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.
Install uv following these instructions.
- 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
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