A simple plugin to use with napari to simulate raw image stacks in Structured illumination microscopy (SIM) with napari.
Project description
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 GPU-accelerated real-time reconstruction in Python of three-dimensional datasets from structured illumination microscopy with hexagonal patterns 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.
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
-
Import napari and create the viewer. The simple code is showed below:
import napari
viewer = napari.Viewer()
napari.run()
-
Launch the widget in Plugin
-
Adjust the parameters in the widget and calculate the raw-image stack.
-
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.
-
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.
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