pathology

There are 20 repositories under pathology topic.

CLAM
mahmoodlab / CLAM
Open source tools for computational pathology - Nature BME
bioimage-informatics camelyon16 camelyon17 clam computational-pathology data-efficient deep-learning digital-pathology histopathology mahmoodlab pathology quantitative-pathology tcga-data weakly-supervised-learning whole-slide-imaging
Language:Python 1278
qupath / qupath
QuPath - Open-source bioimage analysis for research
bioimage-analysis bioimage-informatics cell-analysis cell-segmentation computational-pathology digital-pathology groovy histology image-processing imagej javafx machine-learning opencv pathology tissue-microarray-analysis whole-slide-imaging
Language:Java 1139
baidu-research / NCRF
Cancer metastasis detection with neural conditional random field (NCRF)
deep-learning conditional-random-fields pathology whole-slide-imaging camelyon16
Language:Python 760
mahmoodlab / UNI
Pathology Foundation Model - Nature Medicine
computational-pathology digital-pathology foundation foundation-model histopathology mahmoodlab mass-100k nature-medicine pathology pathology-dinov2 pathology-fm pathology-foundation pathology-foundation-model pathology-self-supervised quantitative-pathology uni uni-foundation-model
Language:Jupyter Notebook 550
basveeling / pcam
The PatchCamelyon (PCam) deep learning classification benchmark.
benchmark dataset deep-learning deep-learning-datasets pathology
Language:Python 489
openslide / openslide
C library for reading virtual slide images
c pathology whole-slide-imaging
Language:C 429
histolab / histolab
Library for Digital Pathology Image Processing
bioinformatics biology data-science digital-pathology digital-pathology-data hacktoberfest pathology python research science-research wsi
Language:Python 422
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 416
mahmoodlab / CONCH
A vision-language foundation model for computational pathology - Nature Medicine
bioimage-analysis bioimage-informatics computational-pathology conch digital-pathology foundation-model health-informatics histopathology mahmoodlab medical-imaging nature-medicine nlp-machine-learning pathology quantitative-pathology vision-language-pathology
Language:Python 342
slideflow
slideflow / slideflow
Powerful, open-source AI tools for digital pathology.
computational-pathology deep-learning histology histopathology machine-learning pathology python whole-slide-imaging
Language:Python 329
mahmoodlab / PathomicFusion
Fusing Histology and Genomics via Deep Learning - IEEE TMI
pathomic fusion multimodal pathology histopathology transcriptomics genomics multimodal-network computational-pathogenomics mahmoodlab
Language:Jupyter Notebook 320
PathologyFoundation / plip
Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI (Nature Medicine). PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.
artificial-intelligence clip pathology vision-and-language
Language:Python 318
BiomedSciAI / histocartography
A standardized Python API with necessary preprocessing, machine learning and explainability tools to facilitate graph-analytics in computational pathology.
machine-learning graph-neural-networks pytorch deep-learning pathology healthcare
Language:Python 252
nadeemlab / DeepLIIF
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
multiplex immunohistochemical-images immunohistochemistry deep-learning multitask-learning pathology pathology-image pathology-gan segmentation cell-segmentation cell-biology cloud-native-applications pytorch ai-ready datasets image-segmentation digital-pathology stitching super-resolution whole-slide-imaging
Language:Python 210
mahmoodlab / MCAT
Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images - ICCV 2021
early-fusion genomics mahmoodlab mcat multimodal multimodal-deep-learning multimodal-fusion pathology
Language:Jupyter Notebook 195
mahmoodlab / NucleiSegmentation
cGAN-based Multi Organ Nuclei Segmentation
nuclei segmentation cgan gan histopathology pathology
Language:Python 190
mahmoodlab / TOAD
AI-based pathology predicts origins for cancers of unknown primary - Nature
histology pathology wsi-images histopathology cancer-imaging-research cancer-research cancer-detection mahmoodlab deep deep-learning bioimage-analysis bioimage-informatics toad unknown-primary cup
Language:Python 172
mahmoodlab / Patch-GCN
Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
wsi wsi-images gcn survival-prediction pathology histopathology mahmoodlab
Language:Python 146
mahmoodlab / SurvPath
Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction - CVPR 2024
histology-transcriptomics mahmoodlab pathology pathology-genomics survpath interpretability pathology-representation pathways
Language:Python 134
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 133
mahmoodlab / PANTHER
Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology - CVPR 2024
histology mixture-model optimal-transport panther pathology protoype
Language:Jupyter Notebook 121
georg-wolflein / pathology-foundation-models
List of pathology feature extractors and foundation models
computational-pathology deep-learning feature-extraction foundation-models pathology self-supervised-learning
112
Project-Evidence / project-evidence.github.io
Evidence SARS-CoV-2 Emerged From a Biological Laboratory in Wuhan, China
sars-cov-2 scribble pathology archive
Language:HTML 111
Project-MONAI / monai-deploy
MONAI Deploy aims to become the de-facto standard for developing, packaging, testing, deploying and running medical AI applications in clinical production.
monai ai medical-imaging inference healthcare guidelines open-standard ai-application-development ai-application-deployment deep-learning machine-learning mlops ml-platform pytorch python dicom fhir radiology pathology
Language:Shell 106
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 102
mahmoodlab / SISH
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
pathology image-retrieval wsi-images histology image-search-engine histopathology mahmoodlab fish deep-learning vqvae bioimage-analysis bioimage-informatics
Language:Python 100
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 99
mahmoodlab / TANGLE
Transcriptomics-guided Slide Representation Learning in Computational Pathology - CVPR 2024
contrastive-learning mahmoodlab pathology tangle histology-transcriptomics pathology-genomics pathology-representation pathology-transcriptomics slide-representation-learning
Language:Python 96
mahmoodlab / MMP
Multimodal prototyping for cancer survival prediction - ICML 2024
multimodal pathology prototype survival optimal-transport
Language:Jupyter Notebook 79
SBU-BMI / wsinfer
🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
deep-learning pathology whole-slide-imaging pytorch classification
Language:Python 68
huangzhii / nuclei.io
nuclei.io: Human-in-the-loop active learning framework for pathology image analysis
ai medical-imaging pathology whole-slide-image
Language:Python 62
lucasrla / wsi-preprocessing
Simple library for preprocessing histopathological whole-slide images (WSI) into tiles (a.k.a. patches) towards deep learning
libvips pyvips openslide whole-slide-imaging wsi pathology preprocessing fastai pytorch histopathology
Language:Python 55
birkhoffkiki / GPFM
The official implementation of GPFM
cancer computational-pathology cpath distillation foundation-model medical-image-analysis pathology gpfm
Language:Python 53
cpystan / Wsi-Caption
Official Inplementation of 《WsiCaption: Multiple Instance Generation of Pathology Reports for Gigapixel Whole Slide Images》(MICCAI 2024 Oral/ Best Paper Candidate)
aigc pathology python visual-language wsi
Language:Python 53
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 53
raccoon
cylab-tw / raccoon
Raccoon is a NoSQL-based medical image archive for managing the DICOM images.
dicomweb fhir-server mongodb fhir-resources wado-uri fhir-imagingstudy qido-rs pathology wsi bluelight
Language:JavaScript 50