Embedded Files
Some of AlliGator's functions can be performed via the top menu bar (and associated shortcuts).
The following menus are provided:
1. File Menu
Open HDF5 Dataset allows loading datasets saved in the open source file format used by AlliGator.
Load Image Folder and Load Image Folder Series are described in the Loading Time-Gated Data pages of this manual and is used with data consisting of series of images.
Reload Dataset and Reload Dataset Series allow reloading the previously loaded data after parameters have been changed in the Settings window that require data reloading and reprocessing (these parameters have labels followed by an asterisk (*) in the Settings window). This function uses the known location of the files to save the user the steps involved in selecting the files anew and works for all supported file formats.
Import is a sub-menu available to beta users and allows importing SwissSPAD data. Details can be found on the Importing SwissSPAD Data page.
Open White Light Image allows opening a single image of the sample (or any other image) which will not be used for data analysis. More information can be found in the Source Image page of this manual.
Open ROI Mask opens a mask image used to define regions of interest for data analysis. More information can be found in the Source Image page of this manual.
Save Source Image: performs the same task as Save Image with Overlay in the Source Image Context Menu described in the Source Image page of this manual.
Save Phasor Plot Image: performs the same task as Save Image with Overlay in the Phasor Plot Image Context Menu (see Phasor Plot page of this manual).
Save HDF5 Dataset saves any file loaded in AlliGator in an open source file format which conveniently packages all gate images and metadata in a multiplatform readable format.
Quit quits AlliGator (with confirmation, offering to save the Notebook).
2. Windows Menu
Notebook opens the Notebook window. The Notebook window is discussed in the Notebook Window page of the manual.
Dataset Information opens the Dataset Information window, discussed in the Dataset Information page of the manual.
Settings opens the Settings window. The Settings window is discussed in the Settings Window page of the manual.
ROI Manager opens the Image Source ROI Manager window, discussed in the Using ROIs manual page..
Fit Status opens the fit monitoring window, discussed in the Fluorescence Decay Fitting manual page.
3. Analysis Menu
Fluorescence Decay Statistics analyzes all single pixel decays within the data set and builds an histogram of the minimum and maximum intensity in each decay. This analysis is discussed in more details in the Fluorescence Decay Statistics page of the manual.
Define Intensity Corrections opens the Define & Save Intensity Corrections File discussed in the Intensity Corrections Definition manual page.
ROI Analysis performs an analysis of the pixels located within the selected ROI (or, if the Use ROI as Search Area button is pressed, in the optimal ROI within that region). This analysis includes:
Fluorescence Decay construction
Phasor calculation
All ROIs Analysis performs the same analysis as above on all ROIs currently defined, in the order they appear in the ROI Manager. There are two different modalities:
Interactive: this emulates the action of selecting each ROI in the list and executing ROI Analysis. In particular, if this option is selected, it will plot the corresponding decay, add a data point to a new phasor plot in the Phasor Graph, and display the current location of the ROI. This can take quite a long time in the case of a very long list of ROIs or for large datasets.
Alternatively, it is possible to use a Non-interactive mode, where no decay is plotted, the phasor plot resulting from the analysis in only displayed at the end, and no ROI is displayed on the Source Image during the analysis. This mode is recommended, as it is much faster (> x10).
In both cases, it is possible to interrupt the analysis by pressing the Abort button at the bottom right of the window.
Whole Image Phasor Scatter Plot computes the phasors of all pixels in the image and displays them as a single phasor plot in the Phasor Graph. Option for binning the image prior to this calculation are set with the Settings>>Source Image>>Image Binning Options.
Global Fit of Selected Decays performs a global fit of decays selected in the Decay Graph (Fluorescence Decay panel). Details can be found in the Fluorescence Decay Fitting page of the manual.
Time-Series Analysis (Phasor) performs the phasor analysis of the loaded dataset series (see the Time-Series Analysis page of the manual for details).
Time-Series Analysis (Fitting) performs a decay fitting analysis of the loaded dataset series (see the Time-Series Analysis page of the manual for details).
Sum All Datasets in Series loads each dataset in a selected series and builds a dataset in which each gate image is the sum of the corresponding gate images of all datasets in the series. If the Average Dataset Sum checkbox in the Settings>>Source Image window is checked, the summed dataset is divided by the number of datasets, obtaining an average dataset.
Warning: This dataset is temporary (as indicated by the asterisk which appears after its name in the AlliGator window title), and can (or should?) be saved immediately using the File>>Save HDF5 Dataset (Ctrl+S) menu item. Indeed, any action that will update the dataset loaded in memory (such as for instance moving the Time Point Slider next to the Source Image), will override this dataset!
Playback will load and display the datasets in a time series, without processing the data (contrary to the Time-Series Analysis menu item). It can be stopped by unchecking the Playback menu item (Ctrl+P) or pressing the Abort button.
Loop performs the same function as playback, but resumes playback from the start when the end of the series is reached. It can be stopped by unchecking the Loop menu item (Ctrl+Shift+P) or pressing the Abort button.
Export Settings to Notebook writes all settings currently used in AlliGator in the Notebook for future reference. Some of these settings are added to the Notebook during the course of data analysis. This function conveniently regroups all settings in one single location in the Notebook
4. Calibration Menu
The menu is comprised of two sub-menus:
Single Phasor Calibration Menu
Use Phasor Calibration performs the same action as checking or unchecking the Use Phasor Calibration checkbox in the Phasor Graph panel. Both are linked (the checkbox is toggled when the menu item is selected and vice versa).
Save Phasor Calibration saves the currently used single calibration phasor to a XML file.
Load Phasor Calibration loads a previously saved calibration phasor and applies it if the Use Phasor Calibration checkbox is checked,
Clear Phasor Calibration removes the stored calibration from memory.
Phasor Calibration Curve Menu
Use Phasor Calibration Curve performs the same action as checking or unchecking the Use Phasor Calibration Curve checkbox in the Phasor Graph panel. Both are linked (the checkbox is toggled when the menu item is selected and vice versa).
Save Phasor Calibration Curve saves the currently used calibration phasor curve to a XML file.
Load Phasor Calibration Curve loads a previously saved calibration phasor curve and applies it if the Use Phasor Calibration Curve checkbox is checked,
Clear Phasor Calibration Curve removes the stored calibration curve from memory.
5. Help Menu
Show Context Help shows a floating window providing basic information on the object pointed at with the mouse pointer.
Online Manual opens a page in the default browser redirecting to this website.
Check for Updates visit the Download & Installation webpage to check the latest released version. If a newer version is found, the software offers to download and install it. The new version will be used on the next time AlliGator is started.
About opens a Dialog window providing basic information on AlliGator.
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