scholarly journals Novel nonlinear reconstruction method with grey-level quantisation units for electron tomography

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Norio Baba ◽  
Kenji Kaneko ◽  
Misuzu Baba
Keyword(s):  
Cross Section ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Reconstruction Technique ◽  
Reconstruction Method ◽  
Back Projection ◽  
Grey Level ◽  
Discrete Processing ◽  
Structural Image ◽  
Tomography Reconstruction

AbstractWe report a new computed tomography reconstruction method, named quantisation units reconstruction technique (QURT), applicable to electron and other fields of tomography. Conventional electron tomography methods such as filtered back projection, weighted back projection, simultaneous iterative reconstructed technique, etc. suffer from the ‘missing wedge’ problem due to the limited tilt-angle range. QURT demonstrates improvements to solve this problem by recovering a structural image blurred due to the missing wedge and substantially reconstructs the structure even if the number of projection images is small. QURT reconstructs a cross-section image by arranging grey-level quantisation units (QU pieces) in three-dimensional image space via unique discrete processing. Its viability is confirmed by model simulations and experimental results. An important difference from recently developed methods such as discrete algebraic reconstruction technique (DART), total variation regularisation—DART, and compressed sensing is that prior knowledge of the conditions regarding the specimen or the expected cross-section image is not necessary.

Three-dimensional organization of chromatin fibers in situ examined by EM tomography

1992 ◽  
Vol 50 (1) ◽  
pp. 498-499
Author(s):  
C.L. Woodcock ◽  
R.A. Horowitz ◽  
D.A. Agard
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Image Data ◽  
Back Projection ◽  
Pixel Size ◽  
Ccd Array ◽  
Chromatin Fibers ◽  
Patiria Miniata ◽  
Em Tomography

Electron tomography is being used to understand the 3D organization of chromatin in situ. As demonstrated previously, the nuclei of Patiria miniata (starfish) sperm contain particularly well-defined chromatin fibers. These studies are being extended through the analysis of 3D reconstructions of material embedded at low temperature in Lowicryl K11M and contrasted with osmium ammine-B, which preferentially stains nucleic acids. Tilt series of sections were recorded at 150KV, over an angular range of +/−75° and tilt increment of 2.5° using a Philips EM430. Image data were collected directly using a 1024x1024 CCD array with 2x2 binning to give a final pixel size of 1.3nm. Gold beads deposited on the sections were used for alignment, and reconstruction was by weighted back projection. Six volumes totalling 0.48um and containing numerous chromatin fibers have been examined utilizing Voxel View (Vital Images, Fairfield Iowa) software running on a Silicon Graphics Iris 4D workstation.

scholarly journals Quantifying Morphology and Diffusion Properties of Mesoporous Carbon From High-Fidelity 3D Reconstructions

2019 ◽  
Vol 25 (4) ◽  
pp. 891-902 ◽  
Author(s):  
Wu Wang ◽  
Artur Svidrytski ◽  
Di Wang ◽  
Alberto Villa ◽  
Horst Hahn ◽  
...  
Keyword(s):  
Mesoporous Carbon ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Morphological Description ◽  
Reconstruction Technique ◽  
Reconstruction Algorithms ◽  
Scanning Transmission ◽  
Dimensional Reconstruction ◽  
Iterative Reconstruction Technique ◽  
Diffusion Properties

AbstractA reliable quantitative analysis in electron tomography, which depends on the segmentation of the three-dimensional reconstruction, is challenging because of constraints during tilt-series acquisition (missing wedge) and reconstruction artifacts introduced by reconstruction algorithms such as the Simultaneous Iterative Reconstruction Technique (SIRT) and Discrete Algebraic Reconstruction Technique (DART). We have carefully evaluated the fidelity of segmented reconstructions analyzing a disordered mesoporous carbon used as support in catalysis. Using experimental scanning transmission electron microscopy (STEM) tomography data as well as realistic phantoms, we have quantitatively analyzed the effect on the morphological description as well as on diffusion properties (based on a random-walk particle-tracking simulation) to understand the role of porosity in catalysis. The morphological description of the pore structure can be obtained reliably both using SIRT and DART reconstructions even in the presence of a limited missing wedge. However, the measured pore volume is sensitive to the threshold settings, which are difficult to define globally for SIRT reconstructions. This leads to noticeable variations of the diffusion coefficients in the case of SIRT reconstructions, whereas DART reconstructions resulted in more reliable data. In addition, the anisotropy of the determined diffusion properties was evaluated, which was significant in the presence of a limited missing wedge for SIRT and strongly reduced for DART.

scholarly journals Rapid Method for Electron Tomographic Reconstruction and Three-Dimensional Modeling of the Murine Synapse Using an Automated Fiducial Marker-Free System

2013 ◽  
Vol 19 (S5) ◽  
pp. 182-187 ◽  
Author(s):  
Hyun-wook Kim ◽  
Seung Hak Oh ◽  
Namkug Kim ◽  
Eiko Nakazawa ◽  
Im Joo Rhyu
Keyword(s):  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
3D Models ◽  
Three Dimension ◽  
Synaptic Organization ◽  
Back Projection ◽  
Virtual Image ◽  
Free System ◽  
Three Dimensional Modeling

