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    131 repositories

    • zarrnii

      Public
      Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations
      transformationsmrinifti
      transformationsmriniftispimzarrome-zarrlightsheet-microscopy
      Python
      •4•9•4•10•Updated Mar 6, 2026Mar 6, 2026

    • vesselFM

      Public
      A foundation model for universal 3D blood vessel segmentation. Paper accepted @ CVPR25.
      Python
      •
      GNU General Public License v3.0
      •23•0•0•1•Updated Mar 6, 2026Mar 6, 2026

    • SPIMquant

      Public
      SnakeBIDS app for quantitative analysis of SPIM (lightsheet) brain data
      mribidsspim
      mribidsspimlightsheetsnakebids
      Python
      •2•5•6•6•Updated Mar 6, 2026Mar 6, 2026

    • cfmm2bids

      Public
      Snakemake workflow for pulling cfmm dicom server data into bids
      Python
      •1•0•3•7•Updated Mar 6, 2026Mar 6, 2026

    • cfmm2tar

      Public
      Tools for dicom-server retrieval, tarballing and conversion to bids
      Python
      •
      GNU General Public License v3.0
      •4•4•1•0•Updated Mar 6, 2026Mar 6, 2026

    • snakebids

      Public
      Snakemake + BIDS
      pythonsnakemakeneuroimaging
      pythonsnakemakeneuroimagingbids
      Python
      •
      MIT License
      •16•22•23•9•Updated Mar 3, 2026Mar 3, 2026

    • khanlab.github.io

      Public
      Khan Lab website
      HTML
      •17•2•1•1•Updated Mar 1, 2026Mar 1, 2026

    • analyze_zona_dmri

      Public
      Python
      •1•0•0•0•Updated Feb 27, 2026Feb 27, 2026

    • hippunfold

      Public
      BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
      pythondeep-learningmri
      pythondeep-learningmrisegmentationhippocampus
      Python
      •
      MIT License
      •22•64•26•4•Updated Feb 27, 2026Feb 27, 2026

    • SPIMprep

      Public
      A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
      Python
      •
      MIT License
      •2•5•9•4•Updated Feb 26, 2026Feb 26, 2026

    • amygdala_atlas_building

      Public
      Python
      •1•0•0•0•Updated Feb 26, 2026Feb 26, 2026

    • FireANTs

      Public
      Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration
      Python
      •
      Other
      •22•0•0•1•Updated Feb 25, 2026Feb 25, 2026

    • SPIMtemplates

      Public
      Python
      •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

    • heudiconv

      Public
      Flexible DICOM conversion into structured directory layouts
      Python
      •
      Other
      •136•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • snakedwi

      Public
      Perl
      •
      MIT License
      •7•2•1•1•Updated Feb 9, 2026Feb 9, 2026

    • hippunfold-atlases

      Public
      Surface-based atlases for hippunfold v2.x
      0•2•1•0•Updated Jan 31, 2026Jan 31, 2026

    • wiki

      Public
      Ruby
      •
      MIT License
      •2•0•2•0•Updated Jan 26, 2026Jan 26, 2026

    • scattr

      Public
      BIDS app for structural connectivity between targeted regions
      Python
      •
      MIT License
      •5•6•5•2•Updated Dec 10, 2025Dec 10, 2025

    • actions

      Public
      Centralized repo of reusable GH actions
      3•1•0•2•Updated Nov 17, 2025Nov 17, 2025

    • spimquant_CellSeg3D

      Public
      A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks
      Python
      •
      MIT License
      •20•0•0•0•Updated Nov 12, 2025Nov 12, 2025

    • conda-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.8k•0•0•0•Updated Nov 11, 2025Nov 11, 2025

    • nibabel

      Public
      Python package to access a cacophony of neuro-imaging file formats
      Python
      •
      Other
      •277•0•0•1•Updated Oct 20, 2025Oct 20, 2025

    • kslurm

      Public
      Helper scripts and wrappers for running commands on SLURM compute clusters.
      pythonclislurm
      pythonclislurmcompute-clusters
      Python
      •
      MIT License
      •4•5•13•3•Updated Sep 18, 2025Sep 18, 2025

    • LOBE_analysis

      Public
      Snakemake workflow for LOBE study
      Jupyter Notebook
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • tar2bids-heuristics

      Public
      Study heuristics for autobids
      Python
      •1•0•0•0•Updated Sep 4, 2025Sep 4, 2025

    • robogui

      Public
      Robocopy GUI for Windows
      PowerShell
      •0•0•0•0•Updated Aug 22, 2025Aug 22, 2025

    • tar2bids

      Public
      Python
      •
      GNU General Public License v3.0
      •9•8•3•2•Updated Aug 14, 2025Aug 14, 2025

    • hippunfold-train-nnunet

      Public
      Workflow for training nnUnet for hippunfold
      Python
      •1•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • labelmerge

      Public
      Merge label maps
      Python
      •
      MIT License
      •5•6•4•2•Updated Jun 18, 2025Jun 18, 2025

    • diffparc-surf

      Public
      Snakebids app for diffparc-surf, including dwi processing
      Python
      •
      MIT License
      •1•0•6•3•Updated Jun 7, 2025Jun 7, 2025