Medical Image Segmentation Transformers Transformer Models

Tools for segmenting anatomical structures and regions in medical images using transformer architectures (including hybrid CNN-transformer models). Does NOT include general medical image diagnosis, classification, or non-transformer segmentation methods.

There are 53 medical image segmentation transformers models tracked. 1 score above 70 (verified tier). The highest-rated is qubvel-org/segmentation_models.pytorch at 84/100 with 11,398 stars. 1 of the top 10 are actively maintained.

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#	Model	Score	Tier	Stars	Language
1	qubvel-org/segmentation_models.pytorch Semantic segmentation models with 500+ pretrained convolutional and...	84	Verified	11,398	Python
2	OSUPCVLab/SegFormer3D Official Implementation of SegFormer3D: an Efficient Transformer for 3D...	47	Emerging	205	Python
3	tue-mps/eomt [CVPR 2025 Highlight] Official code and models for Encoder-only Mask...	46	Emerging	548	Jupyter Notebook
4	jeya-maria-jose/Medical-Transformer Official Pytorch Code for "Medical Transformer: Gated Axial-Attention for...	44	Emerging	857	Python
5	davidiommi/Pytorch--3D-Medical-Images-Segmentation--SALMON Segmentation deep learning ALgorithm based on MONai toolbox: single and...	39	Emerging	124	Python
6	lambdavi/SatDrive-SegFL MLDL '23 Project: Federated Learning and Semantic Segmentation for...	38	Emerging	7	Python
7	MIC-DKFZ/MedNeXt [MICCAI 2023] MedNeXt is a fully ConvNeXt architecture for 3D medical image...	37	Emerging	487	Python
8	snap-research/EfficientFormer EfficientFormerV2 [ICCV 2023] & EfficientFormer [NeurIPs 2022]	37	Emerging	1,109	Python
9	oValach/RailSafeNet Repository of the paper: RailSafeNet: Visual Scene Understanding for Tram Safety	36	Emerging	6	Python
10	amirhossein-kz/HiFormer HiFormer: Hierarchical Multi-scale Representations Using Transformers for...	36	Emerging	144	Jupyter Notebook
11	Kartik-3004/SegFace [AAAI 25] SegFace: Face Segmentation of Long-tail classes	36	Emerging	100	Python
12	amazon-science/unified-ept A Unified Efficient Pyramid Transformer for Semantic Segmentation, ICCVW 2021	33	Emerging	31	Python
13	Omid-Nejati/BEFUnet A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation	33	Emerging	73	Python
14	biswassanket/DocSegTr A Bottom-Up Instance Segmentation Strategy for segmenting document instances...	31	Emerging	59	Python
15	sotiraslab/AgileFormer This the repo for the paper tiltled "AgileFormer: Spatially Agile...	31	Emerging	81	Python
16	DebeshJha/TransNetR Official implementation of TransNetR: Transformer-based Residual Network for...	30	Emerging	24	Python
17	xmindflow/MS-Former [MIDL 2023] MS-Former: Multi-Scale Self-Guided Transformer for Medical Image...	30	Emerging	16	Jupyter Notebook
18	xmindflow/SSCT [ICCV 2023] Self-supervised Semantic Segmentation: Consistency over Transformation	29	Experimental	26	Jupyter Notebook
19	deep-diver/segformer-tf-transformers This repository demonstrates how to use TensorFlow based SegFormer model in...	28	Experimental	30	Jupyter Notebook
20	xmindflow/MSA-2Net [BMVC 2024] Official repository of the paper titled "MSA^2 Net: Multi-scale...	28	Experimental	70	Python
21	rezazad68/transdeeplab TransDeepLab: Convolution-Free Transformer-based DeepLab v3+ for Medical...	27	Experimental	88	Python
22	xmindflow/MMCFormer [MIDL 2023] MMCFormer: Missing Modality Compensation Transformer for Brain...	27	Experimental	20	Python
23	rezazad68/TMUnet Contextual Attention Network: Transformer Meets U-Net	25	Experimental	95	Jupyter Notebook
24	xmindflow/deformableLKA [WACV 2024] Beyond Self-Attention: Deformable Large Kernel Attention for...	24	Experimental	259	Python
25	marqinhos/MedicalLiverSegmentationToolKit Medical Toolkit for Liver Volume Segmentation	24	Experimental	2	Python
