Topic: pathology Goto Github

👇 Here are 174 public repositories matching this topic...

airmec / im4mec
pathology,Code for the im4MEC model described in the paper 'Interpretable deep learning model to predict the molecular classification of endometrial cancer from haematoxylin and eosin-stained whole-slide images: a combined analysis of the PORTEC randomised trials and clinical cohorts'.
Organization: airmec
Home Page: https://doi.org/10.1016/S2589-7500(22)00210-2
ai deep-learning histology pathology pytorch attention-mechanism deep-neural-networks deeplearning self-supervised-learning

baidu-research / ncrf
pathology,Cancer metastasis detection with neural conditional random field (NCRF)
Organization: baidu-research
deep-learning conditional-random-fields pathology whole-slide-imaging camelyon16

basveeling / pcam
pathology,The PatchCamelyon (PCam) deep learning classification benchmark.
User: basveeling
dataset deep-learning benchmark pathology deep-learning-datasets

biomedsciai / histocartography
pathology,A standardized Python API with necessary preprocessing, machine learning and explainability tools to facilitate graph-analytics in computational pathology.
Organization: biomedsciai
deep-learning graph-neural-networks healthcare machine-learning pathology pytorch

cylab-tw / raccoon
pathology,Raccoon is a NoSQL-based medical image archive for managing the DICOM images.
Organization: cylab-tw
dicomweb fhir-server mongodb fhir-resources wado-uri fhir-imagingstudy qido-rs pathology wsi bluelight

dana-farber-aios / pathml
pathology,Tools for computational pathology
Organization: dana-farber-aios
Home Page: https://pathml.org
machine-learning digital-pathology computational-pathology biomedical-image-processing pathology histopathology spatial-transcriptomics image-analysis microscopy fluorescence-microscopy-imaging

diagnijmegen / pathology-whole-slide-data
pathology,A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.
Organization: diagnijmegen
Home Page: https://diagnijmegen.github.io/pathology-whole-slide-data/
histopathology iterator whole-slide-image whole-slide-annotation pathology python whole-slide-imaging deep-learning wsa wsi

dslituiev / slideslicer
pathology,a toolbox for manipulation of digital pathology slides and annotations
User: dslituiev
openslide wsi annotations mask pathology histology slideslicer tissue read-slides

georg-wolflein / pathology-feature-extractors
pathology,List of pathology feature extractors
User: georg-wolflein
computational-pathology deep-learning feature-extraction foundation-models pathology self-supervised-learning

histolab / histolab
pathology,Library for Digital Pathology Image Processing
Organization: histolab
Home Page: http://histolab.readthedocs.io
bioinformatics biology data-science digital-pathology digital-pathology-data hacktoberfest pathology python research science-research wsi

huangzhii / nuclei.io
pathology,nuclei.io: Human-in-the-loop active learning framework for pathology image analysis
User: huangzhii
Home Page: https://huangzhii.github.io/nuclei-HAI/
ai medical-imaging pathology whole-slide-image

jamesdolezal / biscuit
pathology,Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding
User: jamesdolezal
computational-pathology deep-learning histology machine-learning pathology whole-slide-imaging uncertainty-quantification

jamesdolezal / slideflow
pathology,Deep learning library for digital pathology, with both Tensorflow and PyTorch support.
User: jamesdolezal
Home Page: https://slideflow.dev
python machine-learning deep-learning pathology histology computational-pathology whole-slide-imaging histopathology

jopo666 / histoprep
pathology,Preprocessing module for large histological images
User: jopo666
openslide pathology pathology-image tissue-classification tissue-analysis histological-images medical-imaging medical-image-processing medical-image-analysis histological-slides

keiserlab / plaquebox-paper
pathology,Repo for Tang et al, bioRxiv 454793 (2018)
Organization: keiserlab
alzheimers-disease machine-learning amlyoid-plaques deep-learning convolutional-neural-networks interpretable-machine-learning explainable-ai dementia immunohistochemical-images pathology

