A toolbox for analyzing optical mapping and fluorescence imaging data.
Project description
optimap
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, computing activation maps, performing motion compensation and inhibiting motion artifacts, measuring contractility and further post-processing, analyzing and visualizing the results. Refer to the documentation and tutorials for a more detailed list of 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 for more detailed information.
Installing pre-built binaries (Mac OSX, Windows, Linux)
Pre-built binaries can be installed using pip:
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:
pip install opticalmapping
Getting Started
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 very simple example scripts, which explain the usage of optimap, see Tutorials. The example scripts can also be downloaded directly here: example script 1, example script 2. See the Getting Started guide for installation instructions and a quick introduction to optimap. optimap relies on other packages such as numpy, 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.
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