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BCSS
Use this to download all elements of the BCSS dataset described in: Amgad M, Elfandy H, ..., Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz083SurvivalNet
Deep learning survival modelsNuCLS
NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentationHistomicsML2
A tool for training machine-learning models with whole-slide imaging datasetsHistomicsML
An interactive machine learning framework for large histopathology images.HiPS
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosisMuTILs_Panoptic
Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset. medRxiv 2022.01.08.22268814.MatDigitalPathology
Matlab functions to support analysis of digital pathology images.MiscSurvivalUtils
Miscellaneous tools for data management and classical survival analysis.HistXtract
A pipeline for extracting nuclear morphometry features from whole-slide images.IHC-Analysis
glimr
A simplified wrapper for hyperparameter search with Ray Tune.Love Open Source and this site? Check out how you can help us