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Psf is a Python library to calculate Point Spread Functions (PSF) for fluorescence microscopy.
The psf library is no longer actively developed.
:Author: Christoph Gohlke <https://www.cgohlke.com>
_
:License: BSD 3-Clause
:Version: 2025.1.1
Install the psf package and all dependencies from the
Python Package Index <https://pypi.org/project/psf/>
_::
python -m pip install -U "psf[all]"
See Examples
_ for using the programming interface.
Source code and support are available on
GitHub <https://github.com/cgohlke/psf>
_.
This revision was tested with the following requirements and dependencies (other versions may work):
CPython <https://www.python.org>
_ 3.10.11, 3.11.9, 3.12.8, 3.13.1 64-bitNumPy <https://pypi.org/project/numpy/>
_ 2.1.3Matplotlib <https://pypi.org/project/matplotlib/>
_ 3.10.0
(optional for plotting)2025.1.1
2024.5.24
2024.4.24
2024.1.6
2023.4.26
2022.9.26
2022.9.12
2021.6.6
2020.1.1
2019.10.14
2019.4.22
import psf args = dict( ... shape=(32, 32), ... dims=(4, 4), ... ex_wavelen=488, ... em_wavelen=520, ... num_aperture=1.2, ... refr_index=1.333, ... pinhole_radius=0.55, ... pinhole_shape='round', ... ) obsvol = psf.PSF(psf.GAUSSIAN | psf.CONFOCAL, **args) obsvol.sigma.ou (2.588..., 1.370...) obsvol = psf.PSF(psf.ISOTROPIC | psf.CONFOCAL, **args) print(obsvol, end='') PSF ISOTROPIC|CONFOCAL shape: (32, 32) pixel dimensions: (4.00, 4.00) um, (55.64, 61.80) ou, (8.06, 8.06) au excitation wavelength: 488.0 nm emission wavelength: 520.0 nm numeric aperture: 1.20 refractive index: 1.33 half cone angle: 64.19 deg magnification: 1.00 underfilling: 1.00 pinhole radius: 0.550 um, 8.498 ou, 1.1086 au, 4.40 px computing time: ... ms obsvol[0, :3] array([1. , 0.51071, 0.04397])
write the image plane to file
obsvol.slice(0).tofile('_test_slice.bin')
write a full 3D PSF volume to file
obsvol.volume().tofile('_test_volume.bin')
Refer to psf_example.py
in the source distribution for more examples.
FAQs
Point Spread Function calculations for fluorescence microscopy
We found that psf demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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