README.md

MoNuSAC grand-challenge organized at ISBI 2020

Please cite the following paper if you use this repository-

Verma, Ruchika, et al. "MoNuSAC2020: A Multi-organ Nuclei Segmentation and Classification Challenge." IEEE Transactions on Medical Imaging (2021)

File name	Description
Cell_counting	Script to count cells (by type) in each image and store in an excel file
Binary_mask_generation	Use H&E stained images(.svs) along with associated xml files to generate binary masks of each annotated cell-type
n-ary_mask_generation	Use H&E stained images(.svs) along with associated xml files to generate n-ary masks of each annotated cell-type
Compute_PQ_metric	Script to compute Panoptic Quality metric for each n-ary mask image, and store image names and respective PQ values in an excel file