# User Instructions

- [Experiment](/codex/cim/user-instructions/experiment-design-and-run.md): Experiment set up and run CODEX® experiments with the CODEX® Instrument Manager (CIM)
- [Maintenance](/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](/codex/cim/user-instructions/transfer-data.md)
- [Settings](/codex/cim/user-instructions/settings.md): Set up options for logging, ports, updates, and notification, etc.