scholarly journals Progress towards a methodology for high throughput 3D reconstruction of soot nanoparticles via electron tomography

2018 ◽  
Vol 270 (3) ◽  
pp. 272-289 ◽  
Author(s):  
E. HAFFNER-STATON ◽  
A. LA ROCCA ◽  
M.W. FAY
Keyword(s):  
3D Reconstruction ◽  
High Throughput ◽  
Electron Tomography

Embedded Gold Markers for Improved TEM/STEM Tomography Reconstruction

2008 ◽  
Author(s):  
Jian-Shing Luo ◽  
Chia-Chi Huang ◽  
Jeremy D. Russell
Keyword(s):  
3D Reconstruction ◽  
Feature Tracking ◽  
Semiconductor Device ◽  
Electron Tomography ◽  
Tracking Process ◽  
Carbon Coated ◽  
Novel Method ◽  
Tomography Reconstruction ◽  
Tilt Series ◽  
20 Nm

Abstract Electron tomography includes four main steps: tomography data acquisition, image processing, 3D reconstruction, and visualization. After acquisition, tilt-series alignments are performed. Two methods are used to align the tilt-series: cross-correlation and feature tracking. Normally, about 10-20 nm of fiducial markers, such as gold beads, are deposited onto one side of 100 mesh carbon-coated grids during the feature-tracking process. This paper presents a novel method for preparing electron tomography samples with gold beads inside to improve the feature tracking process and quality of 3D reconstruction. Results show that the novel electron tomography sample preparation method improves image alignment, which is essential for successful tomography in many contemporary semiconductor device structures.

scholarly journals Development of High-Throughput, High-Resolution 3D Reconstruction of Large-Volume Biological Tissue Using Automated Tape Collection Ultramicrotomy and Scanning Electron Microscopy

2011 ◽  
Vol 17 (S2) ◽  
pp. 966-967 ◽  
Author(s):  
R Schalek ◽  
N Kasthuri ◽  
K Hayworth ◽  
D Berger ◽  
J Tapia ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
High Resolution ◽  
3D Reconstruction ◽  
High Throughput ◽  
Large Volume ◽  
Biological Tissue ◽  
Scanning Electron

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

Statistical Profiles of PTK1 Kinetochore Microtubule Plus-End Conformations Using High-Throughput Electron Tomography

2004 ◽  
Vol 10 (S02) ◽  
pp. 1194-1195
Author(s):  
K J VandenBeldt ◽  
Xing Meng ◽  
R M Barnard ◽  
P J Hergert ◽  
Bruce F. McEwen
Keyword(s):  
High Throughput ◽  
Electron Tomography

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.

scholarly journals High-Throughput Immunofluorescence and Electron Tomography to Characterize Centrosomal Aberrations in Plasma Cell Neoplasia

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3077-3077
Author(s):  
Tobias Dittrich ◽  
Martin Schorb ◽  
Isabella Haberbosch ◽  
Elena Bausch ◽  
Mandy Börmel ◽  
...  
Keyword(s):  
Board Of Directors ◽  
Cancer Patients ◽  
Genomic Instability ◽  
Cell Lines ◽  
Plasma Cell ◽  
High Throughput ◽  
Research Funding ◽  
Electron Tomography ◽  
Automated Analysis ◽  
Advisory Committees

