General Multispot Analysis

The General Multispot Analysis Script button (General Multispot Analysis, shortcut: Ctrl+Shift+M) allows some level of automation, by providing a list of actions (Script Actions List)  to be performed on each channel pair specified in the Channel Pairs (D, A) list.

To define a script, fill in the Script Action List with actions to be executed in the exact order they need to be executed. Verify that the Channel Pairs (D, A) list contains the proper definitions of pixel pairs.

1. Data Folder & Process all files in Data Folder

    In order to execute a script on multiple files, specify the folder containing those files using the browse button to the right of the path control (or drag the folder in that control). Check the Process all files in Data Folder to let the software know that all files in that folder (of the proper type, see below) are processed. If the box is not checked, only the file selected on the Data File page will be processed.

    To specify which type of files to process, load or preview one of the files via the Data File page, and make sure that the correct File Type is selected. Other file types will be ignored.

Please note that the script (with all its options) is repeated for each file. In general, you will want to make sure that the Clear All Burst Analysis Graphs Before Start checkbox is not checked, and similarly, that the Clear Chart Before Script checkbox on the Monitored Variable tab is not checked, unless you do not want to keep the results of previous files' analysis. Make sure that the Reset all Graphs to Default when Loading a new File option in ALiX Settings>>General Settings window is unchecked, if you not want to lose plots from previous file analyses.

2. Script Actions List

    The Script Actions List is comprised of predefined actions, which correspond to buttons found on the software's user interface (UI). These buttons (or actions) are referred to by their caption, which can be read in the Context Help window (Ctrl+H). Note that not all buttons are available in this list. In particular, script buttons (such as the Run Script button) are not available.

    Adding an action to the list can be done by browsing the pull-down list available for each element, or typing the action/button caption directly. The action list is auto-completing, therefore typing the first few letters will generally be enough to find the corresponding action's precise name.

    An action can be deleted from (right-click >> Delete Element) or inserted into (right-click >> Insert Element Before) the list.

    As an example, the list below reproduces the sequence of actions performed when using the All Analysis Steps item (Ctrl+A) of the Analysis menu and adds to it a final step of 1D ALEX Histograms calculation and 1D Shot Noise Analysis.

3. Script Action Parameters

    Some scripted actions can accept parameters. To add parameters to an action, simply add a semicolon after the action name, followed by each parameter's definition:

Script Action:Parameter_1=Value_1, Parameter_2=Value_2

    For instance, to compute the time trace histogram of the first time trace with a bin of 1.5, the following script action is used:

Time Trace Histogram:ID=0,Bin=1.5

    A list of script actions and description of syntax parameters can be found in the reference section of this manual. 

4. Clear All Burst Analysis Graphs Before Start

    Since the General Script is designed to process several spots sequentially, any step that generates plots (and assuming that the plots are preserved from one analysis to the next), might end up populating graphs in the Burst Analysis page with a potentially large number of plots. Since there are many tabs in this page, the Clear All Burst Analysis Graphs Before Start checkbox allows to automatically clear all these graphs before the script is run.

5. Monitored Variables Tab

    It is often convenient to collect results of some of the analyses performed during a script in the form of plots. This can be done using the Monitored Variables Tab as discussed in the corresponding manual page.

6. Script Archiving (Script Saving & Loading)

    For data analysis reproducibility purposes, it is often important to keep track of every analysis steps, settings and parameter values used during analysis. The Save and Load Multispot Script buttons and the associated checkboxes simplify this task (in principle, all information can be found in the Notebook if options have been selected to export everything to the Notebook, but it is tedious to gather).

    The Include All Control Values option also saves graph cursors having an influence on the analysis (such as the Macrotime Histogram, Nanotime Histogram and ALEX Histogram cursor locations) as well as controls set in the Shot Noise Analysis window. The file saved is a text file (strictly speaking a INI file) and can be edited and reloaded to restore the environment corresponding to a previous analysis (*).

    Note that the script is not executed after it is loaded. The user needs to press the General Script button (or Ctrl+Shift+M) to execute the script. In particular, the script can included a file loading step, which, if the file path is correctly saved by the script, means that a published analysis can be reproduced by the press of two buttons: Load Multispot Script and General Script. In practice, it might be necessary to modify the file path after having loaded the script, as it is unlikely that the original folder structure in which a data file was saved will be preserved on a different computer.

Notes

(*) When editing a script file, be careful not to introduce "invisible" text formatting characters such as tab or carriage returns, etc. It is recommended to use bare bone text editors such as TextEdit (Mac) or Notepad (Windows) and save the files as a text file (not in rich text format, .rtf) in order to not introduce unwanted characters. Be aware that not all quotation mark symbols are equal. In general, editing a script file is not recommended, and could result in part of the information contained in it to not being loaded properly.