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A collection of MRI software projects for simulation, analysis, processing, QA, visualisation and reconstruction.

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MRI Tools

license

A collection of free and open-source software software tools for use in MRI. Free is meant as in free beer (gratis) and freedom (libre).

To add a project, add the project url to the urls.toml file.

Table of Contents

Summary

Repository Description Stars Forks Last Updated
MONAI AI Toolkit for Healthcare Imaging 6119 1136 2025-02-17
torchio Medical imaging processing for deep learning. 2127 241 2025-02-17
Slicer Multi-platform, free open source software for visualization and image computing. 1828 578 2025-02-17
MedicalZooPytorch A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation 1777 298 2025-02-16
fastMRI A large-scale dataset of both raw MRI measurements and clinical MRI images. 1384 384 2025-02-14
medicaldetectiontoolkit The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images. 1317 296 2025-02-15
nilearn Machine learning for NeuroImaging in Python 1239 618 2025-02-17
deepmedic Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans 1039 347 2025-02-08
SimpleITK SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages. 931 207 2025-02-14
medicaltorch A medical imaging framework for Pytorch 861 128 2025-02-07
nipype Workflows and interfaces for neuroimaging packages 761 532 2025-02-14
nibabel Python package to access a cacophony of neuro-imaging file formats 677 260 2025-02-16
freesurfer Neuroimaging analysis and visualization suite 641 254 2025-02-17
SynthSeg Contrast-agnostic segmentation of MRI scans 409 104 2025-02-17
brainchop Brainchop: In-browser 3D MRI rendering and segmentation 405 46 2025-02-16
nipy Neuroimaging in Python FMRI analysis package 385 145 2025-01-22
mriviewer MRI Viewer is a high performance web tool for advanced 2-D and 3-D medical visualizations. 340 107 2025-02-06
intensity-normalization normalize the intensities of various MR image modalities 323 58 2025-02-17
PyMVPA MultiVariate Pattern Analysis in Python 316 136 2025-02-12
mriqc Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain 310 132 2025-02-10
bart BART: Toolbox for Computational Magnetic Resonance Imaging 309 164 2025-02-17
mrtrix3 MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density 299 184 2025-02-14
direct Deep learning framework for MRI reconstruction 254 43 2025-02-14
nitime Timeseries analysis for neuroscience data 244 83 2025-01-31
gadgetron Gadgetron - Medical Image Reconstruction Framework 241 162 2025-02-12
TractSeg Automatic White Matter Bundle Segmentation 233 74 2024-12-11
spinalcordtoolbox Comprehensive and open-source library of analysis tools for MRI of the spinal cord. 216 103 2025-02-17
brainGraph Graph theory analysis of brain MRI data 188 53 2025-02-10
clinicadl Framework for the reproducible processing of neuroimaging data with deep learning methods 166 57 2025-02-14
NiftyMIC NiftyMIC is a research-focused toolkit for motion correction and volumetric image reconstruction of 2D ultra-fast MRI. 145 35 2025-01-17
qsiprep Preprocessing of diffusion MRI 145 58 2025-02-03
mritopng A simple python module to make it easy to batch convert DICOM files to PNG images. 143 50 2025-01-20
smriprep Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools) 136 40 2025-01-21
pypulseq Pulseq in Python 135 69 2025-02-13
KomaMRI.jl Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development. 127 21 2025-02-16
openMorph Curated list of open-access databases with human structural MRI data 127 38 2025-01-30
gif_your_nifti How to create fancy GIFs from an MRI brain image 121 35 2025-01-26
pydeface defacing utility for MRI images 114 42 2025-02-13
ismrmrd ISMRM Raw Data Format 113 88 2025-02-07
quickNAT_pytorch PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty 103 37 2024-12-27
MRQy RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data. 96 30 2025-02-02
MRIReco.jl Julia Package for MRI Reconstruction 88 22 2025-02-17
BraTS-Toolkit Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript. 81 12 2025-01-25
NeSVoR NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction. 76 17 2025-02-08
NIfTI.jl Julia module for reading/writing NIfTI MRI files 74 34 2024-12-27
virtual-scanner An end-to-end hybrid MR simulator/console 64 18 2025-02-07
SIRF Main repository for the CCP SynerBI software 64 29 2025-02-17
QUIT A set of tools for processing Quantitative MR Images 61 21 2024-11-22
SVRTK MIRTK based SVR reconstruction 50 8 2025-02-17
tensorflow-mri A Library of TensorFlow Operators for Computational MRI 40 3 2025-02-10
DCEMRI.jl DCE MRI analysis in Julia 38 16 2025-01-13
DECAES.jl DEcomposition and Component Analysis of Exponential Signals (DECAES) - a Julia implementation of the UBC Myelin Water Imaging (MWI) toolbox for computing voxelwise T2-distributions of multi spin-echo MRI images. 33 5 2024-11-20
popeye A population receptive field estimation tool 33 14 2024-10-09
mialsuperresolutiontoolkit The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework. 28 12 2024-12-06
ukftractography None 26 27 2025-02-13
DL-DiReCT DL+DiReCT - Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation 26 5 2025-01-15
MriResearchTools.jl Specialized tools for MRI 26 8 2025-02-09
disimpy Massively parallel Monte Carlo diffusion MR simulator written in Python. 25 9 2024-12-19
nlsam The reference implementation for the Non Local Spatial and Angular Matching (NLSAM) denoising algorithm for diffusion MRI 24 11 2024-10-26
hazen Quality assurance framework for Magnetic Resonance Imaging 24 12 2025-02-13
MRIgeneralizedBloch.jl None 19 3 2025-02-14
gropt A toolbox for MRI gradient design 18 13 2024-12-17
flow4D Python code for processing 4D flow dicoms and write velocity profiles for CFD simulations. 18 5 2024-09-10
pyCoilGen Magnetic Field Coil Generator for Python, ported from CoilGen 16 7 2025-02-13
sHDR HDR-MRI Algorithms from "Local contrast-enhanced MR images via high dynamic range processing" published in MRM 16 0 2024-11-29
dafne Dafne (Deep Anatomical Federated Network) is a collaborative platform to annotate MRI images and train machine learning models without your data ever leaving your machine. 16 6 2025-01-25
eptlib EPTlib - An open-source, extensible C++ library of electric properties tomography methods 14 2 2025-02-15
scanhub ScanHub combines multimodal data acquisition and complex data processing in one cloud platform. 13 2 2025-02-05
PowerGrid GPU accelerated non-Cartesian magnetic resonance imaging reconstruction toolkit 13 13 2024-12-13
ukat UKRIN Kidney Analysis Toolbox 12 4 2024-10-30
MyoQMRI Quantitative methods for muscle MRI 12 3 2024-09-28
mrQA mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance 11 6 2025-01-09
AFFIRM A deep recursive fetal motion estimation and correction framework based on slice and volume affinity fusion 9 1 2023-11-17
vespa Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis 7 6 2024-12-18
CoSimPy Python electromagnetic cosimulation library 6 3 2024-08-15
fetal-IQA Image quality assessment for fetal MRI 6 0 2024-10-12
dwybss Blind Source Separation of diffusion MRI for free-water elimination and tissue characterization. 2 1 2019-08-01
madym_python Mirror of python wrappers to Madym hosted on Manchester QBI GitLab project 0 0 2021-11-22
MRDQED A Magnetic Resonance Data Quality Evaluation Dashboard 0 1 2021-01-31
MRISafety.jl MRI safety checks 0 0 2025-01-04

