AlliGator Window

AlliGator’s main window (figure below) shows the source dataset intensity image on the left-hand side, and one of many different analysis panels on the right-hand side (the Image Histogram panel is shown in the figure). The pull-down list on the top right (aka panel selector) allows selecting which analysis panel is displayed.

AlliGator Panels

The following panels are available:

• Source Image Panel

• Image Histogram Panel

• Fluorescence Decay Panel

• Fluorescence Decay Statistics Panel

• Intensity Time Trace Panel

• Phasor Plot Panel

• Phasor Graph Panel

• Phasor Ratio Analysis Panel

• Lifetime & Other Parameters Analysis Panel

• Decay Fit Parameter Map Panel

Each panel’s function is discussed in a separate manual page (see the table of content on the left).

A standard menu bar on the top left gives access to different functions, which are sometimes associated with a AlliGator Shortcuts. The different menus are discussed in separate sections of the manual.

The main window can be resized in order to increase the Source Image size. The right-hand side panels do not resize laterally but expand vertically (their content is not resized).

Analysis Status Indicator LEDs

LEDs located on the bottom right of the panel indicate at a glance which parameters or options have been defined, or some user action is required. To see which option they correspond to, hover over each of them and wait for a tip strip to show up.

From left to right, they are:

Top row

• Reference/IRF Defined

• Phasor Calibration Defined

• Phasor Calibration Series Defined

• Phasor Calibration Map Defined

• Phasor Ratio Reference 1 Defined

• Phasor Ratio Reference 2 Defined

• Dataset Update Needed

Bottom row

• Individual IRFs Defined

• Phasor Calibration Used

• Phasor Calibration Series Used

• Phasor Calibration Map Used

• Phasor Ratio Lifetime Reference 1 Defined

• Phasor Ratio Lifetime Reference 2 Defined

• Phasor Plot Update Needed

Other buttons and indicators

Depending on the task being processed, some controls or indicators can appear in the main window. For instance, for some time-consuming tasks, a progress bar is displayed at the bottom of the window. More generally, a spinning-row-of-dots animated icon is displayed while a taks is in progress, and is sometimes associated with an Abort button to allow interrupting these processes.

Finally, audible feedback is provided in the form of chimes to inform the user of the completion of scripts, or the occurence of an error.

More information about the functions and use of the software can be found in the manual pages.