PathologyDataScience/MatDigitalPathology

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MATLAB
Created over 7 years ago
Updated over 7 years ago

PathologyDataScience/MatDigitalPathology

PathologyDataScience

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Matlab functions to support analysis of digital pathology images.

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

HistomicsML2

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

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.

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.