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 126 digital pathology mil frameworks tracked. 4 score above 70 (verified tier). The highest-rated is nilearn/nilearn at 85/100 with 1,370 stars. 3 of the top 10 are actively maintained.

Get all 126 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=ml-frameworks&subcategory=digital-pathology-mil&limit=20"

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#	Framework	Score	Tier	Stars	Language
1	nilearn/nilearn Machine learning for NeuroImaging in Python	85	Verified	1,370	Python
2	aramis-lab/clinica Software platform for clinical neuroimaging studies	78	Verified	272	Python
3	TissueImageAnalytics/tiatoolbox Computational Pathology Toolbox developed by TIA Centre, University of Warwick.	76	Verified	513	Python
4	nipreps/mriqc Automated Quality Control and visual reports for Quality Assessment of...	70	Verified	351	Python
5	nadeemlab/DeepLIIF Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image...	68	Established	241	Python
6	brainiak/brainiak Brain Imaging Analysis Kit	67	Established	371	Python
7	loli/medpy Medical image processing in Python	64	Established	619	Jupyter Notebook
8	Dana-Farber-AIOS/pathml Tools for computational pathology	64	Established	444	Python
9	mahmoodlab/TRIDENT Toolkit for large-scale whole-slide image processing.	63	Established	502	Python
10	ad12/meddlr A flexible ML framework built to simplify medical image reconstruction and...	63	Established	70	Python
11	slideflow/slideflow Powerful, open-source AI tools for digital pathology.	62	Established	353	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	pyanno4rt/pyanno4rt Python-based Advanced Numerical Nonlinear Optimization for Radiotherapy	58	Established	27	Python
15	iitzco/deepbrain Deep Learning tools for brain medical images	56	Established	142	Python
16	prov-gigatime/GigaTIME GigaTIME: Multimodal AI generates virtual population for tumor...	55	Established	117	Jupyter Notebook
17	neuroneural/brainchop Brainchop: In-browser 3D MRI rendering and segmentation	54	Established	523	JavaScript
18	EndoluminalSurgicalVision-IMR/ATM-22-Related-Work [MedIA 2023/MICCAI 2022 Grand Challenge]: Airway Tree Modeling (ATM'22)...	53	Established	163	Python
19	MWod/DeeperHistReg DeeperHistReg - Source Code	53	Established	94	Jupyter Notebook
20	mahmoodlab/MIL-Lab Feather - Lightweight supervised slide foundation models (ICML 2025)	53	Established	141	Python
21	Franblueee/torchmil Deep Multiple Instance Learning library for Pytorch	52	Established	74	Python
22	AICONSlab/MIRACL Multi-modal Image Registration And Connectivity anaLysis	51	Established	48	Python
23	juliandewit/kaggle_ndsb2017 Kaggle datascience bowl 2017	51	Established	626	Python
24	albarqouni/Deep-Learning-for-Medical-Applications Deep Learning Papers on Medical Image Analysis	51	Established	1,608	TeX
25	DIAGNijmegen/pathology-whole-slide-data A package for working with whole-slide data including a fast batch iterator...	51	Established	112	Python
26	SBU-BMI/wsinfer 🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images	51	Established	85	Python
27	MICS-Lab/thunder [NeurIPS25 D&B Spotlight] A tile-level histopathology image understanding benchmark	50	Established	43	Python
28	binli123/dsmil-wsi DSMIL: Dual-stream multiple instance learning networks for tumor detection...	50	Established	458	Python
29	medtorch/awesome-healthcare-ai A curated list of awesome open source healthcare tools, algorithms, datasets...	49	Emerging	309	—
30	viswanath-lab/RadQy RadQy is a quality assurance and checking tool for quantitative assessment...	49	Emerging	115	JavaScript
31	hurcy/awesome-ehr-deeplearning Curated list of awesome papers for electronic health records(EHR) mining,...	49	Emerging	427	—
32	CODAIT/deep-histopath A deep learning approach to predicting breast tumor proliferation scores for...	49	Emerging	208	Jupyter Notebook
33	maduc7/Histopathology-Datasets Ressources of histopathology datasets	49	Emerging	533	—
