Compute CCFs Script

This script goes through all the selected (or all) channels (depending on the Use All Channels slider located on the left hand side of the page) by individual pair (as defined in the Channel Pairs (D, A) list) and computes the CCF for each pair according to the definitions set in the Correlation page.

If the Compute & Save Mean Count Rate checkbox (see below) is checked, an additional step of mean count rate calculation (involving computing the PIH for each channel of the pair and the corresponding average count rate) is inserted. The value of the current mean count rates will be displayed in the Mean Count Rate A (Hz) and Mean Count Rate B (Hz) indicators to the right of the CCFs button.

The corresponding CCF curve(s) (and mean count rates if requested) is then saved as an ASCII file in the same folder as the original file, with the name:

Data_File_Name_CCF of Ch Channel_Name.txt

where Data_File_Name is the data file name without its extension and Channel_Name is the channel name as read on the Data File page. Note that in order to result in a valid file name, any character "\" or ":" in Channel_Name will be replaced by an underscore character.

Like for the Compute ACFs Script, some care needs to be used when defining which channels are selected, which pair to include in the list and which CCF to request in the Correlation page.

For instance, if the user is interested in computing the CCFs of all (D, A) pairs in all spots of a multispot smFRET file, the (Donor, Acceptor) pair should be selected in the Photon Stream Pairs control on the Correlation page:

It is also possible to compute the (A, D) CCF by adding the (Acceptor, Donor) pair to the list above. Note that it is also possible to add the (Donor, Donor) and (Acceptor, Acceptor) pairs to include the ACFs of these streams in the calculation! All curves will be saved in the same file (as separate time and amplitude columns).

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Special consideration for the CCF channel pairs list

To simplify the analysis of optical crosstalk within SPAD arrays, the following syntax is also possible:

• to compute all potential CCF pairs (i < j), where i and j are channel indices in the list of channels as defined on the Data File page, enter the single string "ALL" (without quotes). In order to also compute the pairs i > j, simply set both (Donor, Acceptor) and (Acceptor, Donor) pairs in the CCF settings.

• to compute all potential CCF pairs  (i < j) for i_min <= i < j <= i_max, enter the string "ALL(i_min,i_max)". For instance, if there are two arrays with indices 0 to N-1 for array 1, and N to 2N-1 for array 2, and you are interested in intra-array CCFs only, first run a script with ALL(0,N-1) and then another one with ALL(N,2N-1).

• it is possible to combine these different notations. For instance, to compute all possible CCFs of channel 0 to 7 and channel 8 to 15, enter:

                    ALL(0,7)

                    ALL(8,15)