Mash code 12 - New functionalities "ES linear regression" and "Beta correction factor"

[mca-sh]

Here is a release note:

• Requirements
• Fixed bugs
• Improvements
• New functionalities

Requirements

• delete MASH-FRET\default_param.ini before starting MASH the first time

Fixed bugs

Video processing

Import/export

• fix error occurring when importing old .sira files (2012, 2013)

  Visualization

• correct image rotation when memory is not free from video data
• correct color change of button "Free" when png file is loaded
• correct colorbar scaling when loading a sif file

  Trace processing

  Sample management

• correct image rotation in Trace manager when memory is not free from video data

  Factor corrections

• correct html formatting of mutlifunction button's tooltip string

Improvements

Trace processing

Project

• modify Stoichiometry calculation using the definition used in ES linear regression to be coherent (one FRET pair, one stoichiometry) and restrict choice to defined FRET pairs only
• modify project structure by adding field "ES" to store global ES histograms

  Sample management

• review trace update to use the same scripts in Trace manager, options for ES linear regression and in the regular procedure in TP photobleaching-based gamma calculations (separate updateTraces.m into updateIntensities.m, updateGammaFactor.m and updateStateSequences.m), as well as to use robust gamma/beta factors calculations by ES linear regression (calculated from total processed ES)
• change default parameters structure to add beta factor file import settings (requires to delete file default_param.ini)
• improve import of ASCII traces by identifying FRET pairs in gamma & beta factor files

  Cross-talks

• modify GUI to add panel "Cross-talks" that contains global cross-talk coefficients (not molecule-dependant anymore)
• modify processing parameter structure by moving cross-talks parameters from 5th cell of moelcule parameters to 4th cell of general parameter

  Factor corrections

• modify GUI by moving cross talks to a separate panel in roder to make them globally available
• modify GUI by adding a "beta" field
• modify processing parameter structure by moving factor parameters from the 5th to a 6th cell of molecule parameters and adding beta factors
• adjust photobleaching-based gamma calculations by (1) performing donor & acceptor discretization independently from main trace update, (2) using an individual plot in option window, (3) making the tolerance parameter available for editing, and (4) allowing detection of acceptor photobleaching at any laser excitation

• adapt photobleachin-based gamma calculations to FRET-pair dependent methods (necessary since ES linearization was impl.)
• change processing parameter structure to add the "tolerance" parameter and switch the "show cut off" parameter to the laser index used for photobleaching detection in acceptor trace
• adapt import/export of factor file to new "Beta correction factor" functionality
• change file content of gamma & beta files by adding headers to identify the FRET pair

New functionalities

• Beta correction factor allows to correct stoichiometries from differences in extinction coefficients and excitation intensities between donor and acceptor.

• ES linear regression allows to calculate gamma and beta factors from global FRET-stoichiometry histograms.