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@khanlab

Khan Computational Imaging Lab

  • 22 followers
  • Robarts Research Institute, Western University, London, Canada

Popular repositories Loading

  1. hippunfold hippunfold Public

    BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)

    Python 65 23

  2. snakebids snakebids Public

    Snakemake + BIDS

    Python 22 16

  3. zarrnii zarrnii Public

    Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations

    Python 10 4

  4. tar2bids tar2bids Public

    Python 8 9

  5. mp2rage_genUniDen mp2rage_genUniDen Public

    Generates UNI-DEN image from UNI, Inv1 and Inv2 images

    MATLAB 6 1

  6. scattr scattr Public

    BIDS app for structural connectivity between targeted regions

    Python 6 5

Repositories

Showing 10 of 131 repositories
  • cfmm2bids Public

    Snakemake workflow for pulling cfmm dicom server data into bids

    khanlab/cfmm2bids’s past year of commit activity
    Python 0 1 2 5 Updated Mar 21, 2026
  • hippunfold Public

    BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)

    khanlab/hippunfold’s past year of commit activity
    Python 65 MIT 23 27 (1 issue needs help) 6 Updated Mar 20, 2026
  • hippunfold-tutorials Public
    khanlab/hippunfold-tutorials’s past year of commit activity
    Jupyter Notebook 0 1 1 0 Updated Mar 19, 2026
  • SPIMquant Public

    SnakeBIDS app for quantitative analysis of SPIM (lightsheet) brain data

    khanlab/SPIMquant’s past year of commit activity
    Python 5 2 6 4 Updated Mar 17, 2026
  • zarrnii Public

    Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations

    khanlab/zarrnii’s past year of commit activity
    Python 10 4 3 11 Updated Mar 16, 2026
  • snakebids Public

    Snakemake + BIDS

    khanlab/snakebids’s past year of commit activity
    Python 22 MIT 16 23 6 Updated Mar 13, 2026
  • SPIMprep Public

    A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)

    khanlab/SPIMprep’s past year of commit activity
    Python 5 MIT 2 9 (3 issues need help) 4 Updated Mar 9, 2026
  • vesselFM Public Forked from bwittmann/vesselFM

    A foundation model for universal 3D blood vessel segmentation. Paper accepted @ CVPR25.

    khanlab/vesselFM’s past year of commit activity
    Python 0 GPL-3.0 23 0 0 Updated Mar 8, 2026
  • conda-recipes Public Forked from conda-forge/staged-recipes

    A place to submit conda recipes before they become fully fledged conda-forge feedstocks

    khanlab/conda-recipes’s past year of commit activity
    Python 0 BSD-3-Clause 5,860 0 0 Updated Mar 6, 2026
  • cfmm2tar Public

    Tools for dicom-server retrieval, tarballing and conversion to bids

    khanlab/cfmm2tar’s past year of commit activity
    Python 4 GPL-3.0 4 1 0 Updated Mar 6, 2026
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