Khan Computational Imaging Lab's repositories
hippunfold
BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
neuroglia-helpers
Helper and wrapper scripts for using Singularity locally and on compute canada
labelmerge
Merge label maps
khanlab.github.io
Khan Lab website
subcorticalparc-smk
General-purpose Snakemake workflow for subcortical parcellation with functional and structural connectivity
autobids-globus
Automatically manage globus distribution of Autobids datasets
cvpl_tools
A Python package for utilities and classes related to the file I/O, dataset record keeping for image processing and computer vision.
diffparc-surf
Snakebids app for diffparc-surf, including dwi processing
eplink-redcap2bids
Workflow for exporting redcap braincode data to bids
hippunfold-frozen-2024-04-25
Frozen archive of hippunfold (prior to rewriting history in hippunfold)
hippunfold_deps
Dependencies container for hippocampal_autotop (niftynet, minified fsl/ants, c3d, mcr)
LOBE_analysis
Snakemake workflow for LOBE study
spimquant_cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
spimquant_CellSeg3D
A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks
tar2bids-heuristics
Study heuristics for autobids