Trace file from video processing

Trace files from video are ASCII files with the extension .txt. They are usually found in the main /video_processing/intensities/traces_ASCII or main/video_processing/intensities/traces_ASCII/single_traces analysis folders.

Table of contents

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

Description

These trace files are written in ASCII format and contain the intensity-time traces integrated from the single molecule video (SMV).

They are created in the /video_processing/intensities/traces_ASCII analysis sub-folder if molecules are saved in individual files, or /video_processing/intensities/traces_ASCII/single_traces if all molecules are saved in one file, after creating and exporting ASCII traces in panel Intensity integration of module Video 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, and is appended with an extension depending on the exported format selected in Export options:

  • _mol[n]of[N] if molecules are saved in individual files
  • _all[N] if all molecules are saved in one file

where [n] is the index of the molecule written in the file and [N] the total number of molecules.

Structure

File headers include the date and software version at export, the experiment settings, intensity integration parameters and are written such as:

creation date:
MASH-FRET version:
movie file:
coordinates file:
number of channels:
excitation wavelengths:
frame rate:
integration area:
number of brightest pixels:
experimental parameters:

Molecule coordinates in each video channel are written in the following line such as:

coordinates:		[x],[y]	[x],[y]	[x],[y]

with [x],[y] the respective x- and y-coordinates from the left-most to the right-most channel. If all molecules are saved in the same file, the line is appended with all other molecule coordinates following the same channel order.

Intensity-time traces are organized column-wise with:

  • column time(s) containing time data in second
  • column frames containing frame indexes
  • columns I_[i](a.u.) containing channel-specific intensity-time traces, with [i] the channel index
time(s)		frames	I_1(a.u.)	I_2(a.u.)	I_3(a.u.)
1.017500e-01	1	3181		17475		3741
2.035000e-01	2	14617		6545		3304
3.052500e-01	3	2975		18031		3755

For consistency, intensities are always given as the sum of the brightest pixel intensities per video frame, regardless the units defined in Pixel intensity units.

Compatibility

Trace files from video can be imported in modules Trace processing and Transition analysis for analysis by adjusting the Import options to the actual file structure.