Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/catalystneuro/ahrens-lab-to-nwb

NWB Conversion project for the Ahrens lab at the Janelia research campus. Sponsored by the Simons Foundation.

https://github.com/catalystneuro/ahrens-lab-to-nwb

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords from Contributors

nwb-conversion data-retrieval electrophysiology neuroscience spike-sorting
Last synced: 6 months ago · JSON representation

Repository

NWB Conversion project for the Ahrens lab at the Janelia research campus. Sponsored by the Simons Foundation.

Basic Info
  • Host: GitHub
  • Owner: catalystneuro
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 119 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

ahrens-lab-to-nwb

NWB conversion scripts for the Ahrens lab data to the Neurodata Without Borders data format.

Clone and install

To run the conversion some basic machinery is needed: python, git and pip. For most users, we recommend you to install conda (installation instructions) as it contains all the required machinery in a single and simple install. If your system is windows you might also need to install git (installation instructions) to interact with this repository.

From a terminal (note that conda should install one in your system) you can do the following:

git clone https://github.com/catalystneuro/ahrens-lab-to-nwb cd ahrens-lab-to-nwb conda env create --file make_env.yml conda activate ahrens-lab-to-nwb-env This create a conda environment which isolates the conversion from your system. We recommend that you run all your conversion related tasks and analysis from that environment to minimize the intereference of this code with your own system.

Alternatively, if you want to avoid conda altogether (for example if you use another virtual environment tool) you can install the repository with the following commands using only pip: git clone https://github.com/catalystneuro/ahrens-lab-to-nwb cd ahrens-lab-to-nwb pip install -e .

Note: both of the methods above install the repository in editable mode

Repository structure

Each conversion is organized in a directory of its own in the src directory:

ahrens-lab-to-nwb/
├── LICENSE
├── make_env.yml
├── pyproject.toml
├── README.md
├── requirements.txt
├── setup.py
└── src
    ├── ahrens_lab_to_nwb
    │   ├── conversion_directory_1
    │   └── yu_mu_cell_2019`
    │       ├── yu_mu_cell_2019behaviorinterface.py
    │       ├── yu_mu_cell_2019_convert_script.py
    │       ├── yu_mu_cell_2019_metadata.yml
    │       ├── yu_mu_cell_2019nwbconverter.py
    │       ├── yu_mu_cell_2019_requirements.txt
    │       ├── yu_mu_cell_2019_notes.md

    │       └── __init__.py
    │   ├── conversion_directory_b

    └── __init__.py

For example, for the conversion yu_mu_cell_2019 you can find a directory located in src/ahrens-lab-to-nwb/yu_mu_cell_2019. Inside each conversion directory you can find the following files:

  • yu_mu_cell_2019_convert_script.py: this is the cemtral script that you must run in order to perform the full conversion.
  • yu_mu_cell_2019_requirements.txt: dependencies specific to this conversion specifically.
  • yu_mu_cell_2019_metadata.yml: metadata in yaml format for this specific conversion.
  • yu_mu_cell_2019behaviorinterface.py: the behavior interface. Usually ad-hoc for each conversion.
  • yu_mu_cell_2019nwbconverter.py: the place where the NWBConverter class is defined.
  • yu_mu_cell_2019_notes.md: notes and comments concerning this specific conversion.

The directory might contain other files that are necessary for the conversion but those are the central ones.

Running a specific conversion

To run a specific conversion, you might need to install first some conversion specific dependencies that are located in each conversion directory: pip install -r src/ahrens_lab_to_nwb/yu_mu_cell_2019/yu_mu_cell_2019_requirements.txt

You can run a specific conversion with the following command: python src/ahrens_lab_to_nwb/yu_mu_cell_2019/yu_mu_cell_2019_conversion_script.py

Viewing the NWB files on DANDI

This is very easy through the DANDI Hub platform - simply follow the instructions inside the Interactive Notebook Tutorial

Owner

  • Name: CatalystNeuro
  • Login: catalystneuro
  • Kind: organization
  • Email: hello@catalystneuro.com

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 72
  • Total Committers: 4
  • Avg Commits per committer: 18.0
  • Development Distribution Score (DDS): 0.542
Top Committers
Name Email Commits
Cody Baker c****9@n****u 33
Cody Baker 5****D@u****m 26
pre-commit-ci[bot] 6****]@u****m 12
CodyCBakerPhD c****d@g****m 1
Committer Domains (Top 20 + Academic)
nd.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 3
  • Total pull requests: 20
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.5
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 10
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • CodyCBakerPhD (3)
Pull Request Authors
  • CodyCBakerPhD (10)
  • pre-commit-ci[bot] (10)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 15 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 2
pypi.org: ahrens-lab-to-nwb

NWB conversion scripts, functions, and classes for an the Ahrens lab.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 15 Last month
Rankings
Dependent packages count: 6.6%
Average: 30.1%
Forks count: 30.5%
Dependent repos count: 30.6%
Stargazers count: 39.1%
Downloads: 43.6%
Maintainers (2)
bendichter cbaker9
Last synced: 7 months ago

Dependencies

requirements.txt pypi
  • nwb-conversion-tools *
  • nwbinspector *
  • nwbwidgets *
.github/workflows/add-to-dashboard.yml actions
  • leonsteinhaeuser/project-beta-automations v1.2.1 composite
.github/workflows/auto-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish v1.4.2 composite
src/ahrens_lab_to_nwb/yu_mu_cell_2019/yu_mu_cell_2019_requirements.txt pypi
  • ndx-events ==0.2.0