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 81/100 with 11,398 stars. 2 of the top 10 are actively maintained.

Get all 53 projects as JSON

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#	Model	Score	Tier	Stars	Language
1	qubvel-org/segmentation_models.pytorch Semantic segmentation models with 500+ pretrained convolutional and...	81	Verified	11,398	Python
2	tue-mps/eomt [CVPR 2025 Highlight] Official code and models for Encoder-only Mask...	56	Established	548	Jupyter Notebook
3	OSUPCVLab/SegFormer3D Official Implementation of SegFormer3D: an Efficient Transformer for 3D...	54	Established	205	Python
4	jeya-maria-jose/Medical-Transformer Official Pytorch Code for "Medical Transformer: Gated Axial-Attention for...	51	Established	857	Python
5	davidiommi/Pytorch--3D-Medical-Images-Segmentation--SALMON Segmentation deep learning ALgorithm based on MONai toolbox: single and...	46	Emerging	124	Python
6	lambdavi/SatDrive-SegFL MLDL '23 Project: Federated Learning and Semantic Segmentation for...	45	Emerging	7	Python
7	snap-research/EfficientFormer EfficientFormerV2 [ICCV 2023] & EfficientFormer [NeurIPs 2022]	44	Emerging	1,109	Python
8	MIC-DKFZ/MedNeXt [MICCAI 2023] MedNeXt is a fully ConvNeXt architecture for 3D medical image...	44	Emerging	487	Python
9	oValach/RailSafeNet Repository of the paper: RailSafeNet: Visual Scene Understanding for Tram Safety	43	Emerging	6	Python
10	Kartik-3004/SegFace [AAAI 25] SegFace: Face Segmentation of Long-tail classes	43	Emerging	100	Python
11	amirhossein-kz/HiFormer HiFormer: Hierarchical Multi-scale Representations Using Transformers for...	43	Emerging	144	Jupyter Notebook
12	amazon-science/unified-ept A Unified Efficient Pyramid Transformer for Semantic Segmentation, ICCVW 2021	40	Emerging	31	Python
13	Omid-Nejati/BEFUnet A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation	40	Emerging	73	Python
14	biswassanket/DocSegTr A Bottom-Up Instance Segmentation Strategy for segmenting document instances...	38	Emerging	59	Python
15	sotiraslab/AgileFormer This the repo for the paper tiltled "AgileFormer: Spatially Agile...	38	Emerging	81	Python
16	xmindflow/MS-Former [MIDL 2023] MS-Former: Multi-Scale Self-Guided Transformer for Medical Image...	37	Emerging	16	Jupyter Notebook
17	DebeshJha/TransNetR Official implementation of TransNetR: Transformer-based Residual Network for...	37	Emerging	24	Python
18	deep-diver/segformer-tf-transformers This repository demonstrates how to use TensorFlow based SegFormer model in...	35	Emerging	30	Jupyter Notebook
19	xmindflow/MSA-2Net [BMVC 2024] Official repository of the paper titled "MSA^2 Net: Multi-scale...	35	Emerging	70	Python
20	rezazad68/transdeeplab TransDeepLab: Convolution-Free Transformer-based DeepLab v3+ for Medical...	34	Emerging	88	Python
21	xmindflow/MMCFormer [MIDL 2023] MMCFormer: Missing Modality Compensation Transformer for Brain...	34	Emerging	20	Python
22	xmindflow/SSCT [ICCV 2023] Self-supervised Semantic Segmentation: Consistency over Transformation	32	Emerging	26	Jupyter Notebook
23	rezazad68/TMUnet Contextual Attention Network: Transformer Meets U-Net	32	Emerging	95	Jupyter Notebook
24	xmindflow/deformableLKA [WACV 2024] Beyond Self-Attention: Deformable Large Kernel Attention for...	31	Emerging	259	Python
25	marqinhos/MedicalLiverSegmentationToolKit Medical Toolkit for Liver Volume Segmentation	31	Emerging	2	Python
26	ynes99/BraTS_Segmentation Segmentation of brain tumors (Glioma) in MRIs using Meta's model SAM...	31	Emerging	3	Jupyter Notebook
27	OSUPCVLab/MobileUNETR Official Implementation of MobileUNETR: A Lightweight End-To-End Hybrid...	30	Emerging	61	Python
