napari-psf-simulator

A plugin for simulations of the Point Spread Function, with aberrations


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A plugin for the simulation of the 3D Point Spread Function of an optical systen, particularly a microscope objective.

Calculates the PSF as the squared Fourier Transform of the pupil and uses the angular spectrum to propagate the PSF in 3D.
The following aberrations are included:

  • phase aberration described by a Zernike polynomials with n-m coefficients
  • aberration induced by a slab, with a refractive index different from the one at the object (only scalar approximation is used, polarization not considered yet).

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

Installation

You can install napari-psf-simulator via pip:

pip install napari-psf-simulator

To install latest development version :

pip install git+https://github.com/andreabassi78/napari-psf-simulator.git

Usage

  1. Lauch the plugin and select the parameters of the microscope: NA (numerical aperture), wavelenght, n (refractive index at the object), Nxy (number of pixels), Nz (number of slices), dxy (pixel size, transverse sampling), dz (voxel depth, axial sampling)

  2. Select an aberration type (if needed) and press Calculate PSF to run the simulator. This will create a new image layer with the 3D PSF.

    The option Show Airy disk creates 3 ellipses as a shapes layer, showing the boundaries of the diffraction limited blob.

raw Napari viewer with the psf-simulator widget showing the in-focus plane of an aberrated PSF

raw Slicing through a PSF aberrated with Zernike polynomials of order N=3, M=1 (coma)

  1. Click on the Plot PSF Profile in Console checkbox to see the x and z profiles of the PSF. They will show up in the viewer console when Calculate PSF is executed.

raw Plot profile of the PSF, shown in the Console

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. The plugin has been concived to be modular allowing the insertion of new aberations and pupils. Any suggestions or contributions on this are welcome.

License

Distributed under the terms of the BSD-3 license, "napari-psf-simulator" is free and open source software

Issues

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

Version:

  • 0.1.4

Release date:

  • 12 May 2022

First released:

  • 14 April 2022

License:

  • BSD-3-Clause

Supported data:

  • Information not submitted

GitHub activity:

  • Stars: 9
  • Forks: 1
  • Issues + PRs: 1

Python versions supported:

Operating system:

Requirements:

  • numpy
  • magicgui
  • qtpy

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