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https://github.com/braingeneers/kilosort4

https://github.com/braingeneers/kilosort4

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: braingeneers
  • Language: Python
  • Default Branch: main
  • Size: 23.4 KB
Statistics
  • Stars: 2
  • Watchers: 5
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

Kilosort4 Workflow

Intended to be run on the National Research Platform (NRP). Given a Maxwell hdf5 filepath in s3, this can launch a Job on a Pod, download the Maxwell hdf5 file, run kilosort4 on it, and upload the data back to s3.

NOTE: Currently uses the default parameters that SpikeInterface chooses.

Running on the NRP

To launch this container as a basic Job, modify the kubernetes yaml file with your Maxwell hdf5 filepath in s3, and run the example kubernetes yaml file with:

kubectl apply -f run.yaml

For example, given a Maxwell hdf5 s3 input path at:

"s3://braingeneers/ephys/{uuid}/original/data/{filename}.raw.hdf5"

this will deposit kilosort4 results at:

"s3://braingeneers/ephys/{uuid}/derived/{filename}.raw.hdf5.ks4.zip"

Building and Publishing the Container

To build the kilosort4 container, login to quay.io to host the docker image in quay:

docker login quay.io

To build the image:

docker build . -t quay.io/ucsc_cgl/kilosort4:12.4.1cudnn-runtime-ubuntu22.04

To push the image:

docker push quay.io/ucsc_cgl/kilosort4:12.4.1cudnn-runtime-ubuntu22.04

Owner

  • Name: braingeneers
  • Login: braingeneers
  • Kind: organization

GitHub Events

Total
  • Watch event: 2
  • Push event: 9
  • Pull request review event: 3
  • Pull request review comment event: 7
  • Pull request event: 2
  • Create event: 6
Last Year
  • Watch event: 2
  • Push event: 9
  • Pull request review event: 3
  • Pull request review comment event: 7
  • Pull request event: 2
  • Create event: 6