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

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


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" 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.


"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

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