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
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:
- the user create and saves intensity-time traces in Video processing,
- the user save modifications and calculations in Trace processing, Histogram analysis or Transition analysis.
File name
The file is named by the user.
By default, the file is named after:
- the video file name loaded in Video processing,
- the current project file name loaded in Trace processing.
- the folder containing the trace files imported in Trace processing.
Structure
MASH-FRET project files consist in data structures with the following fields:
Project-related 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' |
Video-related fields
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.