The Surface menu (Figure 7) is divided into two main categories:
- The first category contains tools for 3D surface manipulation.
- The second category includes global analysis tools.
This function can be used to crop data to a region of interest. It crops data to those displayed on the 3D surface panel, which are determined by kinetic and spectrum graph X scale ranges.
Subtract 3D Surface
Use this function to subtract 3D surface data (i.e. solvent response) from the opened surface. Both surfaces have to be taken using the same scales.
CAUTION: Do not choose this option to correct for scattered excitation light. For that choose Subtract Scattered Light option from the Surface menu.
Some data files may have a non-zero spectral baseline, which appears throughout the whole data set even before t0. Such background is usually a result of long-lived species present in the sample (species with lifetimes longer or on the order of the temporal interval between the excitation laser pulses). Additionally such background may be a result of thermal lensing caused by the excitation beam. When you choose the Subtract Background option a new window will pop up (Figure 9).
The spectrum displayed is the first spectrum that appears on your 3D surface. Use the increment button to add as many spectra as needed to produce an averaged background spectrum which will be automatically subtracted from the original data when you hit the Accept button.
Close Subtract Background window if you want to return to the main screen without subtracting the background.
Choose Save File… to save the new surface under a new name.
Subtract Scattered Light
CAUTION: Choose this option when performing correction for scattered pump light or scattered fluorescence (but not stimulated emission).
In some cases your detector picks up scattered light from the sample. This often happens when the excitation wavelength falls into the probing range of your experiment. To correct for such scattered pump or scattered emission (not stimulated emission) you cannot simply subtract the pre-zero background from the data, particularly if the amount of scattered light is significant.
The corrected transient absorption is expressed as follows:
Where S is the experimentally observed ΔA, and S (t<0) is the average of experimentally observed ΔA before time zero.
When you choose the Subtract Scattered Light option a new window will pop up, similar to . The spectrum displayed is the first spectrum that appears on your 3D surface. Add as many spectra as needed to produce an averaged background spectrum.
Long time-window data. Sometimes the time window can be larger than camera integration time that is synchronized with a probe light source. This causes the scattered light to disappear after some delay time on the 3D surface as it is shown on Figure 10.
To take this effect into account click the “Set time Range” button on the bottom left of the “Subtract scattered light” window. This shows a plot that displays the kinetic profile corresponding to the wavelength selected on the “spectra to average” plot cursor (see Figure 11). Use two cursors on the kinetic plot to select the range where the scattered light disappears.
The software subtracts the averaged pre-zero spectrum from the part of the 3D surface that is before the first cursor position.
Spectra corresponding to delay times within the interval between two cursors will be removed from the data set.
The 3D surface will be automatically corrected after you click the Accept button.
Close Subtract Scattered Light window without accepting if you want to return to the main screen without subtracting any background.
Choose Save File… to save the amended surface under a new name.
This function can be used to recalculate measured values to different representation. If currently opened data has ΔA or ΔT/T representation (Z-axis title) the user is asked if he wants to use automatic ΔA ↔ ΔT/T conversion. Data values conversion can also be defined by a custom formula. The dialogue box (Figure 12) also allows changing the Z axis units (see Z-Axis Title section below).
This function allows you to correct the 3D data surface for the chirp of the probe pulse. The main window of the chirp correction utility is shown on Figure 13. It is similar to Surface Xplorer main window. 3D surface, kinetic and spectrum panels with cursors function similarly.
NOTE: To improve the precision of chirp correction, prior to applying the procedure, trim the data matrix on the wavelength axis to include only the useful wavelength range (e.g., to remove spectral regions without sensible data).
To apply chirp correction to the data it is necessary to specify the correct time zero values for every wavelength. The software requires specifying at least 4 time zero – wavelength pairs, others are determined by approximation with a theoretical function. You can specify points to fit in any of the following ways:
- select an active point with cursors and press Add button (or Ctrl+S shortcut);
- manually populate the table with values;
- load fit coefficients file (Add from file button). Usually results of the Fitting solvent response or Resonant fit are used for that purpose. File format is described in Appendix.