28	pranavsinghps1/CASS Official PyTorch implementation of CASS, from the following paper: CASS:...	30	Emerging	20	Jupyter Notebook
29	rekalantar/MedSegmentAnything_SAM_LungCT The code to finetune SAM with bounding box prompt for segmentation of the lungs on CT	27	Experimental	36	Jupyter Notebook
30	CeMOS-IS/GenFormer [ICPR 2024] Official repository of the paper "GenFormer - Generated Images...	27	Experimental	14	Python
31	maggiesong7/FullyAttentional Fully Attentional Network for Semantic Segmentation [AAAI 2022]	27	Experimental	25	Python
32	isaaccorley/segmenter-pytorch PyTorch implementation of "Segmenter: Transformer for Semantic Segmentation"...	27	Experimental	18	Python
33	GhTara/Dose_Prediction A Cascade Transformer-based Model for 3D Dose Distribution Prediction in...	27	Experimental	30	Python
34	csiro-robotics/FactoFormer [IEEE T-GRS 2024] The official repository for Journal Article “FactoFormer:...	26	Experimental	22	Python
35	FlorinAndrei/segmentation_click_train Train an off-the-shelf image segmentation model to respond to user feedback	26	Experimental	5	Jupyter Notebook
36	Mr-TalhaIlyas/segformer PyTorch Implementation of SegFormer: Simple and Efficient Design for...	25	Experimental	7	Python
37	givkashi/Awesome-unet-like-transformers Awesome UNet with Transformer	20	Experimental	69	—
38	mltraore/CompSegNet CompSegNet: An enhanced U-shaped architecture for nuclei segmentation in H&E...	19	Experimental	4	Python
39	maxboels/Surgical-Phase-Recognition Collated a list of useful open-access work related to surgical phase...	19	Experimental	20	—
40	puneetkakkar/road-damage-detection An application for automatic road damage assessment using semantic...	19	Experimental	3	Python
41	shreyanshxt/Mlunet-Brain-Tumor-Segmentation A deep learning–based brain tumor detection framework for MRI scans using an...	18	Experimental	1	Jupyter Notebook
42	nmn-pandey/brain-tumour-segmentation Code for automated brain tumor segmentation from MRI scans using CNNs with...	14	Experimental	17	Python
43	DivyenduDutta/NanoDefectNet End-to-end deep learning app for detecting defects in semiconductor wafermaps	13	Experimental	—	Python
44	usama13o/SwinCup SwinCup Pytorch implementation of SwinCup: Cascaded Swin Transformer for...	13	Experimental	—	Python
45	MHosseinHashemi/NBML_BrTD Implementation of "Realism in action: anomaly-aware diagnosis of brain...	13	Experimental	—	Jupyter Notebook
46	RSandAI/HistRoadSegformer Official implementation of "Automatic Road Extraction from Historical Maps...	12	Experimental	6	Jupyter Notebook
47	abdulvahapmutlu/chest-xray-segmentation A segmentation project that leverages a Swin Transformer-based model to...	11	Experimental	—	Jupyter Notebook
48	Y1D1R/UNETR-2D-Medical-Image-Segmentation From-scratch PyTorch implementation of a 2D variant of the UNETR (U-Net with...	11	Experimental	4	Python
49	Piero24/lossFuncition-4SN This research will show an innovative method useful in the segmentation of...	11	Experimental	—	Python
50	DiTo97/neural-binarization toolkit for efficient semantic document image binarization (DIB)	11	Experimental	—	Jupyter Notebook
51	maxkokot/Semantic-Segmentation-of-Drone-Images Semantic Segmentation of Drone Images With Hugging Face and MLflow	11	Experimental	3	Python
52	iambankaratharva/SegFormer-B0 Implementation of transformer based SegFormer-B0 from scratch for semantic...	11	Experimental	—	Jupyter Notebook
53	Astronauts-Making-Limoncello/Distillo-Ergo-Sum Transformer to CNN heterogeneous knowledge distillation in medical image...	10	Experimental	2	Python