Quick guide 4: Automate analysis

About auto analysis of single-molecule FRET microscopy data

Running the data analysis 100% automated is powerful for a quick screening of data, e.g. for evaluating data during or right after acquisition by the instrument, or as the first step in the following analysis.

The auto-analysis runs all steps in the data analysis using the current settings of the session. Some steps are optionally included which is defined in 'Settings->Autorun settings'. Since the processed data depends on threshold settings and methods used, the settings must be optimized manually to your setup before the auto-analysis is put properly into operation.

Define auto analysis options

Go to 'Settings->Autorun settings'.
In the dialog, specify the steps you want the auto-analysis function to include. If you tick 'Auto-align ROIs as a first step' make sure to check visually whether alignment of the emission channels failed after the analysis. It is recommended to optimize the settings of the bleach detection algorithm and then always to include it in the auto-analysis. See the documentation for how to optimize the bleach finder settings.

Run auto-analysis

Auto-analysis is run by pressing the green "play" button in the toolbar.
The analysis finishes by opening the windows browsing the found FRET-pairs
..and the FRET histogram.
Note that in auto-analysis, the default setting in the histogram window is to plot only time points prior the 1st bleaching events of each molecule.