Digital Pathology MIL ML Frameworks

AI frameworks and tools specifically for analyzing whole-slide histopathology images using multiple instance learning, attention mechanisms, and weakly supervised learning. Does NOT include general medical imaging, segmentation-only approaches, or non-pathology tissue analysis applications.

There are 127 digital pathology mil frameworks tracked. 8 score above 70 (verified tier). The highest-rated is nilearn/nilearn at 98/100 with 1,370 stars and 249,329 monthly downloads. 2 of the top 10 are actively maintained.

Get all 127 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	nilearn/nilearn Machine learning for NeuroImaging in Python	98	Verified	1,370	Python
2	TissueImageAnalytics/tiatoolbox Computational Pathology Toolbox developed by TIA Centre, University of Warwick.	91	Verified	513	Python
3	aramis-lab/clinica Software platform for clinical neuroimaging studies	78	Verified	272	Python
4	nadeemlab/DeepLIIF Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image...	76	Verified	241	Python
5	nipreps/mriqc Automated Quality Control and visual reports for Quality Assessment of...	76	Verified	351	Python
6	loli/medpy Medical image processing in Python	74	Verified	619	Jupyter Notebook
7	brainiak/brainiak Brain Imaging Analysis Kit	73	Verified	371	Python
8	Dana-Farber-AIOS/pathml Tools for computational pathology	70	Verified	444	Python
9	slideflow/slideflow Powerful, open-source AI tools for digital pathology.	69	Established	353	Python
10	ad12/meddlr A flexible ML framework built to simplify medical image reconstruction and...	68	Established	70	Python
11	mahmoodlab/TRIDENT Toolkit for large-scale whole-slide image processing.	67	Established	502	Python
12	ilastik/ilastik ilastik-shell, applets, and workflows to string them together.	61	Established	391	Python
13	ysbecca/py-wsi Python package for dealing with whole slide images (.svs) for machine...	59	Established	164	Jupyter Notebook
14	iitzco/deepbrain Deep Learning tools for brain medical images	56	Established	142	Python
15	maduc7/Histopathology-Datasets Ressources of histopathology datasets	55	Established	533	—
16	prov-gigatime/GigaTIME GigaTIME: Multimodal AI generates virtual population for tumor...	55	Established	117	Jupyter Notebook
17	pyanno4rt/pyanno4rt Python-based Advanced Numerical Nonlinear Optimization for Radiotherapy	54	Established	27	Python
18	neuroneural/brainchop Brainchop: In-browser 3D MRI rendering and segmentation	54	Established	523	JavaScript
19	AICONSlab/MIRACL Multi-modal Image Registration And Connectivity anaLysis	54	Established	48	Python
20	mahmoodlab/MIL-Lab Feather - Lightweight supervised slide foundation models (ICML 2025)	53	Established	141	Python
21	mrphys/tensorflow-mri A Library of TensorFlow Operators for Computational MRI	53	Established	47	Jupyter Notebook
22	MWod/DeeperHistReg DeeperHistReg - Source Code	53	Established	94	Jupyter Notebook
23	EndoluminalSurgicalVision-IMR/ATM-22-Related-Work [MedIA 2023/MICCAI 2022 Grand Challenge]: Airway Tree Modeling (ATM'22)...	53	Established	163	Python
24	Franblueee/torchmil Deep Multiple Instance Learning library for Pytorch	52	Established	74	Python
25	albarqouni/Deep-Learning-for-Medical-Applications Deep Learning Papers on Medical Image Analysis	51	Established	1,608	TeX
26	SBU-BMI/wsinfer 🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images	51	Established	85	Python
27	juliandewit/kaggle_ndsb2017 Kaggle datascience bowl 2017	51	Established	626	Python
28	DIAGNijmegen/pathology-whole-slide-data A package for working with whole-slide data including a fast batch iterator...	51	Established	112	Python
29	MICS-Lab/thunder [NeurIPS25 D&B Spotlight] A tile-level histopathology image understanding benchmark	50	Established	43	Python
30	binli123/dsmil-wsi DSMIL: Dual-stream multiple instance learning networks for tumor detection...	50	Established	458	Python
31	rendeirolab/LazySlide Accessible and interoperable whole slide image analysis	50	Established	187	Python
32	viswanath-lab/RadQy RadQy is a quality assurance and checking tool for quantitative assessment...	49	Emerging	115	JavaScript
