- Last Updated: Friday, 06 October 2017 11:56
- Written by Chavdar Slavov
Global lifetime analysis
Global lifetime analysis (GLA) is the most common analysis technique for time-resolved data (for details see the Data analysis page). This module of OPTIMUS is capable of performing GLA in combination with direct analysis of a number of experimental artifacts typically encountered in ultrafast spectroscopy (see Artifact analysis and Artifact analysis module module). Furthermore, the module allows performing data analysis using a simple sequential kinetic model to obtain the Evolution-Associated Spectra (EAS) (see van Stokkum et al. 2004; Slavov et al., 2015)
Please note that the use of the GLA module is not limited to ultrafast time-resolved data, but it can also be used with time-resolved data recorded on longer timescales (e.g. ns, μs, ms, s).
For the 'Global lifetime analysis' module of OPTIMUS the experimental data files should be supplied in the form of .ana file format.
Global lifetime analysis module of OPTIMUS - Sequential kinetic model
The 'GLA' module is very intuitive and self-explanatory. Nevertheless, here are provided some tips on how to use it.
The operation of the module is similar to the 'Artifact analysis' module
- The lower (lb) and upper (ub) boundary as well as the starting value (start) of each fit parameter in the GLA module of OPTIMUS are specified using a series of edit boxes. The fit value is given in a text box or push button located next to the corresponding start value edit box.
- Panel - Specify general settings
- Edit box: Wavelength range (nm) and Exclude wavelength ranges (nm) - Specify a wavelength range of interest. Dismiss wavelength regions where no relevant signal is present (Format: e.g. 310:350, 420:460, meaning dismiss wavelength regions 310-350 nm and 420-450 nm).
- Edit box - Time range - Specify the time range (typically you can use the complete time range of your measurement).
- Edit box - Sweep period (ps) - An option is included to be used for analysis of fluorescence time-resolved data from Streak camera measurements where long lifetimes contribute to the signal due to the so-called back sweep (for details see van Stokkum et al. 2008; Slavov, 2009). However, this part of the analysis is not yet fully tested and may not work as expected.
- Edit box - # of start points - The fitting of the data can be started automatically from a number of random starting values for the fit parameters in a search for a global minimum. This option is available in The GLA module of OPTIMUS, but it is more relevant when performing Target analysis. Please note the option uses parallel processing and will employ all of the available processor on your computer. To this moment no indicator showing the progress of the multistart analysis is implemented, thus you need to wait until the results are loaded.
- Edit box - Max # of iterations - Specify the maximum number of iterations that will be performed during the optimization.
- Popup menu - Background offset - Background offset option is included in case the data contains a background offset. However, this is rarely the case, thus typically this option is not used.
- Panel - Specify IRF and artifact settings
- Popup menu - IRF with variable FWHMs - Specify whether the IRF FWHM should be varied over the selected wavelength range and if so what kind of variation should be used: i) independent for each wavelength (Option: yes); ii) dispersed (Option: dispersed).
- Pushbuttons - Load and Save - The fitted widths of the IRF can be save in a text file (.wirf), which then can be loaded again. This option allows estimating the IRF widths on a solvent measurements and then use these widths as fixed (option in the Popup menu - IRF with variable FWHMs ) in the analysis of the sample measurements. Note, the .wirf file contains only IRF widths for the analyzed wavelength channels.
- Edit boxes - IRF FWHM (ps) - specifying lower (lb) and upper (ub) boundary and starting value (start) for the IRF width. Note the wavelength dependence of the IRF widths can be viewed as a separate figure by pressing the push button indicating the result of the fit.
- Popup menu - # of artifact components - Specify the number of artifact components to be used in approximating the CA (for details see Artifact analysis). Typically, setting '3' is used.
- Push button- Relative shift - An option is included to allow variation between the center position in time of the different artifact components. Typically the three components should have the same position in time coinciding with the position of the IRF maximum. Thus, this option is almost never used but is included as an option in case it is needed.
- Panel - Specify fit parameters for 'time 0' dispersion
- Popup menu - Dispersion order - Specify the dispersion order to be used for apporximaing the chirp polynomial (for details see Artifact analysis). Order '2' is typically sufficient, while in rare case, e.g. where the chirp is relatively large, also order '3' might be used.
