Opentron vs. Preowned "Premium" Liquid Handler with 50k budget

Hi all,

We are considering purchasing a liquid handler for < 50k. Should we purchase an Opentron Flex or a preowned Hamilton Star (like this one listed by Boston Industries)?

Also, is it possible to purchase the upgraded software from Hamilton, and what would the difference in the quality of support we would receive for these two options be?

For some context, we currently have a Hamilton Prep, and we are struggling with its lack of customizability, reliability, the need to create protocols on the instrument, and the lack of CVS-formated reports. (Its reports are PDF only.)



We have a dog in this hunt, and strongly belive in the quality of Hamilton STARs. Once they are going, they can run for years. Some of the best applications support. Hamilton makes great tips and plastics. Really solid platform.
…That is for the STAR and STARlet.
You have a STARplus linked. Those can be good as well. You just need a great install and understanding of the charateristics of the STARplus units. They need to be very well leveled. I feel in most cases a STAR will do more than most labs need… Are you doing something funky like choping up and integrating something to the plus deck? Or just using this as a liquid handler?

Do you need the 96 head? Looking at the pic on the STARplus, that looks like a good current gen 96 head. Hamilton had 300ul heads(gold annodized bottoms), Mid-gen 1000ul 96 heads(the look boxy and no view window on them), and these 1,000ul 96 heads. The newest ones are great.

Call up your local Hamilton rep. I assume they will sell you the current software. You will need to make sure the systems config/firmware/software all match if you upgrade past a known working system state.

Boston Industries is also solid. Good people, good prices.

Now to OpenTrons - They have been the come out of nowhere new kid on the block. Really amazing approach to democratizing liquid handeling. Outstanding leadership team and vision. Their OT-2s (when set up for appropriate applications) run around the clock. I have seen >20 unit farms running single channel transfers 24/7(almost). They had a heavy python programming charateristic. I am not sure about their ability to format CVS files to the level of the STAR, but assume you can hammer the file into any shape you need.

Happy hunting!


What an interesting (and straight up) question.
In general, I think people are wary to answer a question that asks liquid handling manufacturer 1vs2 because nobody wants to alienate the nice people from these companies helping us solve problems for free in this forum but at the same time balance this with constructive feedback that helps everyone.

So I will start my answer with the classic and political “it depends on your application”. This by itself is a useless statement so let’s go through some examples that give it some meaning.

(The Opentrons Flex has not been released yet in the UK, so I can only talk about what I learned from talking to the fantastic sales reps, deducting from the specs sheet and my years of working with the OT-2.)

