Medical Image Segmentation ML Frameworks

Deep learning models and frameworks for segmenting anatomical structures and tissues in medical images (ultrasound, CT, MRI, OCT). Does NOT include general image segmentation, medical image registration, or non-segmentation medical imaging tasks.

There are 229 medical image segmentation frameworks tracked. 4 score above 70 (verified tier). The highest-rated is Project-MONAI/MONAI at 94/100 with 7,927 stars and 323,705 monthly downloads. 3 of the top 10 are actively maintained.

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#	Framework	Score	Tier	Stars	Language
1	Project-MONAI/MONAI AI Toolkit for Healthcare Imaging	94	Verified	7,927	Python
2	dipy/dipy DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains...	91	Verified	811	Python
3	Project-MONAI/MONAILabel MONAI Label is an intelligent open source image labeling and learning tool.	71	Verified	819	Python
4	neuronets/nobrainer A framework for developing neural network models for 3D image processing.	70	Verified	167	Python
5	axondeepseg/axondeepseg Axon/Myelin segmentation using Deep Learning	68	Established	124	Python
6	FAST-Imaging/FAST A framework for high-performance medical image processing, neural network...	66	Established	501	C++
7	kevinjohncutler/omnipose Omnipose: a high-precision solution for morphology-independent cell segmentation	66	Established	142	Python
8	PortPy-Project/PortPy Opensource Python project for cancer radiation treatment planning [AAPM'23]	65	Established	174	Python
9	Project-MONAI/monai-deploy-app-sdk MONAI Deploy App SDK offers a framework and associated tools to design,...	64	Established	125	Jupyter Notebook
10	tue-bmd/zea zea: A Toolbox for Cognitive Ultrasound Imaging	62	Established	51	Python
11	MedMNIST/MedMNIST [pip install medmnist] 18x Standardized Datasets for 2D and 3D Biomedical...	62	Established	1,323	Python
12	georgeoshardo/SyMBac Accurate segmentation of bacterial microscope images using deep learning...	60	Established	22	Jupyter Notebook
13	frankkramer-lab/MIScnn A framework for Medical Image Segmentation with Convolutional Neural...	58	Established	419	Python
14	GuillaumeMougeot/biom3d Easy Volumetric Segmentation with Deep Learning	56	Established	28	Python
15	PaulRitsche/DeepACSA Automated measurement of muscle anatomical cross-sectional area in...	55	Established	18	Python
16	perone/medicaltorch A medical imaging framework for Pytorch	55	Established	871	Python
17	DCBIA-OrthoLab/SlicerAutomatedDentalTools A 3D Slicer extension to use AMASSS, ALI-CBCT and ALI-IOS	52	Established	146	Python
18	Sentinal4D/cellshape 3D shape analysis using deep learning	52	Established	31	Python
19	ubern-mia/pyradise PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline...	52	Established	53	Python
20	wdika/atommic ATOMMIC: Advanced Toolbox for Multitask Medical Imaging Consistency	49	Emerging	21	Jupyter Notebook
21	koriavinash1/DeepBrainSeg Fully automatic brain tumour segmentation using Deep 3-D convolutional...	49	Emerging	193	Python
22	MuscleMap/MuscleMap MuscleMap: An Open-Source, Community-Supported Consortium for Whole-Body...	48	Emerging	74	Python
23	braph-software/BRAPH-2 BRAPH 2.0 is a comprehensive software package for the analysis and...	48	Emerging	60	MATLAB
24	janelia-cellmap/cellmap-segmentation-challenge Repository of scripts to facilitate participation in CellMap's segmentation...	47	Emerging	40	Python
25	numisveinsson/SeqSeg SeqSeg (Sequential Segmentations)	47	Emerging	15	Python
26	OishiLab/OpenMAP-T1 Whole Brain Segmentation and Parecllation Using OpenMAP-T1 Method for 3D T1 Brain MRI	46	Emerging	37	Python
27	deepmedic/deepmedic Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D...	44	Emerging	1,057	Python
28	mlcommons/GaNDLF A generalizable application framework for segmentation, regression, and...	44	Emerging	191	Python