- Edit boxes - Center (nm) - specifying lower (lb) and upper (ub) boundary and starting value (start) for the center position of the polynomial approximating the chirp. This boxes are typically automatically set using the wavelength information from the loaded dataset.
- Edit boxes - Time offset (ps) - specifying lower (lb) and upper (ub) boundary and starting value (start) for the time zero offset. The starting value should be roughly assigned to the time point of the rise of the signal at the center wavelength (Center (nm)). The boundaries should be set wider enough to allow the program to find the time zero offset.
- Edit boxes - Dispersion - specifying lower (lb) and upper (ub) boundary and starting value (start) for the coefficients of the chirp polynomial (should be between -1 and 1).
- Please note that if in Panel: Specify IRF and artifact settings the option dispersed is selected for the varying the IRF FWHM in dependence of the wavelength, a pushbutton will appear in the Panel: Specify fit parameters for 'time 0' dispersion that will allow setting up dispersion fit parameters also for the IRF width.
- Panel - Specify regularization parameters
- Although the use of regularization is implemented for the 'Lifetime density analysis' module of OPTIMUS it can also be used in the GLA module. The regularization can be useful when the fitting of the experimental data yields compensating lifetime components. Please note, this option has not been evaluated extensively for GLA, thus it is supplied here mainly for testing purposes and should not be used as a primary option.
- Popup menu - regularization - Specify whether the regularization parameter should be used, fixed or variable. Hint: several fixed values can be used to find a reasonable fit.
- Edit boxes - Center (nm) - specifying lower (lb) and upper (ub) boundary and starting value (start) for the center position of the polynomial approximating the chirp. This boxes are initially set using the wavelength information from the loaded dataset.
- Edit boxes - Reg. factor 1 - specifying lower (lb) and upper (ub) boundary and starting value (start) for the regularization factor. Typically between 0 and 1.
- Pushbutton - Other reg. factors - specifying lower (lb) and upper (ub) boundary and starting value (start) for other regularization factors. Do not use!
- Panel - Specify expected lifetimes
- Please note, GLA can be viewed as kinetic modeling with a kinetic scheme with parallel, non-interacting states with equal initial concentrations. Alternatively, if a kinetic scheme can be used where the states evolve in sequence from an initially 100% populated state. The latter analysis results in Evolution-Associated Spectra (EAS) (Slavov et al., 2015).
- Check box - select whether GLA or analysis with sequential kinetic model should be used.
- Table - specifying lower (lb) and upper (ub) boundaries and starting values (start) for the expected lifetimes to be used in the GLA. Hint: if lb, start and ub have the same value the lifetime will be fixed (not variable) during the fitting. In case sequential modeling is selected, the expected lifetime will be used as starting values for the kinetic rates linking the components in the sequential kinetic scheme.
- Pushbutton - Analyze data - starts the data analysis
- Pushbutton - Save results - For consistency, GLA-OPTIMUS saves the complete analysis results before allowing other figures or data to be saved. The file saved after pressing this pushbutton can later be loaded in OPTIMUS-GLA via the Pushbutton: Load results in the Panel: Load datasets for analysis. Please note, all files saved from OPTIMUS are given automatic name related to the name of the original dataset (for details see Files in OPTIMUS).
- 3D plot and 2D plot pushbuttons - at the top-center of the GUI for this module act as tabs for switching between viewing the 3D plots for the dataset and the fit and the 2D plots comparing data and fit traces.
- Additional push buttons are provided for saving the presented figures in a variety of file formats (please explore the options). Push buttons: Save 3D data, Save 3D fit, Residuals, Save 2D plots.
- Pressing 'Save 3D data', 'Save 3D fit' or 'Residuals' push button brings up a new GUI with enlarged 3D plot.
- Pressing 'Save 2D plots' push button brings up a new GUI for exploring the rests.
- Pushbuttons 'Save DAS', 'Save SAS', 'Transient spectra' and 'Transient spectra, expanded' bring popup windows with settings for saving those type of figures.