Stats

  • Total repos: 80
  • Languages:
Language Count
python 47
c++ 12
julia 7
jupyter notebook 4
c 3
r 2
javascript 2
  • Tags:
Tag Count
mri 25
medical-imaging 17
python 16
deep-learning 16
neuroimaging 11
pytorch 10
machine-learning 9
segmentation 7
medical-image-processing 7
brain-imaging 6
quality-control 5
image-processing 4
medical-image-computing 4
diffusion-mri 4
convolutional-neural-networks 4
mri-images 4
itk 3
quality-assurance 3
fmri 3
magnetic-resonance-imaging 2
medical-physics 2
simulation 2
c-plus-plus 2
registration 2
tractography 2
image-reconstruction 2
r 2
tensorflow 2
image-registration 2
fastmri-challenge 2
mri-reconstruction 2
super-resolution 2
fetal 2
bids 2
julia 2
nifti 2
computer-vision 2
dicom 2
medical-images 2
brain-connectivity 2
neuroscience 2
medical-image-analysis 2
qa 2
  • Licenses:
Licence Count
other 23
mit license 17
apache license 2.0 15
bsd 3-clause "new" or "revised" license 8
gnu general public license v3.0 6
gnu affero general public license v3.0 3
none 3
gnu lesser general public license v3.0 2
mozilla public license 2.0 2

Tags

Mri

  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14
  • Neuroimaging analysis and visualization suite
  • License: Other
  • Languages: C++
  • Tags: freesurfer, lcn, mri, neuroimaging
  • Forks: 254
  • Issues: 20
  • Watchers: 641
  • Last updated: 2025-02-17
  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16
  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17
  • Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
  • License: Apache License 2.0
  • Languages: Python
  • Tags: machine-learning, mri, neuroimaging, quality-control, quality-reporter
  • Forks: 132
  • Issues: 59
  • Watchers: 310
  • Last updated: 2025-02-10
  • BART: Toolbox for Computational Magnetic Resonance Imaging
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C
  • Tags: bart-toolbox, compressed-sensing, computational-imaging, deep-learning, iterative-methods, mri
  • Forks: 164
  • Issues: 22
  • Watchers: 309
  • Last updated: 2025-02-17
  • Comprehensive and open-source library of analysis tools for MRI of the spinal cord.
  • License: GNU Lesser General Public License v3.0
  • Languages: Python
  • Tags: mri, neuroimage, python, spinalcord
  • Forks: 103
  • Issues: 365
  • Watchers: 216
  • Last updated: 2025-02-17
  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10
  • Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, image-registration, image-segmentation, mri, structural-mri, surface-reconstruction
  • Forks: 40
  • Issues: 63
  • Watchers: 136
  • Last updated: 2025-01-21
  • Pulseq in Python
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: mri, mri-sequences, pulse-sequences, pulseq, python
  • Forks: 69
  • Issues: 15
  • Watchers: 135
  • Last updated: 2025-02-13
  • Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
  • License: MIT License
  • Languages: Julia
  • Tags: cardiac, diffusion, diffusion-mri, gpu-acceleration, mri, simulation
  • Forks: 21
  • Issues: 89
  • Watchers: 127
  • Last updated: 2025-02-16
  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: glioblastoma, glioma, medical-imaging, mri, segmentation
  • Forks: 12
  • Issues: 8
  • Watchers: 81
  • Last updated: 2025-01-25
  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08
  • Julia module for reading/writing NIfTI MRI files
  • License: Other
  • Languages: Julia
  • Tags: fmri, julia, mri, mri-images, nifti
  • Forks: 34
  • Issues: 32
  • Watchers: 74
  • Last updated: 2024-12-27
  • An end-to-end hybrid MR simulator/console
  • License: GNU Affero General Public License v3.0
  • Languages: Jupyter Notebook
  • Tags: mri
  • Forks: 18
  • Issues: 14
  • Watchers: 64
  • Last updated: 2025-02-07
  • MIRTK based SVR reconstruction
  • License: Apache License 2.0
  • Languages: C++
  • Tags: fetal, mri, reconstruction, retrospecitve, slice-to-volume
  • Forks: 8
  • Issues: 4
  • Watchers: 50
  • Last updated: 2025-02-17
  • A Library of TensorFlow Operators for Computational MRI
  • License: Apache License 2.0
  • Languages: Jupyter Notebook
  • Tags: machine-learning, magnetic-resonance-imaging, ml, mri, python, tensorflow
  • Forks: 3
  • Issues: 8
  • Watchers: 40
  • Last updated: 2025-02-10
  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06
  • DL+DiReCT - Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: cortical-thickness, deep-learning, morphometry, mri
  • Forks: 5
  • Issues: 4
  • Watchers: 26
  • Last updated: 2025-01-15
  • Specialized tools for MRI
  • License: MIT License
  • Languages: Julia
  • Tags: mri, mri-images
  • Forks: 8
  • Issues: 2
  • Watchers: 26
  • Last updated: 2025-02-09
  • Quality assurance framework for Magnetic Resonance Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, mri, mri-phantoms, python, qa, quality-assurance
  • Forks: 12
  • Issues: 49
  • Watchers: 24
  • Last updated: 2025-02-13
  • Magnetic Field Coil Generator for Python, ported from CoilGen
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: magnetic-field-solver, magnetic-resonance-imaging, medical-physics, mri, nmr, physics
  • Forks: 7
  • Issues: 3
  • Watchers: 16
  • Last updated: 2025-02-13
  • HDR-MRI Algorithms from "Local contrast-enhanced MR images via high dynamic range processing" published in MRM
  • License: Other
  • Languages: C++
  • Tags: fusion, hdr, image, medical-image-processing, medical-imaging, mri
  • Forks: 0
  • Issues: 0
  • Watchers: 16
  • Last updated: 2024-11-29
  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Medical-Imaging

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16
  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14
  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15
  • Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, neural-networks
  • Forks: 347
  • Issues: 23
  • Watchers: 1039
  • Last updated: 2025-02-08
  • A medical imaging framework for Pytorch
  • License: Apache License 2.0
  • Languages: Python
  • Tags: computer-vision, deep-learning, machine-learning, medical-imaging, python, pytorch
  • Forks: 128
  • Issues: 17
  • Watchers: 861
  • Last updated: 2025-02-07
  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16
  • Deep learning framework for MRI reconstruction
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, fastmri-challenge, inverse-problems, medical-imaging, mri-reconstruction, pytorch
  • Forks: 43
  • Issues: 3
  • Watchers: 254
  • Last updated: 2025-02-14
  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: glioblastoma, glioma, medical-imaging, mri, segmentation
  • Forks: 12
  • Issues: 8
  • Watchers: 81
  • Last updated: 2025-01-25
  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08
  • Main repository for the CCP SynerBI software
  • License: Other
  • Languages: C++
  • Tags: image-reconstruction, medical-imaging, pet-mr
  • Forks: 29
  • Issues: 158
  • Watchers: 64
  • Last updated: 2025-02-17
  • DCE MRI analysis in Julia
  • License: Other
  • Languages: Julia
  • Tags: analysis, cancer-imaging-research, dce-mri, julia, mat-files, medical-image-processing, medical-imaging
  • Forks: 16
  • Issues: 5
  • Watchers: 38
  • Last updated: 2025-01-13
  • HDR-MRI Algorithms from "Local contrast-enhanced MR images via high dynamic range processing" published in MRM
  • License: Other
  • Languages: C++
  • Tags: fusion, hdr, image, medical-image-processing, medical-imaging, mri
  • Forks: 0
  • Issues: 0
  • Watchers: 16
  • Last updated: 2024-11-29
  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Python

