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Localisation Microscopy

"rainSTORM" MATLAB GUI

We have developed a MATLAB application for Localisation Microscopy image processing, with a simple GUI interface. This application is a set of MATLAB scripts and functions, named rainSTORM, was developed as part of our super-resolution research in collaboration with the Biophysics Group at the National Physical Laboratory and the Advanced Optical Imaging Group at the University of Szeged.

Rees EJ, Erdelyi M, Kaminski-Schierle GS, Knight AE and Kaminski CF, "Elements of image processing in localisation microscopy", Journal of Optics 15, 094012 (2013). DOI | pdf | summary

download (v2.39) | download (v2.37) | User Guide 

Ellipsoid Localisation Microscopy

We have developed a super-resolution method to infer the exact size and order of fluorescent layers in biological structures made up of concentric protein shells, such as bacterial spores and other microbes. The software will be made available pending publication of an article on the method (depending on open access policies).

J. Manetsberger, J.D. Manton, M.J Erdelyi, H. Lin, H.D. Rees, G. Christie, E.J. Rees, Ellipsoid localisation microscopy infers the size and order of protein layers in Bacillus spore coats, (in review).

 

Structured Illumination Microscopy

Joint-Richardson Lucy algorithm

We have developed a MATLAB application for multifocal structured illumination microscopy (MSIM) image reconstruction based on joint Richardson-Lucy deconvolution, named jRL-MSIM. This application is a set of MATLAB scripts and functions and was developed as part of our super-resolution research. The software package is easy to use due to its simple GUI and explained in detail in the respective publication and the accompanying manual.

Stroehl F, Kaminski C F, "A Joint Richardson-Lucy Deconvolution Algorithm for the Reconstruction of Multifocal Structured Illumination Microscopy Data." (2015) , Methods and Applications in Fluorescence 3 014002 DOI pdf summary

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Fluorescence Lifetime Imaging (FLIM)

Multichannel FLIM-FRET analysis

We have developed matlab code for Multichannel FLIM-FRET analysis. It takes advantage of the linear properties of the phasor plot approach, and is able to recover the bound fractions of donors and acceptors in a FRET measurement. The software can be applied to recover the dissociation constant of binding reactions, the concentration of binding partners and the concentration of competitors for the binding. The theory and method used in this software is explained in detail in the publication and accompanying material.

Chen WY, Avezov E, Schlachter S C, Gielen F, Laine R F, Harding H P, Hollfelder F, Ron D and Kaminski C F, "A Method to Quantify FRET Stoichiometry with Phasor Plot Analysis and Acceptor Lifetime In-growth," Biophysical Journal (2015), 108 (5), 2015, pp. 999-1002DOI pdf | summary

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Spectral Imaging of FRET

Sensitised Emission FRET  (seFRET)

This Matlab code is provided to accompany a book chapter on seFRET. In this technique, the fluorescence emission of a specimen in different spectral channels is affected by a contribution from FRET (resonant energy transfer) between two different fluorophores, as well as by the direct emission of each species. This analysis software quantifies the donor-normalised and acceptor-normalised FRET by analysing fluorescence intensity image data in two colour channels (sample data is included). 

Kaminski CF, Rees EJ, Schierle GS, "A quantitative protocol for intensity-based live cell FRET imaging". Methods Mol Biology (2014), 1076:445-454  DOI |pdf summary  

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Molecular Sensing

Stable Calibration Burner

The laser analytics group has developed a novel flat flame calibration burner that supports stable laminar flames and combines many of the advantages of several widely used burner designs without their disadvantages. 

Hartung, G; Hult, J; Kaminski, CF, "A flat flame burner for the calibration of laser thermometry techniques", MEASUREMENT SCIENCE & TECHNOLOGY 17:2485-2493(2006). DOI |pdf | summary

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STED microscopy development for research into molecular mechanisms of disease

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Post Doctoral Research Position Available

Aug 03, 2015

STED microscopy development for research into molecular mechanisms of disease.

Most read articles in Methods and Applications in Fluorescence

Aug 03, 2015

The recent development by the group of a novel reconstruction algorithm for M-SIM features in the top 3 most read papers in the IOP publication Methods and Applications in Fluorescence.

Gabi Kaminski Schierle appointed as Lecturer in Molecular Biotechnology

Jun 29, 2015

Gabi Kaminski Schierle, who heads biological research activities in the Laser Analytics Group, has been appointed as Lecturer in Molecular Biotechnology at this department - many congratulations!

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