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 250 medical image segmentation frameworks tracked. 3 score above 70 (verified tier). The highest-rated is dipy/dipy at 85/100 with 811 stars. 3 of the top 10 are actively maintained.

Get all 250 projects as JSON

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

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#	Framework	Score	Tier	Stars	Language
1	dipy/dipy DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains...	85	Verified	811	Python
2	Project-MONAI/MONAI AI Toolkit for Healthcare Imaging	84	Verified	7,927	Python
3	Project-MONAI/MONAILabel MONAI Label is an intelligent open source image labeling and learning tool.	70	Verified	819	Python
4	neuronets/nobrainer A framework for developing neural network models for 3D image processing.	69	Established	167	Python
5	Project-MONAI/monai-deploy-app-sdk MONAI Deploy App SDK offers a framework and associated tools to design,...	68	Established	125	Jupyter Notebook
6	axondeepseg/axondeepseg Axon/Myelin segmentation using Deep Learning	68	Established	124	Python
7	FAST-Imaging/FAST A framework for high-performance medical image processing, neural network...	67	Established	501	C++
8	kevinjohncutler/omnipose Omnipose: a high-precision solution for morphology-independent cell segmentation	66	Established	142	Python
9	PortPy-Project/PortPy Opensource Python project for cancer radiation treatment planning [AAPM'23]	66	Established	174	Python
10	PaulRitsche/DeepACSA Automated measurement of muscle anatomical cross-sectional area in...	62	Established	18	Python
11	tue-bmd/zea zea: A Toolbox for Cognitive Ultrasound Imaging	60	Established	51	Python
12	MedMNIST/MedMNIST [pip install medmnist] 18x Standardized Datasets for 2D and 3D Biomedical...	59	Established	1,323	Python
13	frankkramer-lab/MIScnn A framework for Medical Image Segmentation with Convolutional Neural...	59	Established	419	Python
14	GuillaumeMougeot/biom3d Easy Volumetric Segmentation with Deep Learning	58	Established	28	Python
15	georgeoshardo/SyMBac Accurate segmentation of bacterial microscope images using deep learning...	58	Established	22	Jupyter Notebook
16	perone/medicaltorch A medical imaging framework for Pytorch	57	Established	871	Python
17	koriavinash1/DeepBrainSeg Fully automatic brain tumour segmentation using Deep 3-D convolutional...	56	Established	193	Python
18	DCBIA-OrthoLab/SlicerAutomatedDentalTools A 3D Slicer extension to use AMASSS, ALI-CBCT and ALI-IOS	56	Established	146	Python
19	ubern-mia/pyradise PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline...	55	Established	53	Python
20	braph-software/BRAPH-2 BRAPH 2.0 is a comprehensive software package for the analysis and...	55	Established	60	MATLAB
21	MuscleMap/MuscleMap MuscleMap: An Open-Source, Community-Supported Consortium for Whole-Body...	52	Established	74	Python
22	wdika/atommic ATOMMIC: Advanced Toolbox for Multitask Medical Imaging Consistency	52	Established	21	Jupyter Notebook
23	ternaus/robot-surgery-segmentation Wining solution and its improvement for MICCAI 2017 Robotic Instrument...	51	Established	639	Jupyter Notebook
24	numisveinsson/SeqSeg SeqSeg (Sequential Segmentations)	51	Established	15	Python
25	microsoft/InnerEye-DeepLearning Medical Imaging Deep Learning library to train and deploy 3D segmentation...	51	Established	578	Python
26	mrirecon/bart BART: Toolbox for Computational Magnetic Resonance Imaging	51	Established	359	C
27	IBBM/Cascaded-FCN Source code for the MICCAI 2016 Paper "Automatic Liver and Lesion...	51	Established	303	Jupyter Notebook
28	NifTK/NiftyNet [unmaintained] An open-source convolutional neural networks platform for...	51	Established	1,381	Python
29	facebookresearch/fastMRI A large-scale dataset of both raw MRI measurements and clinical MRI images.	51	Established	1,508	Python
30	deepmedic/deepmedic Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D...	51	Established	1,057	Python
31	mlcommons/GaNDLF A generalizable application framework for segmentation, regression, and...	51	Established	191	Python
32	janelia-cellmap/cellmap-segmentation-challenge Repository of scripts to facilitate participation in CellMap's segmentation...	51	Established	40	Python