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17
  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14
  • A medical imaging framework for Pytorch
  • License: Apache License 2.0
  • Languages: Python
  • Tags: computer-vision, deep-learning, machine-learning, medical-imaging, python, pytorch
  • Forks: 128
  • Issues: 17
  • Watchers: 861
  • Last updated: 2025-02-07
  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14
  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16
  • Comprehensive and open-source library of analysis tools for MRI of the spinal cord.
  • License: GNU Lesser General Public License v3.0
  • Languages: Python
  • Tags: mri, neuroimage, python, spinalcord
  • Forks: 103
  • Issues: 365
  • Watchers: 216
  • Last updated: 2025-02-17
  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14
  • A simple python module to make it easy to batch convert DICOM files to PNG images.
  • License: MIT License
  • Languages: Python
  • Tags: dicom, dicom-converter, dicom-images, medical, medical-images, png, python
  • Forks: 50
  • Issues: 5
  • Watchers: 143
  • Last updated: 2025-01-20
  • Pulseq in Python
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: mri, mri-sequences, pulse-sequences, pulseq, python
  • Forks: 69
  • Issues: 15
  • Watchers: 135
  • Last updated: 2025-02-13
  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • A Library of TensorFlow Operators for Computational MRI
  • License: Apache License 2.0
  • Languages: Jupyter Notebook
  • Tags: machine-learning, magnetic-resonance-imaging, ml, mri, python, tensorflow
  • Forks: 3
  • Issues: 8
  • Watchers: 40
  • Last updated: 2025-02-10
  • The reference implementation for the Non Local Spatial and Angular Matching (NLSAM) denoising algorithm for diffusion MRI
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: denoising-algorithm, diffusion-mri, machine-learning, python
  • Forks: 11
  • Issues: 7
  • Watchers: 24
  • Last updated: 2024-10-26
  • Quality assurance framework for Magnetic Resonance Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, mri, mri-phantoms, python, qa, quality-assurance
  • Forks: 12
  • Issues: 49
  • Watchers: 24
  • Last updated: 2025-02-13
  • Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis
  • License: Other
  • Languages: Python
  • Tags: fitting, mrs, python, rf-pulse, simulation, spectroscopy, wxpython
  • Forks: 6
  • Issues: 5
  • Watchers: 7
  • Last updated: 2024-12-18

Deep-Learning

  • AI Toolkit for Healthcare Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, healthcare-imaging, medical-image-computing, medical-image-processing, monai, python3, pytorch
  • Forks: 1136
  • Issues: 408
  • Watchers: 6119
  • Last updated: 2025-02-17
  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16
  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14
  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15
  • Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, neural-networks
  • Forks: 347
  • Issues: 23
  • Watchers: 1039
  • Last updated: 2025-02-08
  • A medical imaging framework for Pytorch
  • License: Apache License 2.0
  • Languages: Python
  • Tags: computer-vision, deep-learning, machine-learning, medical-imaging, python, pytorch
  • Forks: 128
  • Issues: 17
  • Watchers: 861
  • Last updated: 2025-02-07
  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16
  • BART: Toolbox for Computational Magnetic Resonance Imaging
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C
  • Tags: bart-toolbox, compressed-sensing, computational-imaging, deep-learning, iterative-methods, mri
  • Forks: 164
  • Issues: 22
  • Watchers: 309
  • Last updated: 2025-02-17
  • Deep learning framework for MRI reconstruction
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, fastmri-challenge, inverse-problems, medical-imaging, mri-reconstruction, pytorch
  • Forks: 43
  • Issues: 3
  • Watchers: 254
  • Last updated: 2025-02-14
  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08
  • DL+DiReCT - Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: cortical-thickness, deep-learning, morphometry, mri
  • Forks: 5
  • Issues: 4
  • Watchers: 26
  • Last updated: 2025-01-15
  • A deep recursive fetal motion estimation and correction framework based on slice and volume affinity fusion
  • License: MIT License
  • Languages: Python
  • Tags: deep-learning, fetus, motion
  • Forks: 1
  • Issues: 0
  • Watchers: 9
  • Last updated: 2023-11-17
  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Neuroimaging

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17
  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14
  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16
  • Neuroimaging analysis and visualization suite
  • License: Other
  • Languages: C++
  • Tags: freesurfer, lcn, mri, neuroimaging
  • Forks: 254
  • Issues: 20
  • Watchers: 641
  • Last updated: 2025-02-17
  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16
  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17
  • Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
  • License: Apache License 2.0
  • Languages: Python
  • Tags: machine-learning, mri, neuroimaging, quality-control, quality-reporter
  • Forks: 132
  • Issues: 59
  • Watchers: 310
  • Last updated: 2025-02-10
  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10
  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14
  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Pytorch

  • AI Toolkit for Healthcare Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, healthcare-imaging, medical-image-computing, medical-image-processing, monai, python3, pytorch
  • Forks: 1136
  • Issues: 408
  • Watchers: 6119
  • Last updated: 2025-02-17
  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16
  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14
  • A medical imaging framework for Pytorch
  • License: Apache License 2.0
  • Languages: Python
  • Tags: computer-vision, deep-learning, machine-learning, medical-imaging, python, pytorch
  • Forks: 128
  • Issues: 17
  • Watchers: 861
  • Last updated: 2025-02-07
  • Deep learning framework for MRI reconstruction
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, fastmri-challenge, inverse-problems, medical-imaging, mri-reconstruction, pytorch
  • Forks: 43
  • Issues: 3
  • Watchers: 254
  • Last updated: 2025-02-14
  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08
  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Machine-Learning

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17
  • Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, neural-networks
  • Forks: 347
  • Issues: 23
  • Watchers: 1039
  • Last updated: 2025-02-08
  • A medical imaging framework for Pytorch
  • License: Apache License 2.0
  • Languages: Python
  • Tags: computer-vision, deep-learning, machine-learning, medical-imaging, python, pytorch
  • Forks: 128
  • Issues: 17
  • Watchers: 861
  • Last updated: 2025-02-07
  • Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
  • License: Apache License 2.0
  • Languages: Python
  • Tags: machine-learning, mri, neuroimaging, quality-control, quality-reporter
  • Forks: 132
  • Issues: 59
  • Watchers: 310
  • Last updated: 2025-02-10
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • A Library of TensorFlow Operators for Computational MRI
  • License: Apache License 2.0
  • Languages: Jupyter Notebook
  • Tags: machine-learning, magnetic-resonance-imaging, ml, mri, python, tensorflow
  • Forks: 3
  • Issues: 8
  • Watchers: 40
  • Last updated: 2025-02-10
  • The reference implementation for the Non Local Spatial and Angular Matching (NLSAM) denoising algorithm for diffusion MRI
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: denoising-algorithm, diffusion-mri, machine-learning, python
  • Forks: 11
  • Issues: 7
  • Watchers: 24
  • Last updated: 2024-10-26

Segmentation

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16
  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15
  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: glioblastoma, glioma, medical-imaging, mri, segmentation
  • Forks: 12
  • Issues: 8
  • Watchers: 81
  • Last updated: 2025-01-25
  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Medical-Image-Processing

  • AI Toolkit for Healthcare Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, healthcare-imaging, medical-image-computing, medical-image-processing, monai, python3, pytorch
  • Forks: 1136
  • Issues: 408
  • Watchers: 6119
  • Last updated: 2025-02-17
  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16
  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15
  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • DCE MRI analysis in Julia
  • License: Other
  • Languages: Julia
  • Tags: analysis, cancer-imaging-research, dce-mri, julia, mat-files, medical-image-processing, medical-imaging
  • Forks: 16
  • Issues: 5
  • Watchers: 38
  • Last updated: 2025-01-13
  • HDR-MRI Algorithms from "Local contrast-enhanced MR images via high dynamic range processing" published in MRM
  • License: Other
  • Languages: C++
  • Tags: fusion, hdr, image, medical-image-processing, medical-imaging, mri
  • Forks: 0
  • Issues: 0
  • Watchers: 16
  • Last updated: 2024-11-29

