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3D Cells and Nuclei Segmentation

This repository is a supplement to the paper On the variability in cell and nucleus shapes by Anusha Devulapally, Varun Parekh, Clint Pazhayidam George, and Sreenath Balakrishnan. This project deals with the segmentation of cells and nuclei confocal images. Folders cells and nuclei show more details.

Data

The folder data contains multiple cells and nuclei types where each folder representing each cell/nuclei type. Each folder has stacks of different cells of the same cell type. For more details, see the documentation.

Acknowledgements

We use the following toolboxes from the Mathworks website

  • Snakes algorithm by D. Kroon, University of Twente
  • Geometry methods by D. Legland, INRA

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