napari OMAAS

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

This plugin is intended to be an analyis and aquisition tool for optical mapping system from panoramic imaging of potentiometric or Ca^2+^ fluorescence signals of intact hearts.

At the moment this pluging is in very early development/experimental stage and only support reading images in .sif format from Andor Technologies powered by the sif_parser python module.

Usage¶

At the moment only can read images generated with Andor Technologies cameras and have been tested on Zyla cameras. Just drag and drop an image to the napari GUI and image will be display. Alternative you can from within a notebook programatically load/read the image

import napari


file = "path/to/my/file/my_image.sif"

viewer = napari.Viewer()
viewer.open(path=file, plugin="napari-omaas", name = "my_image")

to display the metadata just use the standard call to the corresponding layer:

viewer.layers['my_image'].metadata

Roadmap¶

This plugin can be brake down to two mayor components: analysis and aquisition.

Analysis features¶

• Read sif files from Andor Technologies.
• Display time profile of ROIs on image sequences.
• normalize images.
  • segement images and aligne heart ROIs.
  • perform peak analysis of action potential / Calcium traces
  • create activation maps
  • add motion correction
• export results and analysis log.

Aquisition features¶

• Control Zyla camera for aquisition 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.

Installation¶

You can install napari-omaas via pip:

pip install napari-omaas

To install latest development version :

pip install git+https://github.com/rjlopez2/napari-omaas.git

Contributing¶

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays 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 along with a detailed description.