33	medtorch/awesome-healthcare-ai A curated list of awesome open source healthcare tools, algorithms, datasets...	49	Emerging	309	—
34	CODAIT/deep-histopath A deep learning approach to predicting breast tumor proliferation scores for...	49	Emerging	208	Jupyter Notebook
35	hurcy/awesome-ehr-deeplearning Curated list of awesome papers for electronic health records(EHR) mining,...	49	Emerging	427	—
36	analysiscenter/radio RadIO is a library for data science research of computed tomography imaging	48	Emerging	226	Jupyter Notebook
37	raidionics/Raidionics Software for automatic segmentation and generation of standardized clinical...	47	Emerging	44	Python
38	mattaq31/GelGenie Open-Source package for segmentation and analysis of gel electrophoresis...	46	Emerging	87	Python
39	fepegar/awesome-medical-imaging Awesome list of software that I use to do research in medical imaging.	46	Emerging	238	—
40	AICAN-Research/FAST-Pathology ⚡ Open-source software for deep learning-based digital pathology	45	Emerging	141	C++
41	pyvoxel/pyvoxel Fast Pythonic data structures and tools for wrangling medical images.	44	Emerging	28	Python
42	srinidhiPY/SSL_CR_Histo Official code for "Self-Supervised driven Consistency Training for...	43	Emerging	61	Python
43	rendeirolab/wsidata Efficient data structures and IO for whole slide image analysis	43	Emerging	20	Python
44	qimingfan10/SAM-VMNet This is the official code repository for "Deep learning model for coronary...	42	Emerging	26	Python
45	PathologyDataScience/MuTILs_Panoptic Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for...	42	Emerging	28	Python
46	AIRMEC/im4MEC Code for the im4MEC model described in the paper 'Interpretable deep...	42	Emerging	54	Python
47	osirixgrpc/osirixgrpc Source code and documentation for the core OsiriXgrpc plugin	42	Emerging	5	C++
48	suinleelab/MONET Transparent medical image AI via an image–text foundation model grounded in...	42	Emerging	84	Python
49	georg-wolflein/pathology-foundation-models List of pathology feature extractors and foundation models	41	Emerging	177	Makefile
50	TissueImageAnalytics/cerberus One Model is All You Need: Multi-Task Learning Enables Simultaneous...	41	Emerging	100	Python
51	alxndrkalinin/awesome-deepneuroimage A curated list of awesome deep learning applications in the field of...	40	Emerging	152	—
52	OpenImaging/miqa A Medical Imaging Quality Assurance tool	40	Emerging	36	Jupyter Notebook
53	DLinRT-eu/dlinrteu-website Register of deep learning-based products in radiotherapy	40	Emerging	2	TypeScript
54	AntonotnaWang/NaviAirway NaviAirway: a Bronchiole-sensitive Deep Learning-based Airway Segmentation Pipeline	39	Emerging	65	Jupyter Notebook
55	Novestars/Neural_Pre_Processing Neural Pre Processing is an end-to-end weakly supervised learning approach...	39	Emerging	31	Python
56	YashSharma/C2C Implementation of Cluster-to-Conquer: A Framework for End-to-End...	39	Emerging	59	Python
57	GJiananChen/MICCAI2021-OpenReviewAnalysis Starting from MICCAI 2021, all accepted papers and their corresponding...	39	Emerging	58	—
58	raidionics/AeroPath :hugs: AeroPath: An airway segmentation benchmark dataset with challenging pathology	38	Emerging	47	Jupyter Notebook
59	HautaniemiLab/histolytics Interpretable Analysis of Histological WSIs	38	Emerging	15	Python
60	linzixuan45/CMeKG_tools_Version_3 CMeKG Tools for Medical Predict	37	Emerging	65	Jupyter Notebook
61	Erfandarzi/Awesome-MICCAI-2024 A collection of papers published in MICCAI 2024 with their code.	37	Emerging	99	—
62	SBU-BMI/champkit Benchmarking toolkit for patch-based histopathology image classification.	35	Emerging	44	Python
63	jafarinia/snuffy Snuffy: Efficient Whole Slide Image Classifier For Efficient and Performant...	34	Emerging	54	Python
64	AIRMEC/HECTOR Multimodal deep learning to predict distant recurrence-free probability from...	34	Emerging	44	Python
65	pr4deepr/GutAnalysisToolbox Analysis and characterisation of cells within the gut wall using deep...	34	Emerging	7	ImageJ Macro
66	AtlasAnalyticsLab/AtlasPatch AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing	33	Emerging	44	Python
