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

Region Image

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Last updated 5 years ago

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Move region image to window/tab

This feature is available in 1.4.

Starting with version 1.4, you can move region images to a window or tab.

When a region image is placed on a tab, you can find region features in the "Regions" menu.

Open new region

In order to open another region you should click on 'Open region' item in 'File' menu.

Menu bar

You can export region image by clicking on the 'Export as PNG' menu item in the 'Regions' menu. Then you need to specify the location of the file. When the export is finished, you will see a message notification. If extended depth of field (EDF) was used to process data the best focus place is not applicable and will not be available for selection.

When any region image is opened by default it shows best focus z-plane for each tile.

You can disable 'best focus' mode by clicking on the corresponding menu item in the 'Image' menu.

Switching z-plane

FIJI tools

In addition to main frame and region image frames you are able to interact with FIJI tools frame.

Here you can pick a 'lens' tool for zoom in/zoom out region image by clicking on left/right mouse button.

Also you can switch between different selection tools such as Rectangle, Polygon, Oval etc. Once you picked any selection tool your choice will be saved and you can draw selection on any region image.

Creating a population

Remove area

You can always revert removed area. Right click on removed area and choose 'Revert area' option.

When you draw any selection on region image you right click on it and choose ‘Export area’ option in order to save the selection as an image.

When you open any experiment by default first region will be opened. will be selected by default.

When you open any experiment by default first region will be opened. will be selected by default.

When 'best focus' mode is disabled, by default it shows middle z-plane. You can switch z-plane of each region image by adjusting slider at the bottom. When you switch z-plane, corresponding images with selected will be loaded. Also segmentation mask of new z-plane will be loaded if is selected in .

When you draw any selection on region image you can right click on it and choose 'Add population' option in order to create with selected cells (This doesn't work when you without segmentation).

When you draw any selection on region image you can right click on it and choose 'Remove area' option in order to remove this area and cells within in it from the experiment. (This doesn't work when you without segmentation).

open experiment
Overlay manager
open experiment
marker channel
population
Region image window
Region image in tab
'Regions' menu
Open new region
Selecting new region #
z-plane slider
FIJI tools
Zoom in/out tool
FIJI selection tools
Draw selection on region image
Segmentation overlay
Scale bar overlay
Segmentation overlay