33	OishiLab/OpenMAP-T1 Whole Brain Segmentation and Parecllation Using OpenMAP-T1 Method for 3D T1 Brain MRI	50	Established	37	Python
34	Sentinal4D/cellshape 3D shape analysis using deep learning	50	Established	31	Python
35	IAmSuyogJadhav/3d-mri-brain-tumor-segmentation-using-autoencoder-regularization Keras implementation of the paper "3D MRI brain tumor segmentation using...	50	Established	375	Jupyter Notebook
36	JunMa11/MICCAI-OpenSourcePapers MICCAI 2019-2023 Open Source Papers	50	Established	1,293	—
37	oist/Usiigaci Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by...	49	Emerging	204	Jupyter Notebook
38	DengPingFan/PraNet PraNet: Parallel Reverse Attention Network for Polyp Segmentation, MICCAI...	49	Emerging	532	Python
39	sdsubhajitdas/Brain-Tumor-Segmentation Brain Tumor Segmentation done using U-Net Architecture.	49	Emerging	292	Jupyter Notebook
40	leoliuf/MRiLab A Numerical Magnetic Resonance Imaging (MRI) Simulation Platform	49	Emerging	243	MATLAB
41	nitrain/nitrain Train AI models efficiently on medical images using any framework	49	Emerging	1,879	Python
42	KiT-RT/kitrt_code A high performance framework for radiation therapy simulation and numerical...	49	Emerging	27	C++
43	black0017/MedicalZooPytorch A pytorch-based deep learning framework for multi-modal 2D/3D medical image...	49	Emerging	1,906	Python
44	kamalkraj/DATA-SCIENCE-BOWL-2018 DATA-SCIENCE-BOWL-2018 Find the nuclei in divergent images to advance...	48	Emerging	92	Jupyter Notebook
45	MICA-MNI/micaopen Open Scripts and pipelines from the Multimodal Imaging and Connectome...	48	Emerging	84	Jupyter Notebook
46	ardamavi/3D-Medical-Segmentation-GAN 3D Liver Segmentation with GAN	47	Emerging	132	Python
47	open-retina/open-retina Collaborative retina modelling across datasets and species.	47	Emerging	18	Python
48	creatis-myriad/ASCENT cardiAc ultrasound Segmentation & Color-dopplEr dealiasiNg Toolbox (ASCENT)	47	Emerging	44	Python
49	shalabh147/Brain-Tumor-Segmentation-and-Survival-Prediction-using-Deep-Neural-Networks Use of state of the art Convolutional neural network architectures including...	47	Emerging	171	Jupyter Notebook
50	jadevaibhav/Brain-Tumor-Segmentation-using-Deep-Neural-networks Keras implementation of paper by the same name	47	Emerging	96	Jupyter Notebook
51	KibromBerihu/ai4elife This data-centric AI repository implements a robust deep learning method...	46	Emerging	40	Python
52	IlliaOvcharenko/lung-segmentation Lung segmentation for chest X-Ray images	46	Emerging	136	Jupyter Notebook
53	yhygao/CBIM-Medical-Image-Segmentation A PyTorch framework for medical image segmentation	46	Emerging	342	Python
54	Omid-Nejati/MedViT MedViT: A Robust Vision Transformer for Generalized Medical Image...	46	Emerging	237	Python
55	wwu-mmll/deepmriprep Neural network-based MRI preprocessing: Prep 🧠 images in seconds 🔥	46	Emerging	56	Python
56	RazvanDu/DUCK-Net Using DUCK-Net for polyp image segmentation. ( Nature Scientific Reports 2023 )	46	Emerging	127	Jupyter Notebook
57	moverseai/moai moai is a PyTorch-based AI Model Development Kit (MDK) created to improve...	45	Emerging	56	Python
58	ai-med/relaynet_pytorch Pytorch Implementation of retinal OCT Layer Segmentation (with trained models)	45	Emerging	93	Jupyter Notebook
59	hzdr-MedImaging/LyROI nnU-Net-based Lymphoma Total Metabolic Tumor Volume Segmentation	45	Emerging	5	Python
60	YangLabHKUST/STitch3D Construction of a 3D whole organism spatial atlas by joint modeling of...	44	Emerging	70	Python
61	KitwareMedical/SlicerNNUnet 3D Slicer nnUNet integration to streamline usage for nnUNet based AI extensions.	44	Emerging	56	Python
62	NYUMedML/DARTS Code for DARTS: DenseUnet-based Automatic Rapid Tool for brain Segmentation	44	Emerging	69	Jupyter Notebook
63	FZJ-INM1-BDA/celldetection Scalable Instance Segmentation using PyTorch & PyTorch Lightning.	44	Emerging	149	Python
64	wwu-mmll/deepbet Fast brain extraction using neural networks	43	Emerging	50	Python
65	rezazad68/BCDU-Net BCDU-Net : Medical Image Segmentation	43	Emerging	784	Python
66	haakonnese/nect Implicit Neural Representation for Fast 4D Computed Tomography of Multiphase...	43	Emerging	5	Python
67	nadeemlab/DoseRTX Domain knowledge driven 3D radiation dose prediction [PMB'22]	43	Emerging	51	Python
