# napari-omaas
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[](https://pypi.org/project/napari-omaas)
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[](https://codecov.io/gh/rjlopez2/napari-omaas)
[](https://napari-hub.org/plugins/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<sub>m</sub>) or calcium (Ca<sup>2+</sup>) 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 specific image format, 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.
The following example ilustrate how to perform normalization (pixelwise) on a time serie image and plot 2d profile along the t dimension.
## 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
- [x] Read sif files from Andor Technologies.
- [x] Display time profile of ROIs on image sequences.
- [x] Normalize images.
- [x] Perform peak analysis of action potential / Calcium traces.
- [x] Add motion correction.
- [x] APD analysis.
- [ ] Create activation maps.
- [ ] Segment images and align heart ROIs.
- [x] Export results 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.
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started
Also review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->
## 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.
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/rjlopez2/napari-omaas/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
[sif_parser]: https://pypi.org/project/sif-parser/
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"description": "# napari-omaas\n\n[](https://github.com/rjlopez2/napari-omaas/raw/main/LICENSE)\n[](https://pypi.org/project/napari-omaas)\n[](https://python.org)\n[](https://github.com/rjlopez2/napari-omaas/actions)\n[](https://codecov.io/gh/rjlopez2/napari-omaas)\n[](https://napari-hub.org/plugins/napari-omaas)\n\n**napari-OMAAS stands for Optical Mapping Acquisition and Analysis Software for panoramic heart imaging**\n\nThis plugin intends to be an analysis and acquisition tool for optical mapping in potentiometric (V<sub>m</sub>) or calcium (Ca<sup>2+</sup>) fluorescence signals obtained from panoramic imaging of intact hearts.\n\nThis 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.\n\n## Usage\n\nThis 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.\n \n import napari\n \n file = \"path/to/my/file/my_image.sif\"\n\n viewer = napari.Viewer()\n viewer.open(path=file, plugin=\"napari-omaas\", name = \"my_image\")\n\nto display the metadata use the standard call to the corresponding layer:\n\n viewer.layers['my_image'].metadata\n\nIn addition to opening specific image format, 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.\n\nThe following example ilustrate how to perform normalization (pixelwise) on a time serie image and plot 2d profile along the t dimension.\n\n\n\n## Roadmap\n\nThis plugin is composed of two major components: **analysis** and **acquisition**.\n\nBellow is a list of some features this pluggin aims to do.\n\n### Analysis Features\n \n- [x] Read sif files from Andor Technologies.\n- [x] Display time profile of ROIs on image sequences.\n- [x] Normalize images.\n - [x] Perform peak analysis of action potential / Calcium traces.\n - [x] Add motion correction.\n - [x] APD analysis.\n - [ ] Create activation maps.\n - [ ] Segment images and align heart ROIs.\n- [x] Export results and analysis log.\n\n### Acquisition Features\n\n- [ ] Control Zyla camera for the acquisition of data\n - [ ] test using the PYME module\n- [ ] Real-time analysis(?)\n\n \n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nAlso review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Installation\n\nYou can install `napari-omaas` via [pip]:\n\n pip install napari-omaas\n\n\n\nTo install the latest development version (recommended) :\n\n pip install git+https://github.com/rjlopez2/napari-omaas.git\n\n\n## Contributing\n\nContributions are very welcome. Run tests with [tox], ensuring\nthe coverage remains the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-omaas\" is free and open source software.\n\n## Issues\n\nIf you encounter any problems, please [file an issue] and a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/rjlopez2/napari-omaas/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n[sif_parser]: https://pypi.org/project/sif-parser/\n",
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