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viewephys

Neuropixel raw data viewer

https://github.com/int-brain-lab/viewephys

Science Score: 44.0%

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
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Neuropixel raw data viewer

Basic Info
  • Host: GitHub
  • Owner: int-brain-lab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 1.95 MB
Statistics
  • Stars: 2
  • Watchers: 25
  • Forks: 1
  • Open Issues: 4
  • Releases: 0
Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Citation

README.md

viewephys

Neuropixel raw data viewer

Installation

pip install viewephys

Alternatively, in development mode: shell git clone https://github.com/int-brain-lab/viewephys.git cd viewephys pip install -e .

Supported environments

This is compatible with the IBL environment

Otherwise, you can create a new environment as such: shell conda create -n viewephys python=3.12 conda activate viewephys And then follow the install instructions above.

Controls

  • ctrl + z: -3dB gain
  • ctrl + a: +3dB gain
  • ctrl + p: in multi-windows mode, link the displays (pan, zoom and gain)

Pick spikes

When the picking mode is enabled (menu pick) - left button click sets a point - shift + left button removes a point - control + left does not wrap on maximum around pick - space increments the spike group number

Examples

Visualize raw binary file

Activate your environment and type viewephys, you can then load a neuropixel binary file using the file menu.

alt text

Alternatively you can point the viewer to a specific file using the command line: shell viewphys -f /path/to/raw.bin

Load in a numpy array or slice

```python

if running ipython, you may have to use the %gui qt magic command

import numpy as np from viewephys.gui import viewephys nc, ns, fs = (384, 50000, 30000) # this mimics one second of neuropixel data data = np.random.randn(nc, ns) / 1e6 # volts by default ve = viewephys(data, fs=fs) ``` alt text

Contribution

Fork and PR.

Pypi Release checklist: ```shell ruff check rm -fR dist rm -fR build python setup.py sdist bdist_wheel twine upload dist/*

twine upload --repository-url https://test.pypi.org/legacy/ dist/*

```

Owner

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

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software for a publication, please cite it as below."
authors:
  - family-names: Winter
    given-names: Olivier
    orcid: https://orcid.org/0000-0001-9278-2721
title: "viewephys"
version: 0.1.1
doi:
date-released: 2022-02-21
url: "https://github.com/oliche/viewephys"

GitHub Events

Total
  • Issues event: 3
  • Issue comment event: 5
  • Push event: 2
  • Create event: 1
Last Year
  • Issues event: 3
  • Issue comment event: 5
  • Push event: 2
  • Create event: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 4 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 1.67
  • Average comments per pull request: 1.25
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 0
  • Average comments per issue: 1.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • zm711 (1)
  • majidkhalili (1)
  • oliche (1)
Pull Request Authors
  • GaelleChapuis (4)
  • chris-langfield (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 108 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 9
  • Total maintainers: 1
pypi.org: viewephys

Raw Neuropixel data viewer for numpy

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 108 Last month
Rankings
Dependent packages count: 10.1%
Dependent repos count: 11.6%
Average: 23.3%
Stargazers count: 27.8%
Forks count: 29.8%
Downloads: 37.4%
Maintainers (1)
oliche
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • easyqc >=0.6.2
  • ibl-neuropixel *
  • ibllib *
setup.py pypi