68	ChenLiu-1996/CUTS [MICCAI 2024] CUTS: A Deep Learning and Topological Framework for...	43	Emerging	41	Python
69	HINTLab/RibSeg [MICCAI'21 & TMI'23] RibSeg Dataset and Point Cloud Baselines for Rib...	42	Emerging	69	Python
70	AICAN-Research/H2G-Net 🚀 H2G-Net: Segmentation of breast cancer region from whole slide images	42	Emerging	28	Jupyter Notebook
71	volBrain/AssemblyNet AssemblyNet: 3D Whole Brain MRI segmentation pipeline	42	Emerging	71	—
72	anthonyweidai/SvANet [TNNLS 2026] SvANet: Exploiting Scale-Variant Attention for Segmenting Small...	42	Emerging	66	Python
73	andreped/NoCodeSeg 🔬 Code-free deep segmentation for computational pathology	42	Emerging	56	Jupyter Notebook
74	assassint2017/MICCAI-LITS2017 liver segmentation using deep learning	42	Emerging	433	Python
75	Richarizardd/Self-Supervised-ViT-Path Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology...	42	Emerging	143	Jupyter Notebook
76	aiforvision/OCTA-autosegmentation Repository for the paper "Synthetic optical coherence tomography angiographs...	41	Emerging	48	Jupyter Notebook
77	opaserr/dota Data-driven particle transport algorithm for fast dose calculations.	41	Emerging	42	Jupyter Notebook
78	HiLab-git/WORD [MedIA2022]WORD: A large scale dataset, benchmark and clinical applicable...	41	Emerging	172	Python
79	AryaKoureshi/Brain-tumor-detection Implementation of medical image segmentation and deep learning framework...	41	Emerging	74	Jupyter Notebook
80	nadeemlab/CEP Computational Endoscopy Platform (advanced deep learning toolset for...	41	Emerging	82	Python
81	seungjunlee96/U-Net_Lung-Segmentation Application of U-Net in Lung Segmentation-Pytorch	41	Emerging	32	Python
82	tianyu0207/weakly-polyp [MICCAI'22] Contrastive Transformer-based Multiple Instance Learning for...	41	Emerging	43	Python
83	hahnec/rf-ulm RF-ULM: Ultrasound Localization Microscopy Learned from Radio-Frequency Wavefronts	40	Emerging	36	Python
84	wdika/mridc Data Consistency Toolbox for Magnetic Resonance Imaging	40	Emerging	40	Jupyter Notebook
85	limhoyeon/ToothGroupNetwork 3D Dental surface segmentation with Tooth Group Network	40	Emerging	294	Python
86	criticaldata/ShortKit-ML A unified framework to detect, benchmark, and mitigate shortcut learning in...	39	Emerging	3	Python
87	Abe404/RootPainter3D RootPainter3D: Interactive-machine-learning enables rapid and accurate...	39	Emerging	24	Python
88	miac-research/MARS-WMH State-of-the-art, deep learning-based segmentation of brain white matter...	39	Emerging	11	Python
89	WayScience/NF1_organoid_cell_segmentation Deep learning–based vision model for segmentation of cells within NF1 organoids.	39	Emerging	2	Python
90	Brain-Tumor-Segmentation/brain-tumor-segmentation-using-deep-neural-networks The project presents a comparative study of Brain Tumor Segmentation using 3...	38	Emerging	13	Jupyter Notebook
91	ZombaSY/FSG-Net-pytorch Official implementation of the paper, "Full-scale Representation Guided...	38	Emerging	34	Python
92	zekikus/MedSegBench [pip install medsegbench] 35x Standardized Medical Segmentation Datasets...	38	Emerging	29	Python
93	mfaizan-ai/Brain-Tumors-Segmentation Multimodal Brain mpMRI segmentation on BraTS 2023 and BraTS 2021 datasets.	38	Emerging	100	Python
94	arindam369/MedMNIST-ViT Based on our paper "Implementing vision transformer for classifying 2D...	38	Emerging	16	Jupyter Notebook
95	sing-group/deep-learning-colonoscopy Review in Deep Learning for Polyp Detection and Classification in...	38	Emerging	207	—
96	koriavinash1/Fetal-Brain-Segmentation Fully automatic technique for fetal brain segmentation using deep...	37	Emerging	13	Jupyter Notebook
97	LucasKre/dilated_tooth_seg_net DilatedToothSegNet: Tooth Segmentation Network on 3D Dental Meshes Through...	37	Emerging	106	Python
98	sagizty/Multi-Stage-Hybrid-Transformer Official release of MSHT: Multi-stage Hybrid Transformer for the ROSE Image...	36	Emerging	77	Jupyter Notebook
99	alexklwong/subpixel-embedding-segmentation PyTorch Implementation of Small Lesion Segmentation in Brain MRIs with...	36	Emerging	22	Python
100	CedricCaruzzo/pannuke-segmentation An open-source UNet-based pipeline for nuclei segmentation in histopathology...	36	Emerging	10	Python