29	IBBM/Cascaded-FCN Source code for the MICCAI 2016 Paper "Automatic Liver and Lesion...	44	Emerging	303	Jupyter Notebook
30	ternaus/robot-surgery-segmentation Wining solution and its improvement for MICCAI 2017 Robotic Instrument...	44	Emerging	639	Jupyter Notebook
31	NifTK/NiftyNet [unmaintained] An open-source convolutional neural networks platform for...	44	Emerging	1,381	Python
32	facebookresearch/fastMRI A large-scale dataset of both raw MRI measurements and clinical MRI images.	44	Emerging	1,508	Python
33	mrirecon/bart BART: Toolbox for Computational Magnetic Resonance Imaging	44	Emerging	359	C
34	microsoft/InnerEye-DeepLearning Medical Imaging Deep Learning library to train and deploy 3D segmentation...	44	Emerging	578	Python
35	wwu-mmll/deepmriprep Neural network-based MRI preprocessing: Prep 🧠 images in seconds 🔥	44	Emerging	56	Python
36	open-retina/open-retina Collaborative retina modelling across datasets and species.	43	Emerging	18	Python
37	JunMa11/MICCAI-OpenSourcePapers MICCAI 2019-2023 Open Source Papers	43	Emerging	1,293	—
38	IAmSuyogJadhav/3d-mri-brain-tumor-segmentation-using-autoencoder-regularization Keras implementation of the paper "3D MRI brain tumor segmentation using...	43	Emerging	375	Jupyter Notebook
39	black0017/MedicalZooPytorch A pytorch-based deep learning framework for multi-modal 2D/3D medical image...	42	Emerging	1,906	Python
40	wwu-mmll/deepbet Fast brain extraction using neural networks	42	Emerging	50	Python
41	KiT-RT/kitrt_code A high performance framework for radiation therapy simulation and numerical...	42	Emerging	27	C++
42	leoliuf/MRiLab A Numerical Magnetic Resonance Imaging (MRI) Simulation Platform	42	Emerging	243	MATLAB
43	sdsubhajitdas/Brain-Tumor-Segmentation Brain Tumor Segmentation done using U-Net Architecture.	42	Emerging	292	Jupyter Notebook
44	nitrain/nitrain Train AI models efficiently on medical images using any framework	42	Emerging	1,879	Python
45	DengPingFan/PraNet PraNet: Parallel Reverse Attention Network for Polyp Segmentation, MICCAI...	42	Emerging	532	Python
46	oist/Usiigaci Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by...	42	Emerging	204	Jupyter Notebook
47	MICA-MNI/micaopen Open Scripts and pipelines from the Multimodal Imaging and Connectome...	41	Emerging	84	Jupyter Notebook
48	hzdr-MedImaging/LyROI nnU-Net-based Lymphoma Total Metabolic Tumor Volume Segmentation	41	Emerging	5	Python
49	kamalkraj/DATA-SCIENCE-BOWL-2018 DATA-SCIENCE-BOWL-2018 Find the nuclei in divergent images to advance...	41	Emerging	92	Jupyter Notebook
50	shalabh147/Brain-Tumor-Segmentation-and-Survival-Prediction-using-Deep-Neural-Networks Use of state of the art Convolutional neural network architectures including...	40	Emerging	171	Jupyter Notebook
51	jadevaibhav/Brain-Tumor-Segmentation-using-Deep-Neural-networks Keras implementation of paper by the same name	40	Emerging	96	Jupyter Notebook
52	ardamavi/3D-Medical-Segmentation-GAN 3D Liver Segmentation with GAN	40	Emerging	132	Python
53	creatis-myriad/ASCENT cardiAc ultrasound Segmentation & Color-dopplEr dealiasiNg Toolbox (ASCENT)	40	Emerging	44	Python
54	RazvanDu/DUCK-Net Using DUCK-Net for polyp image segmentation. ( Nature Scientific Reports 2023 )	39	Emerging	127	Jupyter Notebook
55	yhygao/CBIM-Medical-Image-Segmentation A PyTorch framework for medical image segmentation	39	Emerging	342	Python
56	Omid-Nejati/MedViT MedViT: A Robust Vision Transformer for Generalized Medical Image...	39	Emerging	237	Python
57	nadeemlab/DoseRTX Domain knowledge driven 3D radiation dose prediction [PMB'22]	39	Emerging	51	Python
58	KibromBerihu/ai4elife This data-centric AI repository implements a robust deep learning method...	39	Emerging	40	Python
59	IlliaOvcharenko/lung-segmentation Lung segmentation for chest X-Ray images	39	Emerging	136	Jupyter Notebook
60	ai-med/relaynet_pytorch Pytorch Implementation of retinal OCT Layer Segmentation (with trained models)	38	Emerging	93	Jupyter Notebook
