Medical Image Registration ML Frameworks

Deep learning frameworks and methods for aligning medical images across modalities and time points, with focus on deformable registration, uncertainty quantification, and foundation models. Does NOT include general image super-resolution, denoising, or restoration without registration components.

There are 29 medical image registration frameworks tracked. 1 score above 70 (verified tier). The highest-rated is voxelmorph/voxelmorph at 70/100 with 2,661 stars.

Get all 29 projects as JSON

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

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#	Framework	Score	Tier	Stars	Language
1	voxelmorph/voxelmorph Unsupervised Learning for Image Registration	70	Verified	2,661	Python
2	uncbiag/uniGradICON uniGradICON: A Foundation Model for Medical Image Registration (MICCAI 2024)	63	Established	212	Python
3	junyuchen245/TransMorph_Transformer_for_Medical_Image_Registration TransMorph: Transformer for Unsupervised Medical Image Registration (PyTorch)	43	Emerging	607	Python
4	DeepRegNet/DeepReg Medical image registration using deep learning	39	Emerging	616	Python
5	MLI-lab/DeepDeWedge Self-supervised deep learning for denoising and missing wedge reconstruction...	37	Emerging	49	Jupyter Notebook
6	AgamChopra/TorchRegister Common 2D and 3D image registration methods such as rigid, affine, and flow...	35	Emerging	25	Python
7	guopengf/ReconFormer ReconFormer: Accelerated MRI Reconstruction Using Recurrent Transformer	34	Emerging	79	Python
8	guopengf/FL-MRCM Multi-institutional Collaborations for Improving Deep Learning-based...	34	Emerging	46	Python
9	ayanglab/SwinMR This is the official implementation of our proposed SwinMR	32	Emerging	77	Python
10	konst-int-i/healnet Multimodal fusion for heterogeneous biomedical data. NeurIPS 2024.	32	Emerging	106	Python
11	MungoMeng/Registration-NICE-Trans [MICCAI2023] NICE-Trans: Non-iterative Coarse-to-fine Transformer Networks...	30	Emerging	27	Python
12	lok-18/GeSeNet IEEE TNNLS \| GeSeNet: A General Semantic-guided Network with Couple Mask...	30	Emerging	21	Python
13	lab-midas/GMARAFT Non-rigid image registration for accelerated MR imaging	29	Experimental	19	Python
14	jianqingzheng/res_aligner_net [Medical Image Analysis] Residual Aligner-based Network (RAN): Motion-Aware...	29	Experimental	34	Python
15	Computer-Assisted-Clinical-Medicine/Networks_for_Affine_Medical_Image_Registration Affine medical image registration using deep learning	29	Experimental	22	Python
16	ayanglab/SwinGANMR Official implementation of SwinGANMR	28	Experimental	17	Python
17	simonZhou86/dilran An attention-based Multi-Scale Feature Learning Framework for Multimodal...	28	Experimental	37	Python
18	MungoMeng/Registration-CorrMLP [CVPR2024 🏆 Best Paper Candidate] CorrMLP: Correlation-aware MLP-based...	26	Experimental	87	Python
19	cxm12/UNiFMIR Pretraining a foundation model for generalizable fluorescence...	26	Experimental	65	Python
20	Arturoprotective670/DIRV-NET 🖼️ Enable precise 2D/3D deformable image registration for medical...	24	Experimental	2	Jupyter Notebook
21	longw010/Low_Field_Enhancement The official implementation of `Quantitative Ischemic Lesions of Portable...	24	Experimental	4	Jupyter Notebook
22	AIRLABkhu/SiNGER Official implementation of SiNGER (ICLR 2026).	23	Experimental	5	Python
23	B9Kang/MD-S2S-Multidimensional-Self2Self [MRM 2024] Self-supervised learning for denoising of multidimensional MRI data	23	Experimental	8	Jupyter Notebook
24	icon-lab/FedGAT Official implementation of FedGAT: Generative Autoregressive Transformers...	22	Experimental	20	Python
25	MungoMeng/Registration-AutoFuse AutoFuse: Automatic Fusion Networks for Unsupervised and Semi-supervised...	20	Experimental	13	Python
26	AllenInstitute/deep_ccf_registration Arbitrary modality registration to CCFv3 using deep learning	16	Experimental	2	Jupyter Notebook
27	kamruleee51/Feedback_DLIR A spatial feedback attention module (FBA) to enhance unsupervised 3D DLIR	15	Experimental	6	Jupyter Notebook
28	junyuchen245/Correlation_Ratio Correlation Ratio for multi- and mono-modal image registration (PyTorch)	13	Experimental	8	Python
29	icai-uma/SRCNN3D_RegSS Deep learning-based SR of 3D MRI by Regularly Spaced Shifting	11	Experimental	2	MATLAB

Comparisons in this category

voxelmorph and TransMorph_Transformer_for_Medical_Image_Registration (70 vs 43) SwinMR and SwinGANMR (32 vs 28)