computational-pathology

There are 11 repositories under computational-pathology topic.

qupath / qupath
QuPath - Bioimage analysis & digital pathology
bioimage-informatics image-processing digital-pathology pathology machine-learning cell-segmentation whole-slide-imaging bioimage-analysis cell-analysis imagej opencv groovy histology javafx tissue-microarray-analysis computational-pathology
Language:Java 980
CLAM
mahmoodlab / CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
histopathology pathology weakly-supervised-learning whole-slide-imaging data-efficient computational-pathology mahmoodlab bioimage-informatics deep-learning tcga-data camelyon16 camelyon17 clam digital-pathology quantitative-pathology
Language:Python 916
mahmoodlab / HIPT
Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)
computational-pathology cvpr cvpr2022 deep-learning hierarchical-attention-networks high-resolution histopathology pretrained-weights pytorch self-supervised-learning transfer-learning unsupervised-learning vision-transformer weakly-supervised-learning
Language:Jupyter Notebook 466
pathml
Dana-Farber-AIOS / pathml
Tools for computational pathology
machine-learning digital-pathology computational-pathology biomedical-image-processing pathology histopathology spatial-transcriptomics image-analysis microscopy fluorescence-microscopy-imaging deep-learning python pytorch research pathml
Language:Python 367
TissueImageAnalytics / tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
python computational-pathology whole-slide-imaging deep-learning digital-pathology histopathology image-analysis machine-learning tissue-analysis tissue-segmentation cell-classification cell-segmentation medical-image-analysis stain-normalization
Language:Python 330
Peter554 / StainTools
Tools for tissue image stain normalisation and augmentation in Python 3
computational-pathology medical-imaging python
Language:Python 304
slideflow
jamesdolezal / slideflow
Deep learning library for digital pathology, with both Tensorflow and PyTorch support.
python machine-learning deep-learning pathology histology computational-pathology whole-slide-imaging histopathology
Language:Python 223
mahmoodlab / UNI
Towards a general-purpose foundation model for computational pathology - Nature Medicine
foundation foundation-model histopathology mahmoodlab pathology uni pathology-foundation-model nature-medicine mass-100k pathology-dinov2 pathology-fm pathology-foundation pathology-self-supervised uni-foundation-model computational-pathology digital-pathology quantitative-pathology
Language:Jupyter Notebook 192
mahmoodlab / CONCH
A vision-language foundation model for computational pathology - Nature Medicine
bioimage-analysis bioimage-informatics conch foundation-model health-informatics histopathology medical-imaging nlp-machine-learning pathology vision-language-pathology nature-medicine computational-pathology digital-pathology mahmoodlab quantitative-pathology
Language:Python 153
owkin / HistoSSLscaling
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
Language:Jupyter Notebook 130
Richarizardd / Self-Supervised-ViT-Path
Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology (LMRL Workshop, NeurIPS 2021)
self-supervised-learning histopathology weakly-supervised-learning vision-transformer unsupervised-learning computational-pathology transfer-learning deep-learning pretrained-weights neurips pytorch
Language:Jupyter Notebook 126
AICAN-Research / FAST-Pathology
⚡ Open-source software for deep learning-based digital pathology
deep-learning machine-learning digital-pathology computational-pathology software free-to-use opencl opengl tensorrt openvino pytorch cplusplus tensorflow inference deployment convolutional-neural-networks fastpathology
Language:C++ 116
MarvinLer / tcga_segmentation
Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024
multiple-instance-learning image-segmentation histopathology tumor-segmentation whole-slide-imaging wsi miccai tcga slide-image-segmentation tcga-data weakly-supervised-learning pathology computational-pathology data-efficient medical-imaging segmentation
Language:Python 113
EIDOSLAB / torchstain
Stain normalization tools for histological analysis and computational pathology
pytorch histopathology stain-normalization computational-pathology medical-imaging python digital-pathology numpy tensorflow
Language:Python 103
hsn_v1
lyndonchan / hsn_v1
HistoSegNet: Semantic Segmentation of Histological Tissue Type in Whole Slide Images (ICCV 2019)
computational-pathology histopathology-images semantic-segmentation wsss
Language:Jupyter Notebook 87
DIAGNijmegen / pathology-whole-slide-data
A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.
