├── .env ├── Dockerfile ├── LICENSE ├── PIPEX.pdf ├── README.md ├── analysis.py ├── disable_swap.sh ├── doc ├── code.jpg ├── doc1.jpg ├── doc10.jpg ├── doc11.jpg ├── doc12.jpg ├── doc13.jpg ├── doc14.jpg ├── doc15.jpg ├── doc2.jpg ├── doc20.jpg ├── doc21.jpg ├── doc22.jpg ├── doc23.jpg ├── doc24.jpg ├── doc25.jpg ├── doc3.jpg ├── doc30.jpg ├── doc4.jpg ├── doc5.jpg ├── doc6.jpg ├── doc7.jpg ├── doc8.jpg ├── doc9.jpg └── preprocessing_presentation.zip ├── docker-compose.yml ├── enable_swap.sh ├── generate_filtered_masks.py ├── generate_geojson.py ├── generate_tissuumaps.py ├── markers_surface.html ├── pipex.py ├── pipex.sh ├── pipexGUI.py ├── pipex_batch_list.txt ├── pipex_batch_list_EXAMPLE.txt ├── preprocessing.py ├── q&a.md ├── q&a.pdf ├── qupath_import_example.groovy ├── requirements.txt └── segmentation.py /.env: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CellProfiling/pipex/HEAD/.env 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