Brain-Imaging

  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17
  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14
  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16
  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10
  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27

Quality-Control

  • Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
  • License: Apache License 2.0
  • Languages: Python
  • Tags: machine-learning, mri, neuroimaging, quality-control, quality-reporter
  • Forks: 132
  • Issues: 59
  • Watchers: 310
  • Last updated: 2025-02-10
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09
  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Image-Processing

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14
  • Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, image-registration, image-segmentation, mri, structural-mri, surface-reconstruction
  • Forks: 40
  • Issues: 63
  • Watchers: 136
  • Last updated: 2025-01-21
  • Quality assurance framework for Magnetic Resonance Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, mri, mri-phantoms, python, qa, quality-assurance
  • Forks: 12
  • Issues: 49
  • Watchers: 24
  • Last updated: 2025-02-13

Medical-Image-Computing

  • AI Toolkit for Healthcare Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, healthcare-imaging, medical-image-computing, medical-image-processing, monai, python3, pytorch
  • Forks: 1136
  • Issues: 408
  • Watchers: 6119
  • Last updated: 2025-02-17
  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Diffusion-Mri

  • Preprocessing of diffusion MRI
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: bids, denoising-images, diffusion-mri, distortion-correction, motion-correction, pipelines
  • Forks: 58
  • Issues: 112
  • Watchers: 145
  • Last updated: 2025-02-03
  • Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
  • License: MIT License
  • Languages: Julia
  • Tags: cardiac, diffusion, diffusion-mri, gpu-acceleration, mri, simulation
  • Forks: 21
  • Issues: 89
  • Watchers: 127
  • Last updated: 2025-02-16
  • Massively parallel Monte Carlo diffusion MR simulator written in Python.
  • License: MIT License
  • Languages: Python
  • Tags: cuda, diffusion-mri, gpu-computing, monte-carlo-simulation
  • Forks: 9
  • Issues: 5
  • Watchers: 25
  • Last updated: 2024-12-19
  • The reference implementation for the Non Local Spatial and Angular Matching (NLSAM) denoising algorithm for diffusion MRI
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: denoising-algorithm, diffusion-mri, machine-learning, python
  • Forks: 11
  • Issues: 7
  • Watchers: 24
  • Last updated: 2024-10-26

Convolutional-Neural-Networks

  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14
  • Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, neural-networks
  • Forks: 347
  • Issues: 23
  • Watchers: 1039
  • Last updated: 2025-02-08
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Mri-Images

  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27
  • Julia module for reading/writing NIfTI MRI files
  • License: Other
  • Languages: Julia
  • Tags: fmri, julia, mri, mri-images, nifti
  • Forks: 34
  • Issues: 32
  • Watchers: 74
  • Last updated: 2024-12-27
  • Specialized tools for MRI
  • License: MIT License
  • Languages: Julia
  • Tags: mri, mri-images
  • Forks: 8
  • Issues: 2
  • Watchers: 26
  • Last updated: 2025-02-09
  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Itk

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14
  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06

Quality-Assurance

  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • Quality assurance framework for Magnetic Resonance Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, mri, mri-phantoms, python, qa, quality-assurance
  • Forks: 12
  • Issues: 49
  • Watchers: 24
  • Last updated: 2025-02-13
  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Fmri

  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17
  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10
  • Julia module for reading/writing NIfTI MRI files
  • License: Other
  • Languages: Julia
  • Tags: fmri, julia, mri, mri-images, nifti
  • Forks: 34
  • Issues: 32
  • Watchers: 74
  • Last updated: 2024-12-27

Magnetic-Resonance-Imaging

  • A Library of TensorFlow Operators for Computational MRI
  • License: Apache License 2.0
  • Languages: Jupyter Notebook
  • Tags: machine-learning, magnetic-resonance-imaging, ml, mri, python, tensorflow
  • Forks: 3
  • Issues: 8
  • Watchers: 40
  • Last updated: 2025-02-10
  • Magnetic Field Coil Generator for Python, ported from CoilGen
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: magnetic-field-solver, magnetic-resonance-imaging, medical-physics, mri, nmr, physics
  • Forks: 7
  • Issues: 3
  • Watchers: 16
  • Last updated: 2025-02-13

Medical-Physics

  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02
  • Magnetic Field Coil Generator for Python, ported from CoilGen
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: magnetic-field-solver, magnetic-resonance-imaging, medical-physics, mri, nmr, physics
  • Forks: 7
  • Issues: 3
  • Watchers: 16
  • Last updated: 2025-02-13

Simulation

  • Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
  • License: MIT License
  • Languages: Julia
  • Tags: cardiac, diffusion, diffusion-mri, gpu-acceleration, mri, simulation
  • Forks: 21
  • Issues: 89
  • Watchers: 127
  • Last updated: 2025-02-16
  • Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis
  • License: Other
  • Languages: Python
  • Tags: fitting, mrs, python, rf-pulse, simulation, spectroscopy, wxpython
  • Forks: 6
  • Issues: 5
  • Watchers: 7
  • Last updated: 2024-12-18

C-Plus-Plus

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Registration

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Tractography

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17
  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Image-Reconstruction

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08
  • Main repository for the CCP SynerBI software
  • License: Other
  • Languages: C++
  • Tags: image-reconstruction, medical-imaging, pet-mr
  • Forks: 29
  • Issues: 158
  • Watchers: 64
  • Last updated: 2025-02-17

R

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14
  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Tensorflow

  • A Library of TensorFlow Operators for Computational MRI
  • License: Apache License 2.0
  • Languages: Jupyter Notebook
  • Tags: machine-learning, magnetic-resonance-imaging, ml, mri, python, tensorflow
  • Forks: 3
  • Issues: 8
  • Watchers: 40
  • Last updated: 2025-02-10
  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Image-Registration

  • Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, image-registration, image-segmentation, mri, structural-mri, surface-reconstruction
  • Forks: 40
  • Issues: 63
  • Watchers: 136
  • Last updated: 2025-01-21
  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Fastmri-Challenge

  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14
  • Deep learning framework for MRI reconstruction
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, fastmri-challenge, inverse-problems, medical-imaging, mri-reconstruction, pytorch
  • Forks: 43
  • Issues: 3
  • Watchers: 254
  • Last updated: 2025-02-14

Mri-Reconstruction

  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14
  • Deep learning framework for MRI reconstruction
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, fastmri-challenge, inverse-problems, medical-imaging, mri-reconstruction, pytorch
  • Forks: 43
  • Issues: 3
  • Watchers: 254
  • Last updated: 2025-02-14

Super-Resolution

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08
  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06

Fetal

  • MIRTK based SVR reconstruction
  • License: Apache License 2.0
  • Languages: C++
  • Tags: fetal, mri, reconstruction, retrospecitve, slice-to-volume
  • Forks: 8
  • Issues: 4
  • Watchers: 50
  • Last updated: 2025-02-17
  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06

Bids

  • Preprocessing of diffusion MRI
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: bids, denoising-images, diffusion-mri, distortion-correction, motion-correction, pipelines
  • Forks: 58
  • Issues: 112
  • Watchers: 145
  • Last updated: 2025-02-03
  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06

