Driven by curiosity. Driving changeFree resources
We have made a number of resources freely available. From methods to MATLAB code to our flat flame calibration burner.
Localisation Microscopy
‘rainSTORM’ MATLAB GUI
We have developed a MATLAB application for Single Molecule 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. Version 2.37 is an older version with simple workspace handling.
- 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 |
- Download (v3.0) | 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.
- 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.” Biophysical Journal (2015), doi: 10.1016/j.bpj.2015.09.023, in press
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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
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Super-resolution optical-sectioning structured illumination microscopy reconstruction software
We have developed a MATLAB application for super-resolution optical-sectioning structured illumination microscopy (SROS-SIM) image reconstruction. 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.
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.
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 | | 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.