Burst Search

Burst Search Parameters Description

1. # Burst to Detect

The default value (-1) should be used if all possible bursts in the file are sought.

2. Time Trace Duration

The default value (-1) should be used to encompass the whole data set.

3. Search Parameters Interpretation

This parameter's definition is discussed in section 6 below.

4. Search Parameters Interpretation

This checkbox (default: unchecked) allows using the "historical" definition of the burst threshold (see Parameter m section below for details). 

5. Photon Stream

The search type specifies which photon stream(s) is (are) included to compute the instantaneous count rate used to identify background-to-burst and burst-to-background transitions. The possible choices are indicated in the snapshot below:

6. Parameter m

This integer parameter indicates how many photons are used to compute the instantaneous count rate mentioned above.

The instantaneous count rate is defined by default as explained in the Count Rate Analysis manual page:

ri = (m - 2) / (ti+m-1 - ti),

where the m consecutive photons have time stamps ti, ..., ti+m-1. The bursts start when this rate is larger than F x B, where B is the background rate computed for the chosen photon stream.

If the Search Parameter Interpretation is checked (Historical interpretation), the criterion is slightly different and reads:

m / (ti+m-1 - ti) > F B

Note that the difference between the two definitions could be accounted for by using a slightly different F value.

The smaller the m parameter, the more "instantaneous" this rate is, but the larger its relative variance. On the other hand, the larger m, the larger the bursts will tend to be, as m will in practice be the typical minimum burst size obtained.

Increasing this parameter has a similar effect to increasing the value of the minimum burst separation (discussed below). Therefore, in order to obtain as "fragmented" as possible a final set of detected bursts, a small value should be used. The default value of 5 should be fine in most cases.

7. Threshold Type

This parameter specifies whether the threshold to which the instantaneous rate is compared is specified as an absolute value (Fixed Rate):

or as a relative value (Proportional to Background) defined in units of background rate:

The proportionality factor F is computed from the specified confidence limit in percent (CL (%)) shown to the right. It is also possible to define an arbitrary value for F, but since no inverse calculation of the corresponding confidence limit is done, the corresponding parameter is meaningless.

or a fixed relative value above background (Fixed Rate above Background):

In the snapshots above, parameters which are not used for the search are crossed.

8. Type of Background Rates

When an Advanced Background Analysis is performed, this checkbox is enabled and allows choosing between a constant background rate (default) or a time-dependent background rate. This option is used for burst threshold calculation.

9. Minimum Burst Separation

This parameter specifies whether bursts separated by less than a minimum duration are fused into a single burst or not.

Since the burst search algorithm proceeds by steps of one photon at a time, it can happen that two consecutive bursts overlap by a few photons (or even just one), even before burst fusion is applied. This is an artifact of the algorithm, and is taken care of by the default parameter (Min Burst Separation = 0), which will fuse those bursts (which should not be "separated" since they overlap).

To preserve this artificial potential overlap (for instance to emulate the default burst search settings of FRETBursts), it is possible to enter a negative Min Burst Separation parameter (the exact value does not matter). In this case, consecutive bursts might overlap and therefore their total number will in general be larger than using the default value of Min Burst Separation = 0 (or a larger value).

10. Logical Combination of Burst Searches

The Burst Search definitions discussed above are in fact part of an array of such definitions (the array can be navigated using the array index visible above it, or using the scrollbar at the bottom).

There are two ways of taking advantage of this feature, using the Logical Combination of Burst Searches string control:

• Typing Si (where i is an integer from 0 to the number of elements in the array) in this string specifies which element to use for the search. This allows defining several different searches and rapidly switching from one to another.

• Typing Si operation Sj (where i and j are integers from 0 to the number of elements in the array and operation is either the & or | character) specifies an AND or OR of two burst searches.

Leaving the string empty instructs the software to use the first set of burst search parameters.

11. Saving/Loading Burst Search Parameters

In order to simplify the reproduction of data analysis, it is possible to save (and retrieve) burst search settings using the two buttons indicated by arrows in the top Figure above. The default file extension is .abs (for ALiX Burst Search parameters). The file is a plain text file and can easily modified with a text editor if needed.