AbstractElectron tomography (ET) has recently afforded new insights into neuronal architecture. However, the tedious process of sample preparation, image acquisition, alignment, back projection, and additional segmentation process of ET repels beginners. We have tried Hitachi's commercial packages integrated with a Hitachi H-7650 TEM to examine the potential of using an automated fiducial-less approach for our own neuroscience research. Semi-thick sections (200–300 nm) were cut from blocks of fixed mouse (C57BL) cerebellum and prepared for ET. Sets of images were collected automatically as each section was tilted by 2° increments (±60°). “Virtual” image volumes were computationally reconstructed in three dimension (3D) with the EMIP software using either the commonly used “weighted back-projection” (WBP) method or “topography-based reconstruction” (TBR) algorithm for comparison. Computed tomograms using the TBR were more precisely reconstructed compared with the WBP method. Following reconstruction, the image volumes were imported into the 3D editing software A-View and segmented according to synaptic organization. The detailed synaptic components were revealed by very thin virtual image slices; 3D models of synapse structure could be constructed efficiently. Overall, this simplified system provided us with a graspable tool for pursuing ET studies in neuroscience.

Generation of grain maps by an algebraic reconstruction technique

2003 ◽  
Vol 36 (4) ◽  
pp. 1062-1068 ◽  
Author(s):  
H. F. Poulsen ◽  
Xiaowei Fu
Keyword(s):  
Grain Boundaries ◽  
Three Dimensional ◽  
Reconstruction Technique ◽  
Reconstruction Method ◽  
Layer By Layer ◽  
X Rays ◽  
Algebraic Reconstruction Technique ◽  
Mosaic Spread ◽  
Average Size ◽  
Non Destructive

A reconstruction method is presented for the generation of three-dimensional maps of the grain boundaries within powders or polycrystals. The grains are assumed to have a mosaic spread below 1°. They are mapped layer by layer in a non-destructive way by diffraction with hard X-rays. First the diffraction spots are sorted with respect to grain of origin by the indexing programGRAINDEX. Next for each grain the reconstruction is performed byART– an iterative algebraic algorithm. The method is optimized by simulations. It is verified by a 50 keV study on one embedded layer in an aluminium specimen. The layer comprises ∼50 grain sections of an average size of 100 µm. Based on the use of five reflections per grain, a resolution of ∼5 µm is inferred.

Compute Three-Dimensional Reconstruction of Brachial Plexus and its Surrounding Tissues by Using Chinese Visible Human (CVH) Data Anatomical Foundation for Brachial Plexus Entrapment

2013 ◽  
Vol 347-350 ◽  
pp. 2728-2733
Author(s):  
Qi Li ◽  
Bing Fang Zeng ◽  
Wei Qing Kong ◽  
Chang Qing Zhang
Keyword(s):  
Brachial Plexus ◽  
Cross Section ◽  
Vertical Section ◽  
Three Dimensional ◽  
Anatomical Study ◽  
Surrounding Tissue ◽  
Reconstruction Technique ◽  
Computer Technique ◽  
Chinese Visible Human ◽  
Visible Human

We selected cervical cross section image from CVH-F1 (Chinese Visible Human Female, No.1) database. After labeling the relative structures, we made 3D reconstruction of brachial plexus and surrounding tissue by computer reconstruction technique. In cervical cross section image, tissues like vertebrae, disc, spinal dura mater, spinal cord, vertebral artery, nerve root and muscles can be recognized, which ensure the ideal effect of 3-D reconstruction. In conclusion, we can make 3-D reconstruction of brachial plexus through computer technique which may serve for anatomical study of brachial plexus compression. After that we made vertical section on the nerve and calculate the ratio between area of nerve and its gap. In result, it is suggested that the nerve passage for root and strand is comparatively narrower.

Reconstruction of grain boundaries in polycrystals by filtered back-projection of diffraction spots

2003 ◽  
Vol 36 (2) ◽  
pp. 319-325 ◽  
Author(s):  
Henning Friis Poulsen ◽  
Soeren Schmidt
Keyword(s):  
Grain Boundaries ◽  
Three Dimensional ◽  
Projection Algorithm ◽  
Reconstruction Method ◽  
X Rays ◽  
Back Projection ◽  
Filtered Back Projection ◽  
Mosaic Spread

A reconstruction method is presented for the generation of three-dimensional maps of the grain boundaries within powders or polycrystals. The grains are assumed to have a mosaic spread below 1°. They are mapped non-destructively by diffraction with hard X-rays, using a uniform mm2-sized beam. First the diffraction spots are sorted with respect to grain of origin by the indexing programGRAINDEX. Next, for each grain the reconstruction is performed by a variant of the filtered back-projection algorithm. The reconstruction method is verified by a simulation over ten grains. Using 64 reflections for each grain, sub-pixel accuracy is obtained. The potential of the method is outlined.

