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Conformal mapping of nuclei in 3D tomographic cell images to assess shape heterogeneity
2012
2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)
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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
2018
Proceedings of the National Academy of Sciences of the United States of America
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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
2008
Journal of Structural Biology
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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
2021
Proceedings of the National Academy of Sciences of the United States of America
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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
2018
Laboratory Investigation
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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
2013
Journal of Cell Biology
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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]
2019
bioRxiv
pre-print
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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
2021
Computers & graphics
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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]
2022
arXiv
pre-print
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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
2012
Ultramicroscopy
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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
2011
Chemical Reviews
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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
2021
Nature Communications
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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]
2019
bioRxiv
pre-print
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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
2020
International Journal of Molecular Sciences
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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]
2007
Handbook of Neurochemistry and Molecular Neurobiology
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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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