Julia

  • Julia module for reading/writing NIfTI MRI files
  • License: Other
  • Languages: Julia
  • Tags: fmri, julia, mri, mri-images, nifti
  • Forks: 34
  • Issues: 32
  • Watchers: 74
  • Last updated: 2024-12-27
  • DCE MRI analysis in Julia
  • License: Other
  • Languages: Julia
  • Tags: analysis, cancer-imaging-research, dce-mri, julia, mat-files, medical-image-processing, medical-imaging
  • Forks: 16
  • Issues: 5
  • Watchers: 38
  • Last updated: 2025-01-13

Nifti

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16
  • Julia module for reading/writing NIfTI MRI files
  • License: Other
  • Languages: Julia
  • Tags: fmri, julia, mri, mri-images, nifti
  • Forks: 34
  • Issues: 32
  • Watchers: 74
  • Last updated: 2024-12-27

Computer-Vision

  • A medical imaging framework for Pytorch
  • License: Apache License 2.0
  • Languages: Python
  • Tags: computer-vision, deep-learning, machine-learning, medical-imaging, python, pytorch
  • Forks: 128
  • Issues: 17
  • Watchers: 861
  • Last updated: 2025-02-07
  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27

Dicom

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16
  • A simple python module to make it easy to batch convert DICOM files to PNG images.
  • License: MIT License
  • Languages: Python
  • Tags: dicom, dicom-converter, dicom-images, medical, medical-images, png, python
  • Forks: 50
  • Issues: 5
  • Watchers: 143
  • Last updated: 2025-01-20

Medical-Images

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • A simple python module to make it easy to batch convert DICOM files to PNG images.
  • License: MIT License
  • Languages: Python
  • Tags: dicom, dicom-converter, dicom-images, medical, medical-images, png, python
  • Forks: 50
  • Issues: 5
  • Watchers: 143
  • Last updated: 2025-01-20

Brain-Connectivity

  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17
  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Neuroscience

  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10
  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Medical-Image-Analysis

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17
  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Qa

  • Quality assurance framework for Magnetic Resonance Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, mri, mri-phantoms, python, qa, quality-assurance
  • Forks: 12
  • Issues: 49
  • Watchers: 24
  • Last updated: 2025-02-13
  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Magnetic-Field-Solver

  • Magnetic Field Coil Generator for Python, ported from CoilGen
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: magnetic-field-solver, magnetic-resonance-imaging, medical-physics, mri, nmr, physics
  • Forks: 7
  • Issues: 3
  • Watchers: 16
  • Last updated: 2025-02-13

Nmr

  • Magnetic Field Coil Generator for Python, ported from CoilGen
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: magnetic-field-solver, magnetic-resonance-imaging, medical-physics, mri, nmr, physics
  • Forks: 7
  • Issues: 3
  • Watchers: 16
  • Last updated: 2025-02-13

Physics

  • Magnetic Field Coil Generator for Python, ported from CoilGen
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: magnetic-field-solver, magnetic-resonance-imaging, medical-physics, mri, nmr, physics
  • Forks: 7
  • Issues: 3
  • Watchers: 16
  • Last updated: 2025-02-13

Fitting

  • Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis
  • License: Other
  • Languages: Python
  • Tags: fitting, mrs, python, rf-pulse, simulation, spectroscopy, wxpython
  • Forks: 6
  • Issues: 5
  • Watchers: 7
  • Last updated: 2024-12-18

Mrs

  • Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis
  • License: Other
  • Languages: Python
  • Tags: fitting, mrs, python, rf-pulse, simulation, spectroscopy, wxpython
  • Forks: 6
  • Issues: 5
  • Watchers: 7
  • Last updated: 2024-12-18

Rf-Pulse

  • Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis
  • License: Other
  • Languages: Python
  • Tags: fitting, mrs, python, rf-pulse, simulation, spectroscopy, wxpython
  • Forks: 6
  • Issues: 5
  • Watchers: 7
  • Last updated: 2024-12-18

Spectroscopy

  • Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis
  • License: Other
  • Languages: Python
  • Tags: fitting, mrs, python, rf-pulse, simulation, spectroscopy, wxpython
  • Forks: 6
  • Issues: 5
  • Watchers: 7
  • Last updated: 2024-12-18

Wxpython

  • Python tools for Magnetic Resonance Spectroscopy - Pulses, Simulation and Analysis
  • License: Other
  • Languages: Python
  • Tags: fitting, mrs, python, rf-pulse, simulation, spectroscopy, wxpython
  • Forks: 6
  • Issues: 5
  • Watchers: 7
  • Last updated: 2024-12-18

3D-Printing

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

3D-Slicer

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Computed-Tomography

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Image-Guided-Therapy

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Kitware

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

National-Institutes-Of-Health

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Nih

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Qt

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Tcia-Dac

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Vtk

  • Multi-platform, free open source software for visualization and image computing.
  • License: Other
  • Languages: C++
  • Tags: 3d-printing, 3d-slicer, c-plus-plus, computed-tomography, image-guided-therapy, image-processing, itk, kitware, medical-image-computing, medical-imaging, national-institutes-of-health, neuroimaging, nih, python, qt, registration, segmentation, tcia-dac, tractography, vtk
  • Forks: 578
  • Issues: 594
  • Watchers: 1828
  • Last updated: 2025-02-17

Pet-Mr

  • Main repository for the CCP SynerBI software
  • License: Other
  • Languages: C++
  • Tags: image-reconstruction, medical-imaging, pet-mr
  • Forks: 29
  • Issues: 158
  • Watchers: 64
  • Last updated: 2025-02-17

Fusion

  • HDR-MRI Algorithms from "Local contrast-enhanced MR images via high dynamic range processing" published in MRM
  • License: Other
  • Languages: C++
  • Tags: fusion, hdr, image, medical-image-processing, medical-imaging, mri
  • Forks: 0
  • Issues: 0
  • Watchers: 16
  • Last updated: 2024-11-29

Hdr

  • HDR-MRI Algorithms from "Local contrast-enhanced MR images via high dynamic range processing" published in MRM
  • License: Other
  • Languages: C++
  • Tags: fusion, hdr, image, medical-image-processing, medical-imaging, mri
  • Forks: 0
  • Issues: 0
  • Watchers: 16
  • Last updated: 2024-11-29

Image

  • HDR-MRI Algorithms from "Local contrast-enhanced MR images via high dynamic range processing" published in MRM
  • License: Other
  • Languages: C++
  • Tags: fusion, hdr, image, medical-image-processing, medical-imaging, mri
  • Forks: 0
  • Issues: 0
  • Watchers: 16
  • Last updated: 2024-11-29

3D-Slicer-Extension

  • None
  • License: Other
  • Languages: C
  • Tags: 3d-slicer-extension
  • Forks: 27
  • Issues: 18
  • Watchers: 26
  • Last updated: 2025-02-13

Cortical-Thickness

  • DL+DiReCT - Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: cortical-thickness, deep-learning, morphometry, mri
  • Forks: 5
  • Issues: 4
  • Watchers: 26
  • Last updated: 2025-01-15

Morphometry

  • DL+DiReCT - Direct Cortical Thickness Estimation using Deep Learning-based Anatomy Segmentation and Cortex Parcellation
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: cortical-thickness, deep-learning, morphometry, mri
  • Forks: 5
  • Issues: 4
  • Watchers: 26
  • Last updated: 2025-01-15

Mri-Sequences

  • Pulseq in Python
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: mri, mri-sequences, pulse-sequences, pulseq, python
  • Forks: 69
  • Issues: 15
  • Watchers: 135
  • Last updated: 2025-02-13