histopathology iterator whole-slide-image whole-slide-annotation pathology python whole-slide-imaging deep-learning wsa wsi wsm whole-slide-mask wsd whole-slide-dataset whole-slide-data computational-pathology
Language:Python 81
mahmoodlab / MI-Zero
Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images - CVPR 2023
mil pathology vision-language-pathology zero-shot-learning image-text-pathology zero-shot-pathology computational-pathology digital-pathology mahmoodlab quantitative-pathology
Language:Python 79
cytomine / Cytomine-core
Cytomine-Core is the main web server implementing the Cytomine API
cytomine digital-pathology machine-learning whole-slide-imaging computational-pathology
Language:Groovy 70
TissueImageAnalytics / cerberus
One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification
computational-pathology deep-learning multi-task-learning python pytorch
Language:Python 62
jgamper / compay-syntax
:microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.
computational-pathology medical-imaging wsis openslide slide-images pathology-image whole-slide-image whole-slide-imaging
Language:Python 55
manuel-munoz-aguirre / PyHIST
A pipeline to segment tissue from the background in histological images
histological-images histology segmentation svs image-segmentation computational-pathology histopathology wsi
Language:Python 55
bianhao123 / Mixed_supervision
MICCAI2022: Multiple Instance Learning with Mixed Supervision in Gleason Grading.
computational-pathology histopathology miccai2022 multiple-instance-learning pytorch pytorch-lightning
Language:Python 50
sebastianffx / stainlib
Python 3 library for the augmentation & normalization of H&E images
histopathology pathology computational-pathology image-normalization image-processing image-augmentation
Language:Jupyter Notebook 50
PingjunChen / pyslide
Digital Pathology Whole Slide Image Analysis Toolbox
pathology whole-slide-imaging deep-learning python image-analysis computational-pathology
Language:Python 48
PingjunChen / tissueloc
Whole Slide Digital Pathology Image Tissue Localization
whole-slide-imaging pathology computational-pathology pathology-image tissue-localization python
Language:Python 44
dazhangyu123 / ACMIL
WSI classification
bracs camelyon16 computational-pathology digital-pathology multiple-instance-learning pathology-image whole-slide-image acmil weakly-supervised-learning histopathology
Language:Python 37
nauyan / Segmentation
Contains code for Semantic Segmentation of MoNuSeg 2018 challenge.
computational-pathology deep-learning deeplabv3 keras medical-imaging segmentation segnet tensorflow u-net
Language:Python 36
PingjunChen / LiverCancerSeg
PAIP2019: Liver Cancer Segmentation
pytorch deep-learning segmentation computational-pathology
Language:Python 32
biscuit
jamesdolezal / biscuit
Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding
computational-pathology deep-learning histology machine-learning pathology whole-slide-imaging uncertainty-quantification
Language:Python 22
mahdihosseini / ADP
Atlas of Digital Pathology for Deep Learning [CVPR2019]
computational-pathology database dataset deep-learning
Language:Python 22
rikiyay / style-transfer-for-digital-pathology
Learning domain-agnostic visual representation for computational pathology using medically-irrelevant style transfer augmentation
computer-vision representation-learning style-transfer computational-pathology digital-pathology data-augumentation deep-learning
Language:Python 22
AICAN-Research / H2G-Net
🚀 H2G-Net: Segmentation of breast cancer region from whole slide images
h2g-net cnn tensorflow-keras digital-pathology computational-pathology u-net agu-net mobilenetv2 breast-cancer clustering convolutional-neural-networks medical-imaging refinement segmentation whole-slide-image deep-learning tensorflow
Language:TeX 19
andreped / fast-stain-normalization
:star2: GPU-accelerated stain normalization command line tool
histopathology-images digital-pathology stain-normalization deep-learning cpp python computational-pathology fast torch tensorflow tensorflow2
Language:Python 19
lunit-io / ocelot23algo
OCELOT 2023: Cell Detection from Cell-Tissue Interaction
cell-detection computational-pathology cvpr2023 miccai2023
Language:Python 17
TissueImageAnalytics / iguana
Interpretable Gland-Graph Networks
computational-pathology deep-learning graph-neural-network python pytorch pytorch-geometric
Language:Python 17
PathologyDataScience / HiPS
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
biomarker-discovery biomedical-image-processing breast-cancer computational-pathology digital-pathology survival-prediction explainable-ai
Language:Python 16