scholarly journals Optimization of Three-Dimensional (3D) Chemical Imaging by Soft X-Ray Spectro-Tomography Using a Compressed Sensing Algorithm

2017 ◽  
Vol 23 (5) ◽  
pp. 951-966 ◽  
Author(s):  
Juan Wu ◽  
Mirna Lerotic ◽  
Sean Collins ◽  
Rowan Leary ◽  
Zineb Saghi ◽  
...  
Keyword(s):  
Compressed Sensing ◽  
Iterative Reconstruction ◽  
Three Dimensional ◽  
Chemical Imaging ◽  
Reconstruction Technique ◽  
Back Projection ◽  
X Ray ◽  
Reconstruction Methods ◽  
Scanning Transmission ◽  
X Ray Absorption

AbstractSoft X-ray spectro-tomography provides three-dimensional (3D) chemical mapping based on natural X-ray absorption properties. Since radiation damage is intrinsic to X-ray absorption, it is important to find ways to maximize signal within a given dose. For tomography, using the smallest number of tilt series images that gives a faithful reconstruction is one such method. Compressed sensing (CS) methods have relatively recently been applied to tomographic reconstruction algorithms, providing faithful 3D reconstructions with a much smaller number of projection images than when conventional reconstruction methods are used. Here, CS is applied in the context of scanning transmission X-ray microscopy tomography. Reconstructions by weighted back-projection, the simultaneous iterative reconstruction technique, and CS are compared. The effects of varying tilt angle increment and angular range for the tomographic reconstructions are examined. Optimization of the regularization parameter in the CS reconstruction is explored and discussed. The comparisons show that CS can provide improved reconstruction fidelity relative to weighted back-projection and simultaneous iterative reconstruction techniques, with increasingly pronounced advantages as the angular sampling is reduced. In particular, missing wedge artifacts are significantly reduced and there is enhanced recovery of sharp edges. Examples of using CS for low-dose scanning transmission X-ray microscopy spectroscopic tomography are presented.

scholarly journals Particle reconstruction of volumetric particle image velocimetry with the strategy of machine learning

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Qi Gao ◽  
Shaowu Pan ◽  
Hongping Wang ◽  
Runjie Wei ◽  
Jinjun Wang
Keyword(s):  
Three Dimensional ◽  
Approximate Solutions ◽  
Optimization Methods ◽  
Initial Guess ◽  
Reconstruction Technique ◽  
Reconstruction Method ◽  
Image Velocimetry ◽  
Order Of Magnitude ◽  
Robustness To Noise ◽  
Particle Reconstruction

AbstractThree-dimensional particle reconstruction with limited two-dimensional projections is an under-determined inverse problem that the exact solution is often difficult to be obtained. In general, approximate solutions can be obtained by iterative optimization methods. In the current work, a practical particle reconstruction method based on a convolutional neural network (CNN) with geometry-informed features is proposed. The proposed technique can refine the particle reconstruction from a very coarse initial guess of particle distribution that is generated by any traditional algebraic reconstruction technique (ART) based methods. Compared with available ART-based algorithms, the novel technique makes significant improvements in terms of reconstruction quality, robustness to noise, and at least an order of magnitude faster in the offline stage.

Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression

2013 ◽  
Vol 19 (6) ◽  
pp. 1669-1677 ◽  
Author(s):  
Cédric Messaoudi ◽  
Nicolas Aschman ◽  
Marcel Cunha ◽  
Tetsuo Oikawa ◽  
Carlos O. Sanchez Sorzano ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Noise Suppression ◽  
Chemical Elements ◽  
Electron Tomography ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Reconstruction Technique ◽  
Chemical Mapping ◽  
Specialized Software ◽  
Alignment Algorithms

AbstractElectron tomography is becoming one of the most used methods for structural analysis at nanometric scale in biological and materials sciences. Combined with chemical mapping, it provides qualitative and semiquantitative information on the distribution of chemical elements on a given sample. Due to the current difficulties in obtaining three-dimensional (3D) maps by energy-filtered transmission electron microscopy (EFTEM), the use of 3D chemical mapping has not been widely adopted by the electron microscopy community. The lack of specialized software further complicates the issue, especially in the case of data with a low signal-to-noise ratio (SNR). Moreover, data interpretation is rendered difficult by the absence of efficient segmentation tools. Thus, specialized software for the computation of 3D maps by EFTEM needs to include optimized methods for image series alignment, algorithms to improve SNR, different background subtraction models, and methods to facilitate map segmentation. Here we present a software package (EFTEM-TomoJ, which can be downloaded from http://u759.curie.fr/fr/download/softwares/EFTEM-TomoJ), specifically dedicated to computation of EFTEM 3D chemical maps including noise filtering by image reconstitution based on multivariate statistical analysis. We also present an algorithm named BgART (for background removing algebraic reconstruction technique) allowing the discrimination between background and signal and improving the reconstructed volume in an iterative way.

Sign in / Sign up

Export Citation Format

Share Document