Projects in Awesome Lists tagged with histopathology
A curated list of projects in awesome lists tagged with histopathology .
https://github.com/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
Last synced: 14 May 2025
https://github.com/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
Last synced: 06 May 2025
https://github.com/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
Last synced: 06 May 2025
https://github.com/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
Last synced: 04 Apr 2025
https://github.com/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
Last synced: 06 May 2025
https://github.com/mahmoodlab/uni
A general-purpose foundation model for computational pathology - 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
Last synced: 15 May 2025
https://github.com/Dana-Farber-AIOS/pathml
Tools for computational pathology
biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics
Last synced: 06 May 2025
https://github.com/dana-farber-aios/pathml
Tools for computational pathology
biomedical-image-processing computational-pathology deep-learning digital-pathology fluorescence-microscopy-imaging histopathology image-analysis machine-learning microscopy pathml pathology python pytorch research spatial-transcriptomics
Last synced: 29 Jan 2025
https://github.com/TissueImageAnalytics/tiatoolbox
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
cell-classification cell-segmentation computational-pathology deep-learning digital-pathology histopathology image-analysis machine-learning medical-image-analysis python stain-normalization tissue-analysis tissue-segmentation whole-slide-imaging
Last synced: 06 May 2025
https://github.com/mahmoodlab/conch
Vision-Language Pathology Foundation Model - 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
Last synced: 16 May 2025
https://github.com/mahmoodlab/CONCH
Vision-Language Pathology Foundation Model - 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
Last synced: 06 May 2025
https://github.com/mahmoodlab/pathomicfusion
Fusing Histology and Genomics via Deep Learning - IEEE TMI
computational-pathogenomics fusion genomics histopathology mahmoodlab multimodal multimodal-network pathology pathomic transcriptomics
Last synced: 06 Apr 2025
https://github.com/mahmoodlab/nucleisegmentation
cGAN-based Multi Organ Nuclei Segmentation
cgan gan histopathology nuclei pathology segmentation
Last synced: 08 May 2025
https://github.com/mahmoodlab/toad
AI-based pathology predicts origins for cancers of unknown primary - Nature
bioimage-analysis bioimage-informatics cancer-detection cancer-imaging-research cancer-research cup deep deep-learning histology histopathology mahmoodlab pathology toad unknown-primary wsi-images
Last synced: 20 Dec 2024
https://github.com/mahmoodlab/Patch-GCN
Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
gcn histopathology mahmoodlab pathology survival-prediction wsi wsi-images
Last synced: 06 May 2025
https://github.com/richarizardd/self-supervised-vit-path
Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology (LMRL Workshop, NeurIPS 2021)
computational-pathology deep-learning histopathology neurips pretrained-weights pytorch self-supervised-learning transfer-learning unsupervised-learning vision-transformer weakly-supervised-learning
Last synced: 10 Apr 2025
https://github.com/Richarizardd/Self-Supervised-ViT-Path
Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology (LMRL Workshop, NeurIPS 2021)
computational-pathology deep-learning histopathology neurips pretrained-weights pytorch self-supervised-learning transfer-learning unsupervised-learning vision-transformer weakly-supervised-learning
Last synced: 06 May 2025
https://github.com/EIDOSLAB/torchstain
Stain normalization tools for histological analysis and computational pathology
computational-pathology digital-pathology histopathology medical-imaging numpy python pytorch stain-normalization tensorflow
Last synced: 06 May 2025
https://github.com/MarvinLer/tcga_segmentation
Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024
computational-pathology data-efficient histopathology image-segmentation medical-imaging miccai multiple-instance-learning pathology segmentation slide-image-segmentation tcga tcga-data tumor-segmentation weakly-supervised-learning whole-slide-imaging wsi
Last synced: 06 May 2025
https://github.com/mahmoodlab/patch-gcn
Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
gcn histopathology mahmoodlab pathology survival-prediction wsi wsi-images
Last synced: 20 Dec 2024
https://github.com/mahmoodlab/sish
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
bioimage-analysis bioimage-informatics deep-learning fish histology histopathology image-retrieval image-search-engine mahmoodlab pathology vqvae wsi-images
Last synced: 28 Apr 2025
https://github.com/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.
computational-pathology deep-learning histopathology iterator pathology python whole-slide-annotation whole-slide-data whole-slide-dataset whole-slide-image whole-slide-imaging whole-slide-mask wsa wsd wsi wsm
Last synced: 06 May 2025
https://github.com/manuel-munoz-aguirre/PyHIST
A pipeline to segment tissue from the background in histological images
computational-pathology histological-images histology histopathology image-segmentation segmentation svs wsi
Last synced: 06 May 2025
https://github.com/srinidhiPY/SSL_CR_Histo
Official code for "Self-Supervised driven Consistency Training for Annotation Efficient Histopathology Image Analysis" Published in Medical Image Analysis (MedIA) Journal, Oct, 2021.
