DeepCSeg

Source code for DeepCSeg plug-in for CellProfiler

Author: Wenchao Han, Biomarker Imaging Research Laboratory (BIRL) https://sunnybrook.ca/research/content/?content=sri-cerigt-birl-about, Sunnybrook Research Institute, Medical Biophysics, University of Toronto, Toronto, ON, Canada. email: wenchao.han@sri.utoronto.ca

This repository provides the code for whole cell and nuclear segmentation for the multiplexed images using two channels of stained images (i.e. DAPI and Na+K+ATPase). This automated software is also distributed as a CellProfiler plug-in for direct use. The plug-in package for the implementation can be found: https://drive.google.com/drive/folders/1WBYFH9bf89s-xjQNZHKSGdFov08h0iFG?usp=sharing. The video for implementation on an example case can be found: https://youtu.be/gpLDjPQJF8Q. The video for Plug-in installation and setup can be found: https://youtu.be/sirRJc-A4tc.

Example nuclear (blue contours) and cell (orange contours) segmentation for an ovarian cancer tissue sample on a synthesized color image(synthesized from the DAPI and Na+K+ATPase images):

Input DAPI and Na+K+ATPase images for the example above:

This repository includes two code files: 1) DeepCSeg.py 2) DeepCSeg plug-in.py

The DeepCSeg.py is the source code for generating the DeepCSeg executable. To generate the executable for implementation, users may execute the code 'pyinstaller -F DeepCSeg.py'. The 'pyinstaller' and 'flask' need to be installed in the environment. This source code includes functions from MaskRCNN implementation developed by Matterport Inc. under the MIT license. The environment needs to meet the requirements for the MaskRCNN implementation. Please refer https://github.com/matterport/Mask_RCNN for configuration details.

For Mac/Linux users, the executable file needs to be generated from the source code in Mac/Linux with all the dependencies/libraries mentioned above.

The DeepCSeg plug-in.py is the python plug-in code for use in CellProfiler.

Citation

Use this bibtex to cite this repository:

@misc{DeepCSeg_2021,
  title={DeepCSeg, a CellProfiler plug-in for whole cell segmentation for immunofluorescence multiplexed images},
  author={Wenchao Han},
  year={2021},
  publisher={Github},
  journal={GitHub repository},
  howpublished={\url{https://github.com/WenchaoHanSRI/DeepCSeg}},
}