34	PathologyDataScience/MuTILs_Panoptic Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for...	49	Emerging	28	Python
35	analysiscenter/radio RadIO is a library for data science research of computed tomography imaging	48	Emerging	226	Jupyter Notebook
36	rendeirolab/wsidata Efficient data structures and IO for whole slide image analysis	47	Emerging	20	Python
37	rendeirolab/LazySlide Accessible and interoperable whole slide image analysis	47	Emerging	187	Python
38	mrphys/tensorflow-mri A Library of TensorFlow Operators for Computational MRI	47	Emerging	47	Jupyter Notebook
39	raidionics/Raidionics Software for automatic segmentation and generation of standardized clinical...	47	Emerging	44	Python
40	pyvoxel/pyvoxel Fast Pythonic data structures and tools for wrangling medical images.	46	Emerging	28	Python
41	mattaq31/GelGenie Open-Source package for segmentation and analysis of gel electrophoresis...	46	Emerging	87	Python
42	fepegar/awesome-medical-imaging Awesome list of software that I use to do research in medical imaging.	46	Emerging	238	—
43	qimingfan10/SAM-VMNet This is the official code repository for "Deep learning model for coronary...	45	Emerging	26	Python
44	osirixgrpc/osirixgrpc Source code and documentation for the core OsiriXgrpc plugin	45	Emerging	5	C++
45	AICAN-Research/FAST-Pathology ⚡ Open-source software for deep learning-based digital pathology	45	Emerging	141	C++
46	srinidhiPY/SSL_CR_Histo Official code for "Self-Supervised driven Consistency Training for...	43	Emerging	61	Python
47	AIRMEC/im4MEC Code for the im4MEC model described in the paper 'Interpretable deep...	42	Emerging	54	Python
48	DLinRT-eu/dlinrteu-website Register of deep learning-based products in radiotherapy	41	Emerging	2	TypeScript
49	georg-wolflein/pathology-foundation-models List of pathology feature extractors and foundation models	41	Emerging	177	Makefile
50	pr4deepr/GutAnalysisToolbox Analysis and characterisation of cells within the gut wall using deep...	41	Emerging	7	ImageJ Macro
51	TissueImageAnalytics/cerberus One Model is All You Need: Multi-Task Learning Enables Simultaneous...	41	Emerging	100	Python
52	OpenImaging/miqa A Medical Imaging Quality Assurance tool	40	Emerging	36	Jupyter Notebook
53	secrierlab/HistoMIL A Python package for handling histopathology whole-slide images using...	40	Emerging	29	Python
54	alxndrkalinin/awesome-deepneuroimage A curated list of awesome deep learning applications in the field of...	40	Emerging	152	—
55	suinleelab/MONET Transparent medical image AI via an image–text foundation model grounded in...	40	Emerging	84	Python
56	HautaniemiLab/histolytics Interpretable Analysis of Histological WSIs	40	Emerging	15	Python
57	agr78/RadDBS-QSM Deep brain stimulation outcome prediction using radiomics on quantitative...	39	Emerging	6	Python
58	GJiananChen/MICCAI2021-OpenReviewAnalysis Starting from MICCAI 2021, all accepted papers and their corresponding...	39	Emerging	58	—
59	YashSharma/C2C Implementation of Cluster-to-Conquer: A Framework for End-to-End...	39	Emerging	59	Python
60	AntonotnaWang/NaviAirway NaviAirway: a Bronchiole-sensitive Deep Learning-based Airway Segmentation Pipeline	39	Emerging	65	Jupyter Notebook
61	Novestars/Neural_Pre_Processing Neural Pre Processing is an end-to-end weakly supervised learning approach...	39	Emerging	31	Python
62	WayScience/Benchmarking_NF1_data Benchmarking data processing strategies for Cell Painting data of NF1...	39	Emerging	6	Jupyter Notebook
63	raidionics/AeroPath :hugs: AeroPath: An airway segmentation benchmark dataset with challenging pathology	38	Emerging	47	Jupyter Notebook
64	Boehringer-Ingelheim/deep-learning-based-quantification-of-NAFLD-NASH Automated liver NAFLD/NASH scoring	38	Emerging	13	Jupyter Notebook
65	linzixuan45/CMeKG_tools_Version_3 CMeKG Tools for Medical Predict	37	Emerging	65	Jupyter Notebook
66	Erfandarzi/Awesome-MICCAI-2024 A collection of papers published in MICCAI 2024 with their code.	37	Emerging	99	—