101	j-morano/rrwnet Official repository of the paper "RRWNet: Recursive Refinement Network for...	36	Emerging	42	Python
102	ZeinebZH/TumorNetSolvers Efficient Deep Learning-based Forward Solvers for Brain Tumor Growth Models	36	Emerging	6	Python
103	AHMEDSANA/Binary-Class-Brain-Tumor-Segmentation-Using-UNET We segmented the Brain tumor using Brats dataset and as we know it is in 3D...	35	Emerging	17	Jupyter Notebook
104	HaamsRee/senoquant Quantifying senescence, the easy way.	35	Emerging	2	Python
105	bmdeep/SegPC2021 Multi-scale Regional Attention Deeplab3+: Multiple Myeloma Plasma Cells...	35	Emerging	9	Jupyter Notebook
106	twpkevin06222/Deep-Attention-Network-for-BraTS20 Deep Supervised Attention Networks for Pixel-wise Brain Tumor Segmentation....	35	Emerging	6	Jupyter Notebook
107	alok-ai-lab/DeepInsight3D_pkg DeepInsight3D package to deal with multi-omics or multi-layered data	35	Emerging	6	MATLAB
108	GorkemP/labeled-images-for-ulcerative-colitis Codes to process and train LIMUC dataset	34	Emerging	35	Python
109	Borda/kaggle_image-segm Simple tooling for instance segmentation aiming at cell biology...	34	Emerging	10	Jupyter Notebook
110	DIAGNijmegen/ULS23 Repository for the Universal Lesion Segmentation Challenge '23	34	Emerging	40	Python
111	codingfisch/niftiai Train neural nets on 3D images (e.g. MRIs) 🧠	34	Emerging	3	Python
112	ViacheslavDanilov/oct_segmentation This repository is dedicated to the segmentation of optical coherence...	34	Emerging	10	Python
113	MJAHMADEE/Cataract-LMM Advanced computer vision framework for surgical video analysis, featuring...	33	Emerging	10	Jupyter Notebook
114	bionlplab/longitudinal_transformer_for_survival_analysis [npj Digital Medicine] "Harnessing the power of longitudinal medical imaging...	33	Emerging	21	Python
115	IAI-ATLAS/SSL-for-Medical-Image-Segmentation TBME: Self-Supervised Learning for Annotation Efficient Biomedical Image Segmentation	33	Emerging	6	Jupyter Notebook
116	edaaydinea/Low-Grade-Glioma-Segmentation This is a capstone project on a real dataset related to segmenting low-grade...	33	Emerging	11	Jupyter Notebook
117	LLeon360/UNetBiomedicalDiagnosis Contains a module for functions that build and evaluate a U-Net Model which...	33	Emerging	8	Python
118	ImagingDataCommons/nnU-Net-BPR-annotations Code accompanying this dataset: Krishnaswamy, D., Bontempi, D., Clunie, D.,...	33	Emerging	8	Jupyter Notebook
119	YigitTurali/HydraViT HydraViT is a PyTorch implementation of the HydraViT model, an adaptive...	33	Emerging	7	—
120	Yulv-git/Awesome-Ultrasound-Standard-Plane-Detection A curated list of awesome ultrasound standard/diagnostic plane...	33	Emerging	56	Python
121	avakanski/Attention-Enriched-DL-Model-for-Breast-Tumor-Segmentation Salient attention U-Net model for tumor segmentation in breast ultrasound...	33	Emerging	45	Jupyter Notebook
122	tkshirakawa/AISegmentation_v141 The public source code of A.I.Segmentation (AIS) version 1.4.1. AIS is a...	33	Emerging	6	Objective-C
123	sinemistoktas/KITE Web-based semi-automated retinal fluid segmentation tool for OCT images....	32	Emerging	2	CSS
124	alok-ai-lab/MRep-DeepInsight Multiple Representation DeepInsight technique	32	Emerging	5	MATLAB
125	vladzalevskyi/brain-segmentation This repository contrains source code and the report for the Brain...	32	Emerging	5	Jupyter Notebook
126	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...	32	Emerging	5	Jupyter Notebook
127	MIC-DKFZ/nnActive nnActive -- code, benchmark and results for the largest study of Active...	31	Emerging	17	Python
128	qianlinyi/hhu-medical-image-group 河海大学医学图像处理组	31	Emerging	120	—
129	thaiminhpv/Doctor-Cyclop-Hackathon-2021 Model for Doctor's Cyclop Project at FPT Edu Hackathon 2021	31	Emerging	4	Python
130	xmindflow/Awesome-Implicit-Neural-Representations-in-Medical-imaging [ICCV 2023] A curated list of resources on implicit neural representations...	31	Emerging	239	—
131	rachitsaluja/BraTS-2023-Metrics Official BraTS 2023 Segmentation Performance Metrics	30	Emerging	21	Python
132	xfetus/xfetus xfetus -- :baby: :brain: :robot: -- A library for ultrasound fetal...	30	Emerging	10	Python
133	Arshad221b/3D-UNet-Image-Segmentation 3D image segmentation using UNet: for MRI/CT scan image data	30	Emerging	6	Jupyter Notebook