61	moverseai/moai moai is a PyTorch-based AI Model Development Kit (MDK) created to improve...	38	Emerging	56	Python
62	YangLabHKUST/STitch3D Construction of a 3D whole organism spatial atlas by joint modeling of...	37	Emerging	70	Python
63	KitwareMedical/SlicerNNUnet 3D Slicer nnUNet integration to streamline usage for nnUNet based AI extensions.	37	Emerging	56	Python
64	NYUMedML/DARTS Code for DARTS: DenseUnet-based Automatic Rapid Tool for brain Segmentation	37	Emerging	69	Jupyter Notebook
65	FZJ-INM1-BDA/celldetection Scalable Instance Segmentation using PyTorch & PyTorch Lightning.	37	Emerging	149	Python
66	zekikus/MedSegBench [pip install medsegbench] 35x Standardized Medical Segmentation Datasets...	36	Emerging	29	Python
67	haakonnese/nect Implicit Neural Representation for Fast 4D Computed Tomography of Multiphase...	36	Emerging	5	Python
68	rezazad68/BCDU-Net BCDU-Net : Medical Image Segmentation	36	Emerging	784	Python
69	ChenLiu-1996/CUTS [MICCAI 2024] CUTS: A Deep Learning and Topological Framework for...	36	Emerging	41	Python
70	AICAN-Research/H2G-Net 🚀 H2G-Net: Segmentation of breast cancer region from whole slide images	35	Emerging	28	Jupyter Notebook
71	andreped/NoCodeSeg 🔬 Code-free deep segmentation for computational pathology	35	Emerging	56	Jupyter Notebook
72	assassint2017/MICCAI-LITS2017 liver segmentation using deep learning	35	Emerging	433	Python
73	ZombaSY/FSG-Net-pytorch Official implementation of the paper, "Full-scale Representation Guided...	35	Emerging	34	Python
74	HINTLab/RibSeg [MICCAI'21 & TMI'23] RibSeg Dataset and Point Cloud Baselines for Rib...	35	Emerging	69	Python
75	anthonyweidai/SvANet [TNNLS 2026] SvANet: Exploiting Scale-Variant Attention for Segmenting Small...	35	Emerging	66	Python
76	Richarizardd/Self-Supervised-ViT-Path Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology...	35	Emerging	143	Jupyter Notebook
77	volBrain/AssemblyNet AssemblyNet: 3D Whole Brain MRI segmentation pipeline	35	Emerging	71	—
78	HiLab-git/WORD [MedIA2022]WORD: A large scale dataset, benchmark and clinical applicable...	34	Emerging	172	Python
79	nadeemlab/CEP Computational Endoscopy Platform (advanced deep learning toolset for...	34	Emerging	82	Python
80	seungjunlee96/U-Net_Lung-Segmentation Application of U-Net in Lung Segmentation-Pytorch	34	Emerging	32	Python
81	tianyu0207/weakly-polyp [MICCAI'22] Contrastive Transformer-based Multiple Instance Learning for...	34	Emerging	43	Python
82	aiforvision/OCTA-autosegmentation Repository for the paper "Synthetic optical coherence tomography angiographs...	34	Emerging	48	Jupyter Notebook
83	AryaKoureshi/Brain-tumor-detection Implementation of medical image segmentation and deep learning framework...	34	Emerging	74	Jupyter Notebook
84	opaserr/dota Data-driven particle transport algorithm for fast dose calculations.	34	Emerging	42	Jupyter Notebook
85	criticaldata/ShortKit-ML A unified framework to detect, benchmark, and mitigate shortcut learning in...	34	Emerging	3	Python
86	WayScience/NF1_organoid_cell_segmentation Deep learning–based vision model for segmentation of cells within NF1 organoids.	33	Emerging	2	Python
87	wdika/mridc Data Consistency Toolbox for Magnetic Resonance Imaging	33	Emerging	40	Jupyter Notebook
88	limhoyeon/ToothGroupNetwork 3D Dental surface segmentation with Tooth Group Network	33	Emerging	294	Python
89	hahnec/rf-ulm RF-ULM: Ultrasound Localization Microscopy Learned from Radio-Frequency Wavefronts	33	Emerging	36	Python
90	HaamsRee/senoquant Quantifying senescence, the easy way.	33	Emerging	2	Python
91	Abe404/RootPainter3D RootPainter3D: Interactive-machine-learning enables rapid and accurate...	32	Emerging	24	Python
92	miac-research/MARS-WMH State-of-the-art, deep learning-based segmentation of brain white matter...	32	Emerging	11	Python
