Janus Liquid Handler-Discarding Supernatant and Adding Labware

We have a Janus automated liquid handling system that we have been trying to set up for a DNA extraction protocol. We have been running into some issues though and were wondering if anyone had any insight.

(1) The first issue we encountered was programming a step for supernatant removal. We were thinking about dispensing waste into a reservoir trough. However, it seems that the program considers a trough as one well and will only dispense one adapter per trough. For example, we want to remove the supernatant out of eight samples and we have two designated troughs for waste. When starting the program, the varispan head will only pick up two tips, remove the supernatant from two samples, dispense supernatant from one tip per trough, drop the tips, then grab two more tips and repeat this process again. If we have three troughs, it will grab three tips at a time and remove and dispense supernatant from each tip per trough. Hopefully this makes sense. A message will also pop up stating a labware change request for the trough every time the varispan head goes to grab new tips. It seems the program does not like using the trough as the location of a dispense.
The goal was to use all eight adapters simultaneously and dispense our waste into one trough, to speed up the process.
We have also attempted to dispense waste into the flush/wash basin, but again it seems to consider this as one well and so will only put one tip per well. If you have any suggestions to remedy this or an alternative method to removing and dispensing waste, we would love any input

(2) Another issue we have been having is the addition of new labware that is not already present in the software. We are using a VWR 96 deep well plate and this is not already pre programmed. We know how to alter the 3D dimensions of the labware we newly created. Based on the dimensions of the other plates, we thought the units of the dimensions were in millimeters. Yet when we measure and input the dimensions of our new plate, they seem to not be accurate in practice. We have resulted in blind trial and error, running a program, doing slight adjustments based on what we see, and running it again, over and over. It’s been very time-consuming. Let us know if you have any advice or knowledge about creating a new labware or if there is a resource that already has these dimensions and can be uploaded online.
Thanks you guys!

Hi Kiki,

Welcome to the hellscape of Janus programming. It’s hot down here.

  1. Supernatant Disposal

I’m assuming that for these steps you’re using a “Single” or “Custom” type transfer correