> For the complete documentation index, see [llms.txt](https://help.codex.bio/codex/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.codex.bio/codex/cim/overview.md).

# Overview

![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-M2enkeJ7yw_LgakhLoD%2F-M2eoJ7AsGzA1AR97HxX%2FCapture%201.PNG?alt=media\&token=e985e232-bda1-4cd9-8882-1297f2caac30)

### 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.

{% hint style="info" %}
The instructions are for CIM version 1.29. If you are working with an older version, please make sure to upgrade the CIM software. 

CIM upgrade installer and install instructions are [here ](https://help.codex.bio/codex/cim/preparing-for-installation/cim-upgrades#installer)
{% endhint %}

### Main Topics

* [User Instructions](https://help.codex.bio/codex/cim/user-instructions)
* Microscope Overview
  * [General recommendations for all Microscopes](https://help.codex.bio/codex/cim/microscope-specific-settings/microscopes)
  * [Keyence specific setup instructions](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence-bz-x800)
  * [Leica specific setup instructions](https://help.codex.bio/codex/cim/microscope-specific-settings/leica-dmi8)
  * [Zeiss specific setup instructions](https://help.codex.bio/codex/cim/microscope-specific-settings/zeiss-axio-observer)
* [Exposure time optimization](https://help.codex.bio/codex/cim/exposure-time-optimization)
* [Determination of signal to noise ratio (SNR)](https://help.codex.bio/codex/cim/determination-of-signal-to-noise-ratio)