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

License:

BSD-3-Clause

Version:

2026.8.8

Quickstart

Install the psf package and all dependencies from the Python Package Index:

python -m pip install -U "psf[all]"

See Examples for using the programming interface.

Source code and support are available on GitHub.

Requirements

This revision was tested with the following requirements and dependencies (other versions may work):

Revisions

2026.8.8

  • Make C extension ABI3 and free-threading compatible.

  • Drop support for Python 3.11 and numpy 2.0 (SPEC0).

  • Support Python 3.15.

2026.1.18

  • Use multi-phase initialization.

  • Improve code quality.

2025.8.1

  • Drop support for Python 3.10, support Python 3.14.

2025.1.1

  • Improve type hints.

  • Drop support for Python 3.9, support Python 3.13.

2024.5.24

  • Fix docstring examples not correctly rendered on GitHub.

2024.4.24

  • Support NumPy 2.

2024.1.6

  • …

Refer to the CHANGES file for older revisions.

References

  1. Electromagnetic diffraction in optical systems. II. Structure of the image field in an aplanatic system. B Richards and E Wolf. Proc R Soc Lond A, 253 (1274), 358-379, 1959.

  2. Focal volume optics and experimental artifacts in confocal fluorescence correlation spectroscopy. S T Hess, W W Webb. Biophys J (83) 2300-17, 2002.

  3. Electromagnetic description of image formation in confocal fluorescence microscopy. T D Viser, S H Wiersma. J Opt Soc Am A (11) 599-608, 1994.

  4. Photon counting histogram: one-photon excitation. B Huang, T D Perroud, R N Zare. Chem Phys Chem (5), 1523-31, 2004. Supporting information: Calculation of the observation volume profile.

  5. Gaussian approximations of fluorescence microscope point-spread function models. B Zhang, J Zerubia, J C Olivo-Marin. Appl. Optics (46) 1819-29, 2007.

  6. The SVI-wiki on 3D microscopy, deconvolution, visualization and analysis. https://svi.nl/NyquistRate

Examples

>>> 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.

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for cgohlke from gravatar.com cgohlke

Credits

Author: Christoph Gohlke

License

BSD-3-Clause

Requires

Python >=3.12

Provides Extra

all

Classifiers

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Release history Release notifications | RSS feed

This release

2026.8.8 This release

25 files

2026.1.18

36 files

2025.8.1

31 files

2025.1.1

24 files

2024.5.24

26 files

2024.4.24

23 files

2024.1.6

23 files

2023.4.26

18 files

2022.9.26

11 files

2022.9.12

10 files

2021.6.6

11 files

2020.1.1

8 files

2019.10.14

11 files

2019.4.22

9 files

2019.2.20

9 files

2019.1.1

11 files

2018.10.18

11 files

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