Background Rates

The Background Rates tab of the Settings window normally displays the background rates resulting from the calculations done in the Background Analysis page, after validation of these results. It also allows choosing what algorithm to use for MLE estimation of background rates.

1. MLE Algorithm

The MLE approach to background rate estimation is described in the Background Analysis page of the manual.

A new option has been introduced in version 4.11 to emulate the procedure implemented in FRETBursts (see the Background Analysis page for reference and Ref. 9 in the Bibliography page of the manual). This option is selected by choosing FRETBursts for the MLE Algorithm. The only adjustable parameter is the MLE Min Time Lag used in the first iteration of the algorithm. The default value (250 us) is usually appropriate for standard single-molecule data.

If you do not want to emulate FRETBurst's approach, the Default algorithm should be used.

2. Background Rates (Hz) array

As a reminder of the Background Analysis page manual, validation of the background rate results has two possible outcomes:

• if the Fitted Rate option was selected for the Background Rate Used for Burst Search parameter (in the Background Analysis page), then the above Background Rates (Hz) values are the fit results found in the top right column on the Background Analysis page (column of rates labeled Fitted Bkgd R).

• if, instead, the MLE Rate option was selected, then the Background Rates (Hz) values are the fit results found in the column labeled MLE Bkgd R.

In both cases, the validated rates are sent to the Settings window and displayed in the Background Rates (Hz) array.

However the values shown in the Background Rates page can later be edited by the user. The implications of such a modification need to be kept in mind and are described below.

The value displayed above are stored internally and used for most calculations requiring average background rate values, among which:

• Time Traces: any statistics involving background correction uses these values for those corrections (time-dependent background correction is not yet supported in time traces)

• Burst Statistics

• ALEX Histograms

• etc.

In other words, it is possible to override values obtained during background analysis by editing this array. As soon as a new background rate analysis is performed, these values are automatically replaced by the new ones.

Notice that overriding the background rate array doesn't affect the result of time-dependent background rate analysis, which remains unchanged.