vbFRET trace files

vbFRET trace files are Matlab binary files with the extension .mat. They are usually found in the main/video_procssing/intensities/traces_vbFRET or main/traces_procssing/traces_vbFRET analysis folder.

Table of contents

  1. Description
  2. File name
  3. Structure
  4. Compatibility
  5. References

Description

These trace files are written in MATLAB binary format importable in the software vbFRET [1]. Each file contains intensity-time traces of a specific FRET pair, integrated from a single molecule video (SMV) or exported after trace processing.

They are created in the /video_processing/intensities/traces_vbFRET analysis sub-folder after creating and exporting vbFRET traces in panel Intensity integration of module Video processing, or in /traces_processing/traces_vbFRET if exported from panel Sample managementof module Trace processing.

File name

The file is named by the user during the export process.

By default, the file is named after the video file loaded in Video processing or the project file in Trace processing from which data are exported, and is appended with an extension _all[N]FRET[D]to[A]_vbFRET where [N] is the number of single molecules, and where [D] and [A] the channel indexes where donor and acceptor fluorescence are specifically detected.

Structure

vbFRET trace files include single molecule data of all N molecules and consist in a 1-by-N cell array with each cell containing donor and acceptor intensity series.

For consistency, intensity-time traces exported from module Video processing or Trace processing are always given as the sum of the brightest pixel intensities per video frame, regardless the units defined in Pixel intensity units or Intensity units respectively.

Compatibility

vbFRET trace files can be imported in external software vbFRET [1].

vbFRET trace files are MATLAB binary files and can be imported in MATLAB’s workspace by simply drag-and-dropping the file, or by typing in MATLAB’s command window:

load('datafolder\vbFRET-file.traces','-mat');

and replacing datafolder\vbFRET-file.traces by your actual file name and directory.

References

  1. J.E. Bronson, J. Fei, J.M. Hofman, R.L. Gonzalez Jr, C.H. Wiggins, Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data, Biophys. J. 2009, DOI: 10.1016/j.bpj.2009.09.031