correct MATLAB's character encoding when machine's default is not windows-1252
Simulation
Molecules
correct re-sorting of coordinates after preset file is imported/removed
correct use and display of FRET deviations when imported from presets
Experimental setup
fix error occurring when importing background image for simulation
Visualization
correct scale of x-axis of intensity histograms
Video processing
Visualization
fix error occurring when loading a video file in VP after deleting default_param.ini
fix error occurring when importing .pma files
Trace processing
Project management
fix error occurring when importing a 1-channel project after saving a multiple-channel project
fix error occurring when processing a project without FRET calculations
fix error occurring when processing a project with multiple stoichiometries
fix error occurring when importing project with lower number of channels/excitations than previously saved
fix error occurring when importing old projects in TP
correct stoichiometry calculations for multiple FRET pairs
correct correction factors down compatibility in Trace processing
correct FRET calculations when FRET between acceptor 1 and 2 is not defined
Sample management
fix error occurring converting rgb color to hexadecimal color and when red/green/blue component is < 16
fix error occurring when wrapping a string with html tags
fix error occurring when exporting only intensity traces
fix error occurring when only one value is present in data histogram
correct plot in Overview when a number of channels different than 2 is used
correct adjustment of molecule selection by adding/removing specific tags
correct range selection with mouse by preventing selection when the cursor is out-of-axes-limits
correct 1D/2D histogram axes label in Auto-sorting
correct molecule sorting when performed on TDP
Factor corrections
fix error occurring when linear regression fails
fix error occurring when importing ASCII data sets and using ES linear regression
fix error occurring when resizing/moving photobleaching-based gamma option window
fix error occurring when no stoichiometry is available and selecting a gamma factor calculation method
Find states
correct identification of already-discretized bottom traces when no stoichiometry is calculated
correct removal of blurr states
Histogram analysis
Project management
correct export of .pdf bootstrap sample figures when less than 12 samples are used
Transition analysis
Project management
fix error occurring when changing to a project that was not visited before
fix error occurring when importing FRET state sequences fom ASCII files of different trace length
correct import and update of BOBA clustering results from .mash file
correct import of FRET state sequences from ASCII files when FRET pairs can not be deduced from column headers
State configuration
fix error occurring when k-mean does not converge during GM model initialization
correct reset of kinetic parameters when exporting a model in panel State transition rates
correct display of cluster centers starting guess and cluster radii
State transition rates
correct histogram building when excluding first and last dwell times in sequences
correct dwell time histogram plot limits
correct order of bootstrap exponential fit results before calculating bootstrap mean and deviation
Tools
fix error occurring when using ALEX data restructuring tool from MASHs menu
correct restructuring of ALEX data when more than 2 lasers are used
Improvements
General
reduce computation time at MASH's start by reviewing wrapping of tooltip strings
Simulation
Molecule
add callbacks to edit fields displaying imported presets/coordinates file that set back file name
review simulation export by not updating data prior exporting (not necessary, time consumming and incompatible with kinsoft routine when removin f externally blurr states from FRET sequences
review transition probabiltiies in the simulation procedure by introducing and using the "weighing factors"
addtrans_prob preset parameter that allows to import "weighing factors"
add the possibility to use user-defined initial state probabilities
Experimental setup
modify GUI by adding an import interface for background image
Trace processing
Sample management
modify GUI by changing the "Add>" pushbutton into a togglebutton
improve all trace update by refreshing plot at the end of the process
review action display when updating all molecules (show info only when discretizing traces)
Background
improve Background analyzer by building the interface programmatically and save callback functions to separate files
Photobleaching
modify GUI by adding a "Split" pushbutton in TP's panel "Photobleaching"
Transition analysis
Project management
add option "export BOBA figures (.pdf)" in export options
adapt import of FRET state sequences from ASCII files for multiple FRET pairs
State configuration
improve display of tooltip strings by wrapping them to a fix width
modify GUI by adding a field to show BIC of selected model
State transition rates
modify GUI by adding a "re-arrange sequences" checkbox
change processing parameters structure by a adding the option "re-arrange state sequences" in kinetic analyiss parameters
Tools
Restructure traces
adapt restructuring of ALEX data for files with multiple headers (ex: coordinates)
Simulation presets template
addtrans_prob preset parameter that allows to import weighing factors
Simulation with multiple FRET pairs
create script to simulate intensity-time traces with multiple FRET pairs
New functionalities
Test routines are used to check the working status of MASH's interface. MASH's modules and menus are tested separately via the menu bar Routines > Test interface. Routine scripts are run on data sets stored in folders $MASH-FRET/source/routines/*/assets. Generated files are stored in $MASH-FRET/source/routines/*/dump (logs are registered in file _logs.txt)
Data analysis routine is used to analyze a set of intensity-time traces written in ASCII files and is accessible from menu via the menu bar Routines > Kinsoft challenge. Run this routine to obtain the FRET state configuration and associated transition rates and probabilities. The routine script is adapted to KinSoft challenge data sets.
Re-arrange sequences is an option used to build Dwell time histograms in module Transition analysis after cancelling transitions out-of-cluster-ranges or contained in diagonal clusters (low-amplitude jumps, usually due to noise discretization). State sequences are re-built by ignoring these transitions and elongating flanking dwell times.
Export sample dwell time histograms (pdf) is an export option in Transition analysis that allows to print figures of sample dwell time histogram used in bootstrap fitting and associated fit results to a multi-paged .pdf file
Simulation of multiple FRET pairs is a side-tool that allows to simulate systems with multiple FRET pairs and generate sets of intensity-time traces written to ASCII files. The script is available at $MASH-FRET/tools/SiM_FRET.m.
Split trace is a method used to split the intensity-time traces of one molecule in 2 at a defined cutoff position. In this case the right-side portion of the trace is added as a new molecule to the molecule list. This functionality allows to ignore long blinking events or interruptions occurring during the measurement from the analysis.
Here is a release note:
Fixed bugs
General
windows-1252Simulation
Molecules
Experimental setup
Visualization
Video processing
Visualization
Trace processing
Project management
Sample management
Factor corrections
Find states
Histogram analysis
Project management
Transition analysis
Project management
State configuration
State transition rates
Tools
Improvements
General
Simulation
Molecule
trans_probpreset parameter that allows to import "weighing factors"Experimental setup
Trace processing
Sample management
Background
Photobleaching
Transition analysis
Project management
State configuration
State transition rates
Tools
Restructure traces
Simulation presets template
trans_probpreset parameter that allows to import weighing factorsSimulation with multiple FRET pairs
New functionalities
Routines > Test interface. Routine scripts are run on data sets stored in folders$MASH-FRET/source/routines/*/assets. Generated files are stored in$MASH-FRET/source/routines/*/dump(logs are registered in file_logs.txt)Routines > Kinsoft challenge. Run this routine to obtain the FRET state configuration and associated transition rates and probabilities. The routine script is adapted to KinSoft challenge data sets.Simulation of multiple FRET pairs is a side-tool that allows to simulate systems with multiple FRET pairs and generate sets of intensity-time traces written to ASCII files. The script is available at
$MASH-FRET/tools/SiM_FRET.m.Split trace is a method used to split the intensity-time traces of one molecule in 2 at a defined cutoff position. In this case the right-side portion of the trace is added as a new molecule to the molecule list. This functionality allows to ignore long blinking events or interruptions occurring during the measurement from the analysis.