The Opentrons Thermocycler Module is an easy-to-use on-deck module that enables automation of upstream and downstream workflow steps. It is a fully automated thermocycler.

For product specifications, see the Opentrons Thermocycler Module White Paper.

Basic setup

For safety information, setup instructions, and basic usage instructions, see the printed manual that came with your thermocycler.

Using your Thermocycler Module in protocols

In Python Protocol API protocols

To see how to use the Thermocycler Module in Python Protocol API protocols, consult the thermocycler section in our API documentation.

The thermocycler is only supported in Python Protocol API version 2.0 and later. You cannot use the thermocycler in API version 1 protocols. Read more about the introduction of APIv2 here.

In Protocol Designer protocols

Protocol Designer does not currently support modules like the thermocycler.

Using your Thermocycler through the Opentrons App

Presetting a target temperature

In the Run tab of the Opentrons App, before starting a protocol that uses the Thermocycler Module, you can set a temperature for the thermocycler block. When you start the protocol, the steps will not actually proceed until that target temperature is reached.

This is useful for pre-heating or pre-cooling samples located on your thermocycler.

Deactivating the module

Sometimes you may wish to deactivate the thermocycler, in order to remove samples from the module or shut the module off after use. Before or after a protocol run, you can click the Deactivate button to ensure that your thermocycler is off before opening the lid.

Note: The Thermocycler Module will hold its temperature, regardless of whether a protocol is running or not. This allows you to cancel a run and be sure that your samples will be held at the temperature specified previously, until you decide to deactivate the module from the Opentrons App as described above.

Using labware with your Thermocycler Module

See: What labware can I use with my modules?

Locating the serial number of your Thermocycler Module

In the Opentrons App, navigate to the PIPETTES & MODULES tab. The serial number is displayed below each detected module.

Alternatively, you can find the serial number of your module by looking on the bottom of the physical device. There will be a sticker with letters and numbers.

Troubleshooting problems with your Thermocycler Module

Unable to close lid

If the lid of the module is not closing properly, it might be due to the latch getting stuck. Try pushing on the orange latch (shown below) several times to unstick it.

Blinking orange light

A blinking orange light indicates an internal problem with your thermocycler.

Blinking orange light because of overheating:

Your thermocycler may be overheating. Long continuous use or hot ambient conditions will make the thermocycler overheat more easily.

  • Check that nothing is blocking airflow from the thermocycler's vent.

  • Ensure your OT-2 is using thermocycler-compatible side panels, as described in the printed Opentrons Thermocycler Module manual.

  • Ensure your OT-2 has adequate spacing from the wall behind it, as described in the printed Opentrons Thermocycler Module manual.

After clearing any obstructions, you must power cycle your Thermocycler Module before trying to use it again.

Blinking orange light because of internal damage:

If the steps above do not resolve the problem, there may be something internally wrong with your Thermocycler Module. Contact Opentrons Support at or through our live chat for assistance.

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