annotation-efficient breastpathq camelyon16 deep-learning digital-pathology histopathology self-supervised-learning semi-supervised-learning teacher-student-training
Last synced: 06 May 2025
https://github.com/lucasrla/wsi-preprocessing
Simple library for preprocessing histopathological whole-slide images (WSI) into tiles (a.k.a. patches) towards deep learning
fastai histopathology libvips openslide pathology preprocessing pytorch pyvips whole-slide-imaging wsi
Last synced: 12 Apr 2025
https://github.com/sebastianffx/stainlib
Python 3 library for the augmentation & normalization of H&E images
computational-pathology histopathology image-augmentation image-normalization image-processing pathology
Last synced: 06 May 2025
https://github.com/SBU-BMI/champkit
Benchmarking toolkit for patch-based histopathology image classification.
benchmark benchmarking deep-learning histopathology image-classification pytorch
Last synced: 08 May 2025
https://github.com/EIDOSLAB/UNITOPATHO
Dataset of 9536 H&E-stained patches for colorectal polyps classification and adenomas grading | ICIP21 https://doi.org/10.1109/ICIP42928.2021.9506198
cancer data health histopathological-image histopathology histopathology-images medical-image-processing medical-images neural-networks
Last synced: 06 May 2025
https://github.com/lucasrla/wsi-tile-cleanup
Image filters for digital pathology: detect pen marks, background, and artifacts. Use them for preprocessing towards deep learning
deep-learning fastai histopathology libvips otsu-threshold pathology preprocessing pytorch pyvips whole-slide-imaging wsi
Last synced: 12 Apr 2025
https://github.com/dazhangyu123/ACMIL
WSI classification
acmil bracs camelyon16 computational-pathology digital-pathology histopathology multiple-instance-learning pathology-image weakly-supervised-learning whole-slide-image
Last synced: 06 May 2025
https://github.com/aican-research/breast-epithelium-segmentation
🌸 Breast epithelium segmentation through IHC-guided supervision
benign breast-cancer cytokeratin deep-learning digital-pathology eosin epithelium fastpathology he hematoxylin hematoxylin-eosin-staining histopathology ihc immunohistochemistry insitu invasive segmentation tissue-microarray tma
Last synced: 23 Apr 2025
https://github.com/andreped/fp-dsa-plugin
Digital Slide Archive plugin to enable FAST deployment of pretrained CNNs for digital pathology
cpp deep-learning digital-pathology digital-slide-archive fast fastpathology gpu histopathology large-image plugin python real-time tensorrt
Last synced: 13 Apr 2025
https://github.com/cedriccaruzzo/pannuke-segmentation
An open-source UNet-based pipeline for nuclei segmentation in histopathology images using the PanNuke dataset. It features an interactive web app for easy data visualization and handling, making AI tools accessible even for non-experts. This project provides a foundation for training and exploring histopathology data.
deep-learning deeplab-v3-plus deeplab-v3-plus-pytorch histopathology histopathology-image-analysis machine-learning python pytorch resnet-50 resunet segmentation semantic-segmentation unet unet-image-segmentation unet-pytorch unet-segmentation unetplusplus
Last synced: 14 Feb 2025
https://github.com/shuyib/cell-explorer-tool
An image explorer tool that uses ipywidgets and image manipulation in Pillow to look for and refine features in a image. This is mostly pitched on cell biology, cytopathology and histopathology.
cell-biology cytopathology histopathology image-processing interactive ipynb ipywidgets medical-imaging mybinder pathology streamlit
Last synced: 19 Apr 2025
https://github.com/lucasrla/wsi-preprocessing-sos-workflow
A pipeline to preprocess whole-slide images (WSI) towards deep learning
deep-learning histopathology pathology preprocessing sos sos-workflow whole-slide-imaging
Last synced: 22 Mar 2025
https://github.com/rendeirolab/wsi
A Python package for the processing of whole slide histopathological images
histopathology openslide-python package python
Last synced: 10 Apr 2025
https://github.com/andreped/pathology-representation-simulation
🚀 Create your own simulation of t-SNE on histopathology images!
clustering dimensionality-reduction histopathology pathology representation simulation t-sne tensorboard tensorboard-projector training wsi
Last synced: 29 Dec 2024
https://github.com/aican-research/dru-net
🫁 DRU-Net: Lung carcinoma Segmentation using multi-lens distortion and fusion refinement network
carcinoma convolutional-neural-networks deep-learning histopathology lung lung-cancer pathology whole-slide-image wsi
Last synced: 23 Apr 2025
https://github.com/pabannier/fgfr3mut
Official Implementation of the "AI allows pre-screening of FGFR3 mutational status using routine histology slides of muscle-invasive bladder cancer" paper
cancer deep-learning histopathology
Last synced: 13 Jan 2025
https://github.com/andreped/wsi-visualization-demo
🔬 Simple containerised whole slide image rendering in the browser
browser deepzoom docker dzi histopathology html http hugging-face hugging-face-spaces huggingface nginx openseadragon pathology real-time web whole-slide-image wsi
Last synced: 24 Mar 2025
https://github.com/uni-creator/lungcancerclassification
This repository contains a deep learning-based cancer type prediction system using a trained convolutional neural network (CNN). The model is deployed using Streamlit, allowing users to upload medical images and receive predictions with a probability distribution displayed in a pie chart.
