Main Menu

CODEX® MAV is organized into tabulated windows. Operations selected from menu items appear in corresponding tabs, e.g., gates appear in gating tab.

When experiment is loaded you will see seven menus at the top of the main frame.

In the 'File' menu you can find the following items:

Open experiment - Open another experiment instead of currently opened.
Open region - Open another region image in addition to currently opened.
Open clustering run - Open another clustering run instead of currently opened.
Import clustering run - Import clustering run that was not performed in CodexMAV.
Open analysis
Save analysis
Save analysis as - see (Save / Open analysis).
Reset experiment - return to the default state of experiment.

Regions menu selections include

Export as PNG – Export region as PNG
Display Best Focus Plane – Disabled when EDF is utilized to process data, because all cells are collapsed into a single z-plane.
Intensity Tracking Marker – select a displayed marker (e.g., CD3) to use for intensity tracking when a line scan is made with CTRL+K command.
To window – pop out region to window.
Close – close region.

In 'Analysis' menu you can click on next items:

X-Shift clustering. - see Clustering.
Box plot. see Box plot.
Voronoi. see Voronoi diagram.
Spatial analysis. see Spatial analysis.
Density heatmap (all cells). see Density heatmap.

See Gating Menu for further details.

All internal frames in the main frame are re-sizable and can be hidden.

Note: Some items will appear in the 'View' menu only after using them first time. (e.g. Gating, Box plot)

Hide / Show

You can manage the visibility of internal frames through the 'View' menu by clicking on item with corresponding internal frame title. When you click on the 'cross' button of any internal frame it also will become hidden.

The fast way to hide or show all internal frames is clicking on 'Hide all' or 'Show all' items in 'View' menu.

Auto-layout

Also as you can always make changes to the location or size of any internal frame, and you can restore the initial state by clicking on 'Auto-layout' item in 'View' menu.

Background activities

One internal frame called 'Backround activities' is hidden by default. You can make it visible and see there information about all long-running tasks such as Voronoi diagram or X-Shift clustering. After any activity is finished you can click on the corresponding 'trash' button to remove this activity from the Background activities panel.

Preferences

Upon clicking on 'Preferences' item in the 'Tools' menu, a frame will appear where the user can change preferences for:

Analysis -
a. Select coloring scheme for heatmaps in Clustering Frame and Population table.
b. Specify analysis state name prefix.
c. Specify 'Random generator seed' which will be used in all algorithms with random operations (e.g. X-Shift). This feature allows the users to reproduce the same results when inputting the same parameters (on different machines, with different runs).
Populations - Here the users can specify the shape and size of population markers.
Export images - Here you can specify image format. This format will be used when you will save different components (gating hierarchy, dendrograms, box plot, etc.)
Logging - Here you can pick logging verbosity that you need and via File chooser select folder where all log files will be stored.

Export Voronoi Diagram

Here you can export Voronoi diagram to any selected folder. If the Voronoi diagram has not been calculated yet, you will see an error message.

Here you can find the following items:

About - You will see information about the current version of app and copyright.
Online help - After clicking on this item web page with online help will be opened in your web-browser.
Feedback - Here you can send feedback by email.