Metadata-Version: 2.1
Name: napari-generic-SIMulator
Version: 0.0.11
Summary: A simple plugin to use with napari to simulate raw image stacks in Structured illumination microscopy (SIM) with napari.
Home-page: https://github.com/Meizhu-Liang/napari-generic-SIMulator
Author: Meizhu Liang
Author-email: ml2618@ic.ac.uk
License: BSD-3-Clause
Project-URL: Bug Tracker, https://github.com/Meizhu-Liang/napari-generic-SIMulator/issues
Project-URL: Documentation, https://github.com/Meizhu-Liang/napari-generic-SIMulator#README.md
Project-URL: Source Code, https://github.com/Meizhu-Liang/napari-generic-SIMulator
Project-URL: User Support, https://github.com/Meizhu-Liang/napari-generic-SIMulator/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: testing
License-File: LICENSE

# napari-generic-SIMulator

[![License BSD-3](https://img.shields.io/pypi/l/napari-generic-SIMulator.svg?color=green)](https://github.com/Meizhu-Liang/napari-generic-SIMulator/raw/main/LICENSE)
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[![Python Version](https://img.shields.io/pypi/pyversions/napari-generic-SIMulator.svg?color=green)](https://python.org)
[![tests](https://github.com/Meizhu-Liang/napari-generic-SIMulator/workflows/tests/badge.svg)](https://github.com/Meizhu-Liang/napari-generic-SIMulator/actions)
[![codecov](https://codecov.io/gh/Meizhu-Liang/napari-generic-SIMulator/branch/main/graph/badge.svg)](https://codecov.io/gh/Meizhu-Liang/napari-generic-SIMulator)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-generic-SIMulator)](https://napari-hub.org/plugins/napari-generic-SIMulator)

A napari plugin to simulate raw-image stacks of Structured illumination microscopy (SIM) with light sheet. 

The simulation is originally based on the paper <strong>GPU-accelerated real-time reconstruction in Python of three-dimensional datasets from structured illumination microscopy with hexagonal patterns</strong> by
Hai Gong, Wenjun Guo and Mark A. A. Neil (https://doi.org/10.1098/rsta.2020.0162). 

The calculation can be GPU-accelerated if cupy is installed.  

Currently applies to:
- conventional 2-beam SIM data with 3 angles and 3 phases
- 3-beam hexagonal SIM data with 7 phases, as described in the paper
- 3-beam hexagonal SIM data with 7 phases at right-angles

----------------------------------

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

and review the napari docs for plugin developers:
https://napari.org/plugins/index.html
-->

## Installation

You can install `napari-generic-SIMulator` via [pip]:

    pip install napari-generic-SIMulator



To install latest development version :

    pip install git+https://github.com/Meizhu-Liang/napari-generic-SIMulator.git

## Usage

1) Import napari and create the viewer. The simple code is showed below:

    ***import napari***
       
    ***viewer = napari.Viewer()***

    ***napari.run()***


2) Launch the widget in ***Plugin***
    ![img.png](img.png)


3) Adjust the parameters in the widget and calculate the raw-image stack.
    ![img_2.png](img_2.png)


4) The sum, psf and otf can be showed. Note the all of these correspond the generated raw-image stack, so the raw images should be recalculated if the parameters change.
    ![img_3.png](img_3.png)


5) The raw image stacks can be then processed by napari-sim-processor (https://www.napari-hub.org/plugins/napari-sim-processor).
## 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-generic-SIMulator" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with 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/Meizhu-Liang/napari-generic-SIMulator/issues

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
