A plugin for simulations of the Point Spread Function, with aberrations
A plugin for the simulation of the 3D Point Spread Function of an optical systen, particularly a microscope objective.
Calculates the PSF using scalar and vectorial models.
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.
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
Lauch the plugin and select the parameters of the microscope:
n(refractive index at the object),
FOV xy(field of view in the transverse direction),
FOV z(field of view in the axial direction),
dxy(pixel size, transverse sampling),
dz(voxel depth, axial sampling),
lens radius(physical aperture of the lens, used in vectorial model)
Select a propagation model between
Select an aberration type (if needed).
Calculate PSFto run the simulator. This will create a new image layer with the 3D PSF.
Show Airy diskcreates a circle with radius given by the diffraction limit (Rayleigh criterion).
Napari viewer with the psf-simulator widget showing the in-focus plane of an aberrated PSF
Slicing through a PSF aberrated with Zernike polynomials of order N=3, M=1 (coma)
- Click on the
Plot PSF Profile in Consolecheckbox to see the x and z profiles of the PSF. They will show up in the viewer console when
Calculate PSFis executed.
Plot profile of the PSF, shown in the Console
An exhaustive documentation of the use of the plugin on scalar and vectoral propagation models can be found in this presentation.
A detailed explanation of the uses and advantages that simulating a PSF brings can be found here.
The vectorial propagation model implements a secondary library: pyfocus. The full documentation of this library can be found at read the docs and in the paper: "PyFocus: A Python package for vectorial calculations of focused optical fields under realistic conditions. Application to toroidal foci." https://doi.org/10.1016/j.cpc.2022.108315
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. Please contact the developers on github for adding new propagations and aberrations types. Any suggestions or contributions are welcome.
Distributed under the terms of the BSD-3 license, "napari-psf-simulator" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
- 31 October 2023
- 14 April 2022
- Information not submitted
- Stars: 21
- Forks: 1
- Issues + PRs: 2