration space flights are currently investigated on three European astronauts that work for nearly half a year at the ISS. Measurements on the hydration, the transepidermal water loss, the surface structure, elasticity and the tissue density by ultrasound are conducted. Furthermore, high-resolution in vivo histology is performed by multiphoton tomography with 300 nm spatial and 200 ps temporal resolution. The mobile certified medical tomograph with a flexible 360° scan head attached to a mechano-optical arm is employed to measure two-photon autofluorescence and SHG in the volar forearm of the astronauts. Modification of the tissue architecture and of the fluorescent biomolecules NAD(P)H, keratin, melanin and elastin are detected as well as of SHG-active collagen. Thinning of the vital epidermis, a decrease of the autofluoresence intensity, an increase in the long fluorescence lifetime, and a reduced skin ageing index SAAID based on an increased collagen level in the upper dermis have been found. Current studies focus on recovery effects.

  14. [Optical coherence tomography].

    PubMed

    von Braunmühl, T

    2015-07-01

    Optical coherence tomography (OCT) was introduced in the 1990s in dermatology and is nowadays established as a noninvasive high-resolution technique for the in vivo evaluation of the skin. To date several studies have been successfully demonstrated the application of OCT for various dermatological questions. The main indication for OCT in the daily practice is the noninvasive diagnosis of nonmelanoma skin cancer such as actinic keratosis and basal cell carcinoma. OCT has also been shown to be a valuable tool in treatment monitoring and evaluation of therapeutic success of noninvasive treatment strategies like topical immune modulators or photodynamic treatment. Other potential applications for OCT include inflammatory diseases, microbial or parasitic infestations of the skin, e.g. scabies mites or onychomycosis. In recent years high-definition OCT devices have been developed that can potentially be used for the evaluation of melanocytic lesions and, due to the higher resolution, for the visualization of intrafollicular demodex mites. Furthermore different commercially available devices offer-in addition to the cross-sectional images-a fast-generated horizontal (en face) imaging mode. With respect to resolution and penetration depth the OCT technique is taking a middle position in comparison to other noninvasive imaging devices in dermatology such as sonography and reflectance confocal microscopy. PMID:25809459

  15. [Optical coherence tomography].

    PubMed

    von Braunmühl, T

    2015-07-01

    Optical coherence tomography (OCT) was introduced in the 1990s in dermatology and is nowadays established as a noninvasive high-resolution technique for the in vivo evaluation of the skin. To date several studies have been successfully demonstrated the application of OCT for various dermatological questions. The main indication for OCT in the daily practice is the noninvasive diagnosis of nonmelanoma skin cancer such as actinic keratosis and basal cell carcinoma. OCT has also been shown to be a valuable tool in treatment monitoring and evaluation of therapeutic success of noninvasive treatment strategies like topical immune modulators or photodynamic treatment. Other potential applications for OCT include inflammatory diseases, microbial or parasitic infestations of the skin, e.g. scabies mites or onychomycosis. In recent years high-definition OCT devices have been developed that can potentially be used for the evaluation of melanocytic lesions and, due to the higher resolution, for the visualization of intrafollicular demodex mites. Furthermore different commercially available devices offer-in addition to the cross-sectional images-a fast-generated horizontal (en face) imaging mode. With respect to resolution and penetration depth the OCT technique is taking a middle position in comparison to other noninvasive imaging devices in dermatology such as sonography and reflectance confocal microscopy.

  16. Cardiac Positron Emission Tomography

    PubMed Central

    Geltman, Edward M.

    1985-01-01

    Positron emission tomography (PET) is a new technique for noninvasively assessing myocardial metabolism and perfusion. It has provided new insight into the dynamics of myocardial fatty acid and glucose metabolism in normal subjects, patients with ischemic heart disease and those with cardiomyopathies, documenting regionally depressed fatty acid metabolism during myocardial ischemia and infarction and spatial heterogeneity of fatty acid metabolism in patients with cardiomyopathy. Regional myocardial perfusion has been studied with PET using water, ammonia and rubidium labeled with positron emitters, permitting the noninvasive detection of hypoperfused zones at rest and during vasodilator stress. With these techniques the relationship between perfusion and the metabolism of a variety of substrates has been studied. The great strides that have been made in developing faster high-resolution instruments and producing new labeled intermediates indicate the promise of this technique for facilitating an increase in the understanding of regional metabolism and blood flow under normal and pathophysiologic conditions. ImagesFigure 5.Figure 6.Figure 7.Figure 8.Figure 9. PMID:3879048

  17. Cardiovascular Optical Coherence Tomography

    NASA Astrophysics Data System (ADS)

    Yonetsu, Taishi; Villiger, Martin; Bouma, Brett E.; Jang, Ik-Kyung

    The potential of optical coherence tomography (OCT) for intravascular imaging and assessing the microstructure of atherosclerosis was suggested already by Huang et al. at the very beginning of OCT [1]. For ophthalmology, the eye provides a natural window for OCT to image the retinal microstructure, and OCT has rapidly become the standard imaging modality to diagnose retinal disease and assess disease progression and response to therapy [1, 2]. Intravascular imaging is more invasive by nature and requires imaging through a catheter probe. This has triggered the development of advanced fiber-optic OCT systems with compact, rotating fiber probes, to image the vessel by circumferentially scanning the luminal wall [3, 4]. In 1998, we established the first cardiac OCT research group at the Massachusetts General Hospital to explore the clinical applications of OCT. The first imaging of rabbit aorta was reported by Fujimoto et al. [5], followed by the first swine measurements in vivo by Tearney et al. [6], and finally the first assessment of coronary arteries in patients by Jang et al. [7]. The scope of this chapter is to highlight the steps taken to bring intravascular OCT from bench to bedside over the last 15 years. We will give a general description of atherosclerosis and its pathophysiology and the specific technical implementation of OCT for intravascular imaging through a fiber-optic probe. The motivation is to provide sufficient medical details to provide a basic introduction to the terminology, principles, and challenges of intracoronary imaging.

  18. Doppler Optical Coherence Tomography

    PubMed Central

    Leitgeb, Rainer A.; Werkmeister, René M.; Blatter, Cedric; Schmetterer, Leopold

    2014-01-01

    Optical Coherence Tomography (OCT) has revolutionized ophthalmology. Since its introduction in the early 1990s it has continuously improved in terms of speed, resolution and sensitivity. The technique has also seen a variety of extensions aiming to assess functional aspects of the tissue in addition to morphology. One of these approaches is Doppler OCT (DOCT), which aims to visualize and quantify blood flow. Such extensions were already implemented in time domain systems, but have gained importance with the introduction of Fourier domain OCT. Nowadays phase-sensitive detection techniques are most widely used to extract blood velocity and blood flow from tissues. A common problem with the technique is that the Doppler angle is not known and several approaches have been realized to obtain absolute velocity and flow data from the retina. Additional studies are required to elucidate which of these techniques is most promising. In the recent years, however, several groups have shown that data can be obtained with high validity and reproducibility. In addition, several groups have published values for total retinal blood flow. Another promising application relates to non-invasive angiography. As compared to standard techniques such as fluorescein and indocyanine-green angiography the technique offers two major advantages: no dye is required and depth resolution is required is provided. As such Doppler OCT has the potential to improve our abilities to diagnose and monitor ocular vascular diseases. PMID:24704352

  19. Computerized tomography calibrator

    NASA Technical Reports Server (NTRS)

    Engel, Herbert P. (Inventor)

    1991-01-01

    A set of interchangeable pieces comprising a computerized tomography calibrator, and a method of use thereof, permits focusing of a computerized tomographic (CT) system. The interchangeable pieces include a plurality of nestable, generally planar mother rings, adapted for the receipt of planar inserts of predetermined sizes, and of predetermined material densities. The inserts further define openings therein for receipt of plural sub-inserts. All pieces are of known sizes and densities, permitting the assembling of different configurations of materials of known sizes and combinations of densities, for calibration (i.e., focusing) of a computerized tomographic system through variation of operating variables thereof. Rather than serving as a phanton, which is intended to be representative of a particular workpiece to be tested, the set of interchangeable pieces permits simple and easy standardized calibration of a CT system. The calibrator and its related method of use further includes use of air or of particular fluids for filling various openings, as part of a selected configuration of the set of pieces.

  20. Endoscopic Optical Coherence Tomography

    NASA Astrophysics Data System (ADS)

    Zhou, Chao; Fujimoto, James G.; Tsai, Tsung-Han; Mashimo, Hiroshi

    New gastrointestinal (GI) cancers are expected to affect more than 290,200 new patients and will cause more than 144,570 deaths in the United States in 2013 [1]. When detected and treated early, the 5-year survival rate for colorectal cancer increases by a factor of 1.4 [1]. For esophageal cancer, the rate increases by a factor of 2 [1]. The majority of GI cancers begin as small lesions that are difficult to identify with conventional endoscopy. With resolutions approaching that of histopathology, optical coherence tomography (OCT) is well suited for detecting the changes in tissue microstructure associated with early GI cancers. Since the lesions are not endoscopically apparent, however, it is necessary to survey a relatively large area of the GI tract. Tissue motion is another limiting factor in the GI tract; therefore, in vivo imaging must be performed at extremely high speeds. OCT imaging can be performed using fiber optics and miniaturized lens systems, enabling endoscopic OCT inside the human body in conjunction with conventional video endoscopy. An OCT probe can be inserted through the working channel of a standard endoscope, thus enabling depth-resolved imaging of tissue microstructure in the GI tract with micron-scale resolution simultaneously with the endoscopic view (Fig. 68.1).

  1. Doppler optical coherence tomography.

    PubMed

    Leitgeb, Rainer A; Werkmeister, René M; Blatter, Cedric; Schmetterer, Leopold

    2014-07-01

    Optical Coherence Tomography (OCT) has revolutionized ophthalmology. Since its introduction in the early 1990s it has continuously improved in terms of speed, resolution and sensitivity. The technique has also seen a variety of extensions aiming to assess functional aspects of the tissue in addition to morphology. One of these approaches is Doppler OCT (DOCT), which aims to visualize and quantify blood flow. Such extensions were already implemented in time domain systems, but have gained importance with the introduction of Fourier domain OCT. Nowadays phase-sensitive detection techniques are most widely used to extract blood velocity and blood flow from tissues. A common problem with the technique is that the Doppler angle is not known and several approaches have been realized to obtain absolute velocity and flow data from the retina. Additional studies are required to elucidate which of these techniques is most promising. In the recent years, however, several groups have shown that data can be obtained with high validity and reproducibility. In addition, several groups have published values for total retinal blood flow. Another promising application relates to non-invasive angiography. As compared to standard techniques such as fluorescein and indocyanine-green angiography the technique offers two major advantages: no dye is required and depth resolution is required is provided. As such Doppler OCT has the potential to improve our abilities to diagnose and monitor ocular vascular diseases. PMID:24704352

  2. 3D imaging of nanomaterials by discrete tomography.