134	Jonghwan-dev/Awesome-Segmentation-in-Medical Welcome, Awesome-segmentation-in-medical project. This repo is robust,...	30	Emerging	9	Python
135	emirhanai/Cell-Instance-Segmentation-Deep-Learning-Project-Emirhan-BULUT Cell Instance Segmentation - Deep Learning Project - Emirhan BULUT	29	Experimental	9	Jupyter Notebook
136	ChrisBotos/ATLAS-Cellpose Created by Christos Botos, ATLAS-Cellpose (Adaptive Tiled Local Analysis...	29	Experimental	1	Python
137	LightersWang/Awesome-Active-Learning-for-Medical-Image-Analysis [MedIA] Paper list and source code for survey "A comprehensive survey on...	29	Experimental	127	Python
138	jytjyt05/Teeth-Seg Teeth segmentation in X-ray images using UNet and Res-UNet	29	Experimental	9	Jupyter Notebook
139	lasopablo/freesurfer-freesurfer-dev-mri_WMHsynthseg MS thesis @Harvard: Deep Learning optimization and data augmentation methods...	29	Experimental	18	Python
140	J-Linaris/retinal-thin-vessels A Python package for computing the recall and precision scores specifically...	29	Experimental	4	Python
141	AntonotnaWang/3DCellSeg Official implementation of "A novel deep learning-based 3D cell segmentation...	29	Experimental	23	Jupyter Notebook
142	sowada23/Brain-Tumor-Segmentation-Project PyTorch 2D U-Net for BraTS brain tumor segmentation (FLAIR+T1CE) with...	29	Experimental	1	Python
143	joewong00/3D-CNN-Segmentation Applying 3D CNN for bio-medical images segmentation with 3D-Unet, Residual...	28	Experimental	22	Jupyter Notebook
144	ChiShengChen/pytorch_deep_learning_medimg_tutorial This project simply implements three common deep learning models (VGG16,...	28	Experimental	20	Python
145	Pablo1990/3D-deep-segmentation-protocol Single cell resolution 3D imaging and segmentation within intact live tissues	28	Experimental	2	Jupyter Notebook
146	Pulkit-Khandelwal/purple-mri Penn Utilities for Registration and ParcelLation of Ex vivo MRI	28	Experimental	23	Python
147	rezazad68/transnorm transnorm	28	Experimental	23	Jupyter Notebook
148	uw-loci/collagen-fiber-metrics Deep generative models for collagen fiber centerline segmentation and...	27	Experimental	12	Jupyter Notebook
149	beasygo1ng/OCT-Retinal-Layer-Segmenter UNet based model that segment retina to 8 layers in OCT images	27	Experimental	85	Jupyter Notebook
150	thierleft/2-5DUNet-supervised-vascular-segmentation-Kaggle Supervised 2.5D U-Net for Vascular Segmentation of Human Renal Arteries on HiP-CT	27	Experimental	2	Jupyter Notebook
151	MultimodalImagingCenter/MIC-MAQ MIC-MAQ for Microscopy Images of Cells - Multi Analyses and Quantifications...	27	Experimental	1	Java
152	miac-research/MARS-brainstem State-of-the-art, deep learning-based segmentation of the brainstem on MRI	26	Experimental	6	Python
153	mu40/babyseg Brain segmentation across the first years of life	26	Experimental	4	Python
154	Belis0811/Unet This is official github repo for Nature InReview paper "AI-enabled live-dead...	25	Experimental	4	Jupyter Notebook
155	RGivisiez/Blood-Vessel-Segmentation Blood vessel segmentation for retina and eggs.	25	Experimental	8	Jupyter Notebook
156	SBriguglio/DLTMIS Deep Learning for Medical Image Segmentation (DLMIS) is intended to help...	25	Experimental	3	Jupyter Notebook
157	jaburke166/deepgpet Repository storing fully automatic DL-based model and mode weights for...	25	Experimental	11	Jupyter Notebook
158	mturja-vf-ic-bd/SlicerSurfaceLearner A Slicer extension to apply convolutional neural network based classifiers...	25	Experimental	2	Shell
159	ecalabr/brain_mask 3D deep convolutional neural network based segmentation and brain masking...	25	Experimental	18	Python
160	Huster-Hq/MonoBox [AAAI 2025] MonoBox: Tightness-free Box-supervised Polyp Segmentation using...	25	Experimental	19	Python
161	Taneja24/Semantic-Segmentation-of-Microscopy-Cell-Images Identify microscopy cells in biomedical images using semantic segmenting...	24	Experimental	5	Jupyter Notebook
162	spsingh37/3D_Liver_Tumor_segmentation This project compares the performance of UNet, ResUNet, SegResNet, and UNETR...	24	Experimental	13	Jupyter Notebook
163	huyquoctrinh/PEFNet The official implementation of paper PEFNet: Positional Embedding Feature...	24	Experimental	15	Python
