lnma-superres

A plugin for 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
• MUSICAL
• 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:

• ESI GitHub repository
• PySOFI GitHub repository
• MUSICAL Google site

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

Installation

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: https://napari.org/stable/

You can install the plugin graphically.

or install latest development version :

pip install git+https://github.com/Dr2-JMM/lnma-superres.git

You might need to install git first.

User guide

A complete user guide with the graphical installation instructions included can be found here.

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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

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Contributing

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.

License

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

Issues

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