Introduction Genomic instability is the basic prerequisite for a Darwinian-type evolution of neoplasia and as such represents a fundamental hallmark of cancer. Centrosomal aberrations have been identified as potent drivers of genomic instability (Cosenza et al., Cell Reports 2017; Krämer et al., Leukemia 2003). The current standard to investigate centrosomal aberrations in cancer patients is immunofluorescence (IF) staining. Although this method is fast and easily scalable, its diagnostic significance is controversially discussed. Moreover, ultrastructural analysis of centrosomes in cancer patients is required to gain a mechanistical understanding of the relationship between genomic instability and centrosomal aberrations. To address this, we combined semi-automated analysis of immunofluorescence (IF) images with high-throughput electron tomography (ET) of different cell lines and subentities of primary plasma cell neoplasia, which serve as surrogate for clonal evolution. Methods CD138+ plasma cells were isolated from bone marrow aspirates of consenting patients with plasma cell neoplasia. Each sample was split to be subsequently processed for IF and ET. The IF workflow included (1) chemical fixation, (2) staining for nuclei, cells, centrin and pericentrin, (3) semi-automated acquisition of >1000 cells, (4) semi-automated analysis of IF data using the software Konstanz Information Miner (KNIME) (Berthold et al., GfKL 2007). The ET workflow included (1) chemical fixation (2) agarose embedding, (3) dehydration and epoxy resin embedding, (4) serial sectioning at 200 nm, (5) semi-automated screening for centrioles with transmission electron microscopy (TEM) (Schorb et al., Nature Methods 2019), (6) semi-automated acquisition of previously identified centriole regions with serial section ET. Results So far, four patients with relapsed refractory myeloma as well as two cell lines (U2OS-PLK4, RPMI.8226) have been screened with TEM. No centrosomal amplification was apparent by IF in any of these patients. Within 5598 cells, 205 centrosomes have been detected. A total of 659 electron tomograms were performed on 141 regions of interest that were distributed on average over five sections. One patient with highly refractory multiple myeloma (resistance to eight prior therapies) showed over-elongated and partially fragmented centrioles (Figure), similar to recently reported findings in tumor cell lines (Marteil et al., Nature Communications 2018). Six out of 10 mother centrioles in this patient were longer than 500 nm, which is supposed to be the physiological length. The dimensions (mean [range]) of mother (decorated with appendages) and daughter centrioles in this patient were: length 919 nm [406 nm - 2620 nm] and 422 nm [367 nm - 476 nm]; diameter 221 nm [99 nm - 470 nm] and 236 nm [178 nm - 450 nm]. Moreover, the mother centrioles showed multiple sets of appendages (mean [range]: 5.9 [2 - 13]), while one set of appendages would be physiological. This is an ongoing study and additional results are expected by the date of presentation. Conclusions We present a semi-automated methodological setup that combines high-throughput IF and cutting-edge ET to study centrosomal aberrations. To our knowledge, this is the first study that systematically analyzes the centrosomal phenotype of cancer patients at the ultrastructural level. Our preliminary IF results suggest that supernumerary centrosomes in plasma cell neoplasia might be less common than previously reported. Moreover, we for the first time describe and characterize over-elongated centrioles in myeloma patients, reminiscent of previous findings in tumor cell lines. With increasing numbers of patients, we will be also able to correlate results from IF and ET to address the current uncertainty with respect to IF screens for centrosomal aberrations. Better insight into centrosomal aberrations will likely increase our understanding on karyotype evolution in plasma cell neoplasia and possibly facilitate the development of novel targeted therapies. Figure Disclosures Goldschmidt: John-Hopkins University: Research Funding; John-Hopkins University: Research Funding; MSD: Research Funding; Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Bristol-Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Dietmar-Hopp-Stiftung: Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding; Adaptive Biotechnology: Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Research Funding; Molecular Partners: Research Funding; Janssen: Consultancy, Research Funding; Mundipharma: Research Funding; Chugai: Honoraria, Research Funding; Novartis: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Müller-Tidow:MSD: Membership on an entity's Board of Directors or advisory committees. Schönland:Medac: Other: Travel Grant; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding; Prothena: Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding. Krämer:Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Research Funding; Daiichi-Sankyo: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bayer: Research Funding.

3D Reconstruction of Plant Leaves for High-Throughput Phenotyping

2018 ◽  
Author(s):  
Feiyu Zhu ◽  
Suresh Thapa ◽  
Tiao Gao ◽  
Yufeng Ge ◽  
Harkamal Walia ◽  
...  
Keyword(s):  
3D Reconstruction ◽  
High Throughput ◽  
Plant Leaves ◽  
High Throughput Phenotyping

A Novel Method for Automated Acquisition of Tilt Series for Electron Tomography Based on Pre-Calibration of the Specimen Stage

