Overview:
Cell nuclear morphology is regulated by complex underlying biological mechanisms related to cell differentiation, development, proliferation, and disease. Changes in the nuclear form are associated with reorganization of chromatin architecture related to altered functional properties such as gene regulation and expression. Thus, nuclear morphological quantification becomes of major relevance as studies of chromatin and DNA architecture reorganization emerge. In this project, we produced imaging datasets and proposed new methodological approaches that combine modeling, analysis, and interpretation of morphometric characteristics of cell nuclei and other compartments in 3D.
Publications:
Alexandr A. Kalinin, Xinhai Hou, Alex S Ade, Gordon-Victor Fon, Walter Meixner, Gerald A Higgins, Jonathan Z Sexton, Xiang Wan, Ivo D. Dinov, Matthew J. O’Meara, Brian D. Athey. 2021. Valproic Acid-Induced Changes of 4D Nuclear Morphology in Astrocyte Cells. Molecular Biology of the Cell. doi: 10.1091/mbc.E20-08-0502
Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Syed S. Husain, Jeffrey R. de Wet, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley, James E. Verdone, Robert W. Veltri, Kenneth J. Pienta, Donald S. Coffey, Brian D. Athey, Ivo D. Dinov. 2018. 3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification. Scientific Reports. doi: 10.1038/s41598-018-31924-2
Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Jeffrey R. de Wet, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley, James E. Verdone, Robert W. Veltri, Kenneth J. Pienta, Donald S. Coffey, Brian D. Athey, Ivo D. Dinov. 2018. 3D Cell Nuclear Morphology: Microscopy Imaging Dataset and Voxel-Based Morphometry Classification Results. Conference on Computer Vision and Pattern Recognition Workshops (CVPRW). doi: 10.1109/CVPRW.2018.00304
Gen Zheng, Alexandr A. Kalinin, Ivo D. Dinov, Walter Meixner, Shengtao Zhu, John Wiley. 2018. Hypothesis: Caco-2 cell rotational 3D mechanogenomic Turing patterns has clinical implications to colon crypts. Journal of Cellular and Molecular Medicine. doi: 10.1111/jcmm.13853
Data and code:
Data: see data download page
Source code and workflow protocols: see GitHub repository