164	mdhabibi/Automated-Cell-Semantic-Segmentation-with-UNet A machine learning solution for automating nucleus detection in biomedical...	24	Experimental	5	Jupyter Notebook
165	Darwin231/Ultrasound-image-classification-and-segmentation Ultrasound Image Recognition	24	Experimental	3	Jupyter Notebook
166	pramod-zillella/Skin-Lesion-Segmentation Fully automatic skin lesion segmentation using the Berkeley wavelet...	24	Experimental	12	Jupyter Notebook
167	Abdalrahmanhassan237/Brain-Tumer-Segmentation--UNET This project focuses on brain tumor segmentation using MRI images, employing...	23	Experimental	3	Jupyter Notebook
168	Jianningli/Autoimplant_II code repository for AutoImplant II submissions	23	Experimental	3	—
169	fisherman611/unet-for-colonoscopy-polyp-segmentation This repository offers an implementation of the UNet model tailored for...	22	Experimental	6	Jupyter Notebook
170	firojalam/medic Multi-Task Learning for Disaster Image Classification using MEDIC	22	Experimental	25	Python
171	mo26-web/Chest-X-Ray-Image_Segmentation_ResUNet Lung segmentation for chest X-Ray images with ResUNet and UNet. In addition,...	22	Experimental	19	Jupyter Notebook
172	tayebiarasteh/vit-med Self-supervised and supervised pretraining for chest radiograph AI	22	Experimental	6	Python
173	ianochieng25/PanNuke-cell-core-region-identification-with-DINO 🧬 Implement nuclei segmentation and classification using DINO...	22	Experimental	—	Python
174	yo3nglau/RealMNet The official implementation of RealMNet [npj Digital Medicine'25]	22	Experimental	5	Python
175	githuseyingur/brain-tumor-segmentation-with-UNet Brain Tumor Segmentation with U-Net (ML Model) - CNN	22	Experimental	2	Jupyter Notebook
176	Bean-Young/PET-Project DeepPET: An Intelligent Brain PET Device with Low Radiation and High Imaging Quality	21	Experimental	3	—
177	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...	21	Experimental	—	MATLAB
178	hamidrezaamirii/WMH-Segmentation-MedSAM-LoRA Parameter-efficient brain lesion segmentation using MedSAM and LoRA on the...	21	Experimental	—	Jupyter Notebook
179	allureking/unet-cell-segmentation U-Net & Attention U-Net for Cell Counting in Microscopy Images \| PyTorch \|...	21	Experimental	—	Python
180	673958639/Convolutional-Neural-Network-for-Brain-Lesion-Segmentation-in-MRI-Images In this work, four popular deep convolutional neural networks (U-NET,...	21	Experimental	12	Jupyter Notebook
181	ugurcanakyuz/3D-Volumetric-MedicalImageSegmentationWithDeepLearning This GitHub repository was created for research focusing on the development...	21	Experimental	9	Jupyter Notebook
182	ChristophReich1996/Yeast-in-Microstructures-Dataset Official and maintained implementation of the dataset paper "An Instance...	21	Experimental	14	Python
183	NIH-NEI/oct-image-segmentation-models Automatic retinal OCT image segmentation for NEI OSIO projects	21	Experimental	—	Python
184	NIH-NEI/oct-segmenter Image processing scripts for automated mouse retinal OCT image segmentation	21	Experimental	—	Python
185	monajemi-arman/dental-canal-cbct Teeth canal detection using deep learning	21	Experimental	4	Python
186	liangzifei/MRH-Net Training a local neural network from multiple MRI to histology	20	Experimental	6	MATLAB
187	fifaak/StrokeSeg-AI AI-Powered Brain Stroke Segmentation using U-Net with ResNet Encoder \|...	20	Experimental	5	Jupyter Notebook
188	akhilchibber/3D-Teeth-Scan-Segmentation Deep Learning based 3D Teeth Scan Segmentation	20	Experimental	5	—
189	ScholarChen20/HCMNet BC-Mamba: A Novel Hybird CNN-Mamba Network For Medical Ultrasound Image Segmentation	20	Experimental	4	Python
190	rachitsaluja/UCSF-BMSR-benchmarks nnUNet benchmarks for The University of California San Francisco Brain...	20	Experimental	10	Jupyter Notebook
191	ARMADILLO-VISION/midline-loss This is a repository of the code used in the "Midline-Constrained Loss in...	20	Experimental	3	Python
192	liu-bodong/CV-Lab A comprehensive CV framework for training and evaluating deep learning...	20	Experimental	3	Jupyter Notebook
193	fignja/microscopy-bubbles-recognition Microscopy bubbles segmentation and size measuring system	20	Experimental	5	Jupyter Notebook