1. Throughput - Liquid handling flexibility
Case study I - cherry picking: The Flex can either have 1x 96-channel head OR 2x pipettes, in addition to what looks like a sturdy plate gripper. This means that in either configuration, if you want to cherry pick liquids from a plate, every transfer needs to run sequentially… this takes a lot of time! Compare this to the independently moving “channels” on the STARlet you are looking at and you can see how all cherry pick source destinations that are in the same x-dimension can be picked up simultaneously, dramatically cutting your processing speed.
Case study II - plate format switching: image you move samples from 4x 24-well plates into one 96-well plate. With the Flex this would require 96-sequential single liquid transfers (because you are switching plate format, even if you had the 96-head you would need to use it as a single channel). If these samples are all unique, i.e. are not allowed to cross-contaminate, you have to get a new tip and eject in every transfer round.
Compare this to the STARlet: the (y-dimension-)independently-movable 8-channels can pick up 8x unique liquids from 2x different 24-well plates simultaneously and then transfer them all at once into the 96-well plate… This means you only need 12 transfer cycles (instead of 96).
2. Throughput - Deck Layout
The STARlet alone has 25 standards SLAS positions. The STARlet plus you linked has even more due to its extension. The Flex has 12 + 4 (extra) SLAS positions. Both Flex and STARlet have stacking capabilities.
3. Codeability
Here, I am biased. I taught myself lab automation using the Opentrons API documentation, and it is incredibly intuitive, elegant and very easy to upgrade. (As mentioned above, Opentrons has truly democratised lab automation, and I got the feeling it made the old bio-robotics companies finally get onto their toes again… a fantastic thing for costumers and science)
I assume you meant CSV file input/ouput generation: with Opentrons you interact with your robot in pure Python, one if not the most used programming language in the world (depending on who you ask). This means you can do virtually anything because you have access to the world’s repository of Python solutions. No proprietary, click-and-drag interface controlled by a single company can ever give the same breath of functionality that a programming language can give you.
There are more reasons in this regard but I leave those for you to read in the PyHamilton and PyLabRobot papers :slight_smile:
4. Usability - Programming
Everything I said in the last point doesn’t matter if you can’t code and either don’t have the time or the willingness to learn. If you cannot code then the VENUS software is probably a bit easier to start with. If you can code a little bit though then you can simply ask ChatGPT to generate Flex protocols for you, and quickly check yourself that they look correct before trying them out.
5. Usability - Calibration
Hamilton machines shine with their precision and (if maintained properly) long-term calibration. You will still have to check that your labware definitions are correct here and there but in general they require very little calibration. On the other hand, the OT-2 was a nightmare to calibrate; you had to calibrate (1) the deck, (2) each pipette, (3) the tips, and finally (4) each labware. In the end, 384-well plate handling was still too inaccurate and only when Opentrons implemented a real-time calibration I was able to reliably use them with this format. I have been told the Flex has an auto-calibrate function… but when I asked for more information it turned out that this only covers the deck calibration and labware still has to be calibrated manually, which can be quite time-consuming.
6. Real-Time Control - Coboting
Maybe you just want to have a lot of “walk-away time” and let the robot do its thing. But maybe your application requires a centrifugation step that cannot be avoided. In such a situation you want a “cobot”, a collaborative robot-human interaction. You can for both Flex and STARlet generate wait() or input() commands that temporarily hold the protocol but sometimes you want to add or remove some steps while you are running it.
This is possible with Opentrons because you can run your machine from a Jupyter Notebook, that means run commands one at a time, in real-time. With VENUS on the STARlet that is to my knowledge absolutely impossible.
7. Support
I am sure both companies have excellent support services (particularly if you are US-based). The question is just how much are you willing to spend. Both companies have protocol writing services, but neither has ‘online protocol writing consultancy services’ (to my knowledge) which is something I would like to see at a lower cost point than the thousands you have to pay for a single day of an engineer to come to your lab.
8. Independence
Opentrons is absolutely amazing with its transparency. You can go to their website and find detailed information not just about their robots but also about absolutely everything they are selling, including modules and their prices. This makes it incredibly easy and fast to generate cost-utility estimates to generate the robot setup that meets your goals at your assigned budget.
I found it incredibly difficult to extract the information I needed out of Hamilton. I spent months figuring out what modules Hamilton offers themselves, which ones they support, which ones I can easily integrate myself and then asking for quotations for various modules which are all very high-end but are accordingly expensive. Hamilton sales reps have their own 3D CAD software that lets them generate robot setups for costumisation and quotations. I have been told this is not available to customers.
9. Running cost
Your main continued cost from the robot side will likely end up being tips. Opentrons tips (not necessary but I do recommend them) are pretty cheap.
Hamilton tips come in two general types: coated tips (for capacitative liquid level detection) and non-coated/clear tips (for everything not requiring cLLD). Coated tips are incredibly expensive and you cannot visually verify the behaviour of your liquids during prototyping. But they do offer capacitative…
10. Liquid level detection
The STARlet offers both capacitative as well as pressure-based LLD which is very nice and can make your liquid transfer much more reliable… if you don’t work with low volumes. If you do then pressure-based LLD might actually suck up your liquid that you are trying to detect, and if you use capacitative LLD the charge of the tip might not dissipate adequately into the liquid due the liquid’s low volume to dissipate through/into.
The Flex has apparently pressure-based LLD, and I am curious how reliable users find it.
11. Pipetting Accuracy
Hamilton is very candid about the fact that their machines require careful adjustment of channel settings to generate accurate liquid transfers, and they sell a liquid verification kit to allow customers to build their own ideal settings (which are then captured in a “liquid class”).
I have never heard Opentrons talk about “liquid classes” but instead you can change all the parameters directly from the default for every liquid transfer step you perform, giving you more ‘in-the-moment’ control. But I am unaware of any on-deck scale or calorimetric system that would allow users to verify the pipetting accuracy with their machines.

