Medical Imaging Reconstruction ML Frameworks

Deep learning frameworks and pipelines for reconstructing medical images from undersampled or low-dose sensor data (MRI, CT, ultrasound, cryo-EM). Includes physics-informed methods, learned optimization, and domain-specific denoising. Does NOT include general image denoising, medical diagnosis systems, or non-reconstruction medical AI applications.

There are 43 medical imaging reconstruction frameworks tracked. 9 score above 50 (established tier). The highest-rated is ProjectNeura/MIPCandy at 69/100 with 245 stars and 574 monthly downloads.

Get all 43 projects as JSON

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#	Framework	Score	Tier	Stars	Language
1	ProjectNeura/MIPCandy Build a complete experiment pipeline for your PyTorch MIP model in 10 seconds.	69	Established	245	Python
2	canlab/CanlabCore Core tools required for running Canlab Matlab toolboxes. The heart of this...	62	Established	165	MATLAB
3	MPI-Dortmund/tomotwin-cryoet cryo-ET particle picking by representation and metric learning	61	Established	42	Python
4	tbepler/topaz Pipeline for particle picking in cryo-electron microscopy images using...	59	Established	208	Jupyter Notebook
5	bioimage-io/core-bioimage-io-python Python libraries for loading, running and packaging bioimage.io models	55	Established	35	Jupyter Notebook
6	sunhongfu/deepMRI MRI reconstruction (e.g., QSM) using deep learning methods	54	Established	38	MATLAB
7	royerlab/cytoself Self-supervised models for encoding protein localization patterns from...	54	Established	82	Python
8	janelia-cellmap/cellmap-data Utility for loading CellMap data for machine learning training, utilizing...	53	Established	7	Python
9	eeulig/ldct-benchmark A benchmark for deep learning-based low dose CT image denoising	50	Established	39	Python
10	chanzuckerberg/octopi Search for Protein 3D Coordinates in CryoET Tomograms	49	Emerging	8	Jupyter Notebook
11	janelia-cellmap/cellmap-models Repository of model architectures and network weights used for CellMap segmentations.	46	Emerging	13	Python
12	CAMMA-public/SelfSupSurg Official repository for "Dissecting Self-Supervised Learning Methods for...	45	Emerging	44	Python
13	llnl/LEAP comprehensive library of 3D transmission Computed Tomography (CT) algorithms...	44	Emerging	220	Cuda
14	CAMMA-public/rendezvous A transformer-inspired neural network for surgical action triplet...	42	Emerging	32	Python
15	lab-midas/ismrm-moco-workshop Hands-on examples for motion estimation and correction in MRI	42	Emerging	48	MATLAB
16	ZauggGroup/DeePiCt Pipeline for the automatic detection and segmentation of particles and...	41	Emerging	41	Python
17	IsoNet-cryoET/spIsoNet Overcoming the preferred orientation problem in cryoEM with self-supervised...	40	Emerging	35	Python
18	dlopezg/mvpalab An easy to use decoding toolbox for Matlab users.	38	Emerging	30	MATLAB
19	cell-observatory/cell_observatory_platform Training backend for Cell Observatory models	38	Emerging	3	Python
20	CAMMA-public/cholect50 A repository for surgical action triplet dataset. Data are videos of...	37	Emerging	76	Python
21	sidgautam95/adaptive-sampling-mri-suno Code for reproducing results for the paper: "Scan-Adaptive MRI Undersampling...	36	Emerging	6	Python
22	IsoNet-cryoET/IsoNet2 IsoNet at higher resolution	36	Emerging	26	Python
23	nadeemlab/Physics-ArX Physics-based data augmentation library for quantifying CT and CBCT images...	36	Emerging	72	Python
24	nipreps/eddymotion Open-source eddy-current and head-motion correction for dMRI.	34	Emerging	20	Python
25	BennyZhang-Codes/LDCT-denoising-with-Deep-Learning-and-Dicom-Viewer Low-dose CT image denoising model based on deep learning & CT image Viewer.	33	Emerging	41	Python
26	janelia-cellmap/cellmap-flow Utility for visualizing results on the fly in neuroglancer	32	Emerging	7	Python
27	PolyRocketMatt/diet4CoLA Displacement and Instantaneous Edge Tracking for Cortical Laser Ablation experiments	32	Emerging	3	Jupyter Notebook
28	pnnl/pychip_gui pyCHIP is a tool for segmentation and feature classification in transmission...	30	Emerging	20	HTML
29	sidgautam95/dynamic-tomography-with-learned-robust-features Code for reproducing results for the paper: "Robust Features for Scatter...	26	Experimental	4	Python
30	MLI-lab/ProPicker Prompt-based segmentation and fine-tuning for data-efficient and flexible...	26	Experimental	11	Jupyter Notebook
31	zs1314/OCTAMamba 【ICASSP2025 Oral】Offical Pytorch Code for "OCTAMamba: A State-Space Model...	26	Experimental	34	Python
32	jacobinsilico/ReconstructUS End-to-end pipeline for ultrasound image reconstruction using DAS, deep...	25	Experimental	6	Jupyter Notebook
33	f78bono/deep-cine-cardiac-mri Exploiting temporal redundancies of multi-coil cine cardiac data for MRI...	24	Experimental	18	Jupyter Notebook
34	xjzhang2365/3D-Reconstruction-Low-Dose-Imaging Physics-informed 3D reconstruction from low-dose 2D images. Novel...	23	Experimental	1	Jupyter Notebook
35	rlpddejong/SurgeNetDINO [MIDL 2026] - Official repo for the paper: "SurgeNetDINO: Towards Effective...	23	Experimental	7	Python
36	sidgautam95/rbicd-dynamic-mri-sampling Code for reproducing results for the paper: "Scan-Adaptive Dynamic MRI...	23	Experimental	1	—
37	EngrEeshaKhan/CZII-CryoET-Object-Identification This project builds machine learning models to automatically detect and...	17	Experimental	2	Jupyter Notebook
38	hdkhunti/pet-gmf Generalized Mapping Function for PET image reconstruction	17	Experimental	2	Jupyter Notebook
39	SamuelSchmidgall/GSViT Code repository for paper: "General surgery vision transformer: A video...	16	Experimental	46	Python
40	MathijsVanhaverbeke/fastMRI-hybrid-modelling Investigate the influence of hybrid modelling on deep learning-based MRI...	15	Experimental	2	Jupyter Notebook
41	jiayangshi/LoDoInd Code for paper "LoDoInd: Introducing A Benchmark Low-dose Industrial CT...	12	Experimental	13	Python
42	jhernandezga/CT_Reconstruction_LEARN_paper Implementation of the paper LEARN: Learned Experts’ Assessment-based...	12	Experimental	19	Python
43	Pei-mao/KeyMorph_Medical_Image This repository refers to keymorph	11	Experimental	2	Python