67	digenoma-lab/HistoMILTrainer Python library to train Multi Instance Learning algorithms in histology for...	37	Emerging	2	Jupyter Notebook
68	DLinRT-eu/website Register of deep learning-based products in radiotherapy	36	Emerging	7	TypeScript
69	Arka-Bhowmik/mri_triage_normal Deep Learning Breast MRI Segmentation and Classification	36	Emerging	10	Jupyter Notebook
70	SBU-BMI/champkit Benchmarking toolkit for patch-based histopathology image classification.	35	Emerging	44	Python
71	AIRMEC/HECTOR Multimodal deep learning to predict distant recurrence-free probability from...	34	Emerging	44	Python
72	sandialabs/PyRIID ML-based radioisotope identification and estimation from gamma spectra in Python.	34	Emerging	18	Python
73	DeepMicroscopy/Cox_AMIL Code for our BVM workshop submission "Attention-based Multiple Instance...	34	Emerging	6	Jupyter Notebook
74	jafarinia/snuffy Snuffy: Efficient Whole Slide Image Classifier For Efficient and Performant...	34	Emerging	54	Python
75	gatsby2016/PhiHER2 [ISMB 2024] Official PyTorch Code for "PhiHER2: Phenotype-informed weakly...	33	Emerging	3	Jupyter Notebook
76	reednaidoo/SurvivMIL_COMPAYL SurvivMIL: A multimodal, Multiple Instance Learning pipeline for survival...	33	Emerging	5	Python
77	zhaoyanglab/ML-for-PSC-differentiation Code and data accompanying "A live-cell image-based machine learning...	33	Emerging	8	Jupyter Notebook
78	ogemarques/deep-network-designer-matlab Example of how to use MATLAB Deep Network Designer to build deep learning...	33	Emerging	4	—
79	CAAI/hnc-tumour-seg Clinical evaluation of deep learning for tumour delineation on...	33	Emerging	6	Jupyter Notebook
80	AtlasAnalyticsLab/AtlasPatch AtlasPatch: An Efficient and Scalable Tool for Whole Slide Image Preprocessing	33	Emerging	44	Python
81	bupt-ai-cz/HSA-NRL Hard Sample Aware Noise Robust Learning forHistopathology Image Classification	32	Emerging	37	Python
82	jamesdolezal/biscuit Bayesian Inference of Slide-level Confidence via Uncertainty Index Thresholding	32	Emerging	30	Python
83	dfsp-spirit/brainnet Machine learning on neuroimaging data, for R.	31	Emerging	4	HTML
84	jafarinia/maxsoft Navigating the MIL Trade-Off: Flexible Pooling for Whole Slide Image Classification	31	Emerging	22	Python
85	wingatesv/SN_IDC_Grading This repo contains source code for the paper: "Evaluating the Effectiveness...	31	Emerging	3	Jupyter Notebook
86	JZK00/AI_MedIA_Library Some code for AI in MedIA.	31	Emerging	4	Python
87	Mr-TalhaIlyas/TSFD Nuclei segmentation and classification (Cancer cells)	30	Emerging	25	Jupyter Notebook
88	OMFSdigital/Automated-PD-L1-Scoring This repository describes a workflow for automated PD-L1 scoring of Tumor...	30	Emerging	2	Groovy
89	caumente/multi_task_breast_cancer Multi-task framework for breast cancer segmentation and classification	30	Emerging	8	Python
90	ilanaliouchouche/Bayesian-Active-Learning-Interface-for-Medical-Imaging This project aims to integrate Domain Knowledge with Bayesian Deep Learning...	30	Emerging	10	JavaScript
91	nyukat/MRI_AI This repository contains code that was used to train and evaluate deep...	29	Experimental	15	Jupyter Notebook
92	naims-aims/awesome-ms-imaging-ai An open source list for MS Imaging & AI tools and resources	29	Experimental	1	—
93	jonahanton/SSL_medicalimaging Codebase for Imperial MSc AI Group Project: How Well Do Self-Supervised...	28	Experimental	10	Jupyter Notebook
94	MungoMeng/Survival-AdaMSS AdaMSS: Adaptive Multi-Modality Segmentation-to-Survival Learning for...	27	Experimental	16	Python
95	sahilsethi0105/scope-mri Resource for getting started with deep learning for MRIs/CTs. This codebase...	26	Experimental	6	Jupyter Notebook
96	uw-loci/qupath-extension-image-export-toolkit QuIET - QuPath Image Export Toolkit: batch export images for ML training and analysis	26	Experimental	2	Java
97	CristianoPatricio/Explainable-Deep-Learning-Methods-in-Medical-Image-Classification-A-Survey Official repository of the paper "Explainable Deep Learning Methods in...	26	Experimental	10	—
