> 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/user-instructions.md).

# User Instructions

- [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.