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 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.
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),
Nxy(number of pixels),
Nz(number of slices),
dxy(pixel size, transverse sampling),
dz(voxel depth, axial sampling)
Select an aberration type (if needed) and press
Calculate PSFto run the simulator. This will create a new image layer with the 3D PSF.
Show Airy diskcreates 3 ellipses in a Shapes layer, showing the boundaries of the diffraction limited blob.
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
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.
- 08 June 2022
- 14 April 2022
- Information not submitted
- Stars: 15
- Forks: 1
- Issues + PRs: 1