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Conformal mapping of nuclei in 3D tomographic cell images to assess shape heterogeneity

Vivek Nandakumar, Xing An, Yalin Wang, Roger Johnson, Deirdre Meldrum
2012 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)  
We used adaptive thresholding schemes to segment cells and nuclei, and applied spherical conformal mapping methods on the 3D nuclear masks to compute 256 rotation invariant coefficients as shape descriptors  ...  We applied ANOVA techniques to assess variations in nuclear shape within each cell type and among the four cell types.  ...  This may be attributed to the underlying biology that results in less uniform staining of the cell membrane and nucleus in cancer cells. 3D segmentation 3D nuclear shape analysis by conformal mapping  ... 
doi:10.1109/isbi.2012.6235524 dblp:conf/isbi/NandakumarAWJM12 fatcat:627k6pwexrga7olc6l3ojnbuya

Cryo-ET reveals the macromolecular reorganization of S. pombe mitotic chromosomes in vivo

Shujun Cai, Chen Chen, Zhi Yang Tan, Yinyi Huang, Jian Shi, Lu Gan
2018 Proceedings of the National Academy of Sciences of the United States of America  
To more reproducibly characterize the heterogeneous complexes in the crowded nucleoplasm, we also took advantage of recent advances in phase-contrast hardware and image-classification software (28, 29)  ...  Knowledge of how chromosomes condense in 3D at the molecular level is needed to explain the nearly global transcriptional repression that happens to the mitotic cells of most eukaryotes (11).  ...  We thank the Centre for BioImaging Sciences microscopy staff for support and training; Snezhka Oliferenko and Mohan Balasubramanian for feedback, sharing yeast strains, and cell-culture advice; and Kazuhiro  ... 
doi:10.1073/pnas.1720476115 fatcat:cj4jyzwgxbcdteryngmgxnj7oa

Unique structures in a tumor herpesvirus revealed by cryo-electron tomography and microscopy

Wei Dai, Qingmei Jia, Eric Bortz, Sanket Shah, Jun Liu, Ivo Atanasov, Xudong Li, Kenneth A. Taylor, Ren Sun, Z. Hong Zhou
2008 Journal of Structural Biology  
The structural characterization of these viruses has been limited due to difficulties in obtaining adequate amount of virion particles.  ...  Two layers of tegument are identified: an inner tegument layer tethered to the underlying capsid and an outer, flexible tegument layer conforming to the overlying, pleomorphic envelope, consistent with  ...  Keck Foundation to the Gulf Coast Consortia. We acknowledge the use of cryoEM facility at the National Center for Macromolecular Imaging (NIH P41RR02250 to Wah Chiu).  ... 
doi:10.1016/j.jsb.2007.10.010 pmid:18096403 pmcid:PMC2714863 fatcat:le57tkaqzvflfhuf2tpluconca

Three-dimensional virtual histology of the human hippocampus based on phase-contrast computed tomography

Marina Eckermann, Bernhard Schmitzer, Franziska van der Meer, Jonas Franz, Ove Hansen, Christine Stadelmann, Tim Salditt
2021 Proceedings of the National Academy of Sciences of the United States of America  
Accordingly, we find that the prototypical transformation between a structure representing healthy granule cells and the pathological state involves a decrease in the volume of granule cell nuclei, as  ...  In view of recent findings suggesting a nuclear origin of AD, we target in particular the nuclear structure of the dentate gyrus (DG) granule cells.  ...  Fig. 5C shows the volume-rendered segmentation of DG cell nuclei. Based on the center of mass of the nuclei, a 3D cell density map was computed as shown in Fig. 5D .  ... 
doi:10.1073/pnas.2113835118 pmid:34819378 pmcid:PMC8640721 fatcat:jmmpgvpbv5gevdtxp5c6cfzab4

Nondestructive, multiplex three-dimensional mapping of immune infiltrates in core needle biopsy

Steve Seung-Young Lee, Vytautas P Bindokas, Mark W Lingen, Stephen J Kron
2018 Laboratory Investigation  
Using T3 imaging, image processing and machine learning to map CD3+CD8+ cytotoxic T cells (CTLs) in whole core needle biopsies from Her2+ murine mammary tumors and human head and neck surgical specimens  ...  Here, we report transparent tissue tomography (T3) as a tool for three-dimensional (3D) imaging cytometry in the complex architecture of the tumor microenvironment, demonstrating multiplexed immunofluorescent  ...  Imaging, image processing, and data analysis were performed at the University of Chicago Integrated Light Microscopy Facility, supported by NCI P30 CA014599.  ... 
doi:10.1038/s41374-018-0156-y pmid:30401959 pmcid:PMC6502706 fatcat:evwysra5t5ggdk47ypg5lrnqh4

