Search Results - RepositoryStats

366

1.1k

gpl-3.0

21

Open source tools for computational pathology - Nature BME

clam pathology tcga-data camelyon16 camelyon17 mahmoodlab deep-learning data-efficient histopathology digital-pathology whole-slide-imaging bioimage-informatics quantitative-pathology computational-pathology weakly-supervised-learning

Created 2020-04-01

119 commits to master branch, last one 7 months ago

qupath qupath

282

1.1k

gpl-3.0

56

QuPath - Open-source bioimage analysis for research

groovy imagej javafx opencv histology pathology cell-analysis image-processing machine-learning bioimage-analysis cell-segmentation digital-pathology whole-slide-imaging bioimage-informatics computational-pathology tissue-microarray-analysis

Created 2016-08-28

4,045 commits to main branch, last one a day ago

HIPT mahmoodlab

90

514

other

11

Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)

cvpr pytorch cvpr2022 deep-learning histopathology high-resolution transfer-learning pretrained-weights vision-transformer unsupervised-learning computational-pathology self-supervised-learning weakly-supervised-learning hierarchical-attention-networks

Created 2022-06-06

89 commits to master branch, last one 8 months ago

pathml Dana-Farber-AIOS

85

394

gpl-2.0

13

Tools for computational pathology

pathml python pytorch research pathology microscopy deep-learning histopathology image-analysis machine-learning digital-pathology computational-pathology spatial-transcriptomics biomedical-image-processing fluorescence-microscopy-imaging

Created 2019-07-31

1,384 commits to master branch, last one 26 days ago

tiatoolbox TissueImageAnalytics

82

389

other

7

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

python deep-learning histopathology image-analysis tissue-analysis machine-learning cell-segmentation digital-pathology cell-classification stain-normalization tissue-segmentation whole-slide-imaging medical-image-analysis computational-pathology

Created 2020-05-28

699 commits to develop branch, last one 8 hours ago

UNI mahmoodlab

49

355

other

7

Towards a general-purpose foundation model for computational pathology - Nature Medicine

uni mass-100k pathology foundation mahmoodlab pathology-fm histopathology nature-medicine foundation-model pathology-dinov2 digital-pathology pathology-foundation uni-foundation-model quantitative-pathology computational-pathology pathology-self-supervised pathology-foundation-model

Created 2024-02-02

27 commits to main branch, last one 2 months ago

CONCH mahmoodlab

22

281

other

3

A vision-language foundation model for computational pathology - Nature Medicine

conch pathology mahmoodlab histopathology medical-imaging nature-medicine foundation-model bioimage-analysis digital-pathology health-informatics bioimage-informatics nlp-machine-learning quantitative-pathology computational-pathology vision-language-pathology

Created 2023-12-31

14 commits to main branch, last one 3 months ago

slideflow slideflow

45

269

apache-2.0

15

Powerful, open-source AI tools for digital pathology.

python histology pathology deep-learning histopathology machine-learning whole-slide-imaging computational-pathology

Created 2019-09-13

3,101 commits to master branch, last one 20 days ago

HEST mahmoodlab

12

169

other

4

HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024

histology computational-pathology spatial-transcriptomics

Created 2024-03-04

37 commits to main branch, last one 10 days ago

HistoSSLscaling owkin

11

146

other

5

Code associated to the publication: Scaling self-supervised learning for histopathology with masked image modeling, A. Filiot et al., MedRxiv (2023). We publicly release Phikon 🚀

computational-pathology

Created 2023-09-01

60 commits to main branch, last one 10 months ago

Self-Supervised-ViT-Path Richarizardd

18

139

gpl-3.0

5

Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology (LMRL Workshop, NeurIPS 2021)

neurips pytorch deep-learning histopathology transfer-learning pretrained-weights vision-transformer unsupervised-learning computational-pathology self-supervised-learning weakly-supervised-learning

Created 2022-03-03

77 commits to master branch, last one 2 years ago

tcga_segmentation MarvinLer

34

127

agpl-3.0

2

Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024

wsi tcga miccai pathology tcga-data segmentation data-efficient histopathology medical-imaging image-segmentation tumor-segmentation whole-slide-imaging computational-pathology slide-image-segmentation multiple-instance-learning weakly-supervised-learning

Created 2020-04-07

36 commits to master branch, last one 3 years ago

FAST-Pathology AICAN-Research

26

122

bsd-2-clause

5

⚡ Open-source software for deep learning-based digital pathology

opencl opengl pytorch openvino software tensorrt cplusplus inference deployment tensorflow free-to-use deep-learning fastpathology machine-learning digital-pathology computational-pathology convolutional-neural-networks

Created 2019-07-09

491 commits to master branch, last one 5 months ago

torchstain EIDOSLAB

21

118

mit

5

Stain normalization tools for histological analysis and computational pathology

numpy python pytorch tensorflow histopathology medical-imaging digital-pathology stain-normalization computational-pathology

Created 2020-12-22

188 commits to main branch, last one about a year ago

pathology-whole-slide-data DIAGNijmegen

27

94

apache-2.0

6

A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.

wsa wsd wsi wsm python iterator pathology deep-learning histopathology whole-slide-data whole-slide-mask whole-slide-image whole-slide-dataset whole-slide-imaging whole-slide-annotation computational-pathology

Created 2021-09-07

643 commits to main branch, last one 26 days ago

MI-Zero mahmoodlab

5

94

other

4

Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images - CVPR 2023

mil pathology mahmoodlab digital-pathology zero-shot-learning zero-shot-pathology image-text-pathology quantitative-pathology computational-pathology vision-language-pathology

Created 2023-04-17

12 commits to main branch, last one about a year ago

WSI-finetuning invoker-LL

14

78

unknown

5

This is the official repository for our CVPR 2023 paper 'Task-Specific Fine-Tuning via Variational Information Bottleneck for Weakly-Supervised Pathology Whole Slide Image Classification'.

wsi end-to-end fine-tuning breast-cancer cervical-cancer mutual-information information-bottleneck computational-pathology

Created 2023-03-14

24 commits to main branch, last one 7 months ago