    PubMed

    Batenburg, K J; Bals, S; Sijbers, J; Kübel, C; Midgley, P A; Hernandez, J C; Kaiser, U; Encina, E R; Coronado, E A; Van Tendeloo, G

    2009-05-01

    The field of discrete tomography focuses on the reconstruction of samples that consist of only a few different materials. Ideally, a three-dimensional (3D) reconstruction of such a sample should contain only one grey level for each of the compositions in the sample. By exploiting this property in the reconstruction algorithm, either the quality of the reconstruction can be improved significantly, or the number of required projection images can be reduced. The discrete reconstruction typically contains fewer artifacts and does not have to be segmented, as it already contains one grey level for each composition. Recently, a new algorithm, called discrete algebraic reconstruction technique (DART), has been proposed that can be used effectively on experimental electron tomography datasets. In this paper, we propose discrete tomography as a general reconstruction method for electron tomography in materials science. We describe the basic principles of DART and show that it can be applied successfully to three different types of samples, consisting of embedded ErSi(2) nanocrystals, a carbon nanotube grown from a catalyst particle and a single gold nanoparticle, respectively. PMID:19269094

  3. Grid-based representation and dynamic visualization of ionospheric tomography

    NASA Astrophysics Data System (ADS)

    He, L. M.; Yang, Y.; Su, C.; Yu, J. Q.; Yang, F.; Wu, L. X.

    2013-10-01

    The ionosphere is a dynamic system with complex structures. With the development of abundant global navigation satellite systems, the ionospheric electron density in different altitudes and its time variations can be obtained by ionospheric tomography technique using GNSS observations collected by the continuously operating GNSS tracking stations distributed over globe. However, it is difficult to represent and analyze global and local ionospheric electron density variations in three-dimensional (3D) space due to its complex structures. In this paper, we introduce a grid-based system to overcome this constraint. First, we give the principles, algorithms and procedures of GNSS-based ionospheric tomography technique. Then, the earth system spatial grid (ESSG) based on the spheroid degenerated octree grid (SDOG) is introduced in detail. Finally, more than 400 continuously operating GNSS receivers from the International GNSS Service are utilized to realize global ionospheric tomography, and then the ESSG is used to organize and express the tomography results in 4D, including 3 spatial dimensions and time.

  4. HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

    PubMed

    Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

    2015-12-01

    The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography.

  5. THE THERMAL SUNYAEV-ZEL'DOVICH TOMOGRAPHY

    SciTech Connect

    Shao Jiawei; Zhang Pengjie; Lin Weipeng; Jing Yipeng

    2011-04-01

    The thermal Sunyaev-Zel'dovich (tSZ) effect directly measures the thermal pressure of free electrons integrated along the line of sight and thus contains valuable information on the thermal history of the universe. However, the redshift information is entangled in the projection along the line of sight. This projection effect severely degrades the power of the tSZ effect to reconstruct the thermal history. We investigate the tSZ tomography technique to recover this otherwise lost redshift information by cross-correlating the tSZ effect with galaxies of known redshifts, or alternatively with matter distribution reconstructed from weak-lensing tomography. We investigate in detail the three-dimensional distribution of the gas thermal pressure and its relation with the matter distribution, through our adiabatic hydrodynamic simulation and the one with additional gastrophysics including radiative cooling, star formation, and supernova feedback. (1) We find a strong correlation between the gas pressure and matter distribution, with a typical cross-correlation coefficient r {approx}> 0.7 at k {approx}< 3 h Mpc{sup -1} and z < 2. This tight correlation will enable robust cross-correlation measurement between SZ surveys such as Planck, ACT, and SPT and lensing surveys such as DES and LSST, at {approx}>20{sigma}-100{sigma} level. (2) We propose a tomography technique to convert the measured cross-correlation into the contribution from gas in each redshift bin to the tSZ power spectrum. Uncertainties in gastrophysics may affect the reconstruction at {approx}2% level, due to the {approx}1% impact of gastrophysics on r found in our simulations. However, we find that the same gastrophysics affects the tSZ power spectrum at {approx}40% level, so it is robust to infer the gastrophysics from the reconstructed redshift-resolved contribution.

  6. Three dimensional rock microstructures: insights from FIB-SEM tomography

    NASA Astrophysics Data System (ADS)

    Drury, Martyn; Pennock, Gill; de Winter, Matthijs

    2016-04-01

    Most studies of rock microstructures investigate two-dimensional sections or thin slices of three dimensional grain structures. With advances of X-ray and electron tomography methods the 3-D microstructure can be(relatively) routinely investigated on scales from a few microns to cm. 3D studies are needed to investigate the connectivity of microstructures and to test the assumptions we use to calculate 3D properties from 2D sections. We have used FIB-SEM tomography to study the topology of melts in synthetic olivine rocks, 3D crystal growth microstructures, pore networks and subgrain structures. The technique uses a focused ion beam to make serial sections with a spacing of tens to hundreds of nanometers. Each section is then imaged or mapped using the electron beam. The 3D geometry of grains and subgrains can be investigated using orientation contrast or EBSD mapping. FIB-SEM tomography of rocks and minerals can be limited by charging of the uncoated surfaces exposed by the ion beam. The newest generation of FIB-SEMs have much improved low voltage imaging capability allowing high resolution charge free imaging. Low kV FIB-SEM tomography is now widely used to study the connectivity of pore networks. In-situ fluids can also be studied using cryo-FIB-SEM on frozen samples, although special freezing techniques are needed to avoid artifacts produced by ice crystallization. FIB-SEM tomography is complementary, in terms of spatial resolution and sampled volume, to TEM tomography and X-ray tomography, and the combination of these methods can cover a wide range of scales. Our studies on melt topology in synthetic olivine rocks with a high melt content show that many grain boundaries are wetted by nanometre scale melt layers that are too thin to resolve by X-ray tomography. A variety of melt layer geometries occur consistent with several mechanisms of melt layer formation. The nature of melt geometries along triple line junctions and quadruple points can be resolved

  7. Transdimensional Seismic Tomography

    NASA Astrophysics Data System (ADS)

    Bodin, T.; Sambridge, M.

    2009-12-01

    In seismic imaging the degree of model complexity is usually determined by manually tuning damping parameters within a fixed parameterization chosen in advance. Here we present an alternative methodology for seismic travel time tomography where the model complexity is controlled automatically by the data. In particular we use a variable parametrization consisting of Voronoi cells with mobile geometry, shape and number, all treated as unknowns in the inversion. The reversible jump algorithm is used to sample the transdimensional model space within a Bayesian framework which avoids global damping procedures and the need to tune regularisation parameters. The method is an ensemble inference approach, as many potential solutions are generated with variable numbers of cells. Information is extracted from the ensemble as a whole by performing Monte Carlo integration to produce the expected Earth model. The ensemble of models can also be used to produce velocity uncertainty estimates and experiments with synthetic data suggest they represent actual uncertainty surprisingly well. In a transdimensional approach, the level of data uncertainty directly determines the model complexity needed to satisfy the data. Intriguingly, the Bayesian formulation can be extended to the case where data uncertainty is also uncertain. Experiments show that it is possible to recover data noise estimate while at the same time controlling model complexity in an automated fashion. The method is tested on synthetic data in a 2-D application and compared with a more standard matrix based inversion scheme. The method has also been applied to real data obtained from cross correlation of ambient noise where little is known about the size of the errors associated with the travel times. As an example, a tomographic image of Rayleigh wave group velocity for the Australian continent is constructed for 5s data together with uncertainty estimates.

  8. Micromagnetic Tomography in Practice

    NASA Astrophysics Data System (ADS)

    Béguin, A.; de Groot, L. V.; Fabian, K.; Reith, P.; Rastogi, A.; Barnhoorn, A.; Hilgenkamp, H.

    2015-12-01

    Methods to derive paleodirections or paleointensities from rocks currently rely on measurements of bulk samples (typically ~10 cc). The process of recording and storing magnetizations as function of temperature, however, differs for grains of various sizes and chemical compositions. Most rocks, by their mere nature, consist of assemblages of grains varying in size, shape, and chemistry. When dealing with lavas, this differing magnetic behavior often hampers paleointensity experiments; while occasionally a reliable paleodirection is obscured (e.g. Coe et al. (2014)). If we would be able to isolate the contribution of each magnetic grain in a sample to the bulk magnetic moment of that sample, a wealth of opportunities for highly detailed magnetic analysis would be opened, possibly leading to an entirely new approach in retrieving paleomagnetic signals from complex mineralogies. Here we take the first practical steps towards this goal by developing a new technique: 'micromagnetic tomography'. Firstly, the distribution and volume of the remanence carrying grains in the sample must be assessed; this is done using a MicroCT scanner capable of detecting grains >1 micron. Secondly, the magnetic stray field perpendicular to the surface of a thin sample is measured using a high-resolution DC SQUID microscope. A mathematical inversion of these measurements yields the isolated direction and magnitude of the magnetic moment of individual grains in the sample. As the measured strength of the magnetic field decreases with the third power as function of distance to the exerting grain (as a result of decay in three dimensions), grains in the top 10-20 microns of the sample can be assessed reliably.

  9. Medical Electronics and Physiological Measurement.

    ERIC Educational Resources Information Center

    Cochrane, T.

    1989-01-01

    Described are developments in medical electronics and physiological measurement. Discussed are electrocardiology, audiology, and urology as mature applications; applied potential tomography, magnetic stimulation of nerves, and laser Doppler flowmetry as new techniques; and optical sensors, ambulatory monitoring, and biosensors as future…

  10. Database tomography for commercial application

    NASA Technical Reports Server (NTRS)

    Kostoff, Ronald N.; Eberhart, Henry J.

    1994-01-01

    Database tomography is a method for extracting themes and their relationships from text. The algorithms, employed begin with word frequency and word proximity analysis and build upon these results. When the word 'database' is used, think of medical or police records, patents, journals, or papers, etc. (any text information that can be computer stored). Database tomography features a full text, user interactive technique enabling the user to identify areas of interest, establish relationships, and map trends for a deeper understanding of an area of interest. Database tomography concepts and applications have been reported in journals and presented at conferences. One important feature of the database tomography algorithm is that it can be used on a database of any size, and will facilitate the users ability to understand the volume of content therein. While employing the process to identify research opportunities it became obvious that this promising technology has potential applications for business, science, engineering, law, and academe. Examples include evaluating marketing trends, strategies, relationships and associations. Also, the database tomography process would be a powerful component in the area of competitive intelligence, national security intelligence and patent analysis. User interests and involvement cannot be overemphasized.

