# 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. ![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M540SNI5JJvcLhrzs29%2F-M541BgqtkXtzxsyV1t5%2FMain%20menu%202.png?alt=media\&token=8a961bb5-e21e-47f2-868c-390f0caf4277) When experiment is loaded you will see seven menus at the top of the main frame. ![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M541Mdper0eei2akp1v%2F-M541n53bhcSZbJE4x5r%2FMain%20menu%203.png?alt=media\&token=a0ca2b39-7483-4299-ae15-31de9643bc24) #### File menu ![File Menu](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M542S0HkR_fYXhzjV_I%2F-M543JKc8fiUFypBD4tk%2FFile%20menu%202.png?alt=media\&token=f5a3f101-e368-4624-a943-0891158ad8e2) 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 ![Regions Menu](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M543NqxARPGWfN_z5KF%2F-M544IR3naAq8HUxJSAi%2FRegions%20menu%202.png?alt=media\&token=e2035700-80ea-4a5a-b470-a08079fd8db4) 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. #### Analysis menu ![Analysis Menu](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M543NqxARPGWfN_z5KF%2F-M54MJ90SCwoJdzezOZE%2FAnalysis%20menu.png?alt=media\&token=2cda1058-3b20-43dd-849f-f4797735f80b) In 'Analysis' menu you can click on next items: * X-Shift clustering. - see [Clustering](https://help.codex.bio/codex/mav/user-instructions/clustering). * Box plot. see [Box plot](https://help.codex.bio/codex/mav/user-instructions/other-analysis-operations#box-plot). * Voronoi. see [Voronoi diagram](https://help.codex.bio/codex/mav/user-instructions/voronoi-diagram). * Spatial analysis. see [Spatial analysis.](https://help.codex.bio/codex/mav/user-instructions/other-analysis-operations#spatial-analysis) * Density heatmap (all cells). [see Density heatmap.](https://help.codex.bio/codex/mav/user-instructions/other-analysis-operations#density-heatmap) #### Gating Menu ![Gating Menu](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M54NS1s7GltnPkymGhZ%2F-M54Ov7tMhyvQh5NPoMI%2FGating%20menu%201.png?alt=media\&token=c390fa2a-1937-49de-aed5-7fd0a870d794) See [Gating Menu](https://help.codex.bio/codex/mav/user-instructions/gating) for further details. #### View menu ![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M54QqIysOcG_OfIEPh9%2F-M54Que4_qmPog0MBg2E%2FView%20menu%201.png?alt=media\&token=458274cb-b7f2-4f5d-9abf-d6d1848a7557) All internal frames in the main frame are re-sizable and can be hidden. ![Resize / close internal frame](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY1K-9k0jJUEQ0jjD3T%2F-LY1_AmWvUUJEPb9wG15%2Fresize.png?alt=media\&token=6f8b7ce9-e5e1-4073-b30b-6183b97f736c) Note: Some items will appear in the 'View' menu only after using them first time. (e.g. [Gating](https://help.codex.bio/codex/mav/user-instructions/gating), [Box plot](https://help.codex.bio/codex/mav/other-analysis-operations#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. ![Show / Hide all](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY1K-9k0jJUEQ0jjD3T%2F-LY1_d_6Kg320A0FpRk9%2FshowAll.png?alt=media\&token=3ca06ccd-aa6e-4d2f-a466-fe66f1d3e0dc) The fast way to hide or show all internal frames is clicking on 'Hide all' or 'Show all' items in 'View' menu. *Auto-layout* ![Auto-layout](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY1K-9k0jJUEQ0jjD3T%2F-LY1a18e0-D7hqlf3d2G%2FautoLayout.png?alt=media\&token=8460fda6-c79e-439a-ada7-32843bd716a7) 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* ![Background activities](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY1K-9k0jJUEQ0jjD3T%2F-LY1aRX7s-Ah0KyOQ_wD%2Fbackground.PNG?alt=media\&token=27aafaa6-8a44-41c1-b6c9-68461563374c) 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](https://help.codex.bio/codex/mav/user-instructions/voronoi-diagram) or [X-Shift clustering](https://help.codex.bio/codex/mav/clustering#run-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. #### Tools menu ![Tools menu](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY1K-9k0jJUEQ0jjD3T%2F-LY1b54ks93kwdYPvodU%2FtoolsMenu.png?alt=media\&token=5b43d30e-a581-49fa-90bb-2f3db917fcf8) *Preferences* ![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-MD-db6pHe-MLFPm7kQ-%2F-MD-lEnxpNS8dblGtnTX%2Fpreferences.PNG?alt=media\&token=7bf72cc0-89ed-405e-878e-a8afd2e96d3f) ![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M54TKgCm7ycNhL8fA2B%2F-M54TRQcgHL1918ny-3b%2FPopulations%20preferences.png?alt=media\&token=ceef42b7-92e0-4585-b6a0-92b7c67aeeb5) ![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M54TKgCm7ycNhL8fA2B%2F-M54TWWYjekHgfXeGRs7%2FExport%20images%20preferences.png?alt=media\&token=e2542480-c791-4ca6-9561-1f012da1a035) ![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M54TKgCm7ycNhL8fA2B%2F-M54TcuQnOL7L9dLNsA6%2FLogging%20preferences.png?alt=media\&token=21cc129f-e61c-4af9-bbc6-187fde1caa7a) Upon clicking on 'Preferences' item in the 'Tools' menu, a frame will appear where the user can change preferences for: 1. Analysis - a. Select coloring scheme for heatmaps in [Clustering Frame](https://help.codex.bio/codex/mav/clustering#clustering-panel) and [Population table](https://help.codex.bio/codex/mav/user-instructions/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). 2. Populations - Here the users can specify the shape and size of [population](https://help.codex.bio/codex/mav/population-table#populations) markers. 3. Export images - Here you can specify image format. This format will be used when you will save different components ([gating hierarchy](https://help.codex.bio/codex/mav/gating#other-gating-tools), dendrograms, [box plot](https://help.codex.bio/codex/mav/other-analysis-operations#box-plot), etc.) 4. 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](https://help.codex.bio/codex/mav/user-instructions/voronoi-diagram) to any selected folder. If the Voronoi diagram has not been calculated yet, you will see an error message. #### Help menu ![Help menu](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-LY1K-9k0jJUEQ0jjD3T%2F-LY1dQf1hKlSLuyevoiv%2FhelpMenu.png?alt=media\&token=38761877-96fb-4119-a332-e6b3a5205533) Here you can find the following items: 1. About - You will see information about the current version of app and copyright. 2. Online help - After clicking on this item web page with online help will be opened in your web-browser. 3. Feedback - Here you can send feedback by email.