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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On this page
  • Microscope
  • Set Log Folder
  • Comm ports
  • Manual
  • Fluidics Check
  • CODEX® Database and Server Connections
  • Updates
  • Email Setup and Test
  • Email Logs to Akoya Support

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  1. CODEX® Instrument Manager (CIM)
  2. User Instructions

Settings

Set up options for logging, ports, updates, and notification, etc.

PreviousTransfer DataNextMicroscope Specific Settings

Last updated 5 years ago

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Select the "Settings" feature from the menu on the CIM window

Microscope

Allows selecting the appropriate Microscope that will be used for CODEX® runs.

Please make sure the Microscope software is also open simultaneously to allow detection of the Microscope by the CIM software.

The microscope software can be selected from the drop-down menu, or automatically detected using the ‘Detect’ button

"Detect" button allows ensuring that CIM can detect the Microscope in use

Select "Yes" to set the selected Microscope for CODEX runs

Set Log Folder

Allows selecting the folder where the CODEX® run logs will be saved.

Comm ports

Click the "Instrument Check" button to allow CIM to perform an Instrument Pre-check

Manual

"Manual" button allows opening the User Manual on a New Window

Please note that this feature requires that the PDF reader is installed on the PC

Fluidics Check

"Fluidics Check" button allows CIM to ensure that the instrument has enough of all the reagents required for the selected number of CODEX® cycles

CODEX® Database and Server Connections

Allows ensuring that the database service is running and the computer is connected to the server.

Updates

"Check for Update" allows the user to check for CIM software updates

Email Setup and Test

This feature allows to set up and save the email addresses that would like to be notified of any warning messages during the run

"Send Test" buttons allow the user(s) to ensure that they are receiving emails from the CIM

Please make sure to enter the emails of all the users wanting to be notified, in the second row, with one email address per line

Email Logs to Akoya Support

Allows uploading all the necessary CODEX® run logs from the Logs folder.

Click the "Upload" Button to send the log files to Akoya Support

Note: User may choose to send several log files at a time