93	Brain-Tumor-Segmentation/brain-tumor-segmentation-using-deep-neural-networks The project presents a comparative study of Brain Tumor Segmentation using 3...	31	Emerging	13	Jupyter Notebook
94	arindam369/MedMNIST-ViT Based on our paper "Implementing vision transformer for classifying 2D...	31	Emerging	16	Jupyter Notebook
95	sing-group/deep-learning-colonoscopy Review in Deep Learning for Polyp Detection and Classification in...	31	Emerging	207	—
96	mfaizan-ai/Brain-Tumors-Segmentation Multimodal Brain mpMRI segmentation on BraTS 2023 and BraTS 2021 datasets.	31	Emerging	100	Python
97	koriavinash1/Fetal-Brain-Segmentation Fully automatic technique for fetal brain segmentation using deep...	30	Emerging	13	Jupyter Notebook
98	codingfisch/niftiai Train neural nets on 3D images (e.g. MRIs) 🧠	30	Emerging	3	Python
99	LucasKre/dilated_tooth_seg_net DilatedToothSegNet: Tooth Segmentation Network on 3D Dental Meshes Through...	30	Emerging	106	Python
100	sagizty/Multi-Stage-Hybrid-Transformer Official release of MSHT: Multi-stage Hybrid Transformer for the ROSE Image...	29	Experimental	77	Jupyter Notebook
101	j-morano/rrwnet Official repository of the paper "RRWNet: Recursive Refinement Network for...	29	Experimental	42	Python
102	alexklwong/subpixel-embedding-segmentation PyTorch Implementation of Small Lesion Segmentation in Brain MRIs with...	29	Experimental	22	Python
103	CedricCaruzzo/pannuke-segmentation An open-source UNet-based pipeline for nuclei segmentation in histopathology...	29	Experimental	10	Python
104	ZeinebZH/TumorNetSolvers Efficient Deep Learning-based Forward Solvers for Brain Tumor Growth Models	29	Experimental	6	Python
105	alok-ai-lab/DeepInsight3D_pkg DeepInsight3D package to deal with multi-omics or multi-layered data	28	Experimental	6	MATLAB
106	AHMEDSANA/Binary-Class-Brain-Tumor-Segmentation-Using-UNET We segmented the Brain tumor using Brats dataset and as we know it is in 3D...	28	Experimental	17	Jupyter Notebook
107	bmdeep/SegPC2021 Multi-scale Regional Attention Deeplab3+: Multiple Myeloma Plasma Cells...	28	Experimental	9	Jupyter Notebook
108	twpkevin06222/Deep-Attention-Network-for-BraTS20 Deep Supervised Attention Networks for Pixel-wise Brain Tumor Segmentation....	28	Experimental	6	Jupyter Notebook
109	MIC-DKFZ/nnActive nnActive -- code, benchmark and results for the largest study of Active...	28	Experimental	17	Python
110	J-Linaris/retinal-thin-vessels A Python package for computing the recall and precision scores specifically...	27	Experimental	4	Python
111	Borda/kaggle_image-segm Simple tooling for instance segmentation aiming at cell biology...	27	Experimental	10	Jupyter Notebook
112	Cardio-AI/cmr-landmark-detection Semantic Segmentation of CMR with a U-Net based architecture. Implemented in...	27	Experimental	6	Jupyter Notebook
113	ardhigagan/Optic-Disc-Detection A comparative study of deep learning (U-Net) and unsupervised computer...	27	Experimental	1	Python
114	alejandro-matos/SlicerUpperAirwaySegmentator 3D Slicer extension for fully automatic segmentation of the upper airway...	27	Experimental	2	Python
115	DIAGNijmegen/ULS23 Repository for the Universal Lesion Segmentation Challenge '23	27	Experimental	40	Python
116	GorkemP/labeled-images-for-ulcerative-colitis Codes to process and train LIMUC dataset	27	Experimental	35	Python
117	ViacheslavDanilov/oct_segmentation This repository is dedicated to the segmentation of optical coherence...	27	Experimental	10	Python
118	MJAHMADEE/Cataract-LMM Advanced computer vision framework for surgical video analysis, featuring...	27	Experimental	10	Jupyter Notebook
119	YigitTurali/HydraViT HydraViT is a PyTorch implementation of the HydraViT model, an adaptive...	26	Experimental	7	—
120	Yulv-git/Awesome-Ultrasound-Standard-Plane-Detection A curated list of awesome ultrasound standard/diagnostic plane...	26	Experimental	56	Python
121	LLeon360/UNetBiomedicalDiagnosis Contains a module for functions that build and evaluate a U-Net Model which...	26	Experimental	8	Python
