napari-omaas 0.1.3

napari-OMAAS stands for Optical Mapping Acquisition and Analysis Software

napari-omaas

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

This 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.

This plugin is in a very early developmental/experimental stage so expect very braking changes at anytime. At the momment supports reading images in .sif format from Andor Technologies powered by the sif_parser python module.

Usage

This plugin can read images generated with Andor Technologies cameras. It has been currently tested on Zyla cameras. Just drag and drop an image to the napari GUI, and the image will display. Alternatively, you can programmatically load/read the image within a notebook.

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 use the standard call to the corresponding layer:

viewer.layers['my_image'].metadata

In addition to opening this specific image format (.sif), it allows the users to perform some basic operations and visualization on images, such as normalization, temporal/spatial filters, motion tracking/compenstaion, plot profile, etc.

Examples

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 average data from the ROI selected.

The next example shows how to compute action potetnial duration in the same image stack.

Roadmap

This plugin is composed of two major components: analysis and acquisition.

Bellow is a list of some features this pluggin aims to do.

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 and align heart ROIs.
• Export results 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.

Installation

You can install napari-omaas via pip:

pip install napari-omaas

To install the latest development version (recommended) :

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

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.