Cryo-electron tomography: The challenge of doing structural biology in situ

Vladan Lučić, Alexander Rigort, Wolfgang Baumeister
2013 Journal of Cell Biology  
JCB: Review Correspondence to Wolfgang Baumeister: baumeist@biochem.mpg.de Abbreviations used in this paper: cryo-ET, cryo-electron tomography; EM, electron microscopy; FIB, focused ion beam; LM, light  ...  Glaeser for many useful comments; Yoshiyuki Fukuda, Miroslava Schaffer, and Julio Ortiz for preparing some of the images; and Gabriela J. Greif and Benjamin D.  ...  Engel for critical reading of the manuscript. This work was supported by the Exzellenzcluster (CIPSM). Submitted: 29 April 2013 Accepted: 11 July 2013  ... 
doi:10.1083/jcb.201304193 pmid:23918936 pmcid:PMC3734081 fatcat:cfj6wuolezbebf2jkxeviaq75u

Ion beam subcellular tomography [article]

Ahmet F Coskun, Guojun Han, Shih-Yu Chen, Xavier Rovira-Clave, Sizun Jiang, Christian M. Schuerch, Yunhao Bai, Chuck Hitzman, Garry P Nolan
2019 bioRxiv   pre-print
Multiplexed ion beam imaging (MIBI) has been previously used to profile multiple parameters in two dimensions in single cells within tissue slices.  ...  IBT also enabled label-free elemental mapping of cells, allowing point of source cellular component measurements not possible for most optical microscopy targets.  ...  Cancer cells and aberrant immune cells (B cell lymphoblasts) typically have large and deformed nuclei with protein compositions and chromatin conformations distinct from those of normal cells; 22,23 very  ... 
doi:10.1101/557728 fatcat:ducvbbzmxbhyxfxb67ba5ms5u4

InShaDe: Invariant Shape Descriptors for visual 2D and 3D cellular and nuclear shape analysis and classification

Khaled Al-Thelaya, Marco Agus, Nauman Ullah Gilal, Yin Yang, Giovanni Pintore, Enrico Gobbetti, Corrado Calí, Pierre J. Magistretti, William Mifsud, Jens Schneider
2021 Computers & graphics  
The framework is based on a novel shape descriptor of closed contours in 2D and 3D.  ...  We present a shape processing framework for visual exploration of cellular nuclear envelopes extracted from microscopic images arising in histology and neuroscience.  ...  Acknowledgments This work was supported by the College of Science and Engineering at Hamad Bin Khalifa University.  ... 
doi:10.1016/j.cag.2021.04.037 fatcat:ga7ckfeqindb7cnhshubkwkwfy

X-ray Phase Contrast Tomography to assess the sequential evolution of multi-organ damage in an animal model of multiple sclerosis [article]

F. Palermo, N. Pieroni, A. Sanna, B. Parodi, C. Venturi, G. Begani, L. Massimi, L. Maugeri, E. Longo, L. Damico, G. Tromba, I. Bukreeva (+4 others)
2022 arXiv   pre-print
A simultaneous imaging of different disease-relevant networks and a multiscale imaging, ranging from the single cell through to the organ as a whole, are required to provide complete reliable information  ...  We use X-ray phase-contrast tomography (XPCT) in a multi-organ approach to identify early imaging markers predictive of multiple sclerosis (MS) in EAE animal model.  ...  of a villus segmented to show the spatial distribution of cell nuclei (in yellow) inside the volume.  ... 
arXiv:2204.12600v1 fatcat:4yfb7owuufagbenq4zjt3utz2q

