napari-psfgenerator

PSF Generator Napari Plugin

The PSF Generator Napari Plugin provides an intuitive, interactive platform for simulating point spread functions (PSFs) directly within the Napari ecosystem. Built on PyTorch, this plugin supports both CPU and GPU-accelerated computations, ensuring fast and efficient simulations for fundamental and advanced optical modeling. Key features include:

Flexible Propagation Models: Scalar and vectorial propagators in Cartesian and spherical coordinates. Customizable Parameters: Configure physical (e.g., numerical aperture, wavelength), numerical (e.g., pixel size, Z-stacks), and optical settings (e.g., Gibson-Lanni corrections, Zernike aberrations). Real-Time Visualization: Seamless integration with Napari for immediate visual feedback. Versatile API: Access propagators programmatically for custom workflows. Image Export: Save computed PSFs in TIFF format.

This plugin is a powerful tool for researchers in optics, computational microscopy, and imaging science, bridging user-friendly interactivity with the computational capabilities of our Python library.

This napari plugin was generated with copier using the napari-plugin-template.

Installation

Set up a Python virtual environment and install napari following this guide.

After activating the virtual environment, you need first to install locally the psf_generator library following the instructions below.

git clone git@github.com:Biomedical-Imaging-Group/psf_generator.git
cd psf_generator
pip install -e .

Move to the correct working directory, then install locally the plugin following the instructions below.

cd .. # move to one directory above
git clone git@github.com:Biomedical-Imaging-Group/napari-psfgenerator.git
pip install -e .
napari

Now you can try the plugin out!

Here we installed the package in "editable mode", so we can modify the code and see the changes in real-time.

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 MIT license, "napari-psfgenerator" is free and open source software

Issues

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