67	digenoma-lab/HistoMILTrainer Python library to train Multi Instance Learning algorithms in histology for...	33	Emerging	2	Jupyter Notebook
68	secrierlab/HistoMIL A Python package for handling histopathology whole-slide images using...	33	Emerging	29	Python
69	jamesdolezal/biscuit Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding	32	Emerging	30	Python
70	WayScience/Benchmarking_NF1_data Benchmarking data processing strategies for Cell Painting data of NF1...	32	Emerging	6	Jupyter Notebook
71	agr78/RadDBS-QSM Deep brain stimulation outcome prediction using radiomics on quantitative...	32	Emerging	6	Python
72	bupt-ai-cz/HSA-NRL Hard Sample Aware Noise Robust Learning forHistopathology Image Classification	32	Emerging	37	Python
73	Boehringer-Ingelheim/deep-learning-based-quantification-of-NAFLD-NASH Automated liver NAFLD/NASH scoring	31	Emerging	13	Jupyter Notebook
74	DLinRT-eu/website Register of deep learning-based products in radiotherapy	30	Emerging	7	TypeScript
75	Arka-Bhowmik/mri_triage_normal Deep Learning Breast MRI Segmentation and Classification	29	Experimental	10	Jupyter Notebook
76	VendenIX/BrainMetaSegmentatorUI-Front Modified OHIF Viewer with an extension for call an API who perform AI and...	28	Experimental	8	TypeScript
77	skr1/Imagene ImaGene: A multi-omic ML/AI software with guided operational reports and...	28	Experimental	6	HTML
78	Edward-E-S-Wang/Radiomics-Feature-Screen-Pipeline A complete radiomics feature selection pipeline for binary classification tasks	27	Experimental	36	Python
79	sandialabs/PyRIID ML-based radioisotope identification and estimation from gamma spectra in Python.	27	Experimental	18	Python
80	DeepMicroscopy/Cox_AMIL Code for our BVM workshop submission "Attention-based Multiple Instance...	27	Experimental	6	Jupyter Notebook
81	CAAI/hnc-tumour-seg Clinical evaluation of deep learning for tumour delineation on...	26	Experimental	6	Jupyter Notebook
82	reednaidoo/SurvivMIL_COMPAYL SurvivMIL: A multimodal, Multiple Instance Learning pipeline for survival...	26	Experimental	5	Python
83	zhaoyanglab/ML-for-PSC-differentiation Code and data accompanying "A live-cell image-based machine learning...	26	Experimental	8	Jupyter Notebook
84	gatsby2016/PhiHER2 [ISMB 2024] Official PyTorch Code for "PhiHER2: Phenotype-informed weakly...	26	Experimental	3	Jupyter Notebook
85	ogemarques/deep-network-designer-matlab Example of how to use MATLAB Deep Network Designer to build deep learning...	26	Experimental	4	—
86	jafarinia/maxsoft Navigating the MIL Trade-Off: Flexible Pooling for Whole Slide Image Classification	25	Experimental	22	Python
87	uw-loci/qupath-extension-image-export-toolkit QuIET - QuPath Image Export Toolkit: batch export images for ML training and analysis	24	Experimental	2	Java
88	wingatesv/SN_IDC_Grading This repo contains source code for the paper: "Evaluating the Effectiveness...	24	Experimental	3	Jupyter Notebook
89	JZK00/AI_MedIA_Library Some code for AI in MedIA.	24	Experimental	4	Python
90	dfsp-spirit/brainnet Machine learning on neuroimaging data, for R.	24	Experimental	4	HTML
91	Mr-TalhaIlyas/TSFD Nuclei segmentation and classification (Cancer cells)	23	Experimental	25	Jupyter Notebook
92	OMFSdigital/Automated-PD-L1-Scoring This repository describes a workflow for automated PD-L1 scoring of Tumor...	23	Experimental	2	Groovy
93	lgy112112/PreProcPipe Easy and Clear Pipeline With LLM-Automation to Preprocess Medical Image for Everybody	23	Experimental	56	Jupyter Notebook
94	caumente/multi_task_breast_cancer Multi-task framework for breast cancer segmentation and classification	23	Experimental	8	Python
95	ilanaliouchouche/Bayesian-Active-Learning-Interface-for-Medical-Imaging This project aims to integrate Domain Knowledge with Bayesian Deep Learning...	23	Experimental	10	JavaScript
96	fabianofilho/awesome-medical-ai A curated list of awesome resources for Medical AI: papers, datasets, tools,...	22	Experimental	—	—
97	naims-aims/awesome-ms-imaging-ai An open source list for MS Imaging & AI tools and resources	22	Experimental	1	—
