Next, you'll need to calibrate the deck. Deck calibration gives your OT-2 a basic notion of how to move pipettes around in 3D space.

This step is required when you first set up your robot. We also recommend redoing it once or twice a year, for maintenance.

To learn more, check out how calibration works on the OT-2.

Materials needed

  • At least one pipette attached to your OT-2.
  • Opentrons tips. (Third-party tips won't work).


Part 1: Begin by attaching a tip

Tip: To make it easier to see what you're doing, turn on the OT-2's deck lights before you begin. Toggle the switch under Robot Controls > Lights. 💡

To begin deck calibration, connect to your robot and select Calibrate.

Make sure the deck is clear. Then, select Move pipette to front. The pipette will move towards the front window and lower itself for access.

Use your hand to place an Opentrons tip on the descended pipette. Make sure the tip is on straight and firm.

Caution: For this, you really do need to attach an Opentrons tip—not a tip made by a third party. If you use a third-party tip, the deck calibration will come out wrong.

Caution: If you're using an 8-Channel pipette, double-check to make sure you put the tip on the correct channel. It should be on the front channel (closest to the front window).

Then, select Confirm tip attached.

Part 2: Calibrate the z-axis

You can now move the pipette around with the arrow keys or on-screen controls.

Move the pipette down until the tip just barely touches the smooth deck surface. This shows the OT-2 how far the pipettes will have to descend in order to reach the deck.

Caution: Be careful with the higher jump sizes. If you accidentally crash the pipette tip into the deck, it could mess up your calibration. 💥

When you're ready, select Save calibration and continue.

Part 3: Calibrate the x-axis and y-axis

The pipette will move near a small cross in deck slot 1.

Move the pipette so the tip is centered in the cross. This shows your OT-2 how the deck is shifted, rotated, and skewed.

Your accuracy here will affect all of your OT-2's movements when it's running a protocol, so do your best to center the tip as closely as you can. This can be tricky, but we've found that it helps to:

  • 💡 Work in a well-lit environment.
  • 👀 Look through the side windows to view the tip from multiple angles.

When you think you've gotten it as close as you can, select Save calibration and continue.

The Opentrons App will have you repeat the process two more times: for the cross in slot 3, and for the cross in slot 7.

Caution: Make sure you don't mistakenly use the cross in slot 10 instead of slot 7. They're next to each other, so it's easy to get them confused.

Part 4: Finish up

After you've calibrated all three crosses, the Opentrons App will prompt you to remove the tip.

Use your hand to pull the tip off the pipette. Then, save the deck calibration by selecting Finish and restart robot.

Wait for your OT-2 to restart. It should only take a few minutes.

While your OT-2 is restarting, it will temporarily lose connection to the Opentrons App. It should reappear in the app shortly after it restarts. (You can listen for the pipette mounts to home to confirm a successful restart.)

If the OT-2 doesn't reappear after a few minutes, try selecting Try again or Refresh list in the Opentrons App. If it still doesn't appear, try troubleshooting connection problems, or reach out to Opentrons Support.

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