Pulse-Sequences

  • Pulseq in Python
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: mri, mri-sequences, pulse-sequences, pulseq, python
  • Forks: 69
  • Issues: 15
  • Watchers: 135
  • Last updated: 2025-02-13

Pulseq

  • Pulseq in Python
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: mri, mri-sequences, pulse-sequences, pulseq, python
  • Forks: 69
  • Issues: 15
  • Watchers: 135
  • Last updated: 2025-02-13

Neuroimage

  • Comprehensive and open-source library of analysis tools for MRI of the spinal cord.
  • License: GNU Lesser General Public License v3.0
  • Languages: Python
  • Tags: mri, neuroimage, python, spinalcord
  • Forks: 103
  • Issues: 365
  • Watchers: 216
  • Last updated: 2025-02-17

Spinalcord

  • Comprehensive and open-source library of analysis tools for MRI of the spinal cord.
  • License: GNU Lesser General Public License v3.0
  • Languages: Python
  • Tags: mri, neuroimage, python, spinalcord
  • Forks: 103
  • Issues: 365
  • Watchers: 216
  • Last updated: 2025-02-17

Freesurfer

  • Neuroimaging analysis and visualization suite
  • License: Other
  • Languages: C++
  • Tags: freesurfer, lcn, mri, neuroimaging
  • Forks: 254
  • Issues: 20
  • Watchers: 641
  • Last updated: 2025-02-17

Lcn

  • Neuroimaging analysis and visualization suite
  • License: Other
  • Languages: C++
  • Tags: freesurfer, lcn, mri, neuroimaging
  • Forks: 254
  • Issues: 20
  • Watchers: 641
  • Last updated: 2025-02-17

Csharp

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Image-Analysis

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Java

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Lua

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Ruby

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Simpleitk

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Swig

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Tcl

  • SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.
  • License: Apache License 2.0
  • Languages: Swig
  • Tags: c-plus-plus, csharp, image-analysis, image-processing, itk, java, lua, python, r, registration, ruby, segmentation, simpleitk, swig, tcl
  • Forks: 207
  • Issues: 60
  • Watchers: 931
  • Last updated: 2025-02-14

Ml

  • A Library of TensorFlow Operators for Computational MRI
  • License: Apache License 2.0
  • Languages: Jupyter Notebook
  • Tags: machine-learning, magnetic-resonance-imaging, ml, mri, python, tensorflow
  • Forks: 3
  • Issues: 8
  • Watchers: 40
  • Last updated: 2025-02-10

Cardiac

  • Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
  • License: MIT License
  • Languages: Julia
  • Tags: cardiac, diffusion, diffusion-mri, gpu-acceleration, mri, simulation
  • Forks: 21
  • Issues: 89
  • Watchers: 127
  • Last updated: 2025-02-16

Diffusion

  • Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
  • License: MIT License
  • Languages: Julia
  • Tags: cardiac, diffusion, diffusion-mri, gpu-acceleration, mri, simulation
  • Forks: 21
  • Issues: 89
  • Watchers: 127
  • Last updated: 2025-02-16

Gpu-Acceleration

  • Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
  • License: MIT License
  • Languages: Julia
  • Tags: cardiac, diffusion, diffusion-mri, gpu-acceleration, mri, simulation
  • Forks: 21
  • Issues: 89
  • Watchers: 127
  • Last updated: 2025-02-16

Cuda

  • Massively parallel Monte Carlo diffusion MR simulator written in Python.
  • License: MIT License
  • Languages: Python
  • Tags: cuda, diffusion-mri, gpu-computing, monte-carlo-simulation
  • Forks: 9
  • Issues: 5
  • Watchers: 25
  • Last updated: 2024-12-19

Gpu-Computing

  • Massively parallel Monte Carlo diffusion MR simulator written in Python.
  • License: MIT License
  • Languages: Python
  • Tags: cuda, diffusion-mri, gpu-computing, monte-carlo-simulation
  • Forks: 9
  • Issues: 5
  • Watchers: 25
  • Last updated: 2024-12-19

Monte-Carlo-Simulation

  • Massively parallel Monte Carlo diffusion MR simulator written in Python.
  • License: MIT License
  • Languages: Python
  • Tags: cuda, diffusion-mri, gpu-computing, monte-carlo-simulation
  • Forks: 9
  • Issues: 5
  • Watchers: 25
  • Last updated: 2024-12-19

Imaging

  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02

Quality-Metrics

  • RadQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) and computed tomography (CT) data.
  • License: BSD 3-Clause Clear License
  • Languages: Python
  • Tags: imaging, machine-learning, medical-image-processing, medical-imaging, medical-physics, mri, python, quality-assurance, quality-control, quality-metrics
  • Forks: 30
  • Issues: 1
  • Watchers: 96
  • Last updated: 2025-02-02

Denoising-Algorithm

  • The reference implementation for the Non Local Spatial and Angular Matching (NLSAM) denoising algorithm for diffusion MRI
  • License: GNU General Public License v3.0
  • Languages: Python
  • Tags: denoising-algorithm, diffusion-mri, machine-learning, python
  • Forks: 11
  • Issues: 7
  • Watchers: 24
  • Last updated: 2024-10-26

Bart-Toolbox

  • BART: Toolbox for Computational Magnetic Resonance Imaging
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C
  • Tags: bart-toolbox, compressed-sensing, computational-imaging, deep-learning, iterative-methods, mri
  • Forks: 164
  • Issues: 22
  • Watchers: 309
  • Last updated: 2025-02-17

Compressed-Sensing

  • BART: Toolbox for Computational Magnetic Resonance Imaging
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C
  • Tags: bart-toolbox, compressed-sensing, computational-imaging, deep-learning, iterative-methods, mri
  • Forks: 164
  • Issues: 22
  • Watchers: 309
  • Last updated: 2025-02-17

Computational-Imaging

  • BART: Toolbox for Computational Magnetic Resonance Imaging
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C
  • Tags: bart-toolbox, compressed-sensing, computational-imaging, deep-learning, iterative-methods, mri
  • Forks: 164
  • Issues: 22
  • Watchers: 309
  • Last updated: 2025-02-17

Iterative-Methods

  • BART: Toolbox for Computational Magnetic Resonance Imaging
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C
  • Tags: bart-toolbox, compressed-sensing, computational-imaging, deep-learning, iterative-methods, mri
  • Forks: 164
  • Issues: 22
  • Watchers: 309
  • Last updated: 2025-02-17

Image-Segmentation

  • Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, image-registration, image-segmentation, mri, structural-mri, surface-reconstruction
  • Forks: 40
  • Issues: 63
  • Watchers: 136
  • Last updated: 2025-01-21

Structural-Mri

  • Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, image-registration, image-segmentation, mri, structural-mri, surface-reconstruction
  • Forks: 40
  • Issues: 63
  • Watchers: 136
  • Last updated: 2025-01-21

Surface-Reconstruction

  • Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, image-registration, image-segmentation, mri, structural-mri, surface-reconstruction
  • Forks: 40
  • Issues: 63
  • Watchers: 136
  • Last updated: 2025-01-21

Fastmri

  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14

Fastmri-Dataset

  • A large-scale dataset of both raw MRI measurements and clinical MRI images.
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fastmri, fastmri-challenge, fastmri-dataset, medical-imaging, mri, mri-reconstruction, pytorch
  • Forks: 384
  • Issues: 18
  • Watchers: 1384
  • Last updated: 2025-02-14

3D-Reconstruction

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

3D-Visualization

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Implicit-Neural-Representation