122	edaaydinea/Low-Grade-Glioma-Segmentation This is a capstone project on a real dataset related to segmenting low-grade...	26	Experimental	11	Jupyter Notebook
123	TimScherr/KIT-GE-3-Cell-Segmentation-for-CTC Distance-transform-prediction-based segmentation method used for our...	26	Experimental	8	Jupyter Notebook
124	tkshirakawa/AISegmentation_v141 The public source code of A.I.Segmentation (AIS) version 1.4.1. AIS is a...	26	Experimental	6	Objective-C
125	ImagingDataCommons/nnU-Net-BPR-annotations Code accompanying this dataset: Krishnaswamy, D., Bontempi, D., Clunie, D.,...	26	Experimental	8	Jupyter Notebook
126	avakanski/Attention-Enriched-DL-Model-for-Breast-Tumor-Segmentation Salient attention U-Net model for tumor segmentation in breast ultrasound...	26	Experimental	45	Jupyter Notebook
127	IAI-ATLAS/SSL-for-Medical-Image-Segmentation TBME: Self-Supervised Learning for Annotation Efficient Biomedical Image Segmentation	26	Experimental	6	Jupyter Notebook
128	bionlplab/longitudinal_transformer_for_survival_analysis [npj Digital Medicine] "Harnessing the power of longitudinal medical imaging...	26	Experimental	21	Python
129	vishal815/Deep-Learning-Models-for-3D-MRI-based-Brain-Tumor-Segmentation-using-Seg-Net-V--Net-and-U-Net This project focuses on the segmentation of brain tumors in 3D MRI images...	25	Experimental	5	Jupyter Notebook
130	MohamedAlaouiMhamdi/3D_teeth_segmentation 3D Teeth Segmentation using PointNet is an advanced deep learning project...	25	Experimental	5	Jupyter Notebook
131	sinemistoktas/KITE Web-based semi-automated retinal fluid segmentation tool for OCT images....	25	Experimental	2	CSS
132	alok-ai-lab/MRep-DeepInsight Multiple Representation DeepInsight technique	25	Experimental	5	MATLAB
133	vladzalevskyi/brain-segmentation This repository contrains source code and the report for the Brain...	25	Experimental	5	Jupyter Notebook
134	Jonghwan-dev/Awesome-Segmentation-in-Medical Welcome, Awesome-segmentation-in-medical project. This repo is robust,...	24	Experimental	9	Python
135	thaiminhpv/Doctor-Cyclop-Hackathon-2021 Model for Doctor's Cyclop Project at FPT Edu Hackathon 2021	24	Experimental	4	Python
136	Pulkit-Khandelwal/purple-mri Penn Utilities for Registration and ParcelLation of Ex vivo MRI	24	Experimental	23	Python
137	qianlinyi/hhu-medical-image-group 河海大学医学图像处理组	24	Experimental	120	—
138	xmindflow/Awesome-Implicit-Neural-Representations-in-Medical-imaging [ICCV 2023] A curated list of resources on implicit neural representations...	24	Experimental	239	—
139	sowada23/Brain-Tumor-Segmentation-Project PyTorch 2D U-Net for BraTS brain tumor segmentation (FLAIR+T1CE) with...	23	Experimental	1	Python
140	ChrisBotos/ATLAS-Cellpose Created by Christos Botos, ATLAS-Cellpose (Adaptive Tiled Local Analysis...	23	Experimental	1	Python
141	Arshad221b/3D-UNet-Image-Segmentation 3D image segmentation using UNet: for MRI/CT scan image data	23	Experimental	6	Jupyter Notebook
142	rachitsaluja/BraTS-2023-Metrics Official BraTS 2023 Segmentation Performance Metrics	23	Experimental	21	Python
143	nextgencodersxyz/DiffuKnee 🩺 Automate knee MRI segmentation using DiffuKnee’s diffusion model and U-Net...	23	Experimental	1	JavaScript
144	xfetus/xfetus xfetus -- :baby: :brain: :robot: -- A library for ultrasound fetal...	23	Experimental	10	Python
145	lasopablo/freesurfer-freesurfer-dev-mri_WMHsynthseg MS thesis @Harvard: Deep Learning optimization and data augmentation methods...	22	Experimental	18	Python
146	ned0624/Retinal-Vessel-Segmentation DRIVE Digital Retinal Images for Vessel Extraction	22	Experimental	—	Jupyter Notebook
147	ianochieng25/PanNuke-cell-core-region-identification-with-DINO 🧬 Implement nuclei segmentation and classification using DINO...	22	Experimental	—	Python
148	titouanlegourrierec/easilastik Easy integration of Ilastik segmentation models in Python.	22	Experimental	—	Python