  11. Double-Difference Adjoint Tomography

    NASA Astrophysics Data System (ADS)

    Yuan, Yanhua O.; Simons, Frederik J.; Tromp, Jeroen

    2016-04-01

    We introduce a double-difference method for the inversion of seismic wavespeed structure by adjoint tomography. Differences between seismic observations and model-based predictions at individual stations may arise from factors other than structural heterogeneity, such as errors in the assumed source-time function, inaccurate timings, and systematic uncertainties. To alleviate the corresponding nonuniqueness in the inverse problem, we construct differential measurements between stations, thereby largely canceling out the source signature and systematic errors. We minimize the discrepancy between observations and simulations in terms of differential measurements made on station pairs. We show how to implement the double-difference concept in adjoint tomography, both theoretically and in practice. We compare the sensitivities of absolute and differential measurements. The former provide absolute information on structure along the ray paths between stations and sources, whereas the latter explain relative (and thus higher-resolution) structural variations in areas close to the stations. Whereas in conventional tomography, a measurement made on a single earthquake-station pair provides very limited structural information, in double-difference tomography, one earthquake can actually resolve significant details of the structure. The double-difference methodology can be incorporated into the usual adjoint tomography workflow by simply pairing up all conventional measurements; the computational cost of the necessary adjoint simulations is largely unaffected. Rather than adding to the computational burden, the inversion of double-difference measurements merely modifies the construction of the adjoint sources for data assimilation.

  12. Imaging of the heart with computed tomography.

    PubMed

    Flohr, Thomas G; Ohnesorge, Bernd M

    2008-03-01

    Imaging of the heart with computed tomography (CT) was already introduced in the 1980Is and has meanwhile entered clinical routine as a consequence of the rapid evolution of CT technology during the last decade. In this review article, we give an overview on the technology and clinical performance of different CT-scanner generations used for cardiac imaging, such as Electron Beam CT (EBCT), single-slice CT und multi-detector row CT (MDCT) with 4, 16 and 64 simultaneously acquired slices. We identify the limitations of current CT-scanners, indicate potential of improvement and discuss alternative system concepts such as CT with area detectors and dual source CT (DSCT). PMID:18324372

  13. 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.

  14. Quantum gate-set tomography

    NASA Astrophysics Data System (ADS)

    Blume-Kohout, Robin

    2014-03-01

    Quantum information technology is built on (1) physical qubits and (2) precise, accurate quantum logic gates that transform their states. Developing quantum logic gates requires good characterization - both in the development phase, where we need to identify a device's flaws so as to fix them, and in the production phase, where we need to make sure that the device works within specs and predict residual error rates and types. This task falls to quantum state and process tomography. But until recently, protocols for tomography relied on a pre-existing and perfectly calibrated reference frame comprising the measurements (and, for process tomography, input states) used to characterize the device. In practice, these measurements are neither independent nor perfectly known - they are usually implemented via exactly the same gates that we are trying to characterize! In the past year, several partial solutions to this self-consistency problem have been proposed. I will present a framework (gate set tomography, or GST) that addresses and resolves this problem, by self-consistently characterizing an entire set of quantum logic gates on a black-box quantum device. In particular, it contains an explicit closed-form protocol for linear-inversion gate set tomography (LGST), which is immune to both calibration error and technical pathologies like local maxima of the likelihood (which plagued earlier methods). GST also demonstrates significant (multiple orders of magnitude) improvements in efficiency over standard tomography by using data derived from long sequences of gates (much like randomized benchmarking). GST has now been applied to qubit devices in multiple technologies. I will present and discuss results of GST experiments in technologies including a single trapped-ion qubit and a silicon quantum dot qubit. Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U

  15. [Computer tomography in acute pyelonephritis].

    PubMed

    Triller, J; Scheidegger, J; Terrier, F

    1983-07-01

    Computer tomography of the kidneys was performed on 30 patients with acute renal infections (acute suppurative pyelonephritis, acute renal abscess, infected cyst, pyelonephrosis, calculus perforation, retroperitoneal abscess). Computer tomography provided more accurate information concerning the extent of the renal and extra-renal inflammatory process than did the urogram or sonogram. This may significantly affect the choice of treatment, particularly concerning the use of drugs or of surgery. Angiography and retrograde pyelography may be used in selected cases, especially where there is a suspicion of acute bacterial nephritis, renal vein thrombosis or ureteric obstruction.

  16. Cardiac Computed Tomography (Multidetector CT, or MDCT)

    MedlinePlus

    ... High Blood Pressure Tools & Resources Stroke More Cardiac Computed Tomography (Multidetector CT, or MDCT) Updated:Sep 3,2015 ... facts MDCT is a very fast type of computed tomography (CT) scan. MDCT creates pictures of the healthy ...

  17. Model-assisted ionospheric tomography: A new algorithm

    SciTech Connect

    Raymund, T.D.; Bresler, Y.; Anderson, D.N.; Daniell, R.E.

    1994-12-01

    Ionospheric tomography uses total electron content (TEC) records collected by longitudinally aligned stations, which receive a beacon satellite orbiting overhead. The electron density distribution is reconstructed for the region bounded by the satellite orbit and the line of ground receivers. A new reconstruction algorithm is describes which satisfies the TEC records, makes use of an ionospheric model, and allows the incorporation of complementary measurements. The new algorithm also accepts relative (rather than absolute) TEC as input data. A comparison of the new algorithm and one used recently shows significant improvement over early techniques, particularly when a scaled ionogram is included in the data.

  18. Anisotropic resistivity tomography

    NASA Astrophysics Data System (ADS)

    Herwanger, J. V.; Pain, C. C.; Binley, A.; de Oliveira, C. R. E.; Worthington, M. H.

    2004-08-01

    , the inversion model is smoother than the true model and the difference in absolute value of anisotropy and conductivity between features is slightly underestimated. Using an anisotropic conductivity distribution aggravates the problem of non-uniqueness of the solution of the inverse electrical problem. This problem can be overcome by applying appropriate structural and anisotropy constraints. We find that running a suite of inversions with varying constraint levels and subsequent examination of the results (including the inspection of residual maps) offers a viable method for choosing appropriate numerical values for the imposed constraints. Inversion of field data reveals a strongly anisotropic subsurface with marked spatial variations of both magnitude of anisotropy and conductivity. Average conductivities range from 0.001 S m-1 (= 1000 Ω m) to 0.003 S m-1 (= 333 Ω m) and anisotropy values range from 0 per cent to more than 300 per cent. As an independent test of the reliability of the structures revealed by anisotropic electric tomography, anisotropic seismic traveltime tomograms were calculated. We find a convincing structural agreement between the two independently derived images. Areas of high electric anisotropy coincide with seismically anisotropic areas and we observe an anticorrelation between electric conductivity and seismic velocity. Both observations are consistent with anisotropy anomalies caused by fracturing or layering.

  19. Atom Probe Tomography of Geomaterials

    NASA Astrophysics Data System (ADS)

    Parman, S. W.; Diercks, D.; Gorman, B.; Cooper, R. F.

    2013-12-01

    From the electron microprobe to the secondary ion microprobe to laser-ablation ICP-MS, steady improvements in the spatial resolution and detection limits of geochemical micro-analysis have been central to generating new discoveries. Atom probe tomography (APT) is a relatively new technology that promises nm-scale spatial resolution (in three dimensions) with ppm level detection limits. The method is substantially different from traditional beam-based (electron, ion, laser) methods. In APT, the sample is shaped (usually with a dual-beam FIB) into a needle with typical dimensions of 1-2 μm height and 100-200 nm diameter. Within the atom probe, the needle is evaporated one atom (ideally) at a time by a high electric field (ten's of V per square nm at the needle tip). A femtosecond laser (12 ps pulse width) is used to assist in evaporating non-conducting samples. The two-dimensional detector locates where the atom was released from the needle's surface and so can reconstruct the positions of all detected atoms in three dimensions. It also records the time of flight of the ion, which is used to calculate the mass/charge ratio of the ion. We will discuss our results analyzing a range of geologic materials. In one case, naturally occurring platinum group alloys (PGA) from the Josephine Ophiolite have been imaged. Such alloys are of interest as recorders of the Os heterogeneity of the mantle [1,2]. Optimal ablation was achieved with a laser power of 120-240 pJ and laser pulse rates 500 kHz. Runs were stopped after 10 million atoms were imaged. An example analysis is: Pt 61(1), Fe 26.1(9), Rh 1.20(4), Ir 7.0(7), Ni 2.65(8), Ru 0.20(9), Cu 1.22(8), Co 0.00029(5). Values are in atomic %; values in parentheses are one-sigma standard deviations on five separate needles from the same FIB lift-out, which was 30 μm long. Assuming the sample is homogenous over the 30 μm from which the needle was extracted, the analyses suggest relative errors for major elements below 5% and for

  20. Computed tomography of intramuscular myxoma

    SciTech Connect

    Ekelund, L.; Herrlin, K.; Rydholm, A.

    1982-11-01

    Computed tomography (CT) was performed in seven patients with intramuscular myxoma. All lesions were well demarcated, of homogeneous appearance and attenuation values ranging from 10 to 60 (HU). The tumor size, as estimated at CT, correlated well with the size of the surgical specimen, which is in contrast to the findings in some high grade malignant sarcomas.

  1. X-ray Computed Tomography.

    ERIC Educational Resources Information Center

    Michael, Greg

    2001-01-01

    Describes computed tomography (CT), a medical imaging technique that produces images of transaxial planes through the human body. A CT image is reconstructed mathematically from a large number of one-dimensional projections of a plane. The technique is used in radiological examinations and radiotherapy treatment planning. (Author/MM)

  2. Multi-wavelength fluorescence tomography

    NASA Astrophysics Data System (ADS)

    Kwong, Tiffany C.; Lo, Pei-An; Cho, Jaedu; Nouizi, Farouk; Chiang, Huihua K.; Kim, Chang-Seok; Gulsen, Gultekin

    2016-03-01

    The strong scattering and absorption of light in biological tissue makes it challenging to model the propagation of light, especially in deep tissue. This is especially true in fluorescent tomography, which aims to recover the internal fluorescence source distribution from the measured light intensities on the surface of the tissue. The inherently ill-posed and underdetermined nature of the inverse problem along with strong tissue scattering makes Fluorescence Tomography (FT) extremely challenging. Previously, multispectral detection fluorescent tomography (FT) has been shown to improve the image quality of FT by incorporating the spectral filtering of biological tissue to provide depth information to overcome the inherent absorption and scattering limitations. We investigate whether multi-wavelength fluorescent tomography can be used to distinguish the signals from multiple fluorophores with overlapping fluorescence spectrums using a unique near-infrared (NIR) swept laser. In this work, a small feasibility study was performed to see whether multi-wavelength FT can be used to detect subtle shifts in the absorption spectrum due to differences in fluorophore microenvironment.

  3. Computed tomography:the details.

    SciTech Connect

    Doerry, Armin Walter

    2007-07-01

    Computed Tomography (CT) is a well established technique, particularly in medical imaging, but also applied in Synthetic Aperture Radar (SAR) imaging. Basic CT imaging via back-projection is treated in many texts, but often with insufficient detail to appreciate subtleties such as the role of non-uniform sampling densities. Herein are given some details often neglected in many texts.

