SMART trace files

SMART trace files are Matlab binary files with the extension .traces. They are usually found in the main/video_processing/intensities/traces_SMART or main/traces_processing/traces_SMART 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 SMART [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_SMART analysis sub-folder after creating and exporting SMART traces in panel Intensity integration of module Video processing, or in or /traces_processing/traces_SMART 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]_SMART 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

SMART trace files include single molecule data of all the N molecules and consist in a N-by-3 cell array with:

  • column 1 containing structures with the following fields:

    field name description data type example
    name file name string 'data_all100FRET1to2_SMART.traces'
    gp_num sub-group index = NaN double 'NaN' (fixed)
    movie_num video index = 1 double 1 (fixed)
    movie_ser video series index = 1 double 1 (fixed)
    trace_num molecule index double 12
    spots_in_movie number of molecules in the set double 100
    position_x x-coordinates in video double 65.5
    position_y y-coordinates in video double 38.5
    positions all molecule cooridnates in the set N-by-4 double  
    fps video frame rate (in s-1) double 9.8280
    len trace length (in frame) double 4000
    nchannels number of detection channels = 2 double 2 (fixed)
  • column 2 containing donor and acceptor intensities written in double precision
  • column 3 containing a boolean vector indicating data points included in /excluded from the analysis

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

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

SMART trace files are MATLAB binary files and can be imported in MATLAB’s workspace by typing in MATLAB’s command window:

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

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

References

  1. M. Greenfeld, D.S. Pavlichin, H. Mabuchi, D. Herschlag, Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data, PLoS ONE 2012, DOI: 10.1371/journal.pone.0030024