napari-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

Repositories available:

Sample dataset

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 following the detailed user guide.

or install latest development version :

pip install git+https://github.com/RoccoDAnt/napari-superres.git

You might need to install git first.

Also a yml file is available.

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