These points are shown as crosses on the Surface graph. When 4 or more points are specified, the software fits them with the following function:
, where a, b, c, d – parameters to determine during the fit, w – wavelength, t0 – time zero. The fit is shown as a black curve on the surface. Buttons Preview chirp correction and Apply & Exit also become available only after enough points have been created.
Use the following elements to control chirp correction tool:
- Click to select point in the table. This will highlight the clicked row, making the point active: move cursors to the corresponding position, update spectrum and kinetic graphs. It will also adjust the graph scales to show this point if it is beyond scale ranges.
- Click existing point on the 3D surface graph to highlight it in the table.
- Button Sort arranges the points in wavelength increasing order.
- Button Remove erased the selected point
- Button Save to file. Save points to text file for future use. File format is described in Appendix, Fit files section
- Button Preview Chirp correction calculates chirp correction, and switches interface to preview mode. Click Back to Setup button to undo changes and return to original surface.
- Button Quick help shows short help tips (Figure 13). Click anywhere within the screen to close help.
After chirp correction, each kinetic profile is shifted based on its time zero value, thus moving them out of the previous borders and causing undefined data – white space on the 3D surface (Figure 14). If this shift is larger than the step in the end of the kinetics, then undefined data will appear also on top of the image (long delay values).
Click Apply & Exit button to perform chirp correction, return to main window and update the data.
Time zero correction
Use this function to shift the time profile on the time axis in order to adjust the zero time setting.
First decide what time corresponds to the instrument zero then choose it with a cursor on kinetics or 3D surface graph, then select Time zero Correction from the Surface menu. A new window will pop up prompting you to enter a new value with default at current delay.
After you click OK the time scale will be adjusted.
This command opens window (Figure 15) to specify the number of adjacent kinetic profiles to average. After you check wavelength scale reduction and confirm values, data spectral resolution will be reduced by averaging every N kinetic profiles (data matrix columns). This serves to improve signal-to-noise ratio.
CAUTION: Use this feature with data having broad spectral bands only.
Delete/Replace Bad Spectra
Sometimes in your data set there are spectra with extra noise, missed points (NaN), etc. Such data points may be caused by laser instabilities, damage in the continuum generator crystal, etc. In this case your data may look like as shown in Figure 16.
In many cases it is sufficient to delete such spectra. However if you are trying to average several surfaces corresponding to different scans of the delay line, a single bad spectrum in one scan will result in a bad spectrum in the averaged data set. The Surface Xplorer “Replace Bad Spectra” function allows you to replace a bad spectrum with one interpolated from two adjacent spectra.
Once this option is chosen from the “Surface” drop-down menu, the dialog window as shown in Figure 17 will appear.
The spectral range to be analyzed for bad data points should be defined in this window. One the OK button is pressed the software will replace every spectrum in this range that contains at least one NaN value by an interpolated one (Figure 17).
Some data (say, from a CCD camera) may contain spikes as it is shown on Figure 19. Remove spikesmenu item opens the window shown on Figure 20. Adjust the slide to set the sensitivity of the spikes detection algorithm. Detected spikes are shown with blinking red points. Click the Accept button to apply the filter. Detected spikes will be replaced with interpolated values.
Global analysis functions
The following functions perform analysis
Principal Components via SVD
This function applies the singular value decomposition procedure to the 3D data matrix.
For more details see the Principal Components.
Reconstruct From Principal Components
This function reconstructs the 3D Surface using the principal components from the SVD procedure. For more details see Principal Components.
This feature allows you to perform Global Fitting of your transient data. For details see the Global Fit.
This feature allows choosing the name of the measured value. The options are: ΔΑ (absorption difference, e.g., transient absorption data), A (absorption, e.g., stopped flow data), I (intensity, e.g., fluorescence data), and ΔT/T (another representation for transient absorption data).
NOTE: this does not change data values. Use 3D Data conversion (page 19) instead.