napari-sim-processor 0.0.1

A napari widget to process Structured Illumination Microscopy data with gpu acceleration

napari-sim-processor

A Napari plugin for the reconstruction of Structured Illumination microscopy (SIM) data with GPU acceleration (with pytorch, if installed). Currently supports:

• conventional data with improved resolution in 1D (1 angle, 3 phases)
• conventional data (3 angles, 3 phases)
• hexagonal SIM (1 angle, 7 phases).

The SIM processing widget accepts image stacks organized in 5D (angle,phase,z,y,x).

For raw image stacks with multiple z-frames each plane is processed as described in: https://doi.org/10.1098/rsta.2020.0162

A reshape widget is availbale, to easily reshape the data if they are organized differently than 5D (angle,phase,z,y,x)

Support for N angles, M phases is in progress. Support for 3D SIM with enhanced resolution in all directions is not yet available. Multicolor reconstruction is not yet available.

---

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-sim-processor via pip:

pip install napari-sim-processor

To install latest development version :

pip install git+https://github.com/andreabassi78/napari-sim-processor.git

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-sim-processor" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.