  4. Maximum entropy beam diagnostic tomography

    SciTech Connect

    Mottershead, C.T.

    1985-01-01

    This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore. 11 refs., 4 figs.

  5. Constrained Deformable-Layer Tomography

    NASA Astrophysics Data System (ADS)

    Zhou, H.

    2006-12-01

    The improvement on traveltime tomography depends on improving data coverage and tomographic methodology. The data coverage depends on the spatial distribution of sources and stations, as well as the extent of lateral velocity variation that may alter the raypaths locally. A reliable tomographic image requires large enough ray hit count and wide enough angular range between traversing rays over the targeted anomalies. Recent years have witnessed the advancement of traveltime tomography in two aspects. One is the use of finite frequency kernels, and the other is the improvement on model parameterization, particularly that allows the use of a priori constraints. A new way of model parameterization is the deformable-layer tomography (DLT), which directly inverts for the geometry of velocity interfaces by varying the depths of grid points to achieve a best traveltime fit. In contrast, conventional grid or cell tomography seeks to determine velocity values of a mesh of fixed-in-space grids or cells. In this study, the DLT is used to map crustal P-wave velocities with first arrival data from local earthquakes and two LARSE active surveys in southern California. The DLT solutions along three profiles are constrained using known depth ranges of the Moho discontinuity at 21 sites from a previous receiver function study. The DLT solutions are generally well resolved according to restoration resolution tests. The patterns of 2D DLT models of different profiles match well at their intersection locations. In comparison with existing 3D cell tomography models in southern California, the new DLT models significantly improve the data fitness. In comparison with the multi-scale cell tomography conducted for the same data, while the data fitting levels of the DLT and the multi-scale cell tomography models are compatible, the DLT provides much higher vertical resolution and more realistic description of the undulation of velocity discontinuities. The constraints on the Moho depth

  6. Double-difference Adjoint Tomography

    NASA Astrophysics Data System (ADS)

    Yuan, Y. O.; Simons, F. J.; Tromp, J.

    2015-12-01

    We introduce the "double-difference" method, hugely popular in source inversion, in adjoint tomography. Differences between seismic observations and simulations may be explained in terms of many factors besides structural heterogeneity, e.g., errors in the source-time function, inaccurate timing, and systematic uncertainties. To alleviate nonuniqueness in the inverse problem, we make a differential measurement between stations, which largely cancels out the source signature and systematic errors. We seek to minimize the difference between differential measurements of observations and simulations at distinct stations. We show how to implement the double-difference concept in adjoint tomography, both theoretically and in practice. In contrast to conventional inversions aiming to maximize absolute agreement between observations and simulations, by differencing pairs of measurements at distinct locations, we obtain gradients of the new differential misfit function with respect to structural perturbations which are relatively insensitive to an incorrect source signature or timing errors. Furthermore, we analyze sensitivities of absolute and differential measurements. The former provide absolute information on structure along the ray paths between stations and sources, whereas the latter explain relative (and thus high-resolution) structural variations in areas close to the stations. In conventional tomography, one earthquake provides very limited structural resolution, as reflected in a misfit gradient consisting of "streaks" between the stations and the source. In double-difference tomography, one earthquake can actually resolve significant details of the structure, i.e., the double-differences provide a hugely powerful constraint on structural variations. Algorithmically, we incorporate the double-difference concept into the conventional adjoint tomography workflow by simply pairing up all regular measurements. Thus, the computational cost of the related adjoint

  7. Three-Dimensional Optical Coherence Tomography

    NASA Technical Reports Server (NTRS)

    Gutin, Mikhail; Wang, Xu-Ming; Gutin, Olga

    2009-01-01

    Three-dimensional (3D) optical coherence tomography (OCT) is an advanced method of noninvasive infrared imaging of tissues in depth. Heretofore, commercial OCT systems for 3D imaging have been designed principally for external ophthalmological examination. As explained below, such systems have been based on a one-dimensional OCT principle, and in the operation of such a system, 3D imaging is accomplished partly by means of a combination of electronic scanning along the optical (Z) axis and mechanical scanning along the two axes (X and Y) orthogonal to the optical axis. In 3D OCT, 3D imaging involves a form of electronic scanning (without mechanical scanning) along all three axes. Consequently, the need for mechanical adjustment is minimal and the mechanism used to position the OCT probe can be correspondingly more compact. A 3D OCT system also includes a probe of improved design and utilizes advanced signal- processing techniques. Improvements in performance over prior OCT systems include finer resolution, greater speed, and greater depth of field.

  8. White-light diffraction tomography of unlabelled live cells

    NASA Astrophysics Data System (ADS)

    Kim, Taewoo; Zhou, Renjie; Mir, Mustafa; Babacan, S. Derin; Carney, P. Scott; Goddard, Lynford L.; Popescu, Gabriel

    2014-03-01

    We present a technique called white-light diffraction tomography (WDT) for imaging microscopic transparent objects such as live unlabelled cells. The approach extends diffraction tomography to white-light illumination and imaging rather than scattering plane measurements. Our experiments were performed using a conventional phase contrast microscope upgraded with a module to measure quantitative phase images. The axial dimension of the object was reconstructed by scanning the focus through the object and acquiring a stack of phase-resolved images. We reconstructed the three-dimensional structures of live, unlabelled, red blood cells and compared the results with confocal and scanning electron microscopy images. The 350 nm transverse and 900 nm axial resolution achieved reveals subcellular structures at high resolution in Escherichia coli cells. The results establish WDT as a means for measuring three-dimensional subcellular structures in a non-invasive and label-free manner.

  9. En-face polarization-sensitive optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Cucu, Radu G.; Podoleanu, Adrian Gh.; Rosen, Richard B.; Boxer, Aaron B.; Jackson, David A.

    2003-10-01

    We report the first (to the best of out knowledge) en face polarization sensitive optical coherence tomography (PS-OCT) system. The transverse raster scanning of the target is achieved using a pair of galvo-scanner mirrors. The set-up is based on incoherent detection in two optical and electronic channels and employs balanced detection to reduce the excess photon noise generated by the low coherence source (superluminescent diode). The outputs of the two channels are processed using software to provide a polarisation insensitive (pure reflectivity) image and a birefringence retardation map. Images from ex vivo (human tooth) and in vivo targets (human retina) have been acquired. Particulars of en face optical coherence tomography imaging of birefringent tissue are discussed.

  10. Mantle dynamics and seismic tomography.

    PubMed

    Tanimoto, T; Lay, T

    2000-11-01

    Three-dimensional imaging of the Earth's interior, called seismic tomography, has achieved breakthrough advances in the last two decades, revealing fundamental geodynamical processes throughout the Earth's mantle and core. Convective circulation of the entire mantle is taking place, with subducted oceanic lithosphere sinking into the lower mantle, overcoming the resistance to penetration provided by the phase boundary near 650-km depth that separates the upper and lower mantle. The boundary layer at the base of the mantle has been revealed to have complex structure, involving local stratification, extensive structural anisotropy, and massive regions of partial melt. The Earth's high Rayleigh number convective regime now is recognized to be much more interesting and complex than suggested by textbook cartoons, and continued advances in seismic tomography, geodynamical modeling, and high-pressure-high-temperature mineral physics will be needed to fully quantify the complex dynamics of our planet's interior.

  11. Computed tomography of the abdomen.

    PubMed

    Leslie, E V; Panaro, V A; Alker, G J; Oh, Y S

    1980-01-01

    In a few short years, computed tomography has become an important diagnostic procedure in the examination of the abdomen and pelvis. Its forte lies in its ability to provide cross-sectional views of excellent anatomical detail. Imaging of deep-seated structures such as the pancreas, adrenal glands, and enlarged retroperitoneal lymph nodes is now possible. The ability to distinguish small variations in tissue density enables the radiologist to evaluate the texture of solid structures, and to differentiate them from cysts or abscesses. The addition of contrast enhancement makes it possible to determine the vascularity of a lesson. The major limitation of CT is poorer delineation of structures in thin patients, and in patients in whom voluntary and involuntary motion cannot be interrupted. Computed tomography is compared with other complementary imaging procedures to include sonography, radionuclide imaging, and conventional radiograph procedures. It has replaced invasive diagnostic procedures in many instances. In a given situation, one or more imaging modalities may be appropriate.

  12. Quantum Process Tomography for Energy Transfer Systems via Ultrafast Spectroscopy

    NASA Astrophysics Data System (ADS)

    Yuen-Zhou, Joel

    2012-02-01

    The description of excited state dynamics in energy transfer systems constitutes a theoretical and experimental challenge in modern chemical physics. A spectroscopic protocol that systematically characterizes both coherent and dissipative processes of the probed chromophores is desired [1,2]. In this talk, I show that a set of two-color photon-echo experiments performs quantum state tomography (QST) of the one-exciton manifold of a dimer by reconstructing its density matrix in real time. This possibility in turn allows for a complete description of excited state dynamics via quantum process tomography (QPT). Simulations of a noisy QPT experiment for an inhomogeneously broadened ensemble of model excitonic dimers show that the protocol distills rich information about dissipative excitonic dynamics, which appears nontrivially hidden in the signal monitored in single realizations of four-wave mixing experiments Progress on the experimental side will be discussed, as well as new insights that QPT has offered on the understanding of 2D electronic and vibrational spectroscopy. [1] J. Yuen-Zhou, J. J. Krich, A. Aspuru-Guzik, Quantum state and process tomography of energy transfer systems via ultrafast spectroscopy Joel Yuen-Zhou, Jacob J. Krich, Masoud Mohseni and Al'an Aspuru-Guzik Proc. Nat. Acad. Sci. USA, Early Edition (2011). [2] J. Yuen-Zhou, A. Aspuru-Guzik, Quantum process tomography of molecular dimers from two-dimensional electronic spectroscopy I: General theory and application to homodimers Joel Yuen-Zhou and Al'an Aspuru-Guzik . Chem. Phys. 134, 134505 (2011).

