{"payload":{"pageCount":4,"repositories":[{"type":"Public","name":"cvpl_tools","owner":"khanlab","isFork":false,"description":"A Python package for utilities and classes related to the file I/O, dataset record keeping for image processing and computer vision.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-17T19:57:51.380Z"}},{"type":"Public","name":"SPIMprep","owner":"khanlab","isFork":false,"description":"A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":10,"starsCount":2,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-17T15:43:39.534Z"}},{"type":"Public","name":"zarrnii","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-09T16:58:22.874Z"}},{"type":"Public","name":"SPIMquant","owner":"khanlab","isFork":false,"description":"SnakeBIDS app for quantiative analysis of SPIM (lightsheet) brain data","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":1,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-01T18:20:07.264Z"}},{"type":"Public","name":"khanlab.github.io","owner":"khanlab","isFork":false,"description":"Khan Lab website","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":1,"issueCount":1,"starsCount":2,"forksCount":8,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-01T05:12:38.084Z"}},{"type":"Public","name":"gcnn_dmri","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-01T01:26:30.642Z"}},{"type":"Public","name":"hippunfold","owner":"khanlab","isFork":false,"description":"BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)","allTopics":["mri","hippocampus","python","deep-learning","segmentation"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":16,"starsCount":47,"forksCount":12,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-30T19:13:11.422Z"}},{"type":"Public","name":"subcorticalparc-smk","owner":"khanlab","isFork":true,"description":"General-purpose Snakemake workflow for subcortical parcellation with functional and structural connectivity","allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":2,"issueCount":0,"starsCount":1,"forksCount":7,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-30T14:05:04.433Z"}},{"type":"Public","name":"snakebids","owner":"khanlab","isFork":false,"description":"Snakemake + BIDS","allTopics":["snakemake","neuroimaging","bids","python"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":21,"starsCount":17,"forksCount":14,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-30T13:47:30.848Z"}},{"type":"Public","name":"SPIMprep-deps","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Dockerfile","color":"#384d54"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-23T15:49:14.374Z"}},{"type":"Public","name":"spimquant_CellSeg3D","owner":"khanlab","isFork":true,"description":"A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":10,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-20T17:18:16.033Z"}},{"type":"Public","name":"actions","owner":"khanlab","isFork":false,"description":"Centralized repo of reusable GH actions","allTopics":[],"primaryLanguage":null,"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-01T13:12:14.842Z"}},{"type":"Public","name":"hippunfold_deps","owner":"khanlab","isFork":false,"description":"Dependencies container for hippocampal_autotop (niftynet, minified fsl/ants, c3d, mcr)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-26T17:42:57.663Z"}},{"type":"Public","name":"autobids-portal","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":9,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-26T17:21:13.998Z"}},{"type":"Public","name":"trident_example_project","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-21T19:19:06.941Z"}},{"type":"Public","name":"spimquant_cellpose","owner":"khanlab","isFork":true,"description":"a generalist algorithm for cellular segmentation with human-in-the-loop capabilities","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":377,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-18T15:34:33.324Z"}},{"type":"Public archive","name":"autobids","owner":"khanlab","isFork":false,"description":"Automated Dicom to BIDS and pipelines using compute canada","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":3,"starsCount":5,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-13T13:09:48.383Z"}},{"type":"Public","name":"tar2bids-heuristics","owner":"khanlab","isFork":false,"description":"Study heuristics for autobids","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-12T14:26:18.006Z"}},{"type":"Public","name":"wiki","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Ruby","color":"#701516"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-17T15:24:09.910Z"}},{"type":"Public","name":"SPIMquant-deps","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Dockerfile","color":"#384d54"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-10T02:16:04.284Z"}},{"type":"Public","name":"LOBE_analysis","owner":"khanlab","isFork":false,"description":"Snakemake workflow for LOBE study","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-09T04:35:13.134Z"}},{"type":"Public archive","name":"hippunfold-frozen-2024-04-25","owner":"khanlab","isFork":false,"description":"Frozen archive of hippunfold (prior to rewriting history in hippunfold)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-25T16:29:30.456Z"}},{"type":"Public","name":"tar2bids","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":2,"starsCount":7,"forksCount":9,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-02T20:47:23.703Z"}},{"type":"Public","name":"scattr","owner":"khanlab","isFork":false,"description":"BIDS app for structural connectivity between targeted regions","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":4,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-20T18:31:14.045Z"}},{"type":"Public","name":"labelmerge","owner":"khanlab","isFork":false,"description":"Merge label maps","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":3,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-15T16:22:25.271Z"}},{"type":"Public","name":"autobids-globus","owner":"khanlab","isFork":false,"description":"Automatically manage globus distribution of Autobids datasets","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-26T19:15:35.878Z"}},{"type":"Public","name":"diffparc-surf","owner":"khanlab","isFork":false,"description":"Snakebids app for diffparc-surf, including dwi processing","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":6,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-15T15:44:48.873Z"}},{"type":"Public","name":"eplink-redcap2bids","owner":"khanlab","isFork":false,"description":"Workflow for exporting redcap braincode data to bids","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-30T19:36:50.548Z"}},{"type":"Public","name":"neuroglia-helpers","owner":"khanlab","isFork":false,"description":"Helper and wrapper scripts for using Singularity locally and on compute canada","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":1,"starsCount":5,"forksCount":7,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-28T13:49:36.123Z"}},{"type":"Public","name":"billing-snakemake","owner":"khanlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-25T19:50:42.839Z"}}],"repositoryCount":111,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"khanlab repositories"}