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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  • Marker Colors
  • Brightness/Contrast Slider
  • Auto-Adjust Brightness/Contrast
  • Min-Max Brightness/Contrast
  • Precise Brightness/Contrast
  • Pseudo-DAB Staining Mode

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

Marker Picker

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Last updated 5 years ago

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Marker Colors

Select markers in the Marker Picker to display the selected marker in the region image with the color of your choice. Up to seven markers can be displayed simultaneously. The available colors are white, red, green, blue, magenta, yellow and cyan (W, R, G, B, M , Y, C).

Brightness/Contrast Slider

Auto-Adjust Brightness/Contrast

To return to auto-adjust brightness and contrast, please press the button shown above.

Min-Max Brightness/Contrast

The next button resets the brightness and contrast to the minimum and maximum values found in the marker image.

Precise Brightness/Contrast

The last buttons allows specifying the minimum and maximum values for precise brightness and contrast setting.

Pseudo-DAB Staining Mode

This feature is available for MAV versions 1.3 and above

Enable DAB mode by clicking the switch button show above.

In this mode, you are able to pick only one marker and it will be highlighted in brown color on the region image. The "nuclear" marker from the same cycle will be automatically highlighted in blue color on the image.

When a marker is selected, brightness and contrast are auto-adjusted using the same optimization used by ImageJ in its . This can be manually adjusted by clicking and dragging the edges of the slider bars.

Auto Brightness/Contrast