  13. Neutron tomography developments and applications.

    PubMed

    Richards, W J; Gibbons, M R; Shields, K C

    2004-10-01

    Neutron radiography has been in use as a nondestructive testing technique for the past 50 years. The neutrons' unique ability to image certain elements and isotopes that are either completely undetectable or poorly detected by other NDI methods makes neutron radiography an important tool for the NDI community. Neutron radiography like other imaging techniques takes a number of different forms (i.e., film, radioscopic, transfer methods, tomography, etc.) This paper will describe the neutron tomography system developed at the University of California, Davis McClellan Nuclear Radiation Center (UC Davis/MNRC), and the applications for both research and commercial uses. The neutron radiography system at the UC Davis/MNRC has been under development for 4 years. The initial system was developed to find very low concentrations of hydrogen (i.e., <200 ppm). In order to achieve these low detection levels, it was necessary to perform both pre- and post-processing of the tomographs. The pre-processing steps include corrections for spatial resolution and random noise effects. Images are corrected for systematic noise errors and beam hardening. From these data the attenuation coefficient is calculated. The post-processing steps include alignment of the collected images, determining the center of mass, and, finally, using the filtered back-projection routine from the Donner Algorithms Library to obtain the final images. Since its initial development, the tomography system has been used very successfully to find low levels of hydrogen in a metal matrix. Further uses of the system have been to verify the exact placement, in three dimensions, of "O-rings" in large metal valve bodies, and to map the location and extent of veins in porous and high-density rocks of various different kinds. These examples show that neutron tomography is becoming a needed inspection technique for the 21st century. PMID:15246398

  14. Computed tomography of gynecologic diseases

    SciTech Connect

    Gross, B.H.; Moss, A.A.; Mihara, K.; Goldberg, H.I.; Glazer, G.M.

    1983-10-01

    Although computed tomography (CT) provides superb images of all areas of the body, sonography, because of its lack of ionizing radiation and its real-time and multiplanar capacities, has become the preferred initial method of evaluating the female pelvis. This has resulted in a relative paucity of information in the literature concerning CT features of benign pelvic disorders in particular and prompted the authors to review our experience with third-generation CT scanning of the uterus and ovaries.

  15. Cranial computed tomography and MRI

    SciTech Connect

    Lee, S.H.; Rao, K.C.V.G.

    1987-01-01

    This book appears to be a hybrid between an atlas and a text. The second edition attempts to depict the current status of both computed tomography (CT) and magnetic resonance (MR) imaging in neuroradiology. Although only the final chapter of the book is completely devoted to cranial MR imaging, MR images are scattered throughout various other chapters. There is coverage of the major anatomic and pathophysiologic entities. There are 17 chapters with images, tables, and diagrams.

  16. Hermaphroditism demonstrated by computed tomography

    SciTech Connect

    Gale, M.E.

    1983-07-01

    The categorization of disorders of gender differentiation is based on chromosome analysis, physical examination, gonadal histology, and endocrine evaluation. In most cases of hermaphroditism, radiologic studies have been limited to assessment of associated urinary tract anomalies before surgical revconstruction. Noninvasive evaluation with computed tomography (CT) or sonography is potentially useful for investigation of internal pelvic anatomy in these cases. A case report of a 65-year-old man is reported. (KRM)

  17. Inherent Limitations of Hydraulic Tomography

    USGS Publications Warehouse

    Bohling, G.C.; Butler, J.J.

    2010-01-01

    We offer a cautionary note in response to an increasing level of enthusiasm regarding high-resolution aquifer characterization with hydraulic tomography. We use synthetic examples based on two recent field experiments to demonstrate that a high degree of nonuniqueness remains in estimates of hydraulic parameter fields even when those estimates are based on simultaneous analysis of a number of carefully controlled hydraulic tests. We must, therefore, be careful not to oversell the technique to the community of practicing hydrogeologists, promising a degree of accuracy and resolution that, in many settings, will remain unattainable, regardless of the amount of effort invested in the field investigation. No practically feasible amount of hydraulic tomography data will ever remove the need to regularize or bias the inverse problem in some fashion in order to obtain a unique solution. Thus, along with improving the resolution of hydraulic tomography techniques, we must also strive to couple those techniques with procedures for experimental design and uncertainty assessment and with other more cost-effective field methods, such as geophysical surveying and, in unconsolidated formations, direct-push profiling, in order to develop methods for subsurface characterization with the resolution and accuracy needed for practical field applications. Copyright ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

  18. FIB–SEM tomography of 4th generation PWA 1497 superalloy

    SciTech Connect

    Ziętara, Maciej Kruk, Adam Gruszczyński, Adam Czyrska-Filemonowicz, Aleksandra

    2014-01-15

    The effect of creep deformation on the microstructure of the PWA 1497 single crystal Ni-base superalloy developed for turbine blade applications was investigated. The aim of the present study was to characterize quantitatively a superalloy microstructure and subsequent development of rafted γ′ precipitates in the PWA 1497 during creep deformation at 982 °C and 248 MPa up to rupture. The PWA1497 microstructure was characterized by scanning electron microscopy and FIB–SEM electron tomography. The 3D reconstruction of the PWA1497 microstructure is presented and discussed. - Highlights: • The microstructure of PWA1497 superalloy was examined using FIB–SEM tomography. • In case of modern single crystal superalloys, measurements of A{sub A} are adequate for V{sub V}. • During creep the γ channel width increases from 65 to 193 nm for ruptured specimen. • Tomography is a useful technique for quantitative studies of material microstructure.

  19. On the Correlation Between Fatigue Striation Spacing and Crack Growth Rate: A Three-Dimensional (3-D) X-ray Synchrotron Tomography Study

    NASA Astrophysics Data System (ADS)

    Williams, Jason J.; Yazzie, Kyle E.; Connor Phillips, N.; Chawla, Nikhilesh; Xiao, Xinghui; de Carlo, Francesco; Iyyer, Nagaraja; Kittur, Maddan

    2011-12-01

    In situ three-dimensional (3-D) X-ray synchrotron tomography of fatigue crack growth was conducted in a 7075-T6 aluminum alloy. Local measurements of da/ dN were possible with the 3-D data sets obtained from tomography. A comparison with fatigue striation spacings obtained from scanning electron microscopy of the fracture surfaces yielded excellent correlation with da/ dN obtained from tomography. The X-ray tomography technique can be used to obtain a highly accurate and representative measurements of crack growth locally in the microstructure of the material.

  20. Finite Quantum Tomography and Semidefinite Programming

    NASA Astrophysics Data System (ADS)

    Mirzaee, M.; Rezaee, M.; Jafarizadeh, M. A.

    2007-06-01

    Using the convex semidefinite programming method and superoperator formalism we obtain the finite quantum tomography of some mixed quantum states such as: truncated coherent states tomography, phase tomography and coherent spin state tomography, qudit tomography, N-qubit tomography, where that obtained results are in agreement with those of References (Buzek et al., Chaos, Solitons and Fractals 10 (1999) 981; Schack and Caves, Separable states of N quantum bits. In: Proceedings of the X. International Symposium on Theoretical Electrical Engineering, 73. W. Mathis and T. Schindler, eds. Otto-von-Guericke University of Magdeburg, Germany (1999); Pegg and Barnett Physical Review A 39 (1989) 1665; Barnett and Pegg Journal of Modern Optics 36 (1989) 7; St. Weigert Acta Physica Slov. 4 (1999) 613).

  1. Computed tomography of the genitourinary tract.

    PubMed

    Stanley, R J; Sagel, S S; Fair, W R

    1978-06-01

    Eighteen months of experience with computed body tomography have revealed that this radiologic modality is useful in the diagnostic evaluation and management of urologic patients. Renal masses, perirenal lesions, poorly functioning kidneys, pelvic tumors and associated retroperitoneal nodal spread and other diagnostic problems related to the urinary tract have been imaged successfully with computed body tomography. Accuracy is high in the differentiation of benign renal cysts from renal neoplasms. Tumor staging and computed body tomography is being explored currently.

  2. Complete Tem-Tomography: 3D Structure of Gems Cluster

    NASA Technical Reports Server (NTRS)

    Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

    2015-01-01

    GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

  3. Therapy response evaluation with positron emission tomography-computed tomography.

    PubMed

    Segall, George M

    2010-12-01

    Positron emission tomography-computed tomography with F-18-fluorodeoxyglucose is widely used for evaluation of therapy response in patients with solid tumors but has not been as readily adopted in clinical trials because of the variability of acquisition and processing protocols and the absence of universal response criteria. Criteria proposed for clinical trials are difficult to apply in clinical practice, and gestalt impression is probably accurate in individual patients, especially with respect to the presence of progressive disease and complete response. Semiquantitative methods of determining tissue glucose metabolism, such as standard uptake value, can be a useful descriptor for levels of tissue glucose metabolism and changes in response to therapy if technical quality control measures are carefully maintained. The terms partial response, complete response, and progressive disease are best used in clinical trials in which the terms have specific meanings and precise definitions. In clinical practice, it may be better to use descriptive terminology agreed upon by imaging physicians and clinicians in their own practice. PMID:21147376

  4. Bayesian statistical ionospheric tomography improved by incorporating ionosonde measurements

    NASA Astrophysics Data System (ADS)

    Norberg, Johannes; Virtanen, Ilkka I.; Roininen, Lassi; Vierinen, Juha; Orispää, Mikko; Kauristie, Kirsti; Lehtinen, Markku S.

    2016-04-01

    We validate two-dimensional ionospheric tomography reconstructions against EISCAT incoherent scatter radar measurements. Our tomography method is based on Bayesian statistical inversion with prior distribution given by its mean and covariance. We employ ionosonde measurements for the choice of the prior mean and covariance parameters and use the Gaussian Markov random fields as a sparse matrix approximation for the numerical computations. This results in a computationally efficient tomographic inversion algorithm with clear probabilistic interpretation. We demonstrate how this method works with simultaneous beacon satellite and ionosonde measurements obtained in northern Scandinavia. The performance is compared with results obtained with a zero-mean prior and with the prior mean taken from the International Reference Ionosphere 2007 model. In validating the results, we use EISCAT ultra-high-frequency incoherent scatter radar measurements as the ground truth for the ionization profile shape. We find that in comparison to the alternative prior information sources, ionosonde measurements improve the reconstruction by adding accurate information about the absolute value and the altitude distribution of electron density. With an ionosonde at continuous disposal, the presented method enhances stand-alone near-real-time ionospheric tomography for the given conditions significantly.

  5. A limited-view-tomography for plasma diagnostics.

    NASA Astrophysics Data System (ADS)

    Denisova, Natalja

    2001-10-01

    In recent years progress in plasma diagnostics has led to the wide use of techniques and algorithms of computerized tomography. An important problem in the diagnostics of a plasma as a spectroscopic source is the determination of spatial distributions of the coefficients of emission (or absorption), which are directly related to the temperature and particle density. There are several methods for the reconstruction of the spatial distributions of the emission (absorption) coefficients from the integrated intensities. This paper describes a Maximum Entropy (ME) algorithm which seems especially attractive in the experimental situations when the number of views is strongly limited.The researcher should have enough justifications for reconstruction from a few views. This problem is discussed with reference to the reconstruction from two views of soft x-ray emissivity profiles in W7-AS stellarator.On the other hand, in experiments of this type there is usually some additional information which can be incorporated into the ME reconstruction algorithm. The crucial role of prior information is illustrated in reconstruction of a spatial distribution of electron density in a laser-produced plasma in a strong transverse magnetic field. References 1.Denisova N.V.Maximum-entropy-based tomography for gas and plasma diagnostics J.Phys.D:Appl.Phys. 31 (1998) 1888-1895. 1.Denisova N.V.Two-view tomography J.Phys.D.:Appl.Phys. 33 (2000) 313-319.

