EMT image analysis code

This repository contains code for reproducing the image analysis used in our manuscript [1]. This repository uses public available data hosted on AWS. The segmentations and 3D meshes generated by this code is further used by EMT_data_analysis to make the plots shwon in the manuscript.

[1] - A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)

Workflow components

• 1 - CytoGFP Groundtruth Segmentation README
• 2 - All Cells Mask Model Training and Inference README
• 3 - H2B and EOMES Nuclear Segmentations README
• 4 - CollagenIV Segmentation README
• 5 - CollagenIV Segmentation Mesh README

Contact

If you have questions about this code, please reach out to us at cells@alleninstitute.org.

Licensing

All code in this repository is provided to you under the Allen Institute Software License.