PathologyDataScience/HistomicsML2

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Created over 5 years ago
Updated 6 months ago

PathologyDataScience/HistomicsML2

PathologyDataScience

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A tool for training machine-learning models with whole-slide imaging datasets

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/btz083

SurvivalNet

Deep learning survival models

SCNN

Survival Convolutional Neural Networks

NuCLS

NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation

Jupyter Notebook

HistomicsML

An interactive machine learning framework for large histopathology images.

HiPS

Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis

MuTILs_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

Jupyter Notebook

glimr

A simplified wrapper for hyperparameter search with Ray Tune.