Estimation of state degeneracy - panel "Kinetic model" - 2D-vbFRET - Linux compatibility - divers bug fixes

[mca-sh]

Here is a release note:

• New functionalities
• Fixed bugs
• Improvements

New functionalities

• Estimation of state degeneracy via exponential fit allows to estimate the optimum fitting model complexity and perform bootstrap fit for all dwell time histograms in one click. Please refer to the dedicated doc sections Workflow and Dwell time histograms for more information.

• Estimation of state degeneracy via DPH selection allows to obtain an optimum configuration of states including state degeneracy by performing BIC-based model selection on discrete-phase type distributions. Please refer to the dedicated doc sections Workflow and Kinetic model for more information.

  

• Kinetic model: This new panel belongs to module Transition analysis and allows to infer the most probable transition rate matrix and associated errors for a given state configuration. It uses the state configuration established from TDP clustering and state degeneracy analysis, and applies the Baum-Welch algorithm to infer the transition probabilities. A set of state sequences is simulated a posteriori to compare with experimental dwell times and validate the given kinetic model. Please refer to the dedicated doc sections Workflow and Kinetic model for more information.

  

Fixed bugs

Routines

Interface testing

• correct testing of project merging

  Simulation

• correct yes/no typo in simulation logs

  Video processing

• fix error occurring when importing a .gif file

  Trace processing

  Project management

• fix error occurring when importing FRET state sequences for more than 1 pair
• correct import of project-associated video (was ignored due to an error in file path)

  Single molecule images

• fix error occurring when refocusing on a video that has an uneven number of frames

  Plot

• correct empty plot when importing one ASCII file

  Transition analysis

  State configuration

• correct axes limits when only one BIC value was inferred

• Improvements

  General

• make compatible with Linux Ubuntu 20.04 distribution

  Video processing

  Edit and export video

• make unavailable the image filters that use the ITALS library (MATLAB freezes every time: there's an issue with the library)

  Routines

  Kinsoft challenge analysis

• adapt the Kinsoft challenge analysis routine to the new kinetic model analysis

• adapt the Kinsoft challenge analysis routine to known number of states and/or non-gaussian noise

  

Simulation

Export options

• add state sequences without blurring effect in (*.txt) Traces from simulation files

Trace processing

Project management

• improve communication by handling ill-sized project

  Find states

• improve deblurr option by only removing the 1-data-point dwell dwell times that are caught between a higher and a lower state values
• add method vbFRET-2D which analyze donor and acceptor intensity as 2D data

Transition analysis

Export

• add files (*.txt) DPH model selection, (*.dt) Dwell times and (*.txt) Kinetic model to export options

  State configuration

• modify GUI to add a "Set" button in order to pick a color for the current cluster (as a replacement to the old *Transition" list)

  

Dwell time histograms

• modify GUI to transform the old "State transition rates" panel into the "Dwell time histogram" panel
• modify parameter structure to store fit parameters for each and all state transitions (fields kin_start and kin_res become lft_start and lft_res to identify the rupture in down-compatibility)
• make available the option to bin state values after clustering

• improve workflow by making the option to exclude/include first & last dwell times available as a general checkbox rather than in a fit-specific popup

  

Kinetic model

• improve transformation from dwell times in state sequences by taking into account time averaging