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.

APD estimation

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

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.

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(?)

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.