fix error occurring when simulating data with transition rates imported from presets file
fix error occurring when importing FRET config withtout corresponding transition rates with a number of states larger than 5
fix error occurring when importing successively presets with increasing number of molecules
Export options
fix error occurring after simulation when output intensity units are set to photon counts
Video processing
Import
correct import of png image containing decimal intensities lower than 0
Edit video
correct donor and acceptor limits on single molecule image during image filtering
Molecule coordinates
correct export of average image with image filters
Trace processing
correct how stoichiometry is corrected with beta factor
Transtition analysis
correct reset of font sizes in BIC and dwell time histogram plots
Improvements
Trace processing
General
review FRET and stoichiometry calculations for mutiple FRET pairs by taking into account gamma factors of other FRET pairs and removing dependency on sym toolbox (increases calculation speed!)
Factor corrections
prevent use of ES linear regression when no stoichiometry is defined for a FRET pair
adapt calculations of correction factors by ES linear regression to mutiple FRET pairs (gamma factors of redder FRET pairs are used in the calculations of ES histograms for greener FRET pairs)
add weight-enhancement exponent for better fit in ES linear regression
Transtition analysis
General
adapt handling of processing parameters to the curr/prm (current settings/last applied) system already implemented in TP
review data processing and plot to make it more robust as in TP
Transition density plot
add display of pointer coordinates when hoovering the TDP
make available the option include statics to include/exclude the last state of each state sequence to the TDP in diagonal bins (activation was previously the default)
modify pdefault rocessing parameters by adding the option include statics
modify GUI by adding the checkbox include statics
modify GUI by adding the text that show pointer coordinated when hoovering the TDP
State configuration
adapt k-mean clustering to square- and diagonal-ellipsis-shaped clusters
make available the clustering constraint matrix to infer cluster configurations where cluster centers are the result of all possible combinations of states (activation was previously the default)
make available the option diagonal clusters to add diagonal clusters to the matrix-constraint configurations (activation was previously the default)
make available the option likelihood to choose in which way the likelihood should be calculated (complete data was previously the default)
modify processing parameter structure by adding options "clustering constraint" (matrix, symmetrical or free), "likelihood calculation" (complete data or incomplete data) and diagonal clusters
modify GUI by converting the k-means and GM toggle buttons to a single method popup menu (appended with new method simple)
modify GUI by adding a popup menu to select a constraint on cluster configurations (matrix, and new constraints symmetrical and free), a diagonal clusters checkbox and a likelihood popup menu
modify GUI by converting the cluster shape popup menu to a series of shape buttons
modify GUI by adding edit fields for setting cluster y-coordinates and radius.
New functionalities
Cluster selection with mouse is used to define the starting guess of the cluster configuration by simply drawing shapes (squares, ellipsis or diagonal ellipsis) on the TDP.
Simple clustering is a clustering method that allows to cluster transitions without inference using the starting guess as the final cluster configuration.
Symmetrical clusters is a constraint applied to the cluster configuration that allows to infer configurations where cluster centers are independent from each other but having a projection on the other side of the TDP diagonal. This offers more flexibility on the cluster configuration without neglecting the inherent symmetry of the TDP.
Constraint-free clustering allows to infer cluster configurations without any constraint on their positions.
Here is a release note:
Fixed bugs
Simulation
Molecules
Export options
Video processing
Import
Edit video
Molecule coordinates
Trace processing
Transtition analysis
Improvements
Trace processing
General
Factor corrections
Transtition analysis
General
Transition density plot
include staticsto include/exclude the last state of each state sequence to the TDP in diagonal bins (activation was previously the default)include staticsinclude staticsState configuration
matrixto infer cluster configurations where cluster centers are the result of all possible combinations of states (activation was previously the default)diagonal clustersto add diagonal clusters to thematrix-constraint configurations (activation was previously the default)likelihoodto choose in which way the likelihood should be calculated (complete datawas previously the default)matrix,symmetricalorfree), "likelihood calculation" (complete dataorincomplete data) anddiagonal clustersk-meansandGMtoggle buttons to a singlemethodpopup menu (appended with new methodsimple)matrix, and new constraintssymmetricalandfree), adiagonal clusterscheckbox and alikelihoodpopup menucluster shapepopup menu to a series of shape buttonsNew functionalities
Simple clustering is a clustering method that allows to cluster transitions without inference using the starting guess as the final cluster configuration.
Symmetrical clusters is a constraint applied to the cluster configuration that allows to infer configurations where cluster centers are independent from each other but having a projection on the other side of the TDP diagonal. This offers more flexibility on the cluster configuration without neglecting the inherent symmetry of the TDP.