https://github.com/alleninstitute/cell_labeling_app
Web app for labeling cells in microscopy recordings
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 3 committers (100.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Repository
Web app for labeling cells in microscopy recordings
Basic Info
- Host: GitHub
- Owner: AllenInstitute
- Language: Python
- Default Branch: master
- Size: 344 KB
Statistics
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 6
- Releases: 0
Metadata Files
README.md
Cell Labeling App
Running the app
- Clone the repository to a computer with access to on-prem resources using
git clone - Run the following:
cd cell_labeling_app conda env create -f environment.yml conda activate cell_labeling_app
Then install the labeling app with
python setup.py install
If you have not already created and populated your SQLALCHEMY_DATABASE, execute python src/server/database/populate_labeling_job.py to populate your database of labeling jobs.
Execute python -m cell_labeling_app.main --input_json <path to app input json> to start the web server.
If this computer does not have access to a browser, then you need to tunnel to port
<PORT>on a computer that does. On linux the command isssh -L <PORT>:localhost:<PORT> -N -f -l <username> <domain name of computer in step (1)>Go to
localhost:<PORT>in a browser
Notes
An ROI that you have not labeled before is randomly sampled until there are no more ROIs left to label.
The projection plot starts out centered on the ROI. Double click the plot to zoom out the entire projection, and double click again to return to the original view. Use the plot tools in the upper right to pan, zoom, etc.
The default video timeframe is argmax(trace magnitude) +- 300 timesteps
To change this timeframe, select a timeframe from the trace and then click the "Go to trace timesteps" button.
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
Last Year
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Adam Amster | a****r@a****g | 292 |
| danielsf | s****l@a****g | 11 |
| Christopher B. Morrison | c****n@a****g | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 32
- Total pull requests: 37
- Average time to close issues: 30 days
- Average time to close pull requests: 7 days
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 0.53
- Average comments per pull request: 0.24
- Merged pull requests: 35
- 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
Top Authors
Issue Authors
- aamster (21)
- danielsf (6)
- wbwakeman (4)
- morriscb (1)
Pull Request Authors
- aamster (30)
- danielsf (4)
- morriscb (3)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- Flask *
- Flask-Login *
- Flask-SQLAlchemy *
- Pillow *
- SQLAlchemy *
- gunicorn *
- h5py *
- matplotlib *
- numpy *
- opencv-python *
- pandas *
- pytest *
- actions/checkout v2 composite
- actions/setup-python v2 composite
- conda-incubator/setup-miniconda v2 composite