pathology

There are 19 repositories under 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 977
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 910
baidu-research / NCRF
Cancer metastasis detection with neural conditional random field (NCRF)
deep-learning conditional-random-fields pathology whole-slide-imaging camelyon16
Language:Python 748
basveeling / pcam
The PatchCamelyon (PCam) deep learning classification benchmark.
dataset deep-learning benchmark pathology deep-learning-datasets
Language:Python 456
openslide / openslide
C library for reading virtual slide images
pathology whole-slide-imaging c
Language:C 382
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 364
histolab / histolab
Library for Digital Pathology Image Processing
digital-pathology-data digital-pathology bioinformatics biology wsi hacktoberfest data-science python science-research research pathology
Language:Python 341
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 254
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 226
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 220
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 217
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 188
mahmoodlab / NucleiSegmentation
cGAN-based Multi Organ Nuclei Segmentation
nuclei segmentation cgan gan histopathology pathology
Language:Python 181
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 168
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 148
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 140
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 140
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
Project-Evidence / project-evidence.github.io
Evidence SARS-CoV-2 Emerged From a Biological Laboratory in Wuhan, China
archive pathology sars-cov-2 scribble
Language:HTML 111
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 103
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 95
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 89
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 78
SBU-BMI / wsinfer
🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
deep-learning pathology whole-slide-imaging pytorch classification
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 50
PingjunChen / pyslide
Digital Pathology Whole Slide Image Analysis Toolbox
pathology whole-slide-imaging deep-learning python image-analysis computational-pathology
Language:Python 48
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 46
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 44
PingjunChen / tissueloc
Whole Slide Digital Pathology Image Tissue Localization
whole-slide-imaging pathology computational-pathology pathology-image tissue-localization python
Language:Python 44
mahmoodlab / HistoFL
Federated Learning for Computational Pathology - Medical Image Analysis
federated-learning pathology histology-images mahmoodlab
Language:Python 43
Path-AI / hif2gene
Data and code to accompany our Nature publication
deep-learning pathology
Language:Jupyter Notebook 41
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 40
MIPT-Oulu / mCTSegmentation
Deep-Learning for Tidemark Segmentation in Human Osteochondral Tissues Imaged with Micro-computed Tomography
pytorch osteoarthritis deep-learning micro-ct pathology 3d
Language:Python 40
rodrigobressan / digipathos
Brazilian Agricultural Research Corporation (EMBRAPA) fully annotated dataset for plant diseases. Plug and play installation over PiP.
dataset plant-disease plant-pathology pathology wrapper python open-data
Language:Python 40
keiserlab / plaquebox-paper
Repo for Tang et al, bioRxiv 454793 (2018)
alzheimers-disease machine-learning amlyoid-plaques deep-learning convolutional-neural-networks interpretable-machine-learning explainable-ai dementia immunohistochemical-images pathology medical-image-analysis plaques saliency-map
Language:Jupyter Notebook 36