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Maintenance

The Maintenance tab has protocols that allow priming the instrument prior to an experiment, routine instrument maintenance, and tissue clearing.

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

Maintenance Wizards

Experiment Preparation

Prime Wash

Used to prime the instrument lines before a run. Critical to performance of the system and sample quality output.
This step is also part of the Experiment Setup Wizard.

Instrument Maintenance

Clean Instrument Wash

Used immediately before and immediately following a run. This will clear all buffers and DMSO from the fluidic lines.
A coverslip needs to be in the Stage insert. If you would like to save the tissue post CODEX run, please use an empty coverslip for this wash.
Please make sure no bottle caps are removed. Water is used from the Water bottle.

Maintenance Wash

To be performed bi-weekly during regular use of the instrument or anytime the instrument is expected to not be in use for a week or longer.
A coverslip needs to be in the Stage insert. Both Bottle 1 and Bottle 2 lids and lines must be placed in water. This will ensure full cleaning of all lines. Bottle lids should be returned to their respective bottles afterward.

Tissue Maintenance

Wash Tissue

Used to gently remove any debris or Nuclear Stain from the tissue. If Reporters are present, this wash will not remove them. This step is also part of the Experiment Setup Wizard.

Clear Tissue

Used when Reporters are likely to be still hybridized to the CODEX antibodies on the tissue. Run "Clear tissue" to remove any Reporters. Both DMSO, 1X CODEX® Buffer, and the clean/empty reservoirs must be present to perform this run.

Instrument Controls

Vacuum Off

Use if the vacuum is left on when any instrument steps have been interrupted.

Move Robot to Home

This will move the Autosampler/Robot/Needle to the home position. To be used if the needle is ever in the way of placing the Reporter plate or sample reservoirs.

Unlock door

This will unlock the door if the lock remains engaged after a run. For user safety, the door will remain locked during a run.

Microscope Management

Microscope Pre-check

Used to check the Microscope settings. When trying different Autofocus or Microscope setup options, use this button prior to the experiment to ensure all new options are being detected.

Run one microscope cycle

Used if the user needs to manually run one microscope cycle. Exposure times, Z-stack, and Cycle data label are set in these fields.
Even though this feature requires that the CODEX instrument is connected, turned on and initialized, this feature will not involve any fluidics, instead only perform the image acquisition steps.
Note that the microscope will save the acquired data, but CIM will not use or track the data as an experiment.