Embedded Files
The Advanced Background Analysis page provides algorithms to obtain time-dependent background rate estimates for the different photon streams. While hopefully not a common concern, time-dependent background rates can occur due to many possible reasons:
Laser intensity fluctuations
Focus drift
Buffer evaporation, etc.
Using a constant (average) background rates in these situations, as obtained with the tools available in the Background Analysis page, will potentially result in longer or shorter bursts than optimal during burst search, and in incorrect background corrections during later stages of the analysis. An example of such a situation is illustrated in the Figure below, where the background rates of the different streams (unit: Hz, read on the right-hand side scale) shows a slowly decreasing background.
Different types of analyses are available, which can be selected using the Background Analysis Type pull-down menu (red box in the Figure above):
Time Trace Based
MLE
1-Exp Fit
The analysis is started by clicking the Compute button and results in one or more background rate time traces plotted in the Background Rate Time Traces graph (green box in the Figure above). Details about these different methods are provided in the sections below.
1. Time Trace Based Analysis
When selecting this method, the following parameters become accessible:
This method uses one of the intensity time trace plotted in the Time Trace page, selected by the Time Trace pull-down list. By definition, at least one time trace must have been plotted in the Time Trace page for this method to be functional.
The Display Time Trace checkbox next to it allows representing the selected time trace in the Background Rate Time Traces graph.
The Window Size (TT Bins) control allows to define the width of the sliding analysis window, in unit of time bins, the value of which is defined by the Time Bin control used to plot the time trace (Time Trace page).
The Threshold (Percentile) control allows to define the threshold used to define time trace bins above the local background level.
The Min Threshold Rate control imposes a minimum threshold Th_min.
The principle of this method is simple: in each window of N bins, the Pth percentile value Th of the time trace window is computed and only bins whose value is below max(Th, Th_min) are retained to compute the local mean background rate.
Note: the results of this method being limited to a single photon stream, they cannot be used for burst search or burst statistics corrections.
2. MLE analysis
When selecting this method, the following parameters become accessible:
Switching the Rate Calculation Type checkbox from Time Trace Bin to # Time Lags reveals a different control:
This approach uses the same MLE calculation of the background rate (for one or all photons streams, depending on the status of the All checkbox) used in the Background Analysis page (see the corresponding manual page for details), limited to a fraction of the data set/time trace.
When the Rate Calculation Type is equal to Time Trace Bin, the data set is divided in consecutive windows of size Time Trace Bin, in which a MLE calculation of the background rate(s) is performed. The minimum time lag used for this calculation can be either determined automatically or specified by the user, depending on the status of the Use Average Count Rate checkbox (see the Background Analysis manual page for details). If specified by the user, the Min Time Lag value is used.
3. 1-Exp Fit analysis
When selecting this method, the following parameters become accessible:
As for the MLE approach, the time window over which the local backround rate(s) is (are) calculated can be defined in terms of duration (Time Trace Bin) or of a constant number of timelags (# Time Lags). The only difference is in the way the background rate is estimated. Here, as in the Background Analysis page (see the corresponding manual page for details), a non-linear fit of the timelag histogram is performed. The timelag histogram's Time Bin (Linear) is user-specified, as is the Fit Method and the type of weighting (Weighted Fit checkbox)
4. Using the time-dependent background rates
As explained before, the Time Trace Based time-dependent background rate analysis results cannot be used for further data processing and is merely provided as an experimental tool.
When using any of the other two methods (MLE or 1-Exp Fit), the resulting background rates can be used only if they have been calculated using a constant time trace bin (Rate Calculation Type = Time Trace Bin). If this is the case, validating (and storing) the results is done by clicking on the Accept All Background Rate Time Traces button next to the Compute button. The green LED next to it lights up when this is done.
The Advanced Background Analysis button (Adv. Background, Ctrl+Shift+B) combines the action of the Compute button and the Accept All Background Rate Time Traces button and is therefore the quickest way of obtaining the desired result. It is one of the functions available in the Analysis menu.
Once this step is accomplished, checking any Use Time-Dependent Background Rates checkbox in another page will have the effect of using the local background rates for any calculation.
Note that if no such time-dependent analysis has been performed (or validated), the background rates used in calculations are the average rates computed in the Background Analysis page.
Finally, it is possible to histogram the background rate time traces and analyze them in the Background Rate Time Trace Histograms Graph (blue box in the figure above).
Page updated
Report abuse