Computational and Integrative Pathology (@PathologyDataScience)
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PathologyDataScience

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Top repositories

1

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
Python
127
star
2

SurvivalNet

Deep learning survival models
Python
112
star
3

SCNN

Survival Convolutional Neural Networks
67
star
4

NuCLS

NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation
Jupyter Notebook
44
star
5

HistomicsML2

A tool for training machine-learning models with whole-slide imaging datasets
JavaScript
22
star
6

HistomicsML

An interactive machine learning framework for large histopathology images.
JavaScript
19
star
7

HiPS

Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
Python
16
star
8

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.
Python
7
star
9

MatDigitalPathology

Matlab functions to support analysis of digital pathology images.
MATLAB
3
star
10

MiscSurvivalUtils

Miscellaneous tools for data management and classical survival analysis.
Python
3
star
11

HistXtract

A pipeline for extracting nuclear morphometry features from whole-slide images.
MATLAB
3
star
12

IHC-Analysis

Jupyter Notebook
2
star
13

glimr

A simplified wrapper for hyperparameter search with Ray Tune.
Python
1
star