Repositories list

• khanlab.github.io

  Public
  Khan Lab website

  HTML

  •10•2•1•2•Updated Mar 1, 2025Mar 1, 2025

• gcnn_dmri

  Public
  Python

  •

  MIT License

  •0•1•0•1•Updated Mar 1, 2025Mar 1, 2025

• hippunfold

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

  mrihippocampuspython+ 2deep-learningsegmentation

  Python

  •

  MIT License

  •15•55•27•5•Updated Feb 28, 2025Feb 28, 2025

• SPIMquant

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

  Jupyter Notebook

  •0•1•2•0•Updated Feb 27, 2025Feb 27, 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

• LOBE_analysis

  Public
  Snakemake workflow for LOBE study

  Jupyter Notebook

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• SPIMprep

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

  Python

  •

  MIT License

  •1•3•9•2•Updated Feb 3, 2025Feb 3, 2025

• snakebids

  Public
  Snakemake + BIDS

  snakemakeneuroimagingbids+ 1python

  Python

  •

  MIT License

  •14•17•21•5•Updated Feb 1, 2025Feb 1, 2025

• zarrnii

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

  transformationsniftizarr+ 1ome-zarr

  Jupyter Notebook

  •1•2•1•0•Updated Jan 31, 2025Jan 31, 2025

• SPIMprep-deps

  Public
  Shell

  •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• wiki

  Public
  Ruby

  •

  MIT License

  •2•0•2•1•Updated Jan 6, 2025Jan 6, 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

• 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

• tar2bids

  Public
  Python

  •

  GNU General Public License v3.0

  •9•7•3•4•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

• hippunfold-train-finetune

  Public
  Workflow for training nnUnet with pre-existing weights

  Python

  •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

• subcorticalparc-smk

  Public
  General-purpose Snakemake workflow for subcortical parcellation with functional and structural connectivity

  MATLAB

  •7•1•0•2•Updated Jul 30, 2024Jul 30, 2024

• spimquant_CellSeg3D

  Public
  A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks

  Python

  •

  MIT License

  •13•0•0•0•Updated Jul 20, 2024Jul 20, 2024

• actions

  Public
  Centralized repo of reusable GH actions

  1•0•0•1•Updated Jul 1, 2024Jul 1, 2024

• autobids-portal

  Public
  Python

  •1•0•9•4•Updated Jun 26, 2024Jun 26, 2024

• trident_example_project

  Public
  0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

• spimquant_cellpose

  Public
  a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •432•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• autobids

  Public archive
  Automated Dicom to BIDS and pipelines using compute canada

  Shell

  •4•5•3•0•Updated Jun 13, 2024Jun 13, 2024

• SPIMquant-deps

  Public
  Dockerfile

  •0•0•0•0•Updated May 10, 2024May 10, 2024

• hippunfold-frozen-2024-04-25

  Public archive
  Frozen archive of hippunfold (prior to rewriting history in hippunfold)

  Python

  •0•0•0•0•Updated Apr 25, 2024Apr 25, 2024

• scattr

  Public
  BIDS app for structural connectivity between targeted regions

  Python

  •

  MIT License

  •3•4•3•0•Updated Mar 20, 2024Mar 20, 2024