26	ynes99/BraTS_Segmentation Segmentation of brain tumors (Glioma) in MRIs using Meta's model SAM...	24	Experimental	3	Jupyter Notebook
27	LankeSathwik7/Urban-Maintenance-Scout AI-powered infrastructure monitoring system that automatically detects and...	24	Experimental	1	Python
28	OSUPCVLab/MobileUNETR Official Implementation of MobileUNETR: A Lightweight End-To-End Hybrid...	23	Experimental	61	Python
29	pranavsinghps1/CASS Official PyTorch implementation of CASS, from the following paper: CASS:...	23	Experimental	20	Jupyter Notebook
30	pavaris-pm/artery-segmentation this repository is the part of Guided Ultrasound Image Segmentation project...	22	Experimental	1	Jupyter Notebook
31	rekalantar/MedSegmentAnything_SAM_LungCT The code to finetune SAM with bounding box prompt for segmentation of the lungs on CT	20	Experimental	36	Jupyter Notebook
32	isaaccorley/segmenter-pytorch PyTorch implementation of "Segmenter: Transformer for Semantic Segmentation"...	20	Experimental	18	Python
33	maggiesong7/FullyAttentional Fully Attentional Network for Semantic Segmentation [AAAI 2022]	20	Experimental	25	Python
34	GhTara/Dose_Prediction A Cascade Transformer-based Model for 3D Dose Distribution Prediction in...	20	Experimental	30	Python
35	CeMOS-IS/GenFormer [ICPR 2024] Official repository of the paper "GenFormer - Generated Images...	20	Experimental	14	Python
36	FlorinAndrei/segmentation_click_train Train an off-the-shelf image segmentation model to respond to user feedback	19	Experimental	5	Jupyter Notebook
37	csiro-robotics/FactoFormer [IEEE T-GRS 2024] The official repository for Journal Article “FactoFormer:...	19	Experimental	22	Python
38	Mr-TalhaIlyas/segformer PyTorch Implementation of SegFormer: Simple and Efficient Design for...	18	Experimental	7	Python
39	Saharsh1005/hubmap-kaggle-competition Binary segmentation of multi organ tissue units while implementing latest...	16	Experimental	4	Python
40	PhucNDA/OE-3DIS Open-Ended 3D Point Cloud Instance Segmentation (ICCV'25 - OpenSUN3D)	15	Experimental	5	Python
41	givkashi/Awesome-unet-like-transformers Awesome UNet with Transformer	13	Experimental	69	—
42	Spectrewolf8/UNET-50-aerial-image-road-segmentation-xp A U-Net-50 model for segmenting road networks in aerial images. Trained on...	12	Experimental	4	Jupyter Notebook
43	mltraore/CompSegNet CompSegNet: An enhanced U-shaped architecture for nuclei segmentation in H&E...	12	Experimental	4	Python
44	techthumb1/Image-Based-Diagnostic-Assistant AI powered Image-Based application for detecting and predicting disease and...	12	Experimental	1	Jupyter Notebook
45	puneetkakkar/road-damage-detection An application for automatic road damage assessment using semantic...	12	Experimental	3	Python
46	shreyanshxt/Mlunet-Brain-Tumor-Segmentation A deep learning–based brain tumor detection framework for MRI scans using an...	12	Experimental	1	Jupyter Notebook
47	maxboels/Surgical-Phase-Recognition Collated a list of useful open-access work related to surgical phase...	12	Experimental	20	—
48	MHosseinHashemi/NBML_BrTD Implementation of "Realism in action: anomaly-aware diagnosis of brain...	11	Experimental	—	Jupyter Notebook
49	sAI-2025/EfficientPS-Med-ConvNeXt-Based-Panoptic-Segmentation-for-Healthcare-Imaging Deep learning project using EfficientPS for panoptic segmentation on medical...	11	Experimental	—	Jupyter Notebook
50	usama13o/SwinCup SwinCup Pytorch implementation of SwinCup: Cascaded Swin Transformer for...	11	Experimental	—	Python
51	DivyenduDutta/NanoDefectNet End-to-end deep learning app for detecting defects in semiconductor wafermaps	11	Experimental	—	Python
52	KaranAnchan/Unetr_3D_Abdomen_Segmentation Abdomen 3D Segmentation Using UNETR: Tool for segmenting abdominal organs...	11	Experimental	2	Python
53	Jacopo00811/segment-like-a-robot Project for the course 02501 Advanced Deep Learning in Computer Vision Spring 25 DTU	11	Experimental	—	Python