Metadata-Version: 2.1
Name: napari-generic-SIMulator
Version: 0.0.14
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 the CUPY (tested with cupy 8.3.0) is installed. In addition, the TORCH package can complete the acceleration both on CPU if TORCH is installed, and on GPU if TORCH is compiled with the CUDA (tested with torch v1.12.0+cu116) enabled.

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) Open napari and create the viewer.


2) Launch the widget in ***Plugin***
    ![raw](https://github.com/Meizhu-Liang/napari-generic-SIMulator/raw/main/images/img.png)
    ![raw](https://github.com/Meizhu-Liang/napari-generic-SIMulator/raw/main/images/img_1.png)


3) Adjust the parameters in the widget and calculate the raw-image stack.
    ![raw](https://github.com/Meizhu-Liang/napari-generic-SIMulator/raw/main/images/img_2.png)


4) The sum, psf and otf can be showed. Note the all of these correspond the generated raw-image stack, so keep the parameters the same before showing the sum (or psf and otf).
    ![raw](https://github.com/Meizhu-Liang/napari-generic-SIMulator/raw/main/images/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/
