# Omni-Stainer Automation Overview

* [ ] Set up Opentrons OT-2 robot. [This set-up guide is a great reference](https://support.opentrons.com/s/ot2-get-started), and our friends at Opentrons are happy to assist you with this if you have any [questions](https://support.opentrons.com/s/information-about-opentrons-support).
* [ ] [Download Opentrons App](https://opentrons.com/ot-app/)
* [ ] [Download Parhelia Bio's base OT-2 scripts and labware definitions from GitHub by clicking here](https://github.com/parheliabio/ot2-scripts/archive/refs/heads/main.zip)
  * [ ] If you would prefer to visit the GitHub and download individual files our GitHub is at <https://github.com/parheliabio/ot2-scripts>
* [ ] Download customized or stock Omni-stainer code from [Stainworks](https://3qcwn6iy48.execute-api.us-east-1.amazonaws.com/)
* [ ] Load protocols and labware definitions into Opentrons software
* [ ] Follow protocol-specific instructions, for preparing and loading your labware and doing protocol setup. We strongly recommend starting with the Blue Dye Demo protocol to get comfortable using the device before conducting actual experiments.

<figure><img src="https://3271682270-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWKyUXOqIKtqE7cAUE2yQ%2Fuploads%2FZpYR9YSQxRTPtOlWYStv%2FScreenshot%202023-05-18%20at%202.44.40%20PM.png?alt=media&#x26;token=09fd7bfc-9147-4442-bd41-a1dde957f360" alt=""><figcaption><p>Example of staining protocol loaded into Opentrons</p></figcaption></figure>

## We suggest starting with the "Blue Dye Demo" Automated Protocol before exploring other protocols. This demo's steps are crafted to generally adapt to various Parhelia protocols. Find the protocol here:

{% content-ref url="../blue-dye-demo-automated-protocol" %}
[blue-dye-demo-automated-protocol](https://docs.parheliabio.com/product-guides/blue-dye-demo-automated-protocol)
{% endcontent-ref %}

Our engaging virtual demonstration serves as an excellent introductory guide for understanding the steps in operating the Parhelia Bio Omni-Stainer C12 and S12, encompassing both manual and automated usage, along with thermal sheath and thermal modules. [**View the virtual demo here!**](https://parheliabio.com/view-virtual-demo/?utm_source=gitbook\&utm_medium=gitbook)

## Step 1 - Place the Omni-Stainer, reagent reservoirs, pipette tip rack, and antibody plate into the dedicated slots on the deck of the liquid handler.

When inserting the labware (plates, reservoirs, Omni-Stainers) into the slot of the liquid handler deck it is important to ensure the complete in-flush alignment of the labware bottom with the surface of the deck. Lack of such alignment may result in tips bending while hitting the bottom of the labware wells. SBS labware should click in or rest fully in a deck location, a common error is one of the back corners not being fully inserted and level with the rest of the labware.

## Step 2 - Create a running protocol using the Staining Works Software

The Python files with staining protocols for an individual experiment can be easily configured using the Staining Works Software. For auditing and accountability we recommend storing the individual day–specific protocols and assigning them a name consisting of the operator name, date, and the purpose of the experiment.

For more information go to our StainWorks documentation page:

{% content-ref url="stainworks" %}
[stainworks](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/stainworks)
{% endcontent-ref %}

You may see a protocol analysis failure in the Opentrons App if the necessary labware definitions have not been uploaded. To learn more see this documentation page:

{% content-ref url="importing-labware-definitions" %}
[importing-labware-definitions](https://docs.parheliabio.com/product-guides/automation-opentrons-ot-2-setup/importing-labware-definitions)
{% endcontent-ref %}

&#x20;

## Step 3 - Start the experiment. Calibration step.

## Step 4 - Start the experiment. Initiate the protocol run.