Software

PICCS: Particle Image-(Cross)Correlation Spectroscopy

A new data analysis tool that resolves correlations on the nanometer length and millisecond timescale is derived. This tool, adapted from methods of spatiotemporal image correlation spectroscopy, exploits the high positional accuracy of single-particle tracking. While conventional tracking methods break down if multiple particle trajectories intersect, our method works in principle for arbitrarily large molecule densities and diffusion coefficients as long as individual molecules can be identified. The method is computationally cheap and robust and requires no a priori knowledge about the dynamical coefficients, as opposed to other methods. We demonstrate the validity of the method by Monte Carlo simulations and by application to single-molecule tracking data of membrane-anchored proteins in live cells. The results faithfully reproduce those obtained by conventional tracking.

references:
– Stefan Semrau and Thomas Schmidt (2007) Particle image correlation spectroscopy (PICS). Retrieving nanometer-scale correlations from High-Density Single-Molecule Position Data, Biophys J., 92, 613.
– Stefan Semrau, Laurent Holtzer, Marcos Gonzalez-Gaitan & Thomas Schmidt (2011) Quantification of biological interactions with Particle Image Cross Correlation, Biophys. J, 100, 1810-8.

downloads (for all you also need the free Matlab 2012a runtime library):
PIC(C)S (Win64)  ||  PIC(C)S (Mac)

 

vEDF: Evaluate data file

vEDF, “Evaluate Data Files”, is a wrapper or batch program. Its sole function is to call the fitting routines with each of a set of given files. It invokes sbe, tests for existence of files, and – if necessary – creates the subdirectories for peak-, trace-, index and msd-data. Subsequently all files are analyzed, trajectories are generated, the mobility is analyzed. Finally all data are summarized by their statistics.
vEDF evaluates several datafiles with a given value for diffusion D and fitoptions. vEDF will create directories for fitting results if necessary. Filespecs are expanded if necessary.

references:
– Th.Schmidt, G.J.Schütz, W.Baumgartner H.J.Gruber and H.Schindler (1995) Characterization of Photophysics and Mobility of Single Molecules in a Fluid Lipid Membrane, J.Phys.Chem, 99, 17662.
– Th.Schmidt, G.J.Schütz, W.Baumgartner, H.J.Gruber and H.Schindler (1996) Imaging of Single Molecule Diffusion, Proc.Natl.Acad.Sci. USA, 93, 2926.

downloads (for all you also need the free Matlab 2012a runtime library):
vEDF (Win64)  ||  vEDF (Mac)  ||  WebEDF service running on our machines