I hope this extensive but by no means exhaustive list of pros and cons shows the nuances behind a question of the liquid handling manufacturer 1vs2 kind.

Side note
In your question you mention the pitfalls of the Microlab Prep nicely but you don’t mention that the deck space/throughput is an issue for you which makes me assume that it isn’t.
If that is the case, have you considered developing a PyLabRobot (PLR) backend for the Microlab Prep yourself?

With PLR you…

  • would code in Python (meaning CSV, json, .txt. TSV, … files are all easy do deal with),
  • could customise the deck to your liking with integrations of 3rd party modules,
  • tremendously increase reliability by choosing all parameters yourself,
  • write protocols in PJs in bed, in a café or in Bali, it doesn’t matter, it’s just Python (no hurting arm muscles from taping onto the Prep touch screen for hours :+1: ),

all while still using the Prep’s amazing hardware (after all it is just a “STARtiny” in my opinion).

Additionally, I would be very interested in a Microlab Prep that can be controlled using PyLabRobot; particularly the ceiling camera for automated labware and tip usage recognition is a Prep-unique feature I have never seen on any liquid handler and could be incredibly useful for programmatic feedback control of sample processing.



Some things to consider:

  • Getting another Hamilton system means that you’ll be familiar with the Hamilton way of doing things (hardware/programming/operation)
  • Getting a Opentrons means that you’ll have to learn new hardware, programming, troubleshooting and teaching the operators a new system.
  • Sticking with Hamilton probably means you’ll deal with one rep rather than two different company support/service people.
  • Supporting two systems (Hamilton/Opentrons) means that you’ll need to stock different tips/consumables, and probably get two different service plans.

On a used Hamilton, I suggest you contact your local Hamilton rep to see if they can service it/support it. On the one you linked I noticed it had CORE I hardware, which isn’t a issue in itself, but is a consideration that its not the newest hardware, and if you decide to upgrade you may have to spend time on that.


One caveat is that the MLPrep I believe uses Instinct underneath the hood, not Venus so it’s not the really the Hamilton way of doing things if you’re exclusively familiar with Venus (as most of this forum appears to be.) Also the MLPrep is incredibly closed so it may actually scare folks from investing in other Hamilton systems if they feel that this is the way Hamilton runs things which is not true. The terminology is similar (for liquid classes) but there’s a massive gap between the ML Prep and the other liquid handlers. I don’t know what it’s in the future for the ML Prep roadmap but a PLR backend would probably help adoption.


I’d be happy to help if you decide to go with this!

I am curious about whether this option is even possible since the Hamilton Prep’s software is rather closed so I’m not sure if there is a way to ‘get into’ the back end.

However, if this could be done, the Prep may become a good option for people capable of coding who want a relatively accurate, reliable, and customizable handler for a relatively low entry price. (< 25k USD)

Thank you for your clear and comprehensive guidance!

I imagine that there is no way of emphasizing how important it is to be able to trust the handler’s reliability.


By the way, I have now seen an example of an ML Prep being controlled by not the on board software.

Since it does use Instinct under the hood, I believe the fw commands are different than STAR’s & their derivatives.

1 Like

With the Vantage, that also has the option to use Instinct, firmware commands are actually (roughly) translated to the VENUS/STAR command set.

1 Like