ai-in-healthcare-and-biology biomedical-ai cancer-classification deeplearning histopathology image-classification lung-cancer-classification machine-learning medical-imaging neural-networks streamlit tensorflow
Last synced: 21 Mar 2025
https://github.com/ambidextrous9/histopathologic-cancer-detection
Histopathologic Cancer Detection
cnn histopathological-images histopathology pytorch pytorch-lightning
Last synced: 01 Mar 2025
https://github.com/PaulNSchofield/mpath
Automatically exported from code.google.com/p/mpath
histopathology mammals mice obofoundry pathology phenotype
Last synced: 11 Mar 2025
https://github.com/saharstudios/lungcancerclassification
This repository contains a deep learning-based cancer type prediction system using a trained convolutional neural network (CNN). The model is deployed using Streamlit, allowing users to upload medical images and receive predictions with a probability distribution displayed in a pie chart.
ai-in-healthcare-and-biology biomedical-ai cancer-classification histopathology image-classification lidc-dataset lung-cancer-classification lung-cancer-detection machine-learning medical-imaging neural-networks pyradiomics streamlit tensorflow
Last synced: 29 Mar 2025
https://github.com/iambg56/lungcancerclassification
This repository contains a deep learning-based cancer type prediction system using a trained convolutional neural network (CNN). The model is deployed using Streamlit, allowing users to upload medical images and receive predictions with a probability distribution displayed in a pie chart.
ai-in-healthcare-and-biology biomedical-ai cancer-classification histopathology image-classification lidc-dataset lung-cancer-classification lung-cancer-detection machine-learning medical-imaging neural-networks pyradiomics streamlit tensorflow
Last synced: 29 Mar 2025
https://github.com/2536ivan/nature
Simple Tailwind CSS and JavaScript project, Nature.
bio-inspired-optimization compiler deep-learning foundation-model histopathology language mahmoodlab metaheuristics nature-inspired-algorithms optimization postgis postgresql qiskit swarm-intelligence
Last synced: 09 May 2025
https://github.com/leonardosabogal/lungcancerclassification
This repository contains a deep learning-based cancer type prediction system using a trained convolutional neural network (CNN). The model is deployed using Streamlit, allowing users to upload medical images and receive predictions with a probability distribution displayed in a pie chart.
ai-in-healthcare-and-biology biomedical-ai cancer-classification histopathology image-classification lidc-dataset lung-cancer-classification machine-learning medical-imaging neural-networks pylidc pyradiomics streamlit tensorflow
Last synced: 29 Mar 2025
https://github.com/mafrs47/lung_cancer_prediction
This project predicts lung cancer risks using machine learning models like Random Forest, Logistic Regression, and SVM. It analyzes patient data with features such as age, smoking habits, and symptoms. Data preprocessing, visualization, and performance evaluation ensure accurate predictions for early diagnosis.
cnn computational-pathology convolutional-neural-networks decision-tree-classifier decision-trees deep-learning gradientboosting histopathology jupyter-notebook lung-cancer multiple-instance-learning scikit-learn svm xgboost
Last synced: 26 Mar 2025
https://github.com/carlpecardal/lung_cancer_prediction
This project predicts lung cancer risks using machine learning models like Random Forest, Logistic Regression, and SVM. It analyzes patient data with features such as age, smoking habits, and symptoms. Data preprocessing, visualization, and performance evaluation ensure accurate predictions for early diagnosis.
algorithm-analysis classification computational-pathology data-analysis decision-tree-classifier gradientboosting histopathology keras logistic-regression lung-cancer multiple-instance-learning svm tissue-microarray-analysis xgboost
Last synced: 31 Mar 2025
https://github.com/anufax99/lungcancerclassification
This repository contains a deep learning-based cancer type prediction system using a trained convolutional neural network (CNN). The model is deployed using Streamlit, allowing users to upload medical images and receive predictions with a probability distribution displayed in a pie chart.
ai-in-healthcare-and-biology biomedical-ai cancer-classification histopathology image-classification lidc-dataset lung-cancer-classification lung-cancer-detection machine-learning medical-imaging neural-networks pylidc streamlit tensorflow
Last synced: 29 Mar 2025
https://github.com/mahtabranjbar/histo_classification-with-deepvit
This project leverages the DeepVit model, a variant of the Vision Transformer (ViT), for the classification of histopathology images from the BreakHis dataset.
computer-vision deep-learning histopathology vision-transformer vit
Last synced: 18 Mar 2025
