Trace file from trace processing

Processed trace files are ASCII files with the extension .txt. They are usually found in the main/traces_processing/traces_ASCII analysis folder.

Table of contents

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

Description

These trace files are written in ASCII format and contain processed intensity- and intensity-ratio-time traces.

They are created in the /trace_processing/traces_ASCII analysis sub-folder after exporting ASCII traces in panel Sample management 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 project file loaded in Trace processing, and is appended with the extension _mol[n]of[N] with [n] the index of the molecule written in the file and [N] the total number of exported molecules.

Structure

If the Export options include processing parameters in the trace file header, processing parameters are first written as described in Processing parameter files.

Intensity-time traces are organized column-wise with:

  • columns time at [L]nm containing time points upon illumination with laser wavelength L (in second)
  • columns frame at [L]nm containing frame indexes upon illumination with laser wavelength L (in second)
  • columns I_[i] at [L]nm and discr.I_[i] at [L]nm containing channel- and illumination-specific intensity-time traces and state trajectories, with [i] the channel index
  • columns FRET_[D]>[A] and discr.FRET_[D]>[A] containing FRET-time traces and state trajectories, with [D] and [A] the channel indexes where donor and acceptor fluorescence of the FRET pair are specifically detected
  • columns S_[D]>[A] and discr.S_[D]>[A] containing stoichiometry-time traces and state trajectories associated with the FRET pair where [D] and [A] are the channel indexes where donor and acceptor fluorescence of the FRET pair are specifically detected
time at 532nm	frame at 532nm	I_1 at 532nm(counts)	I_2 at 532nm(counts)	I_3 at 532nm(counts)	time at 638nm	frame at 638nm	I_1 at 638nm(counts)	I_2 at 638nm(counts)	I_3 at 638nm(counts)	time at 532nm	frame at 532nm	FRET_1>2	discr.FRET_1>2	time at 532nm	frame at 532nm	S_1>2		discr.S_1>2
1.017500e-01	1		-3.162304e+02		-1.248107e+02		-4.999781e+01		2.035000e-01	2		-5.944420e+01		-2.638393e+00		1.688481e+01		1.017500e-01	1		2.541767e-01	-7.502669e-01	1.017500e-01	1		9.157130e-01	1.017316e+00
3.052500e-01	3		-1.323042e+01		-3.182207e+02		-1.269978e+02		4.070000e-01	4		-2.454442e+02		1.573616e+02		1.368848e+02		3.052500e-01	3		6.941246e-01	-7.502669e-01	3.052500e-01	3		1.119132e+00	1.017316e+00
5.087500e-01	5		-7.123042e+01		-4.542065e+01		-3.699781e+01		6.105000e-01	6		-2.514442e+02		-2.963839e+01		-1.181152e+02		5.087500e-01	5		2.956133e-01	-7.502669e-01	5.087500e-01	5		2.779232e-01	8.296395e-01

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

Compatibility

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

For ALEX experiments, files must be restructured prior import in MASH; see Restructure ALEX data for help.