  6. RPC: from High Energy Physics to Positron Emission Tomography

    NASA Astrophysics Data System (ADS)

    Belli, G.; DeVecchi, C.; Giroletti, E.; Musitelli, G.; Nardò, R.; Necchi, M. M.; Pagano, D.; Ratti, S. P.; Riccardi, C.; Sani, G.; Torre, P.; Vitulo, P.; Viviani, C.

    2006-05-01

    A low cost gas-based charged particle detector, the Resistive Plate Counter (RPC) intensively used in fixed target and collider high energy experiments, is proposed as basic detector for Positron Emission Tomography. The performance of RPCs in terms of intrinsic space and time resolution and electronic pulse height response, makes it possible to transform standard RPCs into photon detectors and therefore to compensate for the photon sensitivity of scintillating crystals, when the efficiency of the complex crystal + photomultiplier is turned into standard quantum efficiency (q.e). Prototype multigap glass RPCs were developed which optimize γ detection efficiency and thus might substitute the traditional scintillators setups.

  7. X-ray computerized tomography

    SciTech Connect

    Wellington, S.L.; Vinegar, H.J.

    1987-08-01

    Computerized tomography (CT) is a new radiological imaging technique that measures density and atomic composition inside opaque objects. A revolutionary advance in medical radiology since 1972, CT has only recently been applied in petrophysics and reservoir engineering. This paper discusses several petrophysical applications, including three-dimensional (3D) measurement of density and porosity; rock mechanics studies; correlation of core logs with well logs; characterization of mud invasion, fractures, and disturbed core; and quantification of complex mineralogies and sand/shale ratios. Reservoir engineering applications presented include fundamental studies of CO/sub 2/ displacement in cores, focussing on viscous fingering, gravity segregation, miscibility, and mobility control.

  8. Scanning color optical tomography (SCOT)

    PubMed Central

    Hosseini, Poorya; Sung, Yongjin; Choi, Youngwoon; Lue, Niyom; Yaqoob, Zahid; So, Peter

    2015-01-01

    We have developed an interferometric optical microscope that provides three-dimensional refractive index map of a specimen by scanning the color of three illumination beams. Our design of the interferometer allows for simultaneous measurement of the scattered fields (both amplitude and phase) of such a complex input beam. By obviating the need for mechanical scanning of the illumination beam or detection objective lens; the proposed method can increase the speed of the optical tomography by orders of magnitude. We demonstrate our method using polystyrene beads of known refractive index value and live cells. PMID:26367632

  9. Coherent amplified optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhang, Jun; Rao, Bin; Chen, Zhongping

    2007-07-01

    A technique to improve the signal-to-noise ratio (SNR) of a high speed 1300 nm swept source optical coherence tomography (SSOCT) system was demonstrated. A semiconductor optical amplifier (SOA) was employed in the sample arm to coherently amplify the weak light back-scattered from sample tissue without increasing laser power illuminated on the sample. The image quality improvement was visualized and quantified by imaging the anterior segment of a rabbit eye at imaging speed of 20,000 A-lines per second. The theory analysis of SNR gain is given followed by the discussion on the technologies that can further improve the SNR gain.

  10. Computed tomography of fibrous dysplasia

    SciTech Connect

    Daffner, R.H.; Kirks, D.R.; Gehweiler, J.A. Jr.; Heaston, D.K.

    1982-11-01

    Skeletal fibrous dysplasia produces changes that are usually readily recognized on plain radiographs. Occasionally, routine radiography may not demonstrate the characteristic appearance of the disease. The density of abormal bone in craniofacial fibrous dysplasia may preclude adequate assessment of areas where soft-tissue impingement may occur. Computed tomography (CT) is useful in demonstrating the amorphous ''ground-glass'' texture of the lesion and in defining the extent of craniofacial disease including impingement upon orbital structures. CT was useful in five patients with fibrous dysplasia in whom the nature or extent of involvement was not entirely clear.

  11. Scanning color optical tomography (SCOT).

    PubMed

    Hosseini, Poorya; Sung, Yongjin; Choi, Youngwoon; Lue, Niyom; Yaqoob, Zahid; So, Peter

    2015-07-27

    We have developed an interferometric optical microscope that provides three-dimensional refractive index map of a specimen by scanning the color of three illumination beams. Our design of the interferometer allows for simultaneous measurement of the scattered fields (both amplitude and phase) of such a complex input beam. By obviating the need for mechanical scanning of the illumination beam or detection objective lens; the proposed method can increase the speed of the optical tomography by orders of magnitude. We demonstrate our method using polystyrene beads of known refractive index value and live cells. PMID:26367632

  12. Dual-energy computed tomography.

    PubMed

    Furlow, Bryant

    2015-01-01

    Dual-energy computed tomography (DECT) yields precise anatomic and functional images by exploiting differences in the interactions of high- and low-energy photon spectra with different tissues' and materials' atomic components to more precisely differentiate the chemistry of tissues and disease processes than is possible with traditional single-energy CT scan acquisitions. This article introduces the history of DECT, its physical basis, scanner designs, radiation dose considerations, and postprocessing techniques. DECT's clinical applications also are described, and this relatively new imaging modality's clinical limitations and future prospects are discussed.

  13. NEUTRON IMAGING, RADIOGRAPHY AND TOMOGRAPHY.

    SciTech Connect

    SMITH,G.C.

    2002-03-01

    Neutrons are an invaluable probe in a wide range of scientific, medical and commercial endeavors. Many of these applications require the recording of an image of the neutron signal, either in one-dimension or in two-dimensions. We summarize the reactions of neutrons with the most important elements that are used for their detection. A description is then given of the major techniques used in neutron imaging, with emphasis on the detection media and position readout principle. Important characteristics such as position resolution, linearity, counting rate capability and sensitivity to gamma-background are discussed. Finally, the application of a subset of these instruments in radiology and tomography is described.

  14. Computed tomography of parosteal osteosarcoma

    SciTech Connect

    Hudson, T.M.; Springfield, D.S.; Benjamin, M.; Bertoni, F.; Present, D.A.

    1985-05-01

    Twelve patients with parosteal osteosarcomas were evaluated by computed tomography (CT). CT accurately defined the extent of the tumors for purposes of surgical planning, although tumor bone often could not be distinguished from thickened host bone. Nine tumors invaded the medullary cavity, a feature that implies a poorer prognosis when the tumor also contains high-grade areas. Six CT studies accurately detected the medullary invasion, but three did not. Lucent areas within dense tumors contained either benign tissue or high- or low-grade tumor; CT did not differentiate among these different tissues. CT also did not reveal small satellite nodules of tumor beyond the main tumor mass.

  15. Positron Emission Tomography: A Basic Analysis

    NASA Astrophysics Data System (ADS)

    Kerbacher, M. E.; Deaton, J. W.; Phinney, L. C.; Mitchell, L. J.; Duggan, J. L.

    2007-10-01

    Positron Emission Tomography is useful in detecting biological abnormalities. The technique involves attaching radiotracers to a material used inside the body, in many cases glucose. Glucose is absorbed most readily in areas of unusual cell growth or uptake of nutrients so through natural processes the treated glucose highlights regions of tumors and other degenerative disorders such as Alzheimer's disease. The higher the concentration of isotopes, the more dynamic the area. Isotopes commonly used as tracers are 11C, 18F, 13N, and 15O due to their easy production and short half-lives. Once the tracers have saturated an area of tissue they are detected using coincidence detectors collinear with individual isotopes. As the isotope decays it emits a positron which, upon annihilating an electron, produces two oppositely directioned gamma rays. The PET machine consists of several pairs of detectors, each 180 degrees from their partner detector. When the oppositely positioned detectors are collinear with the area of the isotope, a computer registers the location of the isotope and can compile an image of the activity of the highlighted area based on the position and strength of the isotopes.

  16. Reconstruction of limited computed tomography data of fuel cell components using Direct Iterative Reconstruction of Computed Tomography Trajectories

    NASA Astrophysics Data System (ADS)

    Lange, Axel; Kupsch, Andreas; Hentschel, Manfred P.; Manke, Ingo; Kardjilov, Nikolay; Arlt, Tobias; Grothausmann, Roman

    CT (computed tomography) reconstructions of fuel cell components of a yet unrivaled spatial resolution and quality are presented. This is achieved by application of the novel DIRECTT (Direct Iterative Reconstruction of Computed Tomography Trajectories) algorithm. We focus on two different key issues which essentially rule the fuel cell's durability on different length scales and physical interactions. On the resolution scale of some 100 μm agglomerations of condensed water in flow-field channels are detected by means of quasi- in situ neutron CT (after operation). Five orders of magnitude below nanometer sized Ru catalyst particles on carbon black support are visualized by electron tomography. Both types of experiments are especially adapted to the type of material involved but they are accompanied by severe deviations from ideal CT measuring conditions, as well. In order to overcome the tremendous reconstruction artifacts of standard algorithms, we employ DIRECTT which is described in detail. Comparisons of DIRECTT reconstructions to the conventional filtered back projection, prove the significant improvements in both experimental methods.

  17. Precision-Guaranteed Quantum Tomography

    NASA Astrophysics Data System (ADS)

    Sugiyama, Takanori; Turner, Peter S.; Murao, Mio

    2013-10-01

    Quantum state tomography is currently the standard tool for verifying that a state prepared in the lab is close to an ideal target state, but up to now there have been no rigorous methods for evaluating the precision of the state preparation in tomographic experiments. We propose a new estimator for quantum state tomography, and prove that the (always physical) estimates will be close to the true prepared state with a high probability. We derive an explicit formula for evaluating how high the probability is for an arbitrary finite-dimensional system and explicitly give the one- and two-qubit cases as examples. This formula applies for any informationally complete sets of measurements, arbitrary finite number of data sets, and general loss functions including the infidelity, the Hilbert-Schmidt, and the trace distances. Using the formula, we can evaluate not only the difference between the estimated and prepared states, but also the difference between the prepared and target states. This is the first result directly applicable to the problem of evaluating the precision of estimation and preparation in quantum tomographic experiments.

  18. Computerized Heavy-Ion Tomography

    NASA Astrophysics Data System (ADS)

    Holley, W. R.; Tobias, C. A.; Fabrikant, J. I.; Llacer, J.; Chu, W. T.; Benton, E. V.

    1981-07-01

    Several techniques for heavy-ion computerized tomography are being investigated at Lawrence Berkeley Laboratory. Using beams of carbon and neon from the Bevalac, we have demonstrated that these methods are feasible and capable of high resolution. We describe in some detail the method of heavy-ion CT imaging using nuclear track detectors, including a discussion of procedures for optical scanning and digitization of data and computerized distortion corrections. Comparisons between a heavy-ion CT image and X-ray CT image of a simple phantom are discussed. Preliminary results from two techniques using active, online detector systems for performing heavy-ion computerized tomography are presented. One method uses a multiplane, multiwire ionization chamber for detecting the heavy ions in a mode allowing true three-dimensional reconstructions. The other technique uses a system of position-sensitive silicon solid-state detectors for spacial information and high-purity germanium detectors to measure accurately the residual energy of the ions.

