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    120 repositories

    • SPIMprep

      Public
      A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
      Python
      •
      MIT License
      •1•4•9•4•Updated Aug 15, 2025Aug 15, 2025

    • tar2bids

      Public
      Python
      •
      GNU General Public License v3.0
      •9•7•3•2•Updated Aug 14, 2025Aug 14, 2025

    • hippunfold

      Public
      BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
      mrihippocampuspythondeep-learningsegmentation
      Python
      •
      MIT License
      •19•59•23•6•Updated Aug 8, 2025Aug 8, 2025

    • actions

      Public
      Centralized repo of reusable GH actions
      2•1•0•3•Updated Aug 6, 2025Aug 6, 2025

    • khanlab.github.io

      Public
      Khan Lab website
      HTML
      •11•2•1•3•Updated Aug 1, 2025Aug 1, 2025

    • hippunfold-atlases

      Public
      Surface-based atlases for hippunfold v2.x
      0•1•0•0•Updated Jul 30, 2025Jul 30, 2025

    • hippunfold-train-nnunet

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

    • SPIMquant

      Public
      SnakeBIDS app for quantitative analysis of SPIM (lightsheet) brain data
      Jupyter Notebook
      •2•1•2•0•Updated Jul 24, 2025Jul 24, 2025

    • zarrnii

      Public
      Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations
      transformationsniftizarrome-zarr
      Jupyter Notebook
      •2•3•1•1•Updated Jul 24, 2025Jul 24, 2025

    • scattr

      Public
      BIDS app for structural connectivity between targeted regions
      Python
      •
      MIT License
      •5•5•5•3•Updated Jul 8, 2025Jul 8, 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

    • gcnn_dmri

      Public
      Python
      •
      MIT License
      •0•1•0•1•Updated Jun 1, 2025Jun 1, 2025

    • wiki

      Public
      Ruby
      •
      MIT License
      •2•0•2•0•Updated Apr 23, 2025Apr 23, 2025

    • example-snakemake

      Public
      Snakemake tutorial, to be adapted for Brainhack 2025
      Python
      •2•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • LOBE_analysis

      Public
      Snakemake workflow for LOBE study
      Jupyter Notebook
      •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • snakebids

      Public
      Snakemake + BIDS
      snakemakeneuroimagingbidspython
      Python
      •
      MIT License
      •15•19•22•7•Updated Mar 18, 2025Mar 18, 2025

    • synth_nnunet

      Public
      0•1•1•0•Updated Mar 5, 2025Mar 5, 2025

    • hippunfold_deps

      Public
      Dependencies container for hippocampal_autotop (niftynet, minified fsl/ants, c3d, mcr)
      Python
      •
      MIT License
      •1•0•0•1•Updated Feb 25, 2025Feb 25, 2025

    • SPIMprep-deps

      Public
      Shell
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • tar2bids-heuristics

      Public
      Study heuristics for autobids
      Python
      •1•0•0•1•Updated Dec 20, 2024Dec 20, 2024

    • cvpl_tools

      Public
      A Python package for utilities and classes related to the file I/O, dataset record keeping for image processing and computer vision.
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 19, 2024Dec 19, 2024

    • bidsapps

      Public
      bidsapps
      Python
      •0•1•0•0•Updated Dec 17, 2024Dec 17, 2024

    • dgcnn

      Public
      Python
      •1•1•0•0•Updated Dec 6, 2024Dec 6, 2024

    • hippunfold-plot

      Public
      Plotting functions for hippocampal surface maps from HippUnfold
      Jupyter Notebook
      •
      MIT License
      •0•1•4•0•Updated Dec 6, 2024Dec 6, 2024

    • cc-slurm

      Public
      This profile configures Snakemake to run on Compute Canada with SLURM (e.g. graham).
      Python
      •
      MIT License
      •3•2•0•1•Updated Nov 25, 2024Nov 25, 2024

    • pythondeps-snakeanat

      Public
      Python dependencies for snakeanat
      Dockerfile
      •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • kslurm

      Public
      Helper scripts and wrappers for running commands on SLURM compute clusters.
      pythonclislurmcompute-clusters
      Python
      •
      MIT License
      •4•5•13•3•Updated Nov 20, 2024Nov 20, 2024

    • cbs-server-billing

      Public
      Python
      •1•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • trident-datamgmt-scripts

      Public
      Various scripts for TRIDENT data management
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024