lucasrla / wsi-preprocessing
pathology,Simple library for preprocessing histopathological whole-slide images (WSI) into tiles (a.k.a. patches) towards deep learning
User: lucasrla
libvips pyvips openslide whole-slide-imaging wsi pathology preprocessing fastai pytorch histopathology

lucasrla / wsi-tile-cleanup
pathology,Image filters for digital pathology: detect pen marks, background, and artifacts. Use them for preprocessing towards deep learning
User: lucasrla
libvips pyvips otsu-threshold whole-slide-imaging wsi pathology preprocessing deep-learning fastai pytorch histopathology

mahmoodlab / clam
pathology,Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
Organization: mahmoodlab
Home Page: http://clam.mahmoodlab.org
histopathology pathology weakly-supervised-learning whole-slide-imaging data-efficient computational-pathology mahmoodlab bioimage-informatics deep-learning tcga-data

mahmoodlab / conch
pathology,A vision-language foundation model for computational pathology - Nature Medicine
Organization: mahmoodlab
bioimage-analysis bioimage-informatics conch foundation-model health-informatics histopathology medical-imaging nlp-machine-learning pathology vision-language-pathology

mahmoodlab / crane
pathology,Deep learning enabled assessment of cardiac allograft rejection from endomyocardial biopsies- Nature Medicine
Organization: mahmoodlab
Home Page: http://crane.mahmoodlab.org
biopsy-screening endomyocardial histology pathology weakly-supervised-learning whole-slide-imaging

mahmoodlab / histofl
pathology,Federated Learning for Computational Pathology - Medical Image Analysis
Organization: mahmoodlab
federated-learning pathology histology-images mahmoodlab

mahmoodlab / mcat
pathology,Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images - ICCV 2021
Organization: mahmoodlab
early-fusion genomics mahmoodlab mcat multimodal multimodal-deep-learning multimodal-fusion pathology

mahmoodlab / mi-zero
pathology,Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images - CVPR 2023
Organization: mahmoodlab
mil pathology vision-language-pathology zero-shot-learning image-text-pathology zero-shot-pathology computational-pathology digital-pathology mahmoodlab quantitative-pathology

mahmoodlab / mmp
pathology,Multimodal prototyping for cancer survival prediction - ICML 2024
Organization: mahmoodlab
multimodal optimal-transport pathology prototype survival

mahmoodlab / nucleisegmentation
pathology,cGAN-based Multi Organ Nuclei Segmentation
Organization: mahmoodlab
nuclei segmentation cgan gan histopathology pathology

mahmoodlab / panther
pathology,Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology - CVPR 2024
Organization: mahmoodlab
histology mixture-model optimal-transport panther pathology protoype

mahmoodlab / patch-gcn
pathology,Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
Organization: mahmoodlab
Home Page: http://mahmoodlab.org
wsi wsi-images gcn survival-prediction pathology histopathology mahmoodlab

mahmoodlab / pathomicfusion
pathology,Fusing Histology and Genomics via Deep Learning - IEEE TMI
Organization: mahmoodlab
Home Page: http://www.mahmoodlab.org
pathomic fusion multimodal pathology histopathology transcriptomics genomics multimodal-network computational-pathogenomics mahmoodlab

mahmoodlab / sish
pathology,Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
Organization: mahmoodlab
pathology image-retrieval wsi-images histology image-search-engine histopathology mahmoodlab fish deep-learning vqvae

mahmoodlab / survpath
pathology,Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction - CVPR 2024
Organization: mahmoodlab
histology-transcriptomics mahmoodlab pathology pathology-genomics survpath interpretability pathology-representation pathways

mahmoodlab / tangle
pathology,Transcriptomics-guided Slide Representation Learning in Computational Pathology - CVPR 2024
Organization: mahmoodlab
contrastive-learning mahmoodlab pathology tangle histology-transcriptomics pathology-genomics pathology-representation pathology-transcriptomics slide-representation-learning

mahmoodlab / toad
pathology,AI-based pathology predicts origins for cancers of unknown primary - Nature
Organization: mahmoodlab
Home Page: http://toad.mahmoodlab.org
histology pathology wsi-images histopathology cancer-imaging-research cancer-research cancer-detection mahmoodlab deep deep-learning