149	mu40/babyseg Brain segmentation across the first years of life	22	Experimental	4	Python
150	AntonotnaWang/3DCellSeg Official implementation of "A novel deep learning-based 3D cell segmentation...	22	Experimental	23	Jupyter Notebook
151	LightersWang/Awesome-Active-Learning-for-Medical-Image-Analysis [MedIA] Paper list and source code for survey "A comprehensive survey on...	22	Experimental	127	Python
152	emirhanai/Cell-Instance-Segmentation-Deep-Learning-Project-Emirhan-BULUT Cell Instance Segmentation - Deep Learning Project - Emirhan BULUT	22	Experimental	9	Jupyter Notebook
153	jytjyt05/Teeth-Seg Teeth segmentation in X-ray images using UNet and Res-UNet	22	Experimental	9	Jupyter Notebook
154	Pablo1990/3D-deep-segmentation-protocol Single cell resolution 3D imaging and segmentation within intact live tissues	21	Experimental	2	Jupyter Notebook
155	joewong00/3D-CNN-Segmentation Applying 3D CNN for bio-medical images segmentation with 3D-Unet, Residual...	21	Experimental	22	Jupyter Notebook
156	ChiShengChen/pytorch_deep_learning_medimg_tutorial This project simply implements three common deep learning models (VGG16,...	21	Experimental	20	Python
157	thierleft/2-5DUNet-supervised-vascular-segmentation-Kaggle Supervised 2.5D U-Net for Vascular Segmentation of Human Renal Arteries on HiP-CT	21	Experimental	2	Jupyter Notebook
158	rezazad68/transnorm transnorm	21	Experimental	23	Jupyter Notebook
159	uw-loci/collagen-fiber-metrics Deep generative models for collagen fiber centerline segmentation and...	20	Experimental	12	Jupyter Notebook
160	DebeshJha/Kvasircapsule-SEG NanoNet: Real-Time Polyp Segmentation in Capsule Endoscopy & Colonoscopy...	20	Experimental	7	—
161	beasygo1ng/OCT-Retinal-Layer-Segmenter UNet based model that segment retina to 8 layers in OCT images	20	Experimental	85	Jupyter Notebook
162	MultimodalImagingCenter/MIC-MAQ MIC-MAQ for Microscopy Images of Cells - Multi Analyses and Quantifications...	20	Experimental	1	Java
163	Ji2424/Deep-Learning-Based-Segmentation-of-the-Stratum-Corneum-in-OCT-Images MEng dissertation project on U-Net and DeepLab v3 for automated OCT skin...	19	Experimental	—	MATLAB
164	miac-research/MARS-brainstem State-of-the-art, deep learning-based segmentation of the brainstem on MRI	19	Experimental	6	Python
165	allureking/unet-cell-segmentation U-Net & Attention U-Net for Cell Counting in Microscopy Images \| PyTorch \|...	19	Experimental	—	Python
166	hamidrezaamirii/WMH-Segmentation-MedSAM-LoRA Parameter-efficient brain lesion segmentation using MedSAM and LoRA on the...	19	Experimental	—	Jupyter Notebook
167	NIH-NEI/oct-image-segmentation-models Automatic retinal OCT image segmentation for NEI OSIO projects	19	Experimental	—	Python
168	NIH-NEI/oct-segmenter Image processing scripts for automated mouse retinal OCT image segmentation	19	Experimental	—	Python
169	ecalabr/brain_mask 3D deep convolutional neural network based segmentation and brain masking...	18	Experimental	18	Python
170	Huster-Hq/MonoBox [AAAI 2025] MonoBox: Tightness-free Box-supervised Polyp Segmentation using...	18	Experimental	19	Python
171	sawsanowa/LL3rdM-Segmentation-Detection-Extraction Using deep learning a U-net architecture is used to make segmentation,...	18	Experimental	7	Jupyter Notebook
172	SBriguglio/DLTMIS Deep Learning for Medical Image Segmentation (DLMIS) is intended to help...	18	Experimental	3	Jupyter Notebook
173	RGivisiez/Blood-Vessel-Segmentation Blood vessel segmentation for retina and eggs.	18	Experimental	8	Jupyter Notebook
174	Belis0811/Unet This is official github repo for Nature InReview paper "AI-enabled live-dead...	18	Experimental	4	Jupyter Notebook
175	jaburke166/deepgpet Repository storing fully automatic DL-based model and mode weights for...	18	Experimental	11	Jupyter Notebook
176	mturja-vf-ic-bd/SlicerSurfaceLearner A Slicer extension to apply convolutional neural network based classifiers...	18	Experimental	2	Shell
