Estimation of state degeneracy - panel "Kinetic model" - 2D-vbFRET - Linux compatibility - divers bug fixes#74
Merged
Merged
Conversation
The new kinetic analysis intend to: 1) resolve models with degenerated states 2) use the HMM state definition: single lifetime for each state and different transition probabilities 3) export the whole model with proper transition rate constants - **modify GUI** to separate the "State transition rates" panel into "State lifetimes" and "Kinetic model" - **modify parameter structure** according to the kinetic analysis new procedure - **adapt** dwell time histogram fitting to new procedure (fit all dwell times to get the lifetimes and transition-specific dwell times to estimate the transition probabilities) - **make available** the option to bin state values after clustering - **improve communication** by offering the option to exclude/include first & last dwell times as a general checkbox rather than in a fit-specific popup - **Automated dwell time histogram fitting** allows to fit all data in one click: estimates automatically the optimum number of exponential decays in the model and perform subsequently the model optimization for a particular state (Fit current) or for each of the dwell time histograms (Fit all) - **Estimation of the final kinetic model** allows to obtain an optimum configuration of states and state transitions for the data: optimizes the transition probabilities by comparing experimental distributions and number of transitions with simulation.
- **modify GUI** to add a "Set" button in order to pick a color for the current cluster
- **improve** exponential fit by using amplitudes normalized by the sum and managing infinitely negative gof
- **manage error** occurring when using processing an ill-sized project
- **fix error** occurring when refocusing on a video that has an uneven number of frames
- **improve** state sequence calcualtion from dwell times by taking into accoutnt ime averaging
- **correct** axes limits when only one BIC value was inferred
save function to separate file (commited previously)
- **fix error** occurring when importing FRET state sequences for more than 1 pair
Calculate state sequences from dwell times and pass it to model optimization
create backup ot kinMdlGOF
- compare experimental state sequences to one large simulated sequence with countSeqProb - compare experimental state sequences to one large simulated sequence with calcSeqError - calculate forward probabilities (works well!)
- **correct** how intensities ae improted from ASCII files
use frame-wise simulation instead of dwell time wise and return initial state probabibilties (used for forward ptobabilities calculatons)
correct variable name "rate" into "expT"
adapt script to dwell time matrix having 4 columns
always use crosshair cursor on TDP axes
manage the visibility of the crosshair cursor coordinates on TDP
display logs when starting MASH
update script spec
mca-sh
added
new functionality
…e to lack of data)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Here is a release note:
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
Simulation
Video processing
Trace processing
Project management
Single molecule images
Plot
Transition analysis
State configuration
Improvements
General
Video processing
Edit and export video
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
Trace processing
Project management
Find states
vbFRET-2Dwhich analyze donor and acceptor intensity as 2D dataTransition analysis
Export
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_startandkin_resbecomelft_startandlft_resto 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