Khan Computational Imaging Lab

hippunfold

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

snakebids

Snakemake + BIDS

tar2bids

autobids

Automated Dicom to BIDS and pipelines using compute canada

neuroglia-helpers

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

scattr

BIDS app for structural connectivity between targeted regions

labelmerge

Merge label maps

khanlab.github.io

Khan Lab website

SPIMprep

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

gcnn_dmri

SPIMquant

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

subcorticalparc-smk

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

zarrnii

actions

Centralized repo of reusable GH actions

autobids-globus

Automatically manage globus distribution of Autobids datasets

autobids-newstudy-app

billing-snakemake

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

SPIMprep-deps

SPIMquant-deps

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

trident_example_project

wiki