  19. Numerical tests of stochastic tomography

    NASA Astrophysics Data System (ADS)

    Ru-Shan, Wu; Xiao-Bi, Xie

    1991-05-01

    The method of stochastic tomography proposed by Wu is tested numerically. This method reconstructs the heterospectra (power spectra of heterogeneities) at all depths of a non-uniform random medium using measured joint transverse-angular coherence functions (JTACF) of transmission fluctuations on an array. The inversion method is based on a constrained least-squares inversion implemented via the singular value decomposition. The inversion is also applicable to reconstructions using transverse coherence functions (TCF) or angular coherence functions (ACF); these are merely special cases of JTACF. Through the analysis of sampling functions and singular values, and through numerical examples of reconstruction using theoretically generated coherence functions, we compare the resolution and robustness of reconstructions using TCF, ACF and JTACF. The JTACF can `focus' the coherence analysis at different depths and therefore has a better depth resolution than TCF and ACF. In addition, the JTACF contains much more information than the sum of TCF and ACF, and has much better noise resistance properties than TCF and ACF. Inversion of JTACF can give a reliable reconstruction of heterospectra at different depths even for data with 20% noise contamination. This demonstrates the feasibility of stochastic tomography using JTACF.

  20. Multiphoton tomography for tissue engineering

    NASA Astrophysics Data System (ADS)

    König, Karsten

    2008-02-01

    Femtosecond laser multiphoton tomography has been employed in the field of tissue engineering to perform 3D high-resolution imaging of the extracellular matrix proteins elastin and collagen as well as of living cells without any fixation, slicing, and staining. Near infrared 80 MHz picojoule femtosecond laser pulses are able to excite the endogenous fluorophores NAD(P)H, flavoproteins, melanin, and elastin via a non-resonant two-photon excitation process. In addition, collagen can be imaged by second harmonic generation. Using a two-PMT detection system, the ratio of elastin to collagen was determined during optical sectioning. A high submicron spatial resolution and 50 picosecond temporal resolution was achieved using galvoscan mirrors and piezodriven focusing optics as well as a time-correlated single photon counting module with a fast microchannel plate detector and fast photomultipliers. Multiphoton tomography has been used to optimize the tissue engineering of heart valves and vessels in bioincubators as well as to characterize artificial skin. Stem cell characterization and manipulation are of major interest for the field of tissue engineering. Using the novel sub-20 femtosecond multiphoton nanoprocessing laser microscope FemtOgene, the differentiation of human stem cells within spheroids has been in vivo monitored with submicron resolution. In addition, the efficient targeted transfection has been demonstrated. Clinical studies on the interaction of tissue-engineered products with the natural tissue environment can be performed with in vivo multiphoton tomograph DermaInspect.

  1. Unpowered wireless ultrasound tomography system

    NASA Astrophysics Data System (ADS)

    Zahedi, Farshad; Huang, Haiying

    2016-04-01

    In this paper, an unpowered wireless ultrasound tomography system is presented. The system consists of two subsystems; the wireless interrogation unit (WIU) and three wireless nodes installed on the structure. Each node is designed to work in generation and sensing modes, but operates at a specific microwave frequency. Wireless transmission of the ultrasound signals between the WIU and the wireless nodes is achieved by converting ultrasound signals to microwave signals and vice versa, using a microwave carrier signal. In the generation mode, both a carrier signal and an ultrasound modulated microwave signal are transmitted to the sensor nodes. Only the node whose operating frequency matches the carrier signal will receive these signals and demodulate them to recover the original ultrasound signal. In the sensing mode, a microwave carrier signal with two different frequency components matching the operating frequencies of the sensor nodes is broadcasted by the WIU. The sensor nodes, in turn, receive the corresponding carrier signals, modulate it with the ultrasound sensing signal, and wirelessly transmit the modulated signal back to the WIU. The demodulation of the sensing signals is performed in the WIU using a digital signal processing. Implementing a software receiver significantly reduces the complexity and the cost of the WIU. A wireless ultrasound tomography system is realized by interchanging the carrier frequencies so that the wireless transducers can take turn to serve as the actuator and sensors.

  2. Spectral partitioning in diffraction tomography

    SciTech Connect

    Lehman, S K; Chambers, D H; Candy, J V

    1999-06-14

    The scattering mechanism of diffraction tomography is described by the integral form of the Helmholtz equation. The goal of diffraction tomography is to invert this equation in order to reconstruct the object function from the measured scattered fields. During the forward propagation process, the spatial spectrum of the object under investigation is ''smeared,'' by a convolution in the spectral domain, across the propagating and evanescent regions of the received field. Hence, care must be taken in performing the reconstruction, as the object's spectral information has been moved into regions where it may be considered to be noise rather than useful information. This will reduce the quality and resolution of the reconstruction. We show haw the object's spectrum can be partitioned into resolvable and non-resolvable parts based upon the cutoff between the propagating and evanescent fields. Operating under the Born approximation, we develop a beam-forming on transmit approach to direct the energy into either the propagating or evanescent parts of the spectrum. In this manner, we may individually interrogate the propagating and evanescent regions of the object spectrum.

  3. [Research on Electrical Impedance Tomography Technology].

    PubMed

    Chang, Feiba; Zhang, Hehua; Yan, Lexian; Yin, Jun

    2016-01-01

    This article reviews the principle of electrical impedance tomography imaging and measurement system; focuses on electrical impedance tomography imaging detection system of incentive mode and several typical image reconstruction algorithm of electrical impedance imaging; and objectively compares and effectively evaluates several image reconstruction algorithm.

  4. Electron radiography

    DOEpatents

    Merrill, Frank E.; Morris, Christopher

    2005-05-17

    A system capable of performing radiography using a beam of electrons. Diffuser means receive a beam of electrons and diffuse the electrons before they enter first matching quadrupoles where the diffused electrons are focused prior to the diffused electrons entering an object. First imaging quadrupoles receive the focused diffused electrons after the focused diffused electrons have been scattered by the object for focusing the scattered electrons. Collimator means receive the scattered electrons and remove scattered electrons that have scattered to large angles. Second imaging quadrupoles receive the collimated scattered electrons and refocus the collimated scattered electrons and map the focused collimated scattered electrons to transverse locations on an image plane representative of the electrons' positions in the object.

  5. Dose fractionation theorem in 3-D reconstruction (tomography)

    SciTech Connect

    Glaeser, R.M.

    1997-02-01

    It is commonly assumed that the large number of projections for single-axis tomography precludes its application to most beam-labile specimens. However, Hegerl and Hoppe have pointed out that the total dose required to achieve statistical significance for each voxel of a computed 3-D reconstruction is the same as that required to obtain a single 2-D image of that isolated voxel, at the same level of statistical significance. Thus a statistically significant 3-D image can be computed from statistically insignificant projections, as along as the total dosage that is distributed among these projections is high enough that it would have resulted in a statistically significant projection, if applied to only one image. We have tested this critical theorem by simulating the tomographic reconstruction of a realistic 3-D model created from an electron micrograph. The simulations verify the basic conclusions of high absorption, signal-dependent noise, varying specimen contrast and missing angular range. Furthermore, the simulations demonstrate that individual projections in the series of fractionated-dose images can be aligned by cross-correlation because they contain significant information derived from the summation of features from different depths in the structure. This latter information is generally not useful for structural interpretation prior to 3-D reconstruction, owing to the complexity of most specimens investigated by single-axis tomography. These results, in combination with dose estimates for imaging single voxels and measurements of radiation damage in the electron microscope, demonstrate that it is feasible to use single-axis tomography with soft X-ray microscopy of frozen-hydrated specimens.

  6. X-ray tensor tomography

    NASA Astrophysics Data System (ADS)

    Malecki, A.; Potdevin, G.; Biernath, T.; Eggl, E.; Willer, K.; Lasser, T.; Maisenbacher, J.; Gibmeier, J.; Wanner, A.; Pfeiffer, F.

    2014-02-01

    Here we introduce a new concept for x-ray computed tomography that yields information about the local micro-morphology and its orientation in each voxel of the reconstructed 3D tomogram. Contrary to conventional x-ray CT, which only reconstructs a single scalar value for each point in the 3D image, our approach provides a full scattering tensor with multiple independent structural parameters in each volume element. In the application example shown in this study, we highlight that our method can visualize sub-pixel fiber orientations in a carbon composite sample, hence demonstrating its value for non-destructive testing applications. Moreover, as the method is based on the use of a conventional x-ray tube, we believe that it will also have a great impact in the wider range of material science investigations and in future medical diagnostics. The authors declare no competing financial interests.

  7. [Computer tomography of sports injuries].

    PubMed

    Reiser, M; Rupp, N

    1984-01-01

    Computed tomography (CT) provides axial slices plane and shows excellent details of bones and different soft tissues, favoring its use in traumatic lesions caused by sporting activities. Complex anatomical structures such as the shoulder, the vertebral column, the pelvis, the knee, the tarsal and carpal bones are often better recognized in detail than by conventional radiography. Fracture lines, localization of bone fragments and involvement of soft tissues are clearly demonstrated. Luxations and bone changes leading to luxations can be shown. CT arthrography provides for the first time a direct visualization of joint cartilage and of cruciate ligaments in the knee joint, so traumatic lesions such as chondropathia patellae or rupture of the cruciate ligaments are shown with a high degree of reliability.

  8. Electrical Impedance Tomography of Electrolysis

    PubMed Central

    Meir, Arie; Rubinsky, Boris

    2015-01-01

    The primary goal of this study is to explore the hypothesis that changes in pH during electrolysis can be detected with Electrical Impedance Tomography (EIT). The study has relevance to real time control of minimally invasive surgery with electrolytic ablation. To investigate the hypothesis, we compare EIT reconstructed images to optical images acquired using pH-sensitive dyes embedded in a physiological saline agar gel phantom treated with electrolysis. We further demonstrate the biological relevance of our work using a bacterial E.Coli model, grown on the phantom. The results demonstrate the ability of EIT to image pH changes in a physiological saline phantom and show that these changes correlate with cell death in the E.coli model. The results are promising, and invite further experimental explorations. PMID:26039686

  9. High speed laser tomography system.

    PubMed

    Samsonov, D; Elsaesser, A; Edwards, A; Thomas, H M; Morfill, G E

    2008-03-01

    A high speed laser tomography system was developed capable of acquiring three-dimensional (3D) images of optically thin clouds of moving micron-sized particles. It operates by parallel-shifting an illuminating laser sheet with a pair of galvanometer-driven mirrors and synchronously recording two-dimensional (2D) images of thin slices of the imaged volume. The maximum scanning speed achieved was 120,000 slices/s, sequences of 24 volume scans (up to 256 slices each) have been obtained. The 2D slices were stacked to form 3D images of the volume, then the positions of the particles were identified and followed in the consecutive scans. The system was used to image a complex plasma with particles moving at speeds up to cm/s.

