Repositories list

• 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•1•1•0•Updated Nov 11, 2024Nov 11, 2024

• SPIMquant

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

  Python

  •0•1•1•3•Updated Nov 11, 2024Nov 11, 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•0•1•0•Updated Nov 8, 2024Nov 8, 2024

• cbs-server-billing

  Public
  Python

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

• khanlab.github.io

  Public
  Khan Lab website

  HTML

  •10•2•1•2•Updated Nov 1, 2024Nov 1, 2024

• gcnn_dmri

  Public
  Python

  •

  MIT License

  •0•1•0•1•Updated Nov 1, 2024Nov 1, 2024

• SPIMprep

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

  Python

  •

  MIT License

  •1•3•9•2•Updated Oct 29, 2024Oct 29, 2024

• snakebids

  Public
  Snakemake + BIDS

  snakemakeneuroimagingbids+ 1python

  Python

  •

  MIT License

  •13•17•21•3•Updated Oct 2, 2024Oct 2, 2024

• LOBE_analysis

  Public
  Snakemake workflow for LOBE study

  Jupyter Notebook

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

• SPIMprep-deps

  Public
  Shell

  •0•0•0•0•Updated Sep 28, 2024Sep 28, 2024

• wiki

  Public
  Ruby

  •

  MIT License

  •2•0•2•1•Updated Aug 30, 2024Aug 30, 2024

• tar2bids

  Public
  Python

  •

  GNU General Public License v3.0

  •9•7•3•3•Updated Aug 20, 2024Aug 20, 2024

• hippunfold

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

  mrihippocampuspython+ 2deep-learningsegmentation

  Python

  •

  MIT License

  •13•49•16•1•Updated Jul 30, 2024Jul 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

  •12•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

• hippunfold_deps

  Public
  Dependencies container for hippocampal_autotop (niftynet, minified fsl/ants, c3d, mcr)

  Python

  •

  MIT License

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

  •400•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

• tar2bids-heuristics

  Public
  Study heuristics for autobids

  Python

  •1•0•0•1•Updated Jun 12, 2024Jun 12, 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•2•0•Updated Mar 20, 2024Mar 20, 2024

• labelmerge

  Public
  Merge label maps

  Python

  •2•3•2•0•Updated Mar 15, 2024Mar 15, 2024

• autobids-globus

  Public
  Automatically manage globus distribution of Autobids datasets

  Python

  •1•0•1•0•Updated Feb 26, 2024Feb 26, 2024

• diffparc-surf

  Public
  Snakebids app for diffparc-surf, including dwi processing

  Python

  •

  MIT License

  •0•0•6•2•Updated Dec 15, 2023Dec 15, 2023