> 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.md).

# CODEX® Instrument Manager (CIM)

- [Overview](https://help.codex.bio/codex/cim/overview.md)
- [User Instructions](https://help.codex.bio/codex/cim/user-instructions.md)
- [Experiment](https://help.codex.bio/codex/cim/user-instructions/experiment-design-and-run.md): Experiment set up and run CODEX® experiments with the CODEX® Instrument Manager (CIM)
- [Maintenance](https://help.codex.bio/codex/cim/user-instructions/maintenance.md): The Maintenance tab has protocols that allow priming the instrument prior to an experiment, routine instrument maintenance, and tissue clearing.
- [Transfer Data](https://help.codex.bio/codex/cim/user-instructions/transfer-data.md)
- [Settings](https://help.codex.bio/codex/cim/user-instructions/settings.md): Set up options for logging, ports, updates, and notification, etc.
- [Microscope Specific Settings](https://help.codex.bio/codex/cim/microscope-specific-settings.md)
- [Microscope Requirements - Overview](https://help.codex.bio/codex/cim/microscope-specific-settings/microscopes.md): This section presents an overview of the microscope requirements. Specific microscope requirements are listed within each microscope section.
- [Keyence BZ-X800 and BZ-X700](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence.md)
- [Requirements](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/requirements.md): Specific recommendations for Keyence BZ-800
- [BZ-X800 Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/image-acquisition-settings.md): CODEX®-specific settings for the Keyence BZ-X800.
- [Multi-Point (BZ-X800)](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/image-acquisition-settings/multi-point-bz-x800.md): For imaging more than 10 regions during a CODEX Run.
- [BZ-X700 Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/keyence-bz-x700.md): CODEX specific settings for the Keyence BZ-X700.
- [Multi-Point (BZ-X700)](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/keyence-bz-x700/multipoint-bzx700.md): For imaging more than 10 regions during a CODEX Run.
- [Exposure steps](https://help.codex.bio/codex/cim/microscope-specific-settings/keyence/advanced-options.md): Fractions to msecs
- [Leica DMi8](https://help.codex.bio/codex/cim/microscope-specific-settings/leica-dmi8.md)
- [Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/leica-dmi8/image-acquisition-settings.md)
- [Zeiss Axio Observer](https://help.codex.bio/codex/cim/microscope-specific-settings/zeiss-axio-observer.md)
- [Requirements](https://help.codex.bio/codex/cim/microscope-specific-settings/zeiss-axio-observer/requirements.md)
- [Image Acquisition Settings](https://help.codex.bio/codex/cim/microscope-specific-settings/zeiss-axio-observer/image-acquisition-settings.md): Setting up Zeiss for CODEX runs.
- [Exposure Time Settings Considerations](https://help.codex.bio/codex/cim/microscope-specific-settings/exposure-time-optimization.md): Guidelines on how to set up exposure times for CODEX® experiments such as CODEX® Antibody Screening & Validation and CODEX® Multicycles.
- [Determination of Signal to Noise Ratio](https://help.codex.bio/codex/cim/microscope-specific-settings/determination-of-signal-to-noise-ratio.md): This section offers guidelines on how to measure the Signal to Noise Ratio (SNR) in CODEX fluorescence microscopy images.
- [Technical Notes](https://help.codex.bio/codex/cim/related-documentation.md)
- [Installation](https://help.codex.bio/codex/cim/preparing-for-installation.md)
- [CIM Upgrades](https://help.codex.bio/codex/cim/preparing-for-installation/cim-upgrades.md): The CIM Software will have updates for bug fixes and feature request additions. This page will have the upgrade installers, release notes, and instructions for upgrading the software.