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:
pip install optimap
To update optimap to the latest version run
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.
1 maintainer
Metadata
1 maintainer
Release files for optimap 0.3.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
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Built distributions (wheels)
Total release size: 8.3 MB
Release files / optimap-0.3.1.tar.gz
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