Metadata-Version: 2.1
Name: opticalmapping
Version: 0.2.0
Summary: A toolbox for analyzing optical mapping and fluorescence imaging data.
Home-page: https://github.com/cardiacvision/optimap
Author: Jan Lebert
Author-email: jan.lebert@ucsf.edu
License: MIT
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
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License-File: LICENSE.md
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# optimap

[![docs](https://readthedocs.org/projects/optimap/badge/?version=latest&style=)](https://optimap.readthedocs.org)
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[![DOI](https://zenodo.org/badge/677528623.svg)](https://zenodo.org/badge/latestdoi/677528623)

### optimap: An open-source library for the processing of 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, measuring contractility and further analyzing and visualizing the results. Refer to the [Tutorials](https://optimap.readthedocs.io/en/latest/tutorials/basics/) and the [Documentation](https://optimap.readthedocs.io/en/latest/) for more detailed information about optimap's usage and features.

> ⚠️ optimap is currently in early development, expect breaking changes and bugs.

## Installation

`optimap` is available for Mac OSX, Windows and Linux, see [Installing optimap](https://optimap.readthedocs.io/en/latest/chapters/getting_started/#installing-optimap) for more detailed information.

### Installing pre-built binaries (Mac OSX, Windows, Linux)

Pre-built binaries can be installed using pip:

```bash
pip install opticalmapping[all]
```

The above command will install optimap and all recommended dependencies including OpenCV and PySide2. If you wish to install your own version of OpenCV (e.g. for CUDA support) or Qt implementation use:

```bash
pip install opticalmapping
```

## Getting Started

See [Tutorials](https://optimap.readthedocs.io/en/latest/tutorials/basics/) and the [Getting Started](https://optimap.readthedocs.io/en/latest/chapters/getting_started/) guide for an introduction to optimap and installation instructions.

## About optimap

`optimap` is a script-based software, which means that you run Python-based analysis scripts rather than using a graphical user interface. We provide several example scripts which explain the usage of `optimap`, see [Tutorials](https://optimap.readthedocs.io/en/latest/tutorials/basics/). The example scripts can also be downloaded directly by clicking on the right link in the green box at the top of each tutorial page. `optimap` is developed by members of the [Cardiac Vision Laboratory](https://cardiacvision.ucsf.edu) at the [University of California, San Franicsco](https://www.ucsf.edu). `optimap` was 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. `optimap` is open-source, freely available, and relies on open-source packages such as NumPy, SciPy, matplotlib and OpenCV.

## Links

- [Documentation](https://optimap.readthedocs.io)
- [Issue tracker](https://github.com/cardiacvision/optimap/issues)
- [Source code](https://github.com/cardiacvision/optimap)

## Contributing

We welcome bug reports, questions, ideas for new features and pull-requests to fix issues or add new features to optimap. See [Contributing](https://optimap.readthedocs.io/en/latest/chapters/contributing/) for more information.

## License

optimap is licensed under the [MIT License](https://github.com/cardiacvision/optimap/blob/main/LICENSE.md).