98	Thisen-Ekanayake/BRAINet BRAINet - Brain Radiology Analysis with Intelligent Networks. Deep learning...	26	Experimental	1	JavaScript
99	Edward-E-S-Wang/Radiomics-Feature-Screen-Pipeline A complete radiomics feature selection pipeline for binary classification tasks	26	Experimental	36	Python
100	jamtheim/LUND-PROBE LUND-PROBE – LUND Prostate Radiotherapy Open Benchmarking and Evaluation dataset	25	Experimental	14	Python
101	wlsdzyzl/flemme A flexible and modular learning platform for medical images	25	Experimental	26	Python
102	tanjimin/CANVAS Official repository for Characterization of tumor heterogeneity through...	25	Experimental	14	Python
103	mkldhz/Multi-Cancer-Identification-and-Segmentation-Using-Brain-and-Breast-Scans Identify The Presence of Tumors in Brain and Breast Scans. Segment The...	24	Experimental	5	Jupyter Notebook
104	mdsatria/MultiAttentionMIL ECCV-AIMIA 2022 paper: "Multi-Scale Attention-based Multiple Instance...	24	Experimental	13	Jupyter Notebook
105	lyhkevin/Graph-V-Net A Hierarchical Graph V-Net with Semi-supervised Pre-training for Breast...	24	Experimental	24	Python
106	lgy112112/PreProcPipe Easy and Clear Pipeline With LLM-Automation to Preprocess Medical Image for Everybody	23	Experimental	56	Jupyter Notebook
107	georg-wolflein/good-features Official code for the paper "A Good Feature Extractor Is All You Need for...	23	Experimental	18	Jupyter Notebook
108	junjianli106/LANPC Radiotherapy and Oncology 2025 \| Deep Learning Radiopathomic Model for...	22	Experimental	10	Python
109	paire-tech/paire-deep-psma-submission 🥇 Winning solution for the DeepPSMA Grand Challenge, MICCAI 2025	21	Experimental	5	Python
110	suyashkumar/deeplesion-gcp-loader Get the DeepLesion CT Image data set into a GCP Storage Bucket	21	Experimental	1	Go
111	ntnu-mr-cancer/SegmentationReproducibility The Reproducibility of Deep Learning-Based Segmentation of the Prostate...	21	Experimental	1	MATLAB
112	fabianofilho/awesome-medical-ai A curated list of awesome resources for Medical AI: papers, datasets, tools,...	21	Experimental	—	—
113	diaoquesang/DL4VS :octocat: Deep learning for virtual staining of label-free tissue: A survey....	20	Experimental	4	—
114	paul-tourniaire/MS-CLAM Source code associated to the article "MS-CLAM: Mixed supervision for the...	20	Experimental	5	Jupyter Notebook
115	daviddmc/open-fetal-mri awesome open source tools for fetal MRI analysis	19	Experimental	12	—
116	CamiloSinningUN/CellMIL A Controllable and Flexible Multiple Instance Learning Framework for...	18	Experimental	3	HTML
117	kumeS/biocasia2021-workshop-ja-image Introduction to Bioimage Analysis using R in BioC Asia 2021 Workshop	17	Experimental	1	Dockerfile
118	sofiasannino/LVModel-Cancer-Segmentation Language-vision deep learning model for cancer segmentation with simulations...	15	Experimental	—	Python
119	sparkup/semi-supervised-medical-image Semi-supervised medical image classification pipeline comparing unsupervised...	14	Experimental	1	Jupyter Notebook
120	prasathlab/PathAIData A curated list of publicly available histopathology datasets, accompanied by...	13	Experimental	—	—
121	coryjpugne/medical-imaging-ml Applied ML researcher focused on reliability and interpretability in medical...	13	Experimental	—	—
122	WuJunde/Awesome-Surgical-AI A curated list of surgical AI resources (continually updated)	12	Experimental	6	—
123	dkurt/qupath-extension-openvino Intel OpenVINO extension for QuPath, a digital pathology platform	12	Experimental	6	Java
124	idso-fa1-pathology/.github Welcome to IDSO-FA1-Pathology World!	11	Experimental	—	—
125	mdsatria/npc_digital_tils Code for identifying TILs in H&E images as described in paper: AI-Based Risk...	11	Experimental	4	Jupyter Notebook
126	kumeS/rMiW rMiW: a R package for microscopy-based image analysis workflow	10	Experimental	2	R

Comparisons in this category

nilearn and brainiak (85 vs 67)