98	nyukat/MRI_AI This repository contains code that was used to train and evaluate deep...	22	Experimental	15	Jupyter Notebook
99	jonahanton/SSL_medicalimaging Codebase for Imperial MSc AI Group Project: How Well Do Self-Supervised...	21	Experimental	10	Jupyter Notebook
100	wlsdzyzl/flemme A flexible and modular learning platform for medical images	21	Experimental	26	Python
101	MungoMeng/Survival-AdaMSS AdaMSS: Adaptive Multi-Modality Segmentation-to-Survival Learning for...	20	Experimental	16	Python
102	Thisen-Ekanayake/BRAINet BRAINet - Brain Radiology Analysis with Intelligent Networks. Deep learning...	20	Experimental	1	JavaScript
103	CristianoPatricio/Explainable-Deep-Learning-Methods-in-Medical-Image-Classification-A-Survey Official repository of the paper "Explainable Deep Learning Methods in...	19	Experimental	10	—
104	sahilsethi0105/scope-mri Resource for getting started with deep learning for MRIs/CTs. This codebase...	19	Experimental	6	Jupyter Notebook
105	tanjimin/CANVAS Official repository for Characterization of tumor heterogeneity through...	18	Experimental	14	Python
106	jamtheim/LUND-PROBE LUND-PROBE – LUND Prostate Radiotherapy Open Benchmarking and Evaluation dataset	18	Experimental	14	Python
107	mdsatria/MultiAttentionMIL ECCV-AIMIA 2022 paper: "Multi-Scale Attention-based Multiple Instance...	17	Experimental	13	Jupyter Notebook
108	mkldhz/Multi-Cancer-Identification-and-Segmentation-Using-Brain-and-Breast-Scans Identify The Presence of Tumors in Brain and Breast Scans. Segment The...	17	Experimental	5	Jupyter Notebook
109	lyhkevin/Graph-V-Net A Hierarchical Graph V-Net with Semi-supervised Pre-training for Breast...	17	Experimental	24	Python
110	georg-wolflein/good-features Official code for the paper "A Good Feature Extractor Is All You Need for...	16	Experimental	18	Jupyter Notebook
111	AzizMtg/2D-Image-to-3D-Trauma-Triage-System Transforms a single 2D image into 3D understanding and clinical insights for...	16	Experimental	1	Jupyter Notebook
112	sofiasannino/LVModel-Cancer-Segmentation Language-vision deep learning model for cancer segmentation with simulations...	15	Experimental	—	Python
113	junjianli106/LANPC Radiotherapy and Oncology 2025 \| Deep Learning Radiopathomic Model for...	15	Experimental	10	Python
114	paire-tech/paire-deep-psma-submission 🥇 Winning solution for the DeepPSMA Grand Challenge, MICCAI 2025	15	Experimental	5	Python
115	suyashkumar/deeplesion-gcp-loader Get the DeepLesion CT Image data set into a GCP Storage Bucket	14	Experimental	1	Go
116	prasathlab/PathAIData A curated list of publicly available histopathology datasets, accompanied by...	14	Experimental	—	—
117	ntnu-mr-cancer/SegmentationReproducibility The Reproducibility of Deep Learning-Based Segmentation of the Prostate...	14	Experimental	1	MATLAB
118	diaoquesang/DL4VS :octocat: Deep learning for virtual staining of label-free tissue: A survey....	14	Experimental	4	—
119	CamiloSinningUN/CellMIL A Controllable and Flexible Multiple Instance Learning Framework for...	14	Experimental	3	HTML
120	AITwinMinds/3D-CT-Scan-Viewer A GUI tool for visualizing 3D CT scans with ground truth and predicted...	13	Experimental	7	Python
121	paul-tourniaire/MS-CLAM Source code associated to the article "MS-CLAM: Mixed supervision for the...	13	Experimental	5	Jupyter Notebook
122	sparkup/semi-supervised-medical-image Semi-supervised medical image classification pipeline comparing unsupervised...	12	Experimental	1	Jupyter Notebook
123	shakiliitju/CT-Scan-Image-Analyzer A web-based application for performing basic analysis on CT scan images...	12	Experimental	1	CSS
124	daviddmc/open-fetal-mri awesome open source tools for fetal MRI analysis	12	Experimental	12	—
125	coryjpugne/medical-imaging-ml Applied ML researcher focused on reliability and interpretability in medical...	11	Experimental	—	—
126	edlmar/MorpHista MorpHista is an application for morphology-based histological image...	11	Experimental	—	—
127	kumeS/biocasia2021-workshop-ja-image Introduction to Bioimage Analysis using R in BioC Asia 2021 Workshop	10	Experimental	1	Dockerfile

Comparisons in this category

nilearn and brainiak (98 vs 73)