optimap
An open-source python library for the processing of fluorescence video data
Science Score: 75.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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✓Institutional organization owner
Organization cardiacvision has institutional domain (cardiacvision.ucsf.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary
Keywords
Repository
An open-source python library for the processing of fluorescence video data
Basic Info
- Host: GitHub
- Owner: cardiacvision
- License: mit
- Language: C++
- Default Branch: main
- Homepage: https://cardiacvision.github.io/optimap/
- Size: 5.02 MB
Statistics
- Stars: 15
- Watchers: 1
- Forks: 2
- Open Issues: 1
- Releases: 11
Topics
Metadata Files
README.md
optimap
optimap: An open-source library for processing fluorescence video data
optimap is an open-source Python toolbox for exploring, visualizing, and analyzing high-speed fluorescence imaging data with a focus on cardiac optical mapping data. It includes modules for loading, processing and exporting videos, extracting and measuring optical traces, visualizing action potential or calcium waves, tracking motion and compensating motion artifacts, computing activation maps, conduction velocities, action potential durations, as well as measuring contractility and further analyzing and visualizing the results. Refer to the Tutorials and the Documentation for more information about optimap's features.
Installation
optimap supports macOS, Windows, and Linux. See the Getting Started guide for more information.
You can install optimap using pip:
bash
pip install optimap
To update optimap to the latest version run
bash
pip install --upgrade optimap
About optimap
optimap is an interactive, script or notebook-based software library created for cardiovascular scientists in particular, but might also be useful for scientists in other fields. For instance, when performing calcium imaging or physiological research with moving cells or tissues. It is designed to be a flexible and customizable analysis workflow toolkit, which allows for a wide range of analyses and visualizations. See the Tutorials for examples and more information about the usage of optimap. The tutorials can be downloaded by clicking on the link in the green box at the top of each tutorial page.
optimap is developed by Jan Lebert and Jan Christoph of the Cardiac Vision Laboratory at the University of California, San Franicsco. It is open-source, freely available, and relies on open-source packages such as NumPy, SciPy, Matplotlib and OpenCV.
Links
Contributing
We welcome bug reports, questions, ideas for new features and pull-requests to fix issues or add new features to optimap. See Contributing for more information.
License
optimap is licensed under the MIT License.
Owner
- Name: Cardiac Vision Laboratory
- Login: cardiacvision
- Kind: organization
- Location: United States of America
- Website: https://cardiacvision.ucsf.edu
- Repositories: 1
- Profile: https://github.com/cardiacvision
Cardiovascular Research Institute, University of California, San Francisco
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: >-
optimap: An open-source library for the processing of
fluorescence video data
message: 'If you use this software, please cite it as below.'
type: software
authors:
- family-names: Lebert
given-names: Jan
orcid: 'https://orcid.org/0000-0001-8754-4964'
- family-names: Christoph
given-names: Jan
orcid: 'https://orcid.org/0000-0003-3594-4717'
identifiers:
- type: doi
value: 10.5281/zenodo.8336455
url: 'https://github.com/cardiacvision/optimap'
license: MIT
GitHub Events
Total
- Create event: 8
- Issues event: 1
- Release event: 4
- Watch event: 6
- Delete event: 4
- Push event: 67
- Fork event: 1
Last Year
- Create event: 8
- Issues event: 1
- Release event: 4
- Watch event: 6
- Delete event: 4
- Push event: 67
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 4
- Total pull requests: 1
- Average time to close issues: 26 days
- Average time to close pull requests: 2 minutes
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 0.25
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 2 minutes
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- sitic (3)
- KyrysXYZ (1)
Pull Request Authors
- sitic (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 389 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 1
(may contain duplicates) - Total versions: 16
- Total maintainers: 3
pypi.org: optimap
A toolbox for analyzing optical mapping and fluorescence imaging data.
- Homepage: https://github.com/cardiacvision/optimap
- Documentation: https://optimap.readthedocs.io/
- License: MIT
-
Latest release: 0.3.1
published 11 months ago
Rankings
Maintainers (1)
pypi.org: opticalmapping
Deprecated. Please use the 'optimap' package instead.
- Homepage: https://github.com/cardiacvision/optimap
- Documentation: https://opticalmapping.readthedocs.io/
- License: mit
-
Latest release: 0.2.5
published 12 months ago
Rankings
Maintainers (2)
Dependencies
- actions/checkout v4 composite
- actions/upload-artifact v3 composite
- pypa/cibuildwheel v2.15.0 composite
- actions/checkout v4 composite
- actions/download-artifact v3 composite
- actions/upload-artifact v3 composite
- pypa/cibuildwheel v2.15.0 composite
- pypa/gh-action-pypi-publish release/v1 composite
- matplotlib *
- numpy *
- pooch *
- scikit-image *
- scikit-video *
- scipy *
- seasonal *
- tqdm *