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