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® Instrument Manager (CIM)

Overview

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Last updated 4 years ago

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Purpose

CODEX® Instrument Manager (CIM) allows the user to design and run a complete CODEX® experiment. CIM is installed on the microscope control PC and drives the CODEX instrument. CIM also integrates with the microscope control software to synchronize CODEX® cycles and automate image acquisition.

The instructions are for CIM version 1.29. If you are working with an older version, please make sure to upgrade the CIM software.

Main Topics

  • Microscope Overview

CIM upgrade installer and install instructions are

here
User Instructions
General recommendations for all Microscopes
Keyence specific setup instructions
Leica specific setup instructions
Zeiss specific setup instructions
Exposure time optimization
Determination of signal to noise ratio (SNR)