2000 ◽  
Vol 6 (S2) ◽  
pp. 1148-1149
Author(s):  
U. Ziese ◽  
A.H. Janssen ◽  
T.P. van der Krift ◽  
A.G. van Balen ◽  
W.J. de Ruijter ◽  
...  
Keyword(s):  
High Resolution ◽  
3D Reconstruction ◽  
Cell Biology ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Imaging Method ◽  
3D Images ◽  
Tilt Series ◽  
3D Information ◽  
Structural Arrangements

Electron tomography is a three-dimensional (3D) imaging method with transmission electron microscopy (TEM) that provides high-resolution 3D images of structural arrangements. Conventional TEM images are in first approximation mere 2D-projections of a 3D sample under investigation. With electron tomographya series of images is acquired of a sample that is tilted over a large angular range (±70°) with small angular tilt increments (so called tilt-series). For the subsequent 3D-reconstruction, the images of the tilt series are aligned relative to each other and the 3D-reconstruction is computed. Electron tomography is the only technique that can provide true 3D information with nm-scale resolution of individual and unique samples. For (cell) biology and material science applications the availability of high-resolution 3D images of structural arrangements within individual samples provides unique architectural information that cannot be obtained otherwise. Routine application of electron tomography will comprise a major revolutionary step forward in the characterization of complex materials and cellular arrangements.

Automation of Tilt Series Acquisition in Transmission Electron Microscopy for Applications in Biology and Materials Science

2001 ◽  
Vol 7 (S2) ◽  
pp. 88-89
Author(s):  
Ingo Daberkow ◽  
Bernhard Feja ◽  
Peter Sparlinek ◽  
Hans R. Tietz
Keyword(s):  
3D Reconstruction ◽  
Data Acquisition ◽  
San Francisco ◽  
High Speed ◽  
Materials Science ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Max Planck ◽  
Automatic Data ◽  
Tilt Series

During the last decade, computation of a three-dimensional image from a tilt series (3D reconstruction) has become a well established method, of which a variety of implementations are available. The term “electron tomography” is now generally used for this type of data acquisition and 3D reconstruction. An overview over the techniques involved is given in.With the introduction of micro-processor-controlled TEMs and cooled slow-scan CCD cameras and with the progress in performance of high-speed computers, automation of complex imaging procedures became mainly a task of developing appropriate software, using the control facilities of the microscope. in this way, automated electron tomography was realized in 1990 at the Max- Planck-Institute for Biochemistry in Martinsried, and at about the same time at the University of California in San Francisco (UCSF). New techniques for automatic focusing and alignment, developed somewhat earlier , have been integrated in these automated tomography procedures. in the following we discuss the requirements of automatic data acquisition and the present implementation for several TEMs.

A new approach for 3D reconstruction from bright field TEM imaging: Beam precession assisted electron tomography

2011 ◽  
Vol 111 (9-10) ◽  
pp. 1504-1511 ◽  
Author(s):  
J.M. Rebled ◽  
Ll. Yedra ◽  
S. Estradé ◽  
J. Portillo ◽  
F. Peiró
Keyword(s):  
3D Reconstruction ◽  
Electron Tomography ◽  
Bright Field ◽  
New Approach ◽  
Imaging Beam

Electron Tomography Based 3D Reconstruction of Fuel Cell Catalysts

2013 ◽  
Vol 50 (2) ◽  
pp. 353-359 ◽  
Author(s):  
J. Jankovic ◽  
D. Susac ◽  
T. Soboleva ◽  
J. Stumper
Keyword(s):  
Fuel Cell ◽  
3D Reconstruction ◽  
Electron Tomography ◽  
Fuel Cell Catalysts

scholarly journals Validation of plant part measurements using a 3D reconstruction method suitable for high-throughput seedling phenotyping

2015 ◽  
Vol 27 (5) ◽  
pp. 663-680 ◽  
Author(s):  
Franck Golbach ◽  
Gert Kootstra ◽  
Sanja Damjanovic ◽  
Gerwoud Otten ◽  
Rick van de Zedde
Keyword(s):  
3D Reconstruction ◽  
High Throughput ◽  
Plant Part ◽  
Reconstruction Method
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