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Nerf

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Neural-Network

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Neural-Rendering

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Transformers

  • NeSVoR is a package for GPU-accelerated slice-to-volume reconstruction.
  • License: MIT License
  • Languages: Python
  • Tags: 3d-reconstruction, 3d-visualization, deep-learning, image-reconstruction, image-registration, implicit-neural-representation, medical-imaging, mri, nerf, neural-network, neural-rendering, pytorch, segmentation, super-resolution, transformers
  • Forks: 17
  • Issues: 8
  • Watchers: 76
  • Last updated: 2025-02-08

Fetus

  • A deep recursive fetal motion estimation and correction framework based on slice and volume affinity fusion
  • License: MIT License
  • Languages: Python
  • Tags: deep-learning, fetus, motion
  • Forks: 1
  • Issues: 0
  • Watchers: 9
  • Last updated: 2023-11-17

Motion

  • A deep recursive fetal motion estimation and correction framework based on slice and volume affinity fusion
  • License: MIT License
  • Languages: Python
  • Tags: deep-learning, fetus, motion
  • Forks: 1
  • Issues: 0
  • Watchers: 9
  • Last updated: 2023-11-17

Reconstruction

  • MIRTK based SVR reconstruction
  • License: Apache License 2.0
  • Languages: C++
  • Tags: fetal, mri, reconstruction, retrospecitve, slice-to-volume
  • Forks: 8
  • Issues: 4
  • Watchers: 50
  • Last updated: 2025-02-17

Retrospecitve

  • MIRTK based SVR reconstruction
  • License: Apache License 2.0
  • Languages: C++
  • Tags: fetal, mri, reconstruction, retrospecitve, slice-to-volume
  • Forks: 8
  • Issues: 4
  • Watchers: 50
  • Last updated: 2025-02-17

Slice-To-Volume

  • MIRTK based SVR reconstruction
  • License: Apache License 2.0
  • Languages: C++
  • Tags: fetal, mri, reconstruction, retrospecitve, slice-to-volume
  • Forks: 8
  • Issues: 4
  • Watchers: 50
  • Last updated: 2025-02-17

Bids-Apps

  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06

Nipype

  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06

Workflow

  • The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: C++
  • Tags: bids, bids-apps, fetal, itk, mri, nipype, super-resolution, workflow
  • Forks: 12
  • Issues: 17
  • Watchers: 28
  • Last updated: 2024-12-06

Fetal-Mri

  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Semi-Supervised-Learning

  • Image quality assessment for fetal MRI
  • License: MIT License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, fetal-mri, medical-imaging, pytorch, quality-control, semi-supervised-learning, tensorflow
  • Forks: 0
  • Issues: 0
  • Watchers: 6
  • Last updated: 2024-10-12

Analysis

  • DCE MRI analysis in Julia
  • License: Other
  • Languages: Julia
  • Tags: analysis, cancer-imaging-research, dce-mri, julia, mat-files, medical-image-processing, medical-imaging
  • Forks: 16
  • Issues: 5
  • Watchers: 38
  • Last updated: 2025-01-13

Cancer-Imaging-Research

  • DCE MRI analysis in Julia
  • License: Other
  • Languages: Julia
  • Tags: analysis, cancer-imaging-research, dce-mri, julia, mat-files, medical-image-processing, medical-imaging
  • Forks: 16
  • Issues: 5
  • Watchers: 38
  • Last updated: 2025-01-13

Dce-Mri

  • DCE MRI analysis in Julia
  • License: Other
  • Languages: Julia
  • Tags: analysis, cancer-imaging-research, dce-mri, julia, mat-files, medical-image-processing, medical-imaging
  • Forks: 16
  • Issues: 5
  • Watchers: 38
  • Last updated: 2025-01-13

Mat-Files

  • DCE MRI analysis in Julia
  • License: Other
  • Languages: Julia
  • Tags: analysis, cancer-imaging-research, dce-mri, julia, mat-files, medical-image-processing, medical-imaging
  • Forks: 16
  • Issues: 5
  • Watchers: 38
  • Last updated: 2025-01-13

Ai

  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27

Bayesian

  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27

Biomarkers

  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27

Neuroanatomy

  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27

Uncertainty

  • PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
  • License: MIT License
  • Languages: Python
  • Tags: ai, bayesian, biomarkers, brain-imaging, computer-vision, convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, mri-images, neuroanatomy, pytorch, quality-control, segmentation, uncertainty
  • Forks: 37
  • Issues: 7
  • Watchers: 103
  • Last updated: 2024-12-27

Dicom-Converter

  • A simple python module to make it easy to batch convert DICOM files to PNG images.
  • License: MIT License
  • Languages: Python
  • Tags: dicom, dicom-converter, dicom-images, medical, medical-images, png, python
  • Forks: 50
  • Issues: 5
  • Watchers: 143
  • Last updated: 2025-01-20

Dicom-Images

  • A simple python module to make it easy to batch convert DICOM files to PNG images.
  • License: MIT License
  • Languages: Python
  • Tags: dicom, dicom-converter, dicom-images, medical, medical-images, png, python
  • Forks: 50
  • Issues: 5
  • Watchers: 143
  • Last updated: 2025-01-20

Medical

  • A simple python module to make it easy to batch convert DICOM files to PNG images.
  • License: MIT License
  • Languages: Python
  • Tags: dicom, dicom-converter, dicom-images, medical, medical-images, png, python
  • Forks: 50
  • Issues: 5
  • Watchers: 143
  • Last updated: 2025-01-20

Png

  • A simple python module to make it easy to batch convert DICOM files to PNG images.
  • License: MIT License
  • Languages: Python
  • Tags: dicom, dicom-converter, dicom-images, medical, medical-images, png, python
  • Forks: 50
  • Issues: 5
  • Watchers: 143
  • Last updated: 2025-01-20

Denoising-Images

  • Preprocessing of diffusion MRI
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: bids, denoising-images, diffusion-mri, distortion-correction, motion-correction, pipelines
  • Forks: 58
  • Issues: 112
  • Watchers: 145
  • Last updated: 2025-02-03

Distortion-Correction

  • Preprocessing of diffusion MRI
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: bids, denoising-images, diffusion-mri, distortion-correction, motion-correction, pipelines
  • Forks: 58
  • Issues: 112
  • Watchers: 145
  • Last updated: 2025-02-03

Motion-Correction

  • Preprocessing of diffusion MRI
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: bids, denoising-images, diffusion-mri, distortion-correction, motion-correction, pipelines
  • Forks: 58
  • Issues: 112
  • Watchers: 145
  • Last updated: 2025-02-03

Pipelines

  • Preprocessing of diffusion MRI
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: bids, denoising-images, diffusion-mri, distortion-correction, motion-correction, pipelines
  • Forks: 58
  • Issues: 112
  • Watchers: 145
  • Last updated: 2025-02-03

Complex-Networks

  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Connectome

  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Connectomics

  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Graph-Theory

  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Network-Analysis

  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Statistics

  • Graph theory analysis of brain MRI data
  • License: None
  • Languages: R
  • Tags: brain-connectivity, brain-imaging, complex-networks, connectome, connectomics, fmri, graph-theory, mri, network-analysis, neuroimaging, neuroscience, r, statistics, tractography
  • Forks: 53
  • Issues: 11
  • Watchers: 188
  • Last updated: 2025-02-10

Inverse-Problems

  • Deep learning framework for MRI reconstruction
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, fastmri-challenge, inverse-problems, medical-imaging, mri-reconstruction, pytorch
  • Forks: 43
  • Issues: 3
  • Watchers: 254
  • Last updated: 2025-02-14

