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ibl-neuropixel

Collection of tools to handle Neuropixel 1.0 and 2.0 data

https://github.com/int-brain-lab/ibl-neuropixel

Science Score: 57.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Collection of tools to handle Neuropixel 1.0 and 2.0 data

Basic Info
  • Host: GitHub
  • Owner: int-brain-lab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 2.04 MB
Statistics
  • Stars: 17
  • Watchers: 24
  • Forks: 4
  • Open Issues: 5
  • Releases: 29
Created about 4 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

ibl-neuropixel

Collection of tools to handle Neuropixel 1.0 and 2.0 data (documentation coming soon...)

Installation

Minimum Python version supported is 3.10 pip install ibl-neuropixel

Destriping

Getting started

This relies on a fast fourier transform external library: pip install pyfftw.

Minimal working example to destripe a neuropixel binary file. ```python from pathlib import Path from ibldsp.voltage import decompressdestripecbin srfile = Path('/datadisk/Data/spikesorting/pykilosorttests/imec385100s.ap.bin') outfile = Path('/datadisk/scratch/imec385100s.ap.bin')

decompressdestripecbin(srfile=srfile, outputfile=outfile, nprocesses=8) ```

Viewer

The best way to look at the results is to use viewephys, open an ephys viewer on the raw data.

  • tick the destripe box.
  • move to a desired location in the file
  • ctr+P will make the gain and axis the same on both windows

alt text

You can then move within the raw data file.

White Paper

The following describes the methods implemented in this repository. https://doi.org/10.6084/m9.figshare.19705522

Contribution

Please see our contribution guidelines for details on how to contribute to this project.

Owner

  • Name: International Brain Laboratory
  • Login: int-brain-lab
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 0.0.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: International Brain Laboratory
    given-names: The
    orcid:
title: "ibl-neuropixel"
version:
doi:
date-released: 2021-12-09
url: "https://github.com/int-brain-lab/ibl-neuropixel"

GitHub Events

Total
  • Create event: 23
  • Release event: 5
  • Issues event: 12
  • Watch event: 4
  • Delete event: 18
  • Issue comment event: 12
  • Push event: 47
  • Pull request review event: 2
  • Pull request event: 29
  • Fork event: 1
Last Year
  • Create event: 23
  • Release event: 5
  • Issues event: 12
  • Watch event: 4
  • Delete event: 18
  • Issue comment event: 12
  • Push event: 47
  • Pull request review event: 2
  • Pull request event: 29
  • Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 21
  • Total pull requests: 50
  • Average time to close issues: 3 months
  • Average time to close pull requests: 16 days
  • Total issue authors: 9
  • Total pull request authors: 8
  • Average comments per issue: 1.29
  • Average comments per pull request: 0.22
  • Merged pull requests: 41
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 7
  • Pull requests: 24
  • Average time to close issues: 2 months
  • Average time to close pull requests: 10 days
  • Issue authors: 7
  • Pull request authors: 6
  • Average comments per issue: 1.57
  • Average comments per pull request: 0.17
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • oliche (9)
  • chris-langfield (4)
  • grahamfindlay (1)
  • imontiel92 (1)
  • k1o0 (1)
  • mayofaulkner (1)
  • gersgers (1)
  • grg2rsr (1)
  • JoeZiminski (1)
Pull Request Authors
  • chris-langfield (21)
  • oliche (20)
  • mayofaulkner (7)
  • k1o0 (6)
  • GaelleChapuis (5)
  • grg2rsr (5)
  • kushbanga (1)
  • guidomeijer (1)
Top Labels
Issue Labels
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 7,805 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 5
  • Total versions: 45
  • Total maintainers: 2
pypi.org: ibl-neuropixel

Collection of tools for Neuropixel 1.0 and 2.0 probes data

  • Versions: 45
  • Dependent Packages: 2
  • Dependent Repositories: 5
  • Downloads: 7,805 Last month
Rankings
Dependent packages count: 3.2%
Dependent repos count: 6.6%
Downloads: 7.8%
Average: 10.3%
Forks count: 15.3%
Stargazers count: 18.5%
Maintainers (2)
ibl oliche
Last synced: 10 months ago

Dependencies

requirements-dev.txt pypi
  • flake8 *
  • pytest *
requirements-gpu.txt pypi
  • cudatoolkit <=11.0
  • cupy *
  • pyfftw *
requirements.txt pypi
  • iblutil *
  • joblib *
  • mtscomp *
  • numpy *
  • one-api *
  • pandas *
  • scipy *
.github/workflows/publish_to_pypi.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish 37f50c210e3d2f9450da2cd423303d6a14a6e29f composite
.github/workflows/tests.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
setup.py pypi