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Localisation microscopy | Structured Illumination Microscopy (SIM and mSIM) | Fluorescence Lifetime Imaging (FLIM) | Spectral imaging of FRET | Molecular Sensing

Localisation Microscopy


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 | pdf | summary

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


 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


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


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  


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


STED microscopy development for research into molecular mechanisms of disease

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Major new insights into ALS and other amyloid diseases.

Nov 03, 2015

Research by the Laser Analytics Group recently published in the Journal Neuron contributes major new insights into the molecular pathology of motor neurone disease (also called amyotrophic lateral sclerosis, or ALS) and related neurogenerative disesases such as Alzheimer’s and Parkinson’s.

Register for Sensors Day: A showcase for international sensor research

Sep 24, 2015

The EPSRC Centre for Doctoral Training (CDT) in Sensor Application and Technologies is organising Sensors Day 2015, to celebrate all facets of sensor research ongoing at this University and in research laboratories across the world. The CDT incorporates more than 70 principal investigators from across the University of Cambridge, spanning 20 departments and performing research on sensors all the way from fundamental physical concepts of sensing to sensor middleware and applications.

Research Collaboration launched with Chinese health firm

Sep 04, 2015

The department of Chemical engineering was awarded a major research contract and a donation from Chinese Health company Infinitus. The event was recognised through a signing ceremony with the University's Vice Chancellor on Wednesday the 3rd of September. The deal is worth more than GBP4.0M and includes a very significant donation towards the construction of the department's new building on the University's West Site.

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