Development and application of STEM for the biological sciences

Alioscka A. Sousa, Richard D. Leapman
2012 Ultramicroscopy  
image, it is possible to map the distributions of specific bound elements like phosphorus, calcium and iron in isolated macromolecular assemblies or in compartments within sectioned cells.  ...  reconstruction of micrometer-thick sections of cells.  ...  Daniel Cox for assistance in tomographic reconstruction and 3D modeling; Dr. Christopher Ackerson for valuable discussions on the synthesis of the Au144 clusters; and Ms.  ... 
doi:10.1016/j.ultramic.2012.04.005 pmid:22749213 pmcid:PMC3500455 fatcat:e5tw4nytxrbcnbo4v7ymdmhc24

Structural Analysis of Macromolecular Assemblies by Electron Microscopy

E. V. Orlova, H. R. Saibil
2011 Chemical Reviews  
We are grateful to the Wellcome Trust, BBSRC, EU 3DEM NoE for funding. This review grew out of materials prepared for a series of courses funded by the European Molecular Biology Organization.  ...  The evaluation of variance in the resulting 3D maps and localization of regions with high variance allows assessment of the heterogeneity, and estimation of covariance in the population enables classification  ...  HETEROGENEITY IN 2D AND 3D Sources of Heterogeneity The resolution of macromolecular structure determination by cryo EM is more often limited by conformational variation of the structure than by problems  ... 
doi:10.1021/cr100353t pmid:21919528 pmcid:PMC3239172 fatcat:bx7j3f6dajalzitk63mgx3nxhq

Nanoscopic subcellular imaging enabled by ion beam tomography

Ahmet F. Coskun, Guojun Han, Shambavi Ganesh, Shih-Yu Chen, Xavier Rovira Clavé, Stefan Harmsen, Sizun Jiang, Christian M. Schürch, Yunhao Bai, Chuck Hitzman, Garry P. Nolan
2021 Nature Communications  
AbstractMultiplexed ion beam imaging (MIBI) has been previously used to profile multiple parameters in two dimensions in single cells within tissue slices.  ...  In cultured cancer cells and tissues, IBT enables accessible visualization of 3D volumetric distributions of genomic regions, RNA transcripts, and protein factors with 5 nm axial resolution using isotope-enrichments  ...  Further information on research design is available in the Nature Research Reporting Summary linked to this article.  ... 
doi:10.1038/s41467-020-20753-5 pmid:33542220 fatcat:ze3qnksjmrb2zdmqv7azirywmi

Quantifying Three-dimensional Chromatin Organization Utilizing Scanning Transmission Electron Microscopy: ChromSTEM [article]

Yue Li, Eric W Roth, Vasundhara Agrawal, Adam Eshein, Jane Frederick, Luay Matthew Almassalha, Anne Shim, Reiner Bleher, Vinayak P Dravid, Vadim Backman
2019 bioRxiv   pre-print
imaging of chromatin structure in vitro.  ...  We utilized ChromSTEM to quantify chromatin structure in cultured cells and tissue biopsies through local DNA distribution and the scaling behavior of chromatin polymer.  ...  Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright notation thereon.  ... 
doi:10.1101/636209 fatcat:4c7okh3eajgqpmh2jzzgi7ioue

Correlative Light and Electron Microscopy (CLEM) Analysis of Nuclear Reorganization Induced by Clustered DNA Damage Upon Charged Particle Irradiation

Susanne Tonnemacher, Mikhail Eltsov, Burkhard Jakob
2020 International Journal of Molecular Sciences  
Our observations are discussed in the view of liquid-like phase separation as one of the mechanisms of regulating DNA repair.  ...  Chromatin architecture plays major roles in gene regulation as well as in the repair of DNA damaged by endogenous or exogenous factors, such as after radiation.  ...  Acknowledgments: The authors wish to thank Gudrun Becker and Henrieke Förster for cell culture and excellent technical assistance.  ... 
doi:10.3390/ijms21061911 pmid:32168789 fatcat:pqbhguylyzdapamyyxnq6yn6me

4.2 Mitochondrial Architecture and Heterogeneity [chapter]

G. A. Perkins, M. H. Ellisman
2007 Handbook of Neurochemistry and Molecular Neurobiology  
This aspect makes it possible to correlate live-cell imaging using confocal and two-photon microscopy with highresolution 3D imaging using electron tomography.  ...  imaging, in that computational methods are used to calculate a 3D structure from many two-dimensional (2D) images or projections recorded over a wide range of tilt angles.  ... 
doi:10.1007/978-0-387-30411-3_11 fatcat:rt766dmcmzbmrkc4f2nv6k3vfq
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