194	mazurowski-lab/radiologyintrinsicmanifolds (MICCAI 2022) Code for "The Intrinsic Manifolds of Radiological Images and...	20	Experimental	8	Jupyter Notebook
195	Vidhi1290/Medical-Image-Segmentation-Deep-Learning-Project Our project uses state-of-the-art deep learning techniques to tackle a vital...	20	Experimental	11	Jupyter Notebook
196	pramod-zillella/Brain-Tumor-Segmentation Fully automatic brain tumor segmentation using the Modified 3DUNet...	19	Experimental	16	Jupyter Notebook
197	xfetus/midl2023 :page_facing_up: Short paper to Medical Imaging with Deep Learning 2023...	19	Experimental	12	Jupyter Notebook
198	LightersWang/EndoBoost_FPPD13 Official repo of "EndoBoost: a plug-and-play module for false positive...	19	Experimental	3	—
199	s-shahpouri/DL_PET This repository covers all files that were made and used for Deep learning...	19	Experimental	4	Jupyter Notebook
200	titouanlegourrierec/easilastik Easy integration of Ilastik segmentation models in Python.	19	Experimental	—	Python
201	AIforAnesthesiology/Brachial-Plexus-Segmentation Brachial plexus segmentation on ultrasound imaging by a deep learning model...	19	Experimental	4	HTML
202	wannature/BoostMIS Pytorch implementation of BoostMIS: Boosting Medical Image Semi-supervised...	19	Experimental	56	Python
203	arnejad/FLBS A Fast and Memory-efficient (Light) Brain MRI Segmentation Framework for...	18	Experimental	2	MATLAB
204	TianyiFranklinWang/MedFM_Submission_Only Solution for NeurIPS 2023 - MedFM Challenge	18	Experimental	2	Python
205	pratikshahmit/A_deep_learning_toolkit_for_visualization_and_interpretation_of_segmented_medical_images Public repository for "A deep learning toolkit for visualization and...	18	Experimental	2	—
206	Pengularity/medical-imaging-deep-learning-lab Advanced Deep Learning implementations for Medical Imaging (CT/MRI/X-Ray)....	17	Experimental	—	—
207	Andrewwango/awesome-unsupervised-imaging Resources for solving imaging inverse problems using deep learning without...	17	Experimental	1	—
208	BBQuercus/fluffy Deep learning for cellular and sub-cellular segmentation made easy.	17	Experimental	1	JavaScript
209	steve-zeyu-zhang/Awesome-3D-Medical-Imaging-Segmentation 3D Medical Imaging Segmentation: A Comprehensive Survey	15	Experimental	33	—
210	Sacraniea/BraTS_QML_Segmentation Honours Thesis: Hybrid Quantum-Classical Machine Learning in Brain Tumour...	14	Experimental	—	Python
211	Simran-Sodhi/asrProject2025 Active learning framework for improving cell segmentation in microscopy...	14	Experimental	—	Jupyter Notebook
212	Ivanrs297/endoscopycorruptions The endoscopycorruptions Python package provides utilities to simulate...	13	Experimental	13	Jupyter Notebook
213	ivadomed/model-seg-gm-wm-t2star-7t-unet2d-multiclass A deep learning model that allows robust SC/GM multi-class segmentation...	13	Experimental	3	—
214	prathamhanda/BRATS-2025_Tumor-Prediction Research-grade brain tumor segmentation and classification system leveraging...	13	Experimental	—	Jupyter Notebook
215	OVER-CODER/Nuclei-Segmentation SENLA-ResUNet: Attention-guided Residual U-Net achieving state-of-the-art...	13	Experimental	6	Jupyter Notebook
216	KurtLabUW/brats2023_updated Kurtlab's code for BraTS 2023 submission	13	Experimental	13	Python
217	mahdizynali/Pytorch-UNet-Brain-Tumor-Detection simple pytorch unet model for brain tumor detection on MRI tiff images	13	Experimental	12	Python
218	bogomil-iliev/brain-mri-unet-segmentation 2D U-Net brain MRI segmentation (BraTS2020, FLAIR+T1ce). Dice/IoU. TensorFlow/Keras.	13	Experimental	—	Jupyter Notebook
219	AlinaBaber/Liver-Tumor-Segmentation-Detection-by-ResUNET This repository contains the implementation of the Liver Tumor Segmentation...	12	Experimental	5	Jupyter Notebook
220	an-eve/ISIC-2016-lesion-segmentation-challenge ISIC Challenge - Lesion Segmentation task solved using the U-Net model...	12	Experimental	6	Jupyter Notebook
221	Phirat-Passi/Volumetric-MRI-Validation-of-Additional-Brain-Structures Semantic segmentation in computer vision enables precise brain tumor...	12	Experimental	5	Jupyter Notebook
222	ElmiraYazdani/Machine-Learning-Based-Radiodosiomics-and-Swin-UNETR-Framework-for-Dose-Prediction This repository presents a radiodosiomics framework for personalized...	12	Experimental	3	Jupyter Notebook
