"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.
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 | | summary
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. 999-1002. DOI | | summary
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).