  10. Positron emission tomography wrist detector

    DOEpatents

    Schlyer, David J.; O'Connor, Paul; Woody, Craig; Junnarkar, Sachin Shrirang; Radeka, Veljko; Vaska, Paul; Pratte, Jean-Francois

    2006-08-15

    A method of serially transferring annihilation information in a compact positron emission tomography (PET) scanner includes generating a time signal representing a time-of-occurrence of an annihilation event, generating an address signal representing a channel detecting the annihilation event, and generating a channel signal including the time and address signals. The method also includes generating a composite signal including the channel signal and another similarly generated channel signal concerning another annihilation event. An apparatus that serially transfers annihilation information includes a time signal generator, address signal generator, channel signal generator, and composite signal generator. The time signal is asynchronous and the address signal is synchronous to a clock signal. A PET scanner includes a scintillation array, detection array, front-end array, and a serial encoder. The serial encoders include the time signal generator, address signal generator, channel signal generator, and composite signal generator.

  11. Optical coherence tomography in dermatology

    NASA Astrophysics Data System (ADS)

    Sattler, Elke; Kästle, Raphaela; Welzel, Julia

    2013-06-01

    Optical coherence tomography (OCT) is a noninvasive diagnostic method that offers a view into the superficial layers of the skin in vivo in real-time. An infrared broadband light source allows the investigation of skin architecture and changes up to a depth of 1 to 2 mm with a resolution between 15 and 3 μm, depending on the system used. Thus OCT enables evaluation of skin lesions, especially nonmelanoma skin cancers and inflammatory diseases, quantification of skin changes, visualization of parasitic infestations, and examination of other indications such as the investigation of nails. OCT provides a quick and useful diagnostic imaging technique for a number of clinical questions and is a valuable addition or complement to other noninvasive imaging tools such as dermoscopy, high-frequency ultrasound, and confocal laser scan microscopy.

  12. Photoacoustic tomography: principles and advances

    PubMed Central

    Xia, Jun; Yao, Junjie; Wang, Lihong V.

    2014-01-01

    Photoacoustic tomography (PAT) is an emerging imaging modality that shows great potential for preclinical research and clinical practice. As a hybrid technique, PAT is based on the acoustic detection of optical absorption from either endogenous chromophores, such as oxy-hemoglobin and deoxy-hemoglobin, or exogenous contrast agents, such as organic dyes and nanoparticles. Because ultrasound scatters much less than light in tissue, PAT generates high-resolution images in both the optical ballistic and diffusive regimes. Over the past decade, the photoacoustic technique has been evolving rapidly, leading to a variety of exciting discoveries and applications. This review covers the basic principles of PAT and its different implementations. Strengths of PAT are highlighted, along with the most recent imaging results. PMID:25642127

  13. High speed laser tomography system.

    PubMed

    Samsonov, D; Elsaesser, A; Edwards, A; Thomas, H M; Morfill, G E

    2008-03-01

    A high speed laser tomography system was developed capable of acquiring three-dimensional (3D) images of optically thin clouds of moving micron-sized particles. It operates by parallel-shifting an illuminating laser sheet with a pair of galvanometer-driven mirrors and synchronously recording two-dimensional (2D) images of thin slices of the imaged volume. The maximum scanning speed achieved was 120,000 slices/s, sequences of 24 volume scans (up to 256 slices each) have been obtained. The 2D slices were stacked to form 3D images of the volume, then the positions of the particles were identified and followed in the consecutive scans. The system was used to image a complex plasma with particles moving at speeds up to cm/s. PMID:18377040

  14. State tomography via weak measurements

    PubMed Central

    Wu, Shengjun

    2013-01-01

    Recent work has revealed that the wave function of a pure state can be measured directly and that complementary knowledge of a quantum system can be obtained simultaneously by weak measurements. However, the original scheme applies only to pure states, and it is not efficient because most of the data are discarded by post-selection. Here, we propose tomography schemes for pure states and for mixed states via weak measurements, and our schemes are more efficient because we do not discard any data. Furthermore, we demonstrate that any matrix element of a general state can be directly read from an appropriate weak measurement. The density matrix (with all of its elements) represents all that is directly accessible from a general measurement. PMID:23378924

  15. Collimator-free photon tomography

    DOEpatents

    Dilmanian, F. Avraham; Barbour, Randall L.

    1998-10-06

    A method of uncollimated single photon emission computed tomography includes administering a radioisotope to a patient for producing gamma ray photons from a source inside the patient. Emissivity of the photons is measured externally of the patient with an uncollimated gamma camera at a plurality of measurement positions surrounding the patient for obtaining corresponding energy spectrums thereat. Photon emissivity at the plurality of measurement positions is predicted using an initial prediction of an image of the source. The predicted and measured photon emissivities are compared to obtain differences therebetween. Prediction and comparison is iterated by updating the image prediction until the differences are below a threshold for obtaining a final prediction of the source image.

  16. Collimator-free photon tomography

    DOEpatents

    Dilmanian, F.A.; Barbour, R.L.

    1998-10-06

    A method of uncollimated single photon emission computed tomography includes administering a radioisotope to a patient for producing gamma ray photons from a source inside the patient. Emissivity of the photons is measured externally of the patient with an uncollimated gamma camera at a plurality of measurement positions surrounding the patient for obtaining corresponding energy spectrums thereat. Photon emissivity at the plurality of measurement positions is predicted using an initial prediction of an image of the source. The predicted and measured photon emissivities are compared to obtain differences therebetween. Prediction and comparison is iterated by updating the image prediction until the differences are below a threshold for obtaining a final prediction of the source image. 6 figs.

  17. Single photon emission computed tomography

    SciTech Connect

    Piez, C.W. Jr.; Holman, B.L.

    1985-07-01

    Single photon emission computed tomography (SPECT) is becoming an increasingly important part of routine clinical nuclear medicine. By providing tomographic reconstructions in multiple planes through the patient, SPECT expands the clinical applications in nuclear medicine as well as providing better contrast, edge definition and separation of target from background activities. Imaging techniques have been developed for the evaluation of regional cerebral blood flow using radiolabeled amines. Thus, cerebral functional imaging can be used in the diagnosis of acute cerebral infarction, cerebral vascular disease, dementia and epilepsy. SPECT plays a complementary role in the evaluation of coronary artery disease, particularly when it is coupled with thallium-201 and exercise testing. SPECT extends our diagnostic capabilities in additional areas, such as liver and bone scintigraphy as well as tumor imaging with gallium-67.

  18. Catheters for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Atif, M.; Ullah, H.; Hamza, M. Y.; Ikram, M.

    2011-09-01

    The objective of this review article is to overview technology, clinical evidence, and future applications to date optical coherence tomography (OCT) probes to yield the diagnostic purpose. We have reviewed the designing, construction and working of different categories of OCT probes developed for optical diagnostics having a potential for non invasive and improved detection of different types of cancer as well as other neoplasm. Rotational and balloon catheters, imaging needles and hand-held, linear scanning, multichannel, micro electro mechanical systems (MEMS) technology based, dynamic focusing, forward view imaging, and common path interferometer based probes have been discussed in details. The fiber probes have shown excellent performance for two dimensional and three dimensional higher resolution, cross-sectional imaging of interior and exterior body tissues that can be compared with histopathology to provide the information about the angiogenesis and other lesions in the tissue. The MEMS-technology based probes are found to be more suitable for three dimensional morphological imaging.

  19. Tomography studies of volcanic complexes

    NASA Astrophysics Data System (ADS)

    Koulakov, I.; Gordeev, E. I.; West, M.; Yeguas, A. G.; Luehr, B.-G.; Jakovlev, A.

    2012-04-01

    We present an overview of recent results of seismic tomography studies of different volcanic complexes performed in collaboration with different research teams. In first three examples corresponding to Central Andes, areas around Merapi volcano and Toba caldera, the tomographic images down to 100-200 km depth reveal the paths of fluids and melts which escape from the subducting plate and feed the arc volcanoes. In all these areas, the shapes of the paths are different depending on particular features of the subduction regimes, such as type of the overriding plate, age of the slab, rate of the subduction etc. Next group of studies covers detailed tomographic studies of local structures beneath selected volcanoes. Beneath the Spurr Volcano (Alaska) we clearly observe a thin vertical channel with anomalously high Vp/Vs ratio beneath the main cone. Beneath the volcanoes of Kluchevskoy group (Kamchatka) seismic images reveal complex structure of channels and intermediate magma reservoirs. In the mantle we detect an anomaly with very high Vp/Vs ratio reaching 2.2, which looks as a top of the mantle channel feeding the volcanoes of the group. For this group we observed the time variations of seismic structure based on more than 10 years of continuous data. We detect considerable variations in Vp/Vs ratio in the crust related to large eruptions of Kluchevskoy and Bezymyanny volcanoes in 2005. The last example is another time-lapse tomography model obtained for the El Hierro volcano in Canaries based on earthquake swarm occurred from July to October 2011. During this period we observe regular deepening of a large body with high Vp/Vs ratio, which is interpreted as a magma reservoir, together with lowering of seismicity.

  20. Polarization Sensitive Optical Coherence Tomography

    NASA Astrophysics Data System (ADS)

    Park, B. Hyle; de Boer, Johannes F.

    Optical coherence tomography (OCT) is an interferometric technique capable of noninvasive high-resolution cross-sectional imaging by measuring the intensity of light reflected from within tissue [1]. This results in a noncontact imaging modality that provides images similar in scale and geometry to histology. Just as different stains can be used to enhance the contrast in histology, various extensions of OCT allow for visualization of features not readily apparent in traditional OCT. For example, optical Doppler tomography [2] can enable depth-resolved imaging of flow by observing differences in phase between successive depth scans [3-5]. This chapter will focus on polarization-sensitive OCT (PS-OCT), which utilizes depth-dependent changes in the polarization state of detected light to determine the light-polarization changing properties of a sample [6-11]. These properties, including birefringence, dichroism, and optic axis orientation, can be determined directly by studying the depth evolution of Stokes parameters [7-10, 12-16] or indirectly by using the changing reflected polarization states to first determine Jones or Mueller matrices [11, 17-21]. PS-OCT has been used in a wide variety of applications, including correlating burn depth with a decrease in birefringence [14], measuring the birefringence of the retinal nerve fiber layer [22, 23], and monitoring the onset and progression of caries lesions [24]. In this chapter, a discussion of polarization theory and its application to PS-OCTwill be followed by clinical uses of the technology and will conclude with mentionof more recent work and future directions of PS-OCT.