177	Darwin231/Ultrasound-image-classification-and-segmentation Ultrasound Image Recognition	17	Experimental	3	Jupyter Notebook
178	pramod-zillella/Skin-Lesion-Segmentation Fully automatic skin lesion segmentation using the Berkeley wavelet...	17	Experimental	12	Jupyter Notebook
179	spsingh37/3D_Liver_Tumor_segmentation This project compares the performance of UNet, ResUNet, SegResNet, and UNETR...	17	Experimental	13	Jupyter Notebook
180	huyquoctrinh/PEFNet The official implementation of paper PEFNet: Positional Embedding Feature...	17	Experimental	15	Python
181	Taneja24/Semantic-Segmentation-of-Microscopy-Cell-Images Identify microscopy cells in biomedical images using semantic segmenting...	17	Experimental	5	Jupyter Notebook
182	mdhabibi/Automated-Cell-Semantic-Segmentation-with-UNet A machine learning solution for automating nucleus detection in biomedical...	17	Experimental	5	Jupyter Notebook
183	Jianningli/Autoimplant_II code repository for AutoImplant II submissions	16	Experimental	3	—
184	Abdalrahmanhassan237/Brain-Tumer-Segmentation--UNET This project focuses on brain tumor segmentation using MRI images, employing...	16	Experimental	3	Jupyter Notebook
185	Zoha-Arif/DeepMReye_Validation BrainHack Vanderbilt 2025: A validation project for DeepMReye, a...	16	Experimental	3	—
186	fisherman611/unet-for-colonoscopy-polyp-segmentation This repository offers an implementation of the UNet model tailored for...	15	Experimental	6	Jupyter Notebook
187	Pengularity/medical-imaging-deep-learning-lab Advanced Deep Learning implementations for Medical Imaging (CT/MRI/X-Ray)....	15	Experimental	—	—
188	firojalam/medic Multi-Task Learning for Disaster Image Classification using MEDIC	15	Experimental	25	Python
189	yo3nglau/RealMNet The official implementation of RealMNet [npj Digital Medicine'25]	15	Experimental	5	Python
190	githuseyingur/brain-tumor-segmentation-with-UNet Brain Tumor Segmentation with U-Net (ML Model) - CNN	15	Experimental	2	Jupyter Notebook
191	mo26-web/Chest-X-Ray-Image_Segmentation_ResUNet Lung segmentation for chest X-Ray images with ResUNet and UNet. In addition,...	15	Experimental	19	Jupyter Notebook
192	tayfurertas/vlm3d_project VLM3D-Efficient-Pipeline: Weakly Supervised Disease Localization with Transformers	15	Experimental	—	Python
193	tayebiarasteh/vit-med Self-supervised and supervised pretraining for chest radiograph AI	15	Experimental	6	Python
194	Toliol/mu-net-polyp-segmentation 🔍 Enhance polyp detection in colonoscopy with μ-Net, a robust architecture...	14	Experimental	—	—
195	673958639/Convolutional-Neural-Network-for-Brain-Lesion-Segmentation-in-MRI-Images In this work, four popular deep convolutional neural networks (U-NET,...	14	Experimental	12	Jupyter Notebook
196	liu-bodong/CV-Lab A comprehensive CV framework for training and evaluating deep learning...	14	Experimental	3	Jupyter Notebook
197	monajemi-arman/dental-canal-cbct Teeth canal detection using deep learning	14	Experimental	4	Python
198	Simran-Sodhi/asrProject2025 Active learning framework for improving cell segmentation in microscopy...	14	Experimental	—	Jupyter Notebook
199	Sacraniea/BraTS_QML_Segmentation Honours Thesis: Hybrid Quantum-Classical Machine Learning in Brain Tumour...	14	Experimental	—	Python
200	Bean-Young/PET-Project DeepPET: An Intelligent Brain PET Device with Low Radiation and High Imaging Quality	14	Experimental	3	—
201	ARMADILLO-VISION/midline-loss This is a repository of the code used in the "Midline-Constrained Loss in...	14	Experimental	3	Python
202	ScholarChen20/HCMNet BC-Mamba: A Novel Hybird CNN-Mamba Network For Medical Ultrasound Image Segmentation	14	Experimental	4	Python
203	ugurcanakyuz/3D-Volumetric-MedicalImageSegmentationWithDeepLearning This GitHub repository was created for research focusing on the development...	14	Experimental	9	Jupyter Notebook
