This article provides recommendations on where to locate your modules to maximize deck space, limit interference between modules, and avoid physical collisions.

General Guidelines

  1. The OT-2 is limited to one of each type of module on the deck.

  2. Temperature and Magnetic modules should only be placed in the leftmost (1, 4, 7, 10) or rightmost (3, 6, 9) slots, with cords oriented to the outside.

  3. The Thermocycler module must be placed in the back-left slots (occupying all of 7, 8, 10 and 11).

Avoiding Temperature Interference

The heat of the Thermocycler and Temperature modules may interfere with adjacent modules or labware.


  1. Separate the Thermocycler and Temperature modules by at least one slot, as they may affect each other’s performance.

  2. Avoid placing temperature-sensitive samples immediately adjacent to the temperature module’s heating plate. This is primarily a concern for labware elevated to the same height as the heating plate: for example, labware on top of a magnetic module. Labware directly on the deck is not affected.

Avoiding Pipette Collisions

Multi-channel pipettes may have limited access to slots adjacent to modules. Using modules in the following configurations may result in collisions between pipettes and modules.

The following limitations apply only to OT-2s with either ‘Gen1’ modules or ‘Gen1’ multi-channel pipettes. ‘Gen1’ modules and pipettes shipped through mid-May 2020; all orders received after mid-May 2020 included ‘Gen2’ pipettes and modules. To learn more about Gen1 vs Gen2 and confirm your pipette or module version, click here.

Gen1 Multi Channel Pipette and Any Module

Gen1 multi-channel pipettes may not be used to access slots above or below any module (the Gen1 pipettes are slightly ‘taller’, extending into the slots above and below).

For example, if any Temperature or Magnetic module is placed in slot 4, the Gen1 multichannel pipette should not be used to access labware in slots 1 or 7.

Gen2 Multi Channel Pipette and Gen1 Modules

Gen2 multi-channel pipettes may not be used to access slots to the right or left of Gen1 modules (the Gen1 modules are slightly ‘wider’, extending into the slots to the left and right).

For example, if a Gen1 Temperature or Magnetic module is placed in slot 1, the Gen2 multichannel pipette may not access labware in slot 2.

Gen2 Multi Channel Pipettes and Gen2 Modules

Gen2 multi-channel pipettes may be used without restriction alongside Gen2 modules. That is: Gen2 pipettes can safely access all slots adjacent to a Gen2 module.

If using all three modules (Thermocycler, Magnetic, and Temperature), we recommend starting with the Magnetic Module in slot 1, the Temperature Module in Slot 3, and the Thermocycler in slots 7, 8, 10, and 11. This minimizes temperature interference between modules and maximizes usable deck space.

Note on Protocol Designer

The Protocol Designer will automatically place modules in the recommended locations outlined above.

To set the modules up in a different location on the deck, toggle on the ‘disable the ‘module placement restrictions’ setting.

For more information on using modules in Protocol Designer, click here.

Did this answer your question?