Application Snapshot: Automated Liquid Handling

Customers around the world have used Opentrons to automate a variety of basic wet lab liquid handling tasks. Here’s how.

NOTE: In addition to more complex tasks like NGS library preparation, nucleic acid extraction, and qPCR, you can also automate a slew of basic liquid handling wet lab tasks using the Opentrons platform.  

In this snapshot, you will learn how to automate basic pipetting wet lab tasks—including tube filling, microplate filling, serial dilution, and compound serial dilution—using Opentrons hardware, software, consumables, and protocols. You will also learn best practices for optimizing your lab’s workflow to automate these tasks, and which tasks already have downloadable Opentrons protocols.


Q: How will the Opentrons platform work in my lab?

A: The platform is open-source so any lab can use it, customizable for different workflows, and kit agnostic.

Q: How can I make a basic liquid handling protocol?

A: You have 3 different options for making a basic liquid handling protocol:

-- OPTION 1: Design your own with our interactive, user-friendly Protocol Designer tool

-- OPTION 2: Code your own using our open-source Python Protocol API

-- OPTION 3: Have our Applications Engineering team create a protocol for you

Q: Do you have any pre-written protocols I can use?

A: We have many downloadable protocols in our Protocol Library, including these for basic wet lab liquid handling assays:

-- Normalization

-- Tube Filling

-- Mass Spec

-- Plate Filling

-- Aliquoting

-- Serial Dilution

-- Pooling & Consolidation

-- Cherry picking

-- Cell Seeding

Q: What kind of labware can I use with the Opentrons platform?

A: Out of the box, the OT-2 can support any standard, automation-compatible / SBS footprint well plates, plus a wide range of snap-cap and screw-cap tubes up to a 50mL conical with our 4-in-1 Tube Rack. You can see the full range of supported labware in our Labware Library.

Q: Do you support custom labware?

A: The OT-2 can work with almost any piece of labware you’re using today, even if it’s custom-made.

If you need to use custom labware that has the same footprint as a common microplate, you can create a custom labware definition of your own in minutes using our Labware Creator.

If you need to use custom labware that doesn’t have the same footprint as a common microplate, our Applications Engineers can create one for you. Or, if you have some coding knowledge, you can create one yourself and 3D print a bracket or adapter to use it on the deck.

Q: Do I need to know how to code to use the Opentrons platform?

A: You do not need to know how to code to use the Opentrons platform. Protocols can be created using Opentrons’ plug-and-play protocol design tools. We also have an Applications Engineering team to help customers build protocols.

Q: Can I see a sample protocol?

A: All of our protocols are open-source and free to access on GitHub.

Q: How long does the OT-2 take to ______?

A: Distribute 20uL to all 96 wells in a plate?

Q: Add 1uL to all wells of a 384-well plate?

A: 2 minutes at the fastest settings with an Opentrons Single Channel P20 GEN2 Electronic Pipette

Q: Fill a 1mL tube?

A: 7 seconds with an Opentrons Single-Channel P20 GEN2 Electronic Pipette

Q: Can I handle small volume transfers with the OT-2?

A: You can accurately and precisely handle volumes from 1-20µL with either our Opentrons 8-Channel P20 GEN2 Electronic Pipette or Opentrons Single-Channel P20 GEN2 Electronic Pipette. Pipettes are calibrated and factory tested at the 1µL setpoint, and come with a calibration certificate. However, even with testing and certification, handling low volume transfers via automated air displacement pipetting requires testing and optimization to ensure they meet your specifications.

Q: Can you transfer viscous liquids on the robot?

A: Some customers use the OT-2 to transfer viscous liquids including honey and blood. But, since the OT-2 uses air displacement pipetting technology, it isn’t optimized for viscous liquids. The volume transferred by the robot will differ from the volume you enter into the OT-2 software, so additional optimization may be needed (e.g. heating the liquid, spinning down the liquid, using wide-bore tips).

Q: Can I create a clean environment in the OT-2?

A: Yes. When equipped with our HEPA module, the OT-2 enclosure can be turned into a clean work environment. However, Opentrons Electronic Pipettes can’t be autoclaved, so you’ll need to use filter tips to prevent contamination inside the pipette. Also, the OT-2 does NOT support UV light disinfecting.

Q: Can I use 384-well plates?

A: Standard full skirted 384-well plates are fully compatible with the OT-2. But because of the size of the wells, we recommend using only the Opentrons Single-Channel P20 GEN2 Electronic Pipette when working with 384-well plates. Using larger volume pipettes like the Opentrons 8-Channel P300 GEN2 Electronic Pipettes would be tricky because these tips have a large diameter, making the precise labware calibration required to access the small wells of a 384-well plate challenging to achieve consistently.

If you require temperature control for your 384-well plate, you need to find an aluminum thermal block with a standard SBS footprint to use in conjunction with the Opentrons Temperature Module.

Q: Do I need to use your tips?

A: You are required to use Opentrons Tips to setup and calibrate your Opentrons OT-2 after purchase.

While it is possible to use any universal bore tip with Opentrons pipettes, we highly recommend you use Opentrons Tips with the Opentrons system because they have been specifically engineered and thoroughly tested to ensure volumetric accuracy and precision when used with Opentrons Electronic Pipettes. Our tips are competitively priced and come pre-built into the Opentrons software.

In order to use 3rd party tips, you need a custom labware definition and, in many cases, a 3D-printed adapter to fit the tip box into an OT-2 deck slot.

Q: How do you prevent cross contamination?

A: The OT-2 has a few special features to manage droplet formation from the pipettes like air gap, touch tip, and blow out.

The most important thing you can do to prevent contamination is set up the deck and the robot’s movements to avoid maneuvering dirty pipettes over clean samples. You can ensure this by visualizing the deck layout of your experiment in our Protocol Designer, or using Python to specify your own XYZ path for the robot to follow.

You might need to use a reservoir on the deck as a liquid waste receptacle to avoid long movements of contamination prone samples. If so, and you need help, our Application Engineering team is available to help you.

Q: Can you take reformat samples from tubes to plates and vice versa? (i.e tubes to 96 well plate and multiple 96 well plates into 384)

A: You can reformat samples using the Opentrons platform: the only constraint is the pipette volume. An Opentrons 8-Channel GEN2 Electronic Pipette can’t be used to access a tube or all of the wells in a 384-well plate. In order to reformat samples with an Opentrons 8-Channel GEN2 Electronic Pipette, you’ll either need to handle accessing every other well on the 384-well plate in your downstream assay, or use an Opentrons Single-Channel GEN2 Electronic Pipette.

Here’s an example of 4 96-well plates consolidated to a 384-well plate with an Opentrons 8-Channel GEN2 Electronic Pipette:

Q: What kind of input does Opentrons accept for plate reformatting/cherrypicking?

A: We have several pre-built protocols for different kinds of input—like our cherry picking protocol that can use a CSV for the source and destination well input. If you need a different protocol, our Application Engineering team can customize one for you.

Q: Can you integrate with my LIMS system?

A: Opentrons does not offer any officially supported LIMS integration at this time. However if your LIMS can output a CSV, some of our pre-built protocols can accept that file as an input. If you need additional customization beyond that, you can always ask our Application Engineering team to write a protocol for you that accepts your LIMS formatted CSV as an input. Additionally, since the Opentrons API is completely open-source, if someone on your team has the coding ability, you can write your own two-way integration with your LIMS and even run protocols remotely.

Ready for next steps? Reach out to our sales team to schedule a free consultation.