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

Marker Manager

PreviousCellsNextGating

Last updated 4 years ago

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Using the Marker manager window, the users can manage all markers. Any changes made to marker selection in this window will affect all features involving markers (, ,, , ).

Change visibility

By clicking on any marker checkbox the corresponding marker will be hidden/shown in all features with markers. By default any markers with type 'Nuclear' (DAPI, HOECHST) and 'Blank' will be unselected.

Change order

You can sort markers by any column by clicking on the corresponding table header. It will cause marker order changes in all CodexMAV features that support marker sorting.

Note: Changing marker order in the Manager will not affect the marker dendrogram order.

Also you can click on the 'Default sort' button and return markers sorting to the default.

Change name

If you click on any marker name then you can change it. You can't set duplicate and empty marker names. After setting new name all features with markers will be updated.

Reset markers

The users can deselect all markers at once, except for the first two, by clicking on the 'Reset markers' button.

Marker picker
Clustering
Population table
Table view
Box plot
Marker Manager
Return to default sort order
Reset markers button