Monitored Variables

1. Monitored Variables List

    The Monitored Variables List is used by both the General Multispot Analysis script and the Sliding Window Analysis script (a beta feature) described in separate pages of this manual.

    At the end of each iteration of these scripts, the updated values of the variables listed in this list are collected and added to their separate plot in the chart. There are as many plots as there are variables in the list, with the caveat that array variables are represented by N separate plots, where N is the number of array elements. The plots' "length" is equal to the number of iterations in the script (in general, the number of spots, but possibly, the number of pixels).

    Each element of the list is an internal numeric variable, or an indicator or control value. The supported variables are accessible via a pull-down list, or can be auto-completed when typing the beginning of the variable name. Note, however, that it is possible to edit these names and therefore introduce typographic errors which will render the name of a variable unrecognizable. In this case, the variable output will be zero.

The reason why the variable names are editable is that array variables are possible.

Array Variables

    A number of variables within ALiX are arrays (some are clusters, and are discussed next). Their name appears as:

Variable_Name[]

where the brackets indicate an array indexing possibility. An example is Average Rates (Hz)[], which refers to the Average Rates (Hz) array indicator found on the Background Analysis page and represents the average count rates measured for each photon streams in the data set.

    Leaving the Monitored Variable name as is will result in as many plots as there are elements in the array.

    However, in most cases, not all values are of interest to the user. In this case, it is possible to specify which element of the array is desired by adding the index of that element in the brackets (the first element's index is 0, and so on). For instance, to monitor the average count rate in the Donor and Acceptor streams, add the following two elements to the Monitored Variables List:

Average Rates (Hz)[5]

Average Rates (Hz)[6]

Cluster Variables

    Some of the variable names in the list appear with a period separating two names, to indicate elements of a cluster (or structure) of parameters.

For instance, the variable:

ALEX Statistics.E

represents the mean E value of the selected bursts in the ALEX Histogram, as shown in the cluster of indicators to the right of the histogram's scale legend. The cluster comprises 4 elements: E, S, dE and dS, all accessible individually in the list.           

2. Monitored Variables Chart

    The Monitored Variables Chart is updated after each iteration. The example shown in the figure above corresponds to a series of 8 spots smFRET experiment. The selected variables are the 2nd and 3rd fit parameters of the E Histogram fit, which was selected to be an unweighted least-square fit using a Gaussian Fit Model. In this case, according to the corresponding manual page, these parameters are the Center and Standard Deviation of the Gaussian. Note that there is a single vertical scale, therefore variables having different dynamic ranges may need some scale adjustment to be clearly legible.

As usual, these plots can be exported to the clipboard.

3. Checkboxes

    If it is not cleared before starting a script (i.e., if the Clear Chart Before Script checkbox is left unchecked), new data points are added to the existing plots.

    The Keep Current Plot Names checkbox can be used to give user-defined plot names to different plots, as illustrated in the figure above. Otherwise, the plots take the name of the variable they represent.