SOCR 3D Cell Morphometry Project
This is the repository for workflows, source code, and documentation associated with the 3D Cell Morphometry Project.
3D microscopic imaging data and derived binary masks are available for downloading from the project data webpage.
Materials are provided in 3 parts corresponding to publications:
- 3D cell nuclear morphology: microscopy imaging dataset
- 3D cell nuclear shape modeling, morphometry, and classification
- 4D nuclear morphometry of VPA-treated astrocytes
We also provide an example of how to use these materials in the pipeline workflow:
Nuclear morphometric classification demo workflow
If you find this work useful please cite a corresponding publication:
- 3D cell nuclear morphology: microscopy imaging dataset and voxel-based morphometry classification results
@inproceedings{kalinin20183ddata,
title={3D cell nuclear morphology: microscopy imaging dataset and voxel-based morphometry classification results},
author={Kalinin, Alexandr A and Allyn-Feuer, Ari and Ade, Alex and Fon, Gordon-Victor and Meixner, Walter and Dilworth, David and De Wet, Jeffrey R and Higgins, Gerald A and Zheng, Gen and Creekmore, Amy and Wiley, John W and Verdone, James E and Veltri, Robert W and Pienta, Kenneth J and Coffey, Donald S and Athey, Brian D and Dinov, Ivo D},
booktitle={Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition Workshops},
pages={2272--2280},
year={2018}
}
- 3D shape modeling for cell nuclear morphological analysis and classification
@article{kalinin20183dshape,
title={3D shape modeling for cell nuclear morphological analysis and classification},
author={Kalinin, Alexandr A and Allyn-Feuer, Ari and Ade, Alex and Fon, Gordon-Victor and Meixner, Walter and Dilworth, David and Husain, Syed S and de Wett, Jeffrey R and Higgins, Gerald A and Zheng, Gen and and Creekmore, Amy and Wiley, John W and Verdone, James E and Veltri, Robert W and Pienta, Kenneth J and Coffey, Donald S and Athey, Brian D and Dinov, Ivo D},
journal={Scientific reports},
volume={8},
year={2018},
publisher={Nature Publishing Group}
}
- Valproic Acid-Induced Changes of 4D Nuclear Morphology in Astrocyte Cells
Molecular Biology of the Cell, 2021
@article{kalinin20214dvpa,
title={Valproic Acid-Induced Changes of 4D Nuclear Morphology in Astrocyte Cells},
author={Kalinin, Alexandr A and Hou, Xinhai and Ade, Alex S and Fon, Gordon-Victor and Meixner, Walter and Higgins, Gerald A and Sexton, Jonathan Z and Wan, Xiang and Dinov, Ivo D and O’Meara, Matthew J and Athey, Brian D},
journal={Molecular Biology of the Cell},
volume={32},
number={18},
pages={1624--1633},
year={2021},
publisher={American Society for Cell Biology}
}
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