CODEX® Support
  • Welcome
  • CODEX® Instrument Manager (CIM)
    • Overview
    • User Instructions
      • Experiment
      • Maintenance
      • Transfer Data
      • Settings
    • Microscope Specific Settings
      • Microscope Requirements - Overview
      • Keyence BZ-X800 and BZ-X700
        • Requirements
        • BZ-X800 Image Acquisition Settings
          • Multi-Point (BZ-X800)
        • BZ-X700 Image Acquisition Settings
          • Multi-Point (BZ-X700)
        • Exposure steps
      • Leica DMi8
        • Image Acquisition Settings
      • Zeiss Axio Observer
        • Requirements
        • Image Acquisition Settings
      • Exposure Time Settings Considerations
      • Determination of Signal to Noise Ratio
    • Technical Notes
    • Installation
      • CIM Upgrades
  • CODEX® Processor
    • Overview
    • Installation
      • Install
      • Update
      • Version History
    • User Instructions
      • Quick Start
      • Processing Options
      • Segmentation Options
      • Image Analysis Report
    • Technical Notes
      • Expected Input
      • Expected Output
      • Cycle Alignment
      • Background Subtraction
      • Deconvolution
      • Extended Depth of Field
      • Shading Correction
      • Tile Registration
      • Segmentation & Spillover
      • t-SNE
      • FCS Format
    • Troubleshooting
  • CODEX® Multiplex Analysis Viewer (MAV)
    • Overview
    • Installation
      • System Requirements
      • CODEX® MAV - Download & Install
      • Release Notes
    • User Instructions
      • Quick Start
      • Open Experiment
      • Main Menu
      • Overlay Manager
      • Marker Picker
      • Region Image
      • History Panel
      • Save / Open Analysis
      • Clustering
      • Population Table
      • Cells
      • Marker Manager
      • Gating
      • Voronoi Diagram
      • Other Analysis Operations
    • Technical Notes
      • Algorithm Details
      • FCS Format
    • Public Datasets
    • Troubleshooting
  • Workflow Documents
    • CODEX and microscope setup
    • Reagents and staining
  • Appendix
    • End User License Agreement
    • Third-party Licenses
      • CIM
      • Processor
      • MAV
  • PhenoCycler Analysis
Powered by GitBook
On this page

Was this helpful?

  1. CODEX® Multiplex Analysis Viewer (MAV)
  2. User Instructions

Main Menu

PreviousOpen ExperimentNextOverlay Manager

Last updated 4 years ago

Was this helpful?

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.

File menu

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 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

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

Gating Menu

View menu

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

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

Tools menu

Preferences

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

  1. Analysis -

    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. 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

Help menu

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.

X-Shift clustering. - see .

Box plot. see .

Voronoi. see .

Spatial analysis. see

Density heatmap (all cells).

See for further details.

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

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 or . After any activity is finished you can click on the corresponding 'trash' button to remove this activity from the Background activities panel.

a. Select coloring scheme for heatmaps in and .

Populations - Here the users can specify the shape and size of markers.

Export images - Here you can specify image format. This format will be used when you will save different components (, dendrograms, , etc.)

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

Clustering
Box plot
Voronoi diagram
Spatial analysis.
see Density heatmap.
Gating Menu
Voronoi diagram
Gating
Voronoi diagram
Population table
Box plot
box plot
gating hierarchy
population
File Menu
Regions Menu
Analysis Menu
Gating Menu
Resize / close internal frame
Show / Hide all
Auto-layout
Background activities
Tools menu
Help menu
X-Shift clustering
Clustering Frame