MASH-FRET project files

MASH-FRET project files are Matlab binary files with the extension .mash. They are usually found in the main/video_processing analysis folder.

Table of contents

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

Description

MASH project files are the main analysis files. They contain information about loaded experimental data, calculated data and method settings.

They are created at a user-defined location.

They are created/updated when:

File name

The file is named by the user.

By default, the file is named after:

Structure

MASH-FRET project files consist in data structures with the following fields:

field name description data type example
date_creation date of project creation in format DD-Mon-YYYY hh:mm:ss string '05-Feb-2019 12:51:06'
date_last_modif date of last project modification in format DD-Mon-YYYY hh:mm:ss string '20-Mar-2019 14:02:32'
MASH_version version of MASH when project was created string '1.1.2'
proj_file path to project file string 'C:\MyDataFolder\experiment_01\data.mash'
is_movie a video file is/isn’t attached to the project 1/0 1
movie_file path to video file string 'C:\MyDataFolder\experiment_01\data.sira'
movie_dim video dimensions in pixel (width,height) 1-by-2 double [256,256]
movie_dat parameters used to read pixel data in video file 1-by-3 cell  
sampling_time acquisition time of one video frame in second double 0.1
resampling_time sampling time in second after trajectory re-sampling double 0.3

Experiment settings fields

nb_channel number of spectroscopic channel nC double 2
nb_excitations number of alternated lasers nL double 2
excitations excitation wavelengths 1-by-nL double [638,532]
chanExc laser indexes for channel direct excitation 1-by-nC double channel 1 is directly excited by 2nd laser: [2,1]
labels labels for spectroscopic channel 1-by-nC cell { 'Cy3','Cy5' }
colours RGB colors used to plot trajectories and labels (intensities, FRET, S) 1-by-3 cell for 2 channel and 2 alternated lasers: { {[0,0.5,0],[0.5,0.5,0];[0,1,0],[1,1,0]}, [0,0,0], [0,0,1] }
exp_parameters a number nP of user-defined project parameters (name, value, units) nP-by-3 cell { 'Project title','data_D135_01',[]; 'Molecule name','D135',[]; '[Mg2+]','100','mM'; '[K+]','500','mM' }
traj_import_opt options for the import of trajectory files (trajectory-based projects) 1-by-6 cell see setParam.m for defaults
hist_import_opt options for the import of histogram files (histogram-based projects) 1-by-4 double [0,1,1,2]
spltime_from_video sampling time is/isn’t determined from the video file or the simulation 1/0 0
spltime_from_traj sampling time is/isn’t determined from trajectory files 1/0 0

Molecule fields

is_coord molecule coordinates are/aren’t attached to the project 1/0 1
coord a number M of molecule coordinates (x,y) M-by-2*nC double  
coord_file file from which molecule coordinates were read string 'C:\MyDataFolder\experiment_01\video_processing\coordinates\transformed\data_ave.coord'
coord_imp_param parameters that were used to import molecule coordinates from file 1-by-nC cell  
coord_incl molecule is selected/unselected 1-by-M true/false  
molTag molecule’s tag (1,2 or 3) 1-by-M double  
molTagNames default tag name cell array { static, dynamic, D-only, A-only }
molTagClr hexadecimal default tag colors cell array { '#B3D9FF, '#0066CC }

Intensity fields

intensities raw intensity trajectories with a number L of data point L-by-nC*M double  
pix_intgr pixel area size and number of pixels used to integrate intensity 1-by-2 double [5,8]
cnt_p_pix units are/aren’t counts per pixel 1/0 1
cnt_p_sec units are/aren’t counts per second 1/0 1
intensities_bgCorr background-corrected intensity trajectories L-by-nC*M double  
intensities_bin re-sampled intensity trajectories L'-by-nC*M double  
intensities_crossCorr background- & cross-talk-corrected intensity trajectories L'-by-nC*M double  
intensities_denoise corrected and smoothed intensity trajectories L'-by-nC*M double  
intensities_DTA discretized intensity trajectories L'-by-nC*M double  
bool_intensities included/ignored intensity data points L'-by-M true/false  

FRET- and stoichiometry- fields

FRET a number nF of different FRET pair (don, acc) channel indexes for FRET calculations nF-by-2 double FRET from channel 1 to 2: [1,2]
FRET_DTA discretized FRET trajectories L-by-nF*M double  
FRET_DTA_import discretized FRET trajectories imported from ASCII files for trajectory-based projects, or from module Simulation for simulation-based projects L-by-nF*M double  
S a number nS of different FRET pair (don, acc) channel indexes for stoichiometry calculations nS-by-2 double S of FRET pair from channel 1 to 2: [1,2]
S_DTA discretized stoichiometry trajectories L-by-nS*M double  
ES 2D histograms of FRET-inverse of associated stoichiometry used for estimation of gamma and beta factors 1-by-nF cell  

Analysis settings

sim parameter settings and simulation results of module Simulation struct  
VP parameter settings and processing outcome of module Video processing struct  
TP parameter settings and processing outcome of module Trace processing struct  
HA parameter settings and analysis results of module Histogram analysis struct  
TA parameter settings and analysis results of module Transition analysis struct  

For more information about how the analysis settings fields are structured, please refer to the respective function in the source code:

MASH-FRET/source/project/setDefPrm_sim.m
MASH-FRET/source/project/setDefPrm_VP.m
MASH-FRET/source/project/setDefPrm_traces.m
MASH-FRET/source/project/setDefPrm_thm.m
MASH-FRET/source/project/setDefPrm_TDP.m

Compatibility

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

load('datafolder\project-file.mash','-mat');

and replacing datafolder\project-file.mash by your actual file name and directory.