napari OMAAS

napari-OMAAS stands for Optical Mapping Acquisition and Analysis Software for panoramic heart imaging.

This napari plugin intends to be an analysis and acquisition tool for optical mapping in potentiometric (V_m) or calcium (Ca²⁺) fluorescence signals obtained from panoramic imaging of intact hearts.

It supports reading images in .sif format and binary files generated from Andor Technologies cameras powered by the sif_parser python module.

Examples¶

Plot profile¶

The following example ilustrate how to perform normalization (pixelwise) on a time serie image and plot its 2d profile along the t dimension withing the averaged ROI selected pixels.

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APD estimation¶

The next example shows how to compute action potential duration (APD) in the same image stack.

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You can also perform additional operations on images, such as normalization, temporal/spatial filters, segmentation, but also apply more advanced image processing methods such as motion tracking/compensation, etc.

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Roadmap¶

This plugin was aimed to have two major components: analysis and acquisition. Bellow is a list of the current features that napari-omaas supports:

Analysis Features¶

• Read sif files from Andor Technologies.
• Display time profile of ROIs on image sequences.
• Normalize images.
  • Perform peak analysis of action potential / Calcium traces.
  • Add motion correction.
  • APD analysis.
  • Create activation maps.
  • Segment images.
  • Automatic crop and alignment of heart ROIs.
• Export results, metadata and analysis log.

Acquisition Features¶

• Control Zyla camera for the acquisition of data
  • test using the PYME module
• Real-time analysis(?)

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This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Contributing¶

Contributions are very welcome. Run tests with tox, ensuring the coverage remains the same before you submit a pull request.

License¶

Distributed under the terms of the BSD-3 license, "napari-omaas" is free and open source software.

Issues¶

If you encounter any problems, please file an issue and a detailed description.