How separated are cells in tissue?

This tutorial teaches how to quantify the extent of cell-cell separation in histopathology tissue. Examples shown are on cell-cell separation of inflammed and healthy H&E slices of mouse pancreases.
This tutorial requires basic familiarity with python.

Dependencies

Install uv following these instructions.

It follows these steps:

• Quality control
• Segment tissue (forground vs background)
• Segment gaps between cells in the foreground region
• Export segmentation masks from QuPath
• Tile output images
  -- To run: uvx juv run 4_Tile_images_uv.ipynb
• Count and export the density of branchpoints
  -- To run: uvx juv run 5_Count_branchpoints_uv.ipynb

Acknowledgements

This tutorial heavily builds on QuPath functions
Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Scientific Reports (2017).
https://doi.org/10.1038/s41598-017-17204-5