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Fluorescence Fluctuation-based Super Resolution (FF-SRM) Methods

Project description


License BSD-3 PyPI Python Version tests codecov napari hub

A collection of super-resolution microscopy FF-SRM methods.

Open-source implementation of methods for Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM):

Review: Alva et al., 2022. “Fluorescence Fluctuation-Based Super-Resolution Microscopy: Basic Concepts for an Easy Start.” Journal of Microscopy, August.

MSSR article: Torres-García, E., Pinto-Cámara, R., Linares, A. et al. Extending resolution within a single imaging frame. Nat Commun 13, 7452 (2022).

ESI article: Idir Yahiatene, Simon Hennig, Marcel Müller, Thomas Huser (2015/2016). "Entropy-based Super-resolution Imaging (ESI): From Disorder to Fine Detail" ACS Photonics 8, 2 (2015)

SOFI article: T. Dertinger, R. Colyer, G. Iyer, and J. Enderlein. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). PNAS 52, 106 (2009)

SRRF article: Gustafsson, N., Culley, S., Ashdown, G., D. M. Owen, P. Matos Pereira, and R. Henriques. Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations. Nat Commun 7, 12471 (2016)

MUSICAL article: K. Agarwal and R. Machan, Multiple Signal Classification Algorithm for super-resolution fluorescence microscopy, Nature Communications, vol. 7, article id. 13752, (2016)

Methods implemented:

  • MSSR
  • ESI
  • SOFI
  • SRRF
  • Split channels
Super Resolution Radial Fluctuations (SRRF) Mean-Shift Super Resolution (MSSR) Entropy-based Super-resolution Imaging (ESI)
from Fig. 7 of Alva et al., 2022 from Fig. 2 of García et al., 2021 from Fig. 6 of Alva et al., 2022

Repositories available:

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


First install napari viewer (if you haven't):

conda create -y -n napari-env -c conda-forge python=3.9
conda activate napari-env
pip install "napari[all]"

For details check:

You can install the plugin graphically.

or install latest development version :

pip install git+

You might need to install git first.

Examples of use:

Original tMSSR

Parameters: Amplification: 2, Order: 0, PSF FWHM: 6,
Interpolation: Bicubic, Statistical integration: CV*sigma
Original ESI

Parameters: image in output: 2, bins: 2, Order: 2
Original SOFI

Parameters: Amplification factor: 2, Moment Order: 4, lambda parameter: 1.5, No. Iterations: 20, Window size: 100
Original SRRF

Parameters: Amplification: 2, Spatial radius: 5, Symmetry Axis: 6, Start frame: 0, End frame: 48
Original MUSICAL

Parameters: Emission [nm]: 510 NA: 1.4, Mag: 100, Pizel size: 8000, Threshold: -0.5, Alpha: 4, Subpixels per pixel: 20


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.


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


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

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