Computational and Integrative Pathology
Organization for the Computational and Integrative Pathology Group at Northwestern University
Chicago, IL, USA
Pinned Repositories
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
HiPS
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
histolab
Library for Digital Pathology Image Processing
HistomicsML
An interactive machine learning framework for large histopathology images.
HistomicsML2
A tool for training machine-learning models with whole-slide imaging datasets
MatDigitalPathology
Matlab functions to support analysis of digital pathology images.
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.
NuCLS
NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation
SCNN
Survival Convolutional Neural Networks
SurvivalNet
Deep learning survival models
Computational and Integrative Pathology's Repositories
PathologyDataScience/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
PathologyDataScience/SurvivalNet
Deep learning survival models
PathologyDataScience/SCNN
Survival Convolutional Neural Networks
PathologyDataScience/NuCLS
NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation
PathologyDataScience/HistomicsML2
A tool for training machine-learning models with whole-slide imaging datasets
PathologyDataScience/HiPS
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
PathologyDataScience/HistomicsML
An interactive machine learning framework for large histopathology images.
PathologyDataScience/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.
PathologyDataScience/histolab
Library for Digital Pathology Image Processing
PathologyDataScience/MatDigitalPathology
Matlab functions to support analysis of digital pathology images.
PathologyDataScience/HistomicsTK
A Python library for pathology image analysis algorithms.
PathologyDataScience/HistXtract
A pipeline for extracting nuclear morphometry features from whole-slide images.
PathologyDataScience/MiscSurvivalUtils
Miscellaneous tools for data management and classical survival analysis.
PathologyDataScience/hif2gene
PathologyDataScience/IHC-Analysis
PathologyDataScience/glimr
A simplified wrapper for hyperparameter search with Ray Tune.
PathologyDataScience/Mask_RCNN
Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
PathologyDataScience/pathology-hooknet
PathologyDataScience/RipleyK
Calculation of the Ripley K (spatial statistics) value in python