https://github.com/alleninstitute/openscope_databook
OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
Science Score: 54.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
6 of 19 committers (31.6%) from academic institutions -
✓Institutional organization owner
Organization alleninstitute has institutional domain (alleninstitute.org) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
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Repository
OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://alleninstitute.github.io/openscope_databook
- Size: 533 MB
Statistics
- Stars: 69
- Watchers: 4
- Forks: 23
- Open Issues: 22
- Releases: 15
Topics
Metadata Files
README.md
OpenScope Databook
The Deployed Databook can be found here: https://alleninstitute.github.io/openscope_databook
The citeable DOI page on Zenodo can be found here: https://zenodo.org/records/12614664
The OpenScope Databook is meant to store code and documentation used for reproducible brain data analysis and visualization, primarily working with NWB files and the DANDI archive. It is provided by the Allen Institute's OpenScope Project, a component of The Allen Institute for Neural Dynamics. OpenScope is a platform for high-throughput and reproducible neurophysiology open to external scientists to test theories of brain function. Through Jupyter Book, this code is structured as a series of documented Jupyter notebooks intended to explain and educate users on how to work with brain data.
We are releasing this code to the public as a tool we expect others to use and are actively updating and maintaining this project. Issue submissions are encouraged. Questions can be directed to @rcpeene or @jeromelecoq. Below, you can see a working list of the content goals for this databook. We are open to hearing input from users about what types of analysis and visualization might be useful for reproducible neuroscience, particularly when working with the NWB file standard.
Content Goals
Chapter 1: Using DANDI/getting data
- Downloading NWB files from DANDI
- Reading NWB files
- Exploring NWB files with NWBWidgets
- Streaming NWB files from DANDI
- Querying metadata across sessions from DANDI
Chapter 2: Data visualization
- Visualizing eye-tracking gaze locations, eye area, and running speed
- Visualizing 2P raw movie
- Visualizing Neuropixels probe locations
- Visualizing Neuropixels recorded unit quality metrics
- Visualizing LFP responses to stimulus events
- Visualizing neuronal spike matrices
- Visualizing neuronal unit responses to stimulus events in different epochs and spike waveforms
- Visualizing 2P responses to stimulus events in different epochs
Chapter 3: First-order analysis
- Neuropixels: Plotting receptive fields
- Neuropixels: Identifying opto-tagged cells
- Neuropixels: Extracting Current Source Density plots
- 2P: Cell matching across days
- 2P: Stimuli averages with 2P data
- Neuropixels: Stimuli averages with neuropixels data
- 2P: How to align timestamps across modalities
- Sending NWB raw data to a segmentation pipeline: example with Suite2p
- Classifying spike waveform between fast spiking and normal spiking cells
Chapter 4: Higher-order analysis
- Neural dynamics using time-analysis with CEBRA
CEBRA Demo on the CEBRA Repository - Extracting clusters of correlated neurons with TCA
- Estimating behavioral state given trial choices and relating states to pupil size
Chapter 5: Replicating figures
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Create event: 7
- Release event: 1
- Issues event: 10
- Watch event: 7
- Delete event: 1
- Issue comment event: 22
- Push event: 91
- Pull request event: 27
- Fork event: 5
Last Year
- Create event: 7
- Release event: 1
- Issues event: 10
- Watch event: 7
- Delete event: 1
- Issue comment event: 22
- Push event: 91
- Pull request event: 27
- Fork event: 5
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Carter Peene | c****e@a****g | 1,248 |
| Katrina Ager | k****r@a****g | 59 |
| sjara | s****a@u****u | 13 |
| Colleen J. Gillon | c****n@h****m | 13 |
| Jerome Lecoq | j****q@g****m | 13 |
| Yaroslav Halchenko | d****n@o****m | 10 |
| Steph Prince | 4****e | 9 |
| Kabilar Gunalan | k****i@m****u | 9 |
| Song Jiatai | l****7@g****m | 7 |
| KimYeerim | y****4@s****r | 4 |
| GitHub Authors Action | 4 | |
| Mackenzie Mathis | m****s@r****u | 2 |
| Ben Dichter | b****r@g****m | 1 |
| Katrina Ager | 1****r | 1 |
| KimYeerim | 1****m | 1 |
| Publishing Bot | a****n@g****m | 1 |
| github-actions[bot] | 4****] | 1 |
| shailajaAkella | 6****a | 1 |
| sytseng | s****g@g****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 69
- Total pull requests: 56
- Average time to close issues: 18 days
- Average time to close pull requests: 8 days
- Total issue authors: 5
- Total pull request authors: 4
- Average comments per issue: 4.0
- Average comments per pull request: 1.16
- Merged pull requests: 50
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 7
- Pull requests: 18
- Average time to close issues: 2 days
- Average time to close pull requests: 22 days
- Issue authors: 4
- Pull request authors: 3
- Average comments per issue: 0.14
- Average comments per pull request: 2.06
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rcpeene (79)
- jeromelecoq (20)
- bendichter (5)
- RobertoDF (1)
- cspurandare (1)
- Laohusong (1)
- NilsNyberg (1)
- sytseng (1)
- stephprince (1)
- colleenjg (1)
- satra (1)
Pull Request Authors
- rcpeene (91)
- kabilar (8)
- yarikoptic (4)
- sjara (3)
- KimYeerim (3)
- colleenjg (3)
- stephprince (2)
- Laohusong (2)
- camila-maura (1)
- jeromelecoq (1)
- shailajaAkella (1)
- yrk24 (1)
- Mikakoki (1)
- bendichter (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- actions/checkout v3 composite
- peaceiris/actions-gh-pages v3.6.1 composite
- actions/checkout v3 composite
- pozetroninc/github-action-get-latest-release master composite
- stefanzweifel/git-auto-commit-action v4 composite
- Ana06/get-changed-files v2.2.0 composite
- actions/checkout v3 composite
- Pillow ==9.3.0
- ccfwidget ==0.5.3
- cebra *
- dandi ==0.55.1
- elephant ==0.12.0
- fsspec ==2022.11.0
- h5py ==3.7.0
- jupyter ==1.0.0
- matplotlib ==3.6.2
- mpl-interactions ==0.22.0
- neo ==0.12.0
- numpy ==1.22.4
- nwbwidgets ==0.10.0
- pandas ==1.5.2
- pynwb ==2.2.0
- quantities ==0.14.1
- scikit-image ==0.19.3
- scipy ==1.9.3
- suite2p ==0.12.1
- tensortools ==0.4
- zarr ==2.13.3