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Open Source Science

https://github.com/alleninstitute/v1dd_physiology

https://github.com/alleninstitute/v1dd_physiology

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 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 62.5 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created about 4 years ago · Last pushed almost 4 years ago
Metadata Files
Readme License

README.md

v1dd_physiology

This python package allows the interaction with the Allen Institute V1 DeepDive Physiology data set. This data set contains dense calcium imaging (two-photon and three-photon) of excitatory neurons at the center of mouse primary visual cortex while displaying various visual stimuli. In total, data were collected from four mice expressing GCaMP6s as calcium indicator in excitatory neurons. The base data format loosely follows the Neurodata Without Borders (nwb) standard.

Importantly, the imaged tissue of one mouse were processed by volumetric EM processing and reconstruction to reveal detailed anatomical structures and synaptic-level connectome.

The description of the data set can be found here.

The project white paper can be found here and additional meta data can be found here.

The example for using this package can be found in these ipython notebooks.

A recorded video introducing this database can be found here or as a mp4 file: \\allen\programs\mindscope\workgroups\surround\v1dd_in_vivo_new_segmentation\v1dd_physiology_intro_JunZhuang-20220701.mp4

 

Special dependency

 

Install

Create environment

```

conda create -n v1dd python=3 conda activate v1dd ```

Install volumeimaging2P_analysis

```

pip install v1dd-physiology ```

or

```

git clone https://github.com/AllenInstitute/v1ddphysiology.git cd v1ddphysiology pip install . ```

Install Jupyter Notebook

```

conda install jupyter jupyterlab python -m ipykernel install --user --name v1dd --display-name "Python3 (v1dd)" ```

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 75
  • Total Committers: 2
  • Avg Commits per committer: 37.5
  • Development Distribution Score (DDS): 0.027
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jun Zhuang w****r@h****m 73
Jun Zhuang j****z@a****g 2
Committer Domains (Top 20 + Academic)
alleninstitute.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 33
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 33
  • Bot issues: 0
  • Bot pull requests: 0
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
Pull Request Authors
  • zhuangjun1981 (33)
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 6 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 3
  • Total maintainers: 1
pypi.org: v1dd-physiology

SDK for volumetric multi-photon data of V1 DeepDive project

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 6 Last month
Rankings
Dependent packages count: 9.8%
Dependent repos count: 21.8%
Forks count: 22.7%
Average: 32.3%
Stargazers count: 38.9%
Downloads: 68.2%
Maintainers (1)
zhuangjun1981
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • NeuroAnalysisTools *
  • cython *
  • h5py *
  • matplotlib *
  • numpy *
  • opencv-python *
  • pandas *
  • pillow *
  • pytest *
  • scikit-image *
  • scipy *
  • tifffile *