mahmoodlab / uni
pathology,Towards a general-purpose foundation model for computational pathology - Nature Medicine
Organization: mahmoodlab
foundation foundation-model histopathology mahmoodlab pathology uni pathology-foundation-model nature-medicine mass-100k pathology-dinov2

marvinler / tcga_segmentation
pathology,Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024
User: marvinler
multiple-instance-learning image-segmentation histopathology tumor-segmentation whole-slide-imaging wsi miccai tcga slide-image-segmentation tcga-data

mipt-oulu / mctsegmentation
pathology,Deep-Learning for Tidemark Segmentation in Human Osteochondral Tissues Imaged with Micro-computed Tomography
Organization: mipt-oulu
3d deep-learning micro-ct osteoarthritis pathology pytorch

nadeemlab / deepliif
pathology,Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
Organization: nadeemlab
Home Page: https://deepliif.org
multiplex immunohistochemical-images immunohistochemistry deep-learning multitask-learning pathology pathology-image pathology-gan segmentation cell-segmentation

openslide / openslide
pathology,C library for reading virtual slide images
Organization: openslide
Home Page: https://openslide.org/
pathology whole-slide-imaging c

path-ai / hif2gene
pathology,Data and code to accompany our Nature publication
Organization: path-ai
Home Page: https://www.nature.com/articles/s41467-021-21896-9
deep-learning pathology

pathologyfoundation / plip
pathology,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.
Organization: pathologyfoundation
artificial-intelligence clip pathology vision-and-language

pingjunchen / pyslide
pathology,Digital Pathology Whole Slide Image Analysis Toolbox
User: pingjunchen
Home Page: https://pyslide.readthedocs.io
computational-pathology deep-learning image-analysis pathology python whole-slide-imaging

pingjunchen / tissueloc
pathology,Whole Slide Digital Pathology Image Tissue Localization
User: pingjunchen
Home Page: https://tissueloc.readthedocs.io
whole-slide-imaging pathology computational-pathology pathology-image tissue-localization python

project-evidence / project-evidence.github.io
pathology,Evidence SARS-CoV-2 Emerged From a Biological Laboratory in Wuhan, China
User: project-evidence
Home Page: https://project-evidence.github.io
sars-cov-2 scribble pathology archive

project-monai / monai-deploy
pathology,MONAI Deploy aims to become the de-facto standard for developing, packaging, testing, deploying and running medical AI applications in clinical production.
Organization: project-monai
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

qupath / qupath
pathology,QuPath - Bioimage analysis & digital pathology
Organization: qupath
Home Page: https://qupath.github.io
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

rodrigobressan / digipathos
pathology,Brazilian Agricultural Research Corporation (EMBRAPA) fully annotated dataset for plant diseases. Plug and play installation over PiP.
User: rodrigobressan
dataset open-data pathology plant-disease plant-pathology python wrapper

sbu-bmi / wsinfer
pathology,🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
Organization: sbu-bmi
Home Page: https://wsinfer.readthedocs.io
deep-learning pathology whole-slide-imaging pytorch classification

sebastianffx / stainlib
pathology,Python 3 library for the augmentation & normalization of H&E images
User: sebastianffx
histopathology pathology computational-pathology image-normalization image-processing image-augmentation

smujiang / re-stained_wsis_registration
pathology,Re-stained whole slide image alignment
User: smujiang
image registration re-stained alignment pathology whole-slide-image

spawaskar-cora / cora-docs
pathology,CoRA Docs
Organization: spawaskar-cora
cora forensics anthropology commingled-human-remains human-remains dna bones data-science data-analytics articulations

stanfordmlgroup / dlbcl-morph
pathology,DLBCL-Morph dataset containing high resolution tissue microarray scans from 209 DLBCL cases, with geometric features computed using deep learning
Organization: stanfordmlgroup
dataset deep-learning medical-imaging pathology survival-prediction