napari generic SIMulator

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

Meizhu Liang

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

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 the CUPY (tested with cupy-cuda11x) 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 v1.13.1+cu117) 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 5 phases at right-angles
conventional 3-beam 3-D data with 3 angles and 5 phases

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

This plugin is compatible with napari 0.4.17 or above, older versions of napari would show errors in interpolation.

Usage¶

Open napari and create the viewer.
Launch two widgets: Point cloud generator and SIM data generator in Plugin.

The two widgets can be tabbed together.
Choose the type and other parameters of point cloud as a sample in Point cloud generator.

The point cloud can be displayed in three dimensions, and be saved and loaded as .pcd files.
Adjust parameters in SIM data generator to simulate a raw image stack.

Apart from basic parameters such as the refractive index, the wavelengths and so on, the z scanning can be either z drift: the conventional SIM (imaging a raw stack at the same z-position) or z step: the drifting case in the papaer mentioned above (imaging only one raw image at a z-position).

The parameters used in the simulation can be saved with the image stack by clicking save tif with tags. Tags (of current or of one stack dragged into napari viewer) can be printed in Python by print tags.
Three-dimensional point spread function (PSF), optical transfer function (OTF) and illumination patterns applied in the simulation can be showed by buttons. Note the all of these correspond the generated raw-image stack, so keep the parameters the same before showing the PSF (or OTF and illumination).
The raw image stacks can be then processed by napari-sim-processor (https://www.napari-hub.org/plugins/napari-sim-processor).