223	therakeshjoshi/Brain-Tumor-Segmentation-from-MRI-Scans-Using-CNN-Based-U-Net-Architecture Building a deep learning model to automatically segment brain tumors from MRI scans	12	Experimental	1	—
224	koesan/Brain_Segmentation Deep learning brain tumor segmentation using U-Net architecture on BRATS2015...	12	Experimental	2	Jupyter Notebook
225	TheAlphaJas/Liver-Tumor-Seg-Implements This repository contains codes of various state-of-the-art methods and...	12	Experimental	7	Jupyter Notebook
226	parsakhavarinejad/Breast_cancer_image_segmentation This project leverages the power of U-Net architecture implemented in...	12	Experimental	7	Jupyter Notebook
227	inferno73/AI-for-Identifying-the-Origin-of-Scattered-Gamma-Rays---GammaTPC A research repository exploring advanced Analytical, Deep Learning, and...	12	Experimental	1	HTML
228	renato-umeton/self-supervised-learning-review-in-medicine Self-Supervised Learning in Medicine Review	12	Experimental	5	—
229	Taiwan-CVAI/HeaortaNet HeaortaNet is a pre-trained model for 3D segmentation of heart and aorta...	12	Experimental	8	Python
230	yugantgajera/Dilated-Inception-U-Net-for-Nuclei-Segmentation-in-Multi-Organ-Histology-Images Medical image processing using machine learning is an emerging field of...	12	Experimental	8	Jupyter Notebook
231	vtsynergy/DL-FACT DL-FACT: Deep Learning-based Fast and Accurate Computed Tomography	12	Experimental	8	—
232	Inc0mple/3D_Brain_Tumor_Seg_V2 Using the BraTS2020 dataset, we test several approaches for brain tumour...	12	Experimental	8	Jupyter Notebook
233	Abdennacer-Badaoui/Segmenation_of_nerf_optic_sheath This project focused on ultrasound image segmentation of the optic nerve...	11	Experimental	3	Jupyter Notebook
234	NorhanAwad848/HUPMAP-Segmentation-ReactJS The goal is to segment instances of microvascular structures, including...	11	Experimental	—	HTML
235	cassxw/SAMSeg 🧠 U-SAM: Enhancing brain tumour segmentation by integrating SAM with U-Net...	11	Experimental	—	Python
236	ShrutiSemwal/MTech.-Dissertation-UNet-with-Attention-Mechanism UNet with Attention-DL Model for green building domain	11	Experimental	1	—
237	MosesKKhoza/Deep-Learning-on-Cassava-Leaves-Diseases Deep Learning - This solution trains a U-Net Model (primarily used in...	11	Experimental	—	Jupyter Notebook
238	lucianoscarpaci/UNet-Brain-Image-Segmentation This project applies segmentation techniques to a set of brain imaging data...	11	Experimental	—	Jupyter Notebook
239	Rachinder3/MRI-Tumor-Explorer Goal: Build a solution capable of generating masks to identify the presence...	11	Experimental	—	Jupyter Notebook
240	NirmalPb/Automated-Method-For-Brain-Tumor-Segmentation-And-Classification Machine trying to be a doctor	11	Experimental	—	HTML
241	rachitsaluja/UCSF-ALPTDG-benchmarks nnUNet benchmarks for The University of California San Francisco Adult...	11	Experimental	3	Jupyter Notebook
242	jvoliveira/Volumetric-Medical-Imaging-2025 This survey aims to review the main advances in the application of DL to...	11	Experimental	2	—
243	diaazg/image_segmentation COVID-19 lung segmentation using U-Net and MobileNet-U-Net with MLflow for...	11	Experimental	2	Jupyter Notebook
244	sohaamir/brainslicer A tool for slicing and upscaling T1-anatomical NIFTIs	11	Experimental	—	Jupyter Notebook
245	PhuocPhat1005/TransUNet_Segmentation_In_Medical_Image This is final project about TransUNet, an approach for Segmentation in Medical Image.	11	Experimental	—	Jupyter Notebook
246	ersinerzurum/MONAI 2D-3D segmentation using monai	11	Experimental	—	Jupyter Notebook
247	uniMedic/uniMedic-Models Lista de los modelos de Deep Learning disponibles que serán llamados por...	11	Experimental	—	—
248	Medical-Radiation-Physics-NTNU/knuth_2021_mri MRI-based automatic segmentation of rectal cancer using 2D UNet on two...	11	Experimental	—	—
249	Jack47744/ultrasound_subset Efficient Ultrasound Video Frame Subset Selection via Generative Dataset...	10	Experimental	2	Jupyter Notebook
250	sheeraz-prog/BraTS20_FYP Brain Tumor Segmentation And Overall Survival Prediction. My final year...	10	Experimental	2	Jupyter Notebook

Comparisons in this category

MONAI and medicaltorch (84 vs 57) MONAI and MONAILabel (84 vs 70) MONAI and monai-deploy-app-sdk (84 vs 68)