3D-Segmentation

  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16

Frontend-App

  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16

Javascript

  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16

Mri-Segmentation

  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16

Pyodide

  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16

Tensorflowjs

  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16

Three-Js

  • Brainchop: In-browser 3D MRI rendering and segmentation
  • License: MIT License
  • Languages: Javascript
  • Tags: 3d-segmentation, deep-learning, frontend-app, javascript, medical-imaging, mri, mri-segmentation, neuroimaging, pyodide, tensorflowjs, three-js
  • Forks: 46
  • Issues: 3
  • Watchers: 405
  • Last updated: 2025-02-16

Quality-Reporter

  • Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
  • License: Apache License 2.0
  • Languages: Python
  • Tags: machine-learning, mri, neuroimaging, quality-control, quality-reporter
  • Forks: 132
  • Issues: 59
  • Watchers: 310
  • Last updated: 2025-02-10

Fcm

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Harmonization

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Intensity-Normalization

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Normalization

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Ravel

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Standardization

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Whitestripe

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Zscore

  • normalize the intensities of various MR image modalities
  • License: Other
  • Languages: Python
  • Tags: fcm, harmonization, intensity-normalization, mri, neuroimaging, normalization, ravel, standardization, whitestripe, zscore
  • Forks: 58
  • Issues: 12
  • Watchers: 323
  • Last updated: 2025-02-17

Healthcare-Imaging

  • AI Toolkit for Healthcare Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, healthcare-imaging, medical-image-computing, medical-image-processing, monai, python3, pytorch
  • Forks: 1136
  • Issues: 408
  • Watchers: 6119
  • Last updated: 2025-02-17

Monai

  • AI Toolkit for Healthcare Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, healthcare-imaging, medical-image-computing, medical-image-processing, monai, python3, pytorch
  • Forks: 1136
  • Issues: 408
  • Watchers: 6119
  • Last updated: 2025-02-17

Python3

  • AI Toolkit for Healthcare Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: deep-learning, healthcare-imaging, medical-image-computing, medical-image-processing, monai, python3, pytorch
  • Forks: 1136
  • Issues: 408
  • Watchers: 6119
  • Last updated: 2025-02-17

3D-Mask-Rcnn

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

3D-Models

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

3D-Object-Detection

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Deep-Neural-Networks

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Detection

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Mask-Rcnn

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Object-Detection

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Pytorch-Cnn

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Pytorch-Deeplearning

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Pytorch-Implementation

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Retina-Net

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Retina-Unet

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Semantic-Segmentation

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

U-Net

  • The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: 3d-mask-rcnn, 3d-models, 3d-object-detection, deep-learning, deep-neural-networks, detection, mask-rcnn, medical-image-analysis, medical-image-computing, medical-image-processing, medical-imaging, object-detection, pytorch-cnn, pytorch-deeplearning, pytorch-implementation, retina-net, retina-unet, segmentation, semantic-segmentation, u-net
  • Forks: 296
  • Issues: 47
  • Watchers: 1317
  • Last updated: 2025-02-15

Augmentation

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17

Data-Augmentation

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17

Medical-Imaging-Datasets

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17

Medical-Imaging-With-Deep-Learning

  • Medical imaging processing for deep learning.
  • License: Apache License 2.0
  • Languages: Python
  • Tags: augmentation, data-augmentation, deep-learning, machine-learning, medical-image-analysis, medical-image-computing, medical-image-processing, medical-images, medical-imaging-datasets, medical-imaging-with-deep-learning, python, pytorch
  • Forks: 241
  • Issues: 38
  • Watchers: 2127
  • Last updated: 2025-02-17

Neural-Networks

  • Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans
  • License: BSD 3-Clause "New" or "Revised" License
  • Languages: Python
  • Tags: convolutional-neural-networks, deep-learning, machine-learning, medical-imaging, neural-networks
  • Forks: 347
  • Issues: 23
  • Watchers: 1039
  • Last updated: 2025-02-08

3D-Convolutional-Network

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Brats2018

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Brats2019

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Densenet

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Iseg

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Iseg-Challenge

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Medical-Image-Segmentation

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Mrbrains18

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Resnet

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Segmentation-Models

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Unet

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Unet-Image-Segmentation

  • A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
  • License: MIT License
  • Languages: Python
  • Tags: 3d-convolutional-network, brats2018, brats2019, deep-learning, densenet, iseg, iseg-challenge, medical-image-processing, medical-image-segmentation, medical-imaging, mrbrains18, pytorch, resnet, segmentation, segmentation-models, unet, unet-image-segmentation
  • Forks: 298
  • Issues: 20
  • Watchers: 1777
  • Last updated: 2025-02-16

Big-Data

  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14

Brainweb

  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14

Data-Science

  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14

Dataflow

  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14

Dataflow-Programming

  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14

Workflow-Engine

  • Workflows and interfaces for neuroimaging packages
  • License: Other
  • Languages: Python
  • Tags: big-data, brain-imaging, brainweb, data-science, dataflow, dataflow-programming, neuroimaging, python, workflow-engine
  • Forks: 532
  • Issues: 424
  • Watchers: 761
  • Last updated: 2025-02-14

Afni-Brik-Head

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Cifti-2

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Data-Formats

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Ecat

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Gifti

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Minc

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Streamlines

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Tck

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Trk

  • Python package to access a cacophony of neuro-imaging file formats
  • License: Other
  • Languages: Python
  • Tags: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
  • Forks: 260
  • Issues: 135
  • Watchers: 677
  • Last updated: 2025-02-16

Brain-Mri

  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17

Decoding

  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17

Mvpa

  • Machine learning for NeuroImaging in Python
  • License: Other
  • Languages: Python
  • Tags: brain-connectivity, brain-imaging, brain-mri, decoding, fmri, machine-learning, mvpa, neuroimaging, python
  • Forks: 618
  • Issues: 263
  • Watchers: 1239
  • Last updated: 2025-02-17

Alzheimer-Disease

  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14

Convolutional-Neural-Network

  • Framework for the reproducible processing of neuroimaging data with deep learning methods
  • License: MIT License
  • Languages: Python
  • Tags: alzheimer-disease, brain-imaging, convolutional-neural-network, deep-learning, medical-imaging, neuroimaging, python, pytorch
  • Forks: 57
  • Issues: 27
  • Watchers: 166
  • Last updated: 2025-02-14

Glioblastoma

  • Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: glioblastoma, glioma, medical-imaging, mri, segmentation
  • Forks: 12
  • Issues: 8
  • Watchers: 81
  • Last updated: 2025-01-25

Glioma

  • Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
  • License: GNU Affero General Public License v3.0
  • Languages: Python
  • Tags: glioblastoma, glioma, medical-imaging, mri, segmentation
  • Forks: 12
  • Issues: 8
  • Watchers: 81
  • Last updated: 2025-01-25

Brain

  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Ismrm

  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Mr-Image

  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Mri-Brain

  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Niqc

  • mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance
  • License: Apache License 2.0
  • Languages: Python
  • Tags: brain, ismrm, mr-image, mri, mri-brain, mri-images, neuroimaging, neuroscience, niqc, qa, quality-assurance, quality-control
  • Forks: 6
  • Issues: 38
  • Watchers: 11
  • Last updated: 2025-01-09

Mri-Phantoms

  • Quality assurance framework for Magnetic Resonance Imaging
  • License: Apache License 2.0
  • Languages: Python
  • Tags: image-processing, mri, mri-phantoms, python, qa, quality-assurance
  • Forks: 12
  • Issues: 49
  • Watchers: 24
  • Last updated: 2025-02-13

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A collection of MRI software projects for simulation, analysis, processing, QA, visualisation and reconstruction.

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