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@Deep-MI Deep Medical Imaging Lab (PI Reuter)

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    20 repositories

    • WhipperSnapPy

      Public
      Publication-quality OpenGL surface renderer with overlays — off-screen, Jupyter, and GUI support
      Python
      •
      MIT License
      •9•2•1•1•Updated Feb 22, 2026Feb 22, 2026

    • LaPy

      Public
      Toolbox for Differential Geometry on Triangle and Tetrahedra Meshes (FEM, Laplace, Poisson, Heat Flow ...)
      Python
      •
      MIT License
      •15•96•2•1•Updated Feb 22, 2026Feb 22, 2026

    • neurolit

      Public
      Neuro Lesion Inpainting Tool (neuroLIT / FastSurfer-LIT) for lesion inpainting e.g. for whole brain segmentation and cortical surface reconstruction in the pres…
      Python
      •
      Apache License 2.0
      •3•18•0•0•Updated Feb 21, 2026Feb 21, 2026

    • Deep-MI.github.io

      Public
      Deep Medical Imaging Lab Webpage
      TeX
      •
      MIT License
      •16•3•0•1•Updated Feb 18, 2026Feb 18, 2026

    • FastSurfer

      Public
      PyTorch implementation of FastSurferCNN
      Python
      •
      Apache License 2.0
      •145•583•21•3•Updated Feb 17, 2026Feb 17, 2026

    • fsqc

      Public
      A set of quality control scripts for FreeSurfer- and FastSurfer-processed structural MRI data
      Python
      •
      MIT License
      •16•74•2•1•Updated Jan 26, 2026Jan 26, 2026

    • hipsta

      Public
      HIPSTA - a python package for hippocampal shape and thickness analysis
      Python
      •
      MIT License
      •1•6•0•1•Updated Dec 15, 2025Dec 15, 2025

    • BrainPrint

      Public
      A python-only derivative of the original BrainPrint scripts
      Python
      •
      MIT License
      •9•15•0•0•Updated Dec 15, 2025Dec 15, 2025

    • YODA

      Public
      You Only Denoise once or Average (YODA) - A diffusion-based 2.5D medical image translation model with noise-supression
      Python
      •
      Apache License 2.0
      •1•7•0•0•Updated Oct 16, 2025Oct 16, 2025

    • olf-bulb-segmentation

      Public
      Automated Olfactory Bulb Segmentation Pipeline for T2-Weighted MRI
      olfactory-bulb-segmentation
      Python
      •
      Apache License 2.0
      •3•11•0•0•Updated Aug 4, 2025Aug 4, 2025

    • segmentation_labeling

      Public
      A labeling tool for comparative segmentation labeling
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

    • fslmer

      Public
      Univariate and mass-univariate linear mixed-effects analysis for FreeSurfer imaging data.
      R
      •
      Other
      •1•8•1•0•Updated Jan 22, 2025Jan 22, 2025

    • VINNA4neonates

      Public
      Newborn Whole Brain Segmentation with VINNA
      Python
      •
      Apache License 2.0
      •0•0•1•0•Updated Jan 9, 2025Jan 9, 2025

    • head-motion-tools

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Nov 11, 2024Nov 11, 2024

    • DISCUS

      Public
      The repository contains code for the Geometric Deep Learning for Diffusion MRI Signal Reconstruction with Continuous Samplings (DISCUS) project
      Python
      •0•5•1•0•Updated Apr 22, 2024Apr 22, 2024

    • head-motion-from-MRI

      Public
      Code for the paper "Estimating Head Motion from MRI", which predicts motion scores directly from MRI images.
      Python
      •
      Apache License 2.0
      •2•4•0•0•Updated Mar 22, 2024Mar 22, 2024

    • 3d-neuro-seg

      Public
      Repository to our 3d neuro-anatomic segmentation method submitted to the MIDL 2022 conference
      Python
      •
      Apache License 2.0
      •1•4•1•0•Updated Jul 25, 2022Jul 25, 2022

    • FatSegNet

      Public
      Deep CNN for Abdominal Adipose Tissue Segmentation on Dixon MRI
      deep-learningimage-segmentationmedical-image-processingmri-segmentationabdominal-adipose-tissuedixon-mri
      Python
      •
      Apache License 2.0
      •13•24•1•0•Updated Apr 7, 2022Apr 7, 2022

    • fastsurfer-webpage

      Public
      Jekyll Webpage for the FastSurfer project
      HTML
      •
      MIT License
      •160•1•0•0•Updated Jan 15, 2022Jan 15, 2022

    • BrainPrint-legacy

      Public
      Python scripts for shape analysis of neuroimaging data (wrapping around shapeDNA and FreeSurfer)
      Python
      •7•21•0•0•Updated Feb 3, 2021Feb 3, 2021