Repositories list

• zarrnii

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

  transformationsmrinifti+ 4

  transformationsmriniftispimzarrome-zarrlightsheet-microscopy

  Python

  •44 forks•1010 stars•22 issues•88 pull requests•Updated Apr 26, 2026Apr 26, 2026

• cfmm2bids

  Public
  Snakemake workflow for pulling cfmm dicom server data into bids

  Python

  •11 fork•33 stars•33 issues•66 pull requests•Updated Apr 25, 2026Apr 25, 2026

• hippunfold

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

  pythondeep-learningmri+ 2

  pythondeep-learningmrisegmentationhippocampus

  Python

  •

  MIT License

  •2323 forks•6565 stars•2828 issues•66 pull requests•Updated Apr 23, 2026Apr 23, 2026

• SPIMquant

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

  mribidsspim+ 2

  mribidsspimlightsheetsnakebids

  Python

  •22 forks•66 stars•55 issues•99 pull requests•Updated Apr 21, 2026Apr 21, 2026

• neuroglia-helpers

  Public
  Helper and wrapper scripts for using Singularity locally and on compute canada

  Shell

  •

  GNU General Public License v3.0

  •77 forks•55 stars•11 issue•00 pull requests•Updated Apr 14, 2026Apr 14, 2026

• billing-snakemake

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• cbs-server-billing

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• SPIMprep

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

  Python

  •

  MIT License

  •33 forks•55 stars•1010 issues•44 pull requests•Updated Apr 13, 2026Apr 13, 2026

• anatprep

  Public
  Anatomical preprocessing snakebids app for TRIDENT (15T) mouse data

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• SPIMquant-intro

  Public template
  Introduction and tutorial for SPIMquant

  00 forks•11 star•00 issues•00 pull requests•Updated Apr 2, 2026Apr 2, 2026

• mind-lightsheet-validator

  Public
  Validator for file/folder naming standards for raw lightsheet data in the MIND project

  TypeScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 2, 2026Apr 2, 2026

• snakebids

  Public
  Snakemake + BIDS

  pythonsnakemakeneuroimaging+ 1

  pythonsnakemakeneuroimagingbids

  Python

  •

  MIT License

  •1616 forks•2222 stars•2323 issues•88 pull requests•Updated Apr 1, 2026Apr 1, 2026

• khanlab.github.io

  Public
  Khan Lab website

  HTML

  •1717 forks•22 stars•11 issue•11 pull request•Updated Apr 1, 2026Apr 1, 2026

• cfmm2bids-intro

  Public
  Intro slides for cfmm2bids, providing motivation and overview of the approach

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• vesselFM

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

  Python

  •

  GNU General Public License v3.0

  •2626 forks•00 stars•00 issues•11 pull request•Updated Mar 29, 2026Mar 29, 2026

• pythondeps-nnunetv2

  Public
  Python dependencies for nnunet-v2

  Dockerfile

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2026Mar 25, 2026

• hippunfold-tutorials

  Public
  Jupyter Notebook

  •11 fork•00 stars•11 issue•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• 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

  •5.9k5.9k forks•00 stars•00 issues•00 pull requests•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

  •44 forks•44 stars•11 issue•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• analyze_zona_dmri

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 27, 2026Feb 27, 2026

• amygdala_atlas_building

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 26, 2026Feb 26, 2026

• FireANTs

  Public
  Adaptive Riemannian Optimization for Multi-Scale Diffeomorphic Registration

  Python

  •

  Other

  •2323 forks•00 stars•00 issues•11 pull request•Updated Feb 25, 2026Feb 25, 2026

• SPIMtemplates

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• heudiconv

  Public
  Flexible DICOM conversion into structured directory layouts

  Python

  •

  Other

  •136136 forks•00 stars•00 issues•00 pull requests•Updated Feb 20, 2026Feb 20, 2026

• snakedwi

  Public
  Perl

  •

  MIT License

  •77 forks•22 stars•11 issue•11 pull request•Updated Feb 9, 2026Feb 9, 2026

• hippunfold-atlases

  Public
  Surface-based atlases for hippunfold v2.x

  00 forks•22 stars•11 issue•00 pull requests•Updated Jan 31, 2026Jan 31, 2026

• wiki

  Public
  Ruby

  •

  MIT License

  •22 forks•00 stars•22 issues•00 pull requests•Updated Jan 26, 2026Jan 26, 2026

• scattr

  Public
  BIDS app for structural connectivity between targeted regions

  Python

  •

  MIT License

  •55 forks•66 stars•55 issues•22 pull requests•Updated Dec 10, 2025Dec 10, 2025

• actions

  Public
  Centralized repo of reusable GH actions

  33 forks•11 star•00 issues•22 pull requests•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

  •2121 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025