AUTOMATED BLOOD VESSEL SEGMENTATION ON CD3-STAINED WSI

A research project.

REQUIREMENTS

The built-in functions require rasterio and aicspylibczi libraries for tif and czi file management. The code was executed with python 3.11.

CONTENT

├── annotations          # ground truth 
├── code             
│   ├── datasets         # custom dataset backbones for torchgeo, csv  
│   ├── datasets         # custom dataset backbones for torchgeo, csv  
│   ├── datasets         # custom dataset backbones for torchgeo, csv  
│   └── samplers         # custom samplers for torchgeo               
├── results              # result masks
├── scenes               # original files 
├── prat_demo.ipynb      # demo notebook                 
└── pdf/slides                

HOW TO USE

Simply run the notebook.
It provides a step-by-step usage guide.