204	ChristophReich1996/Yeast-in-Microstructures-Dataset Official and maintained implementation of the dataset paper "An Instance...	14	Experimental	14	Python
205	rachitsaluja/UCSF-BMSR-benchmarks nnUNet benchmarks for The University of California San Francisco Brain...	13	Experimental	10	Jupyter Notebook
206	fifaak/StrokeSeg-AI AI-Powered Brain Stroke Segmentation using U-Net with ResNet Encoder \|...	13	Experimental	5	Jupyter Notebook
207	Vidhi1290/Medical-Image-Segmentation-Deep-Learning-Project Our project uses state-of-the-art deep learning techniques to tackle a vital...	13	Experimental	11	Jupyter Notebook
208	OMFSdigital/Cyto-R-CNN Source code for the paper "Cyto R-CNN and CytoNuke Dataset: Towards reliable...	13	Experimental	5	Python
209	mazurowski-lab/radiologyintrinsicmanifolds (MICCAI 2022) Code for "The Intrinsic Manifolds of Radiological Images and...	13	Experimental	8	Jupyter Notebook
210	akhilchibber/3D-Teeth-Scan-Segmentation Deep Learning based 3D Teeth Scan Segmentation	13	Experimental	5	—
211	liangzifei/MRH-Net Training a local neural network from multiple MRI to histology	13	Experimental	6	MATLAB
212	fignja/microscopy-bubbles-recognition Microscopy bubbles segmentation and size measuring system	13	Experimental	5	Jupyter Notebook
213	LightersWang/EndoBoost_FPPD13 Official repo of "EndoBoost: a plug-and-play module for false positive...	12	Experimental	3	—
214	AIforAnesthesiology/Brachial-Plexus-Segmentation Brachial plexus segmentation on ultrasound imaging by a deep learning model...	12	Experimental	4	HTML
215	s-shahpouri/DL_PET This repository covers all files that were made and used for Deep learning...	12	Experimental	4	Jupyter Notebook
216	pramod-zillella/Brain-Tumor-Segmentation Fully automatic brain tumor segmentation using the Modified 3DUNet...	12	Experimental	16	Jupyter Notebook
217	wannature/BoostMIS Pytorch implementation of BoostMIS: Boosting Medical Image Semi-supervised...	12	Experimental	56	Python
218	xfetus/midl2023 :page_facing_up: Short paper to Medical Imaging with Deep Learning 2023...	12	Experimental	12	Jupyter Notebook
219	jrodriguezortega/CHaRM Code to reproduce all the experiments in the paper "CHaRM: Conditioned...	12	Experimental	1	—
220	pratikshahmit/A_deep_learning_toolkit_for_visualization_and_interpretation_of_segmented_medical_images Public repository for "A deep learning toolkit for visualization and...	11	Experimental	2	—
221	arnejad/FLBS A Fast and Memory-efficient (Light) Brain MRI Segmentation Framework for...	11	Experimental	2	MATLAB
222	dlepre01/Semi-Automatic-Pipeline-for-Muscle-Cell-Segmentation-and-Quantitative-Index-Computation Semi-automatic deep learning pipeline for nuclei detection, muscle fibre...	11	Experimental	—	—
223	TianyiFranklinWang/MedFM_Submission_Only Solution for NeurIPS 2023 - MedFM Challenge	11	Experimental	2	Python
224	motasemwed/eyetech-liver-segmentation Deep learning system for automatic liver & tumor segmentation from CT scans...	11	Experimental	—	Jupyter Notebook
225	prathamhanda/BRATS-2025_Tumor-Prediction Research-grade brain tumor segmentation and classification system leveraging...	11	Experimental	—	Jupyter Notebook
226	bogomil-iliev/brain-mri-unet-segmentation 2D U-Net brain MRI segmentation (BraTS2020, FLAIR+T1ce). Dice/IoU. TensorFlow/Keras.	11	Experimental	—	Jupyter Notebook
227	BBQuercus/fluffy Deep learning for cellular and sub-cellular segmentation made easy.	10	Experimental	1	JavaScript
228	Andrewwango/awesome-unsupervised-imaging Resources for solving imaging inverse problems using deep learning without...	10	Experimental	1	—
229	WestCoastGod/Carotid-Artery-Segmentation-with-nnU-Net This project uses nnU-Net to automatically segment carotid arteries from 2D...	10	Experimental	3	Python

Comparisons in this category

MONAI and medicaltorch (94 vs 55) MONAI and MONAILabel (94 vs 71) MONAI and monai-deploy-app-sdk (94 vs 64)