Segment Anything for Histopathology Experiment Scripts

This directory contains all experiment scripts for building and benchmarking segment anything model for histopathology.

Here is a brief description of relevant folders:

• benchmarking: Contains scripts to run reference methods (eg. HoVerNet, HoVerNeXt, CellViT, InstanSeg, StarDist)
• data: Contains scripts for preprocessing images and corresponding labels for all experiments.
• patho-sam: Contains scripts for running SAM-models (eg. default SAM, micro-sam and patho-sam models for automatic and interactive instance segmentation).
• semantic_segmentation: Contains scripts for training and evaluation semantic segmentation using patho-sam generalist models.
• training: Contains scripts for training the specialist and generalist patho-sam models.

NOTE 1: There are scripts where the expected filepaths / directories might be hard-coded. Replace them with your respective paths where you would like to store / fetch files from.

NOTE 2: We provide example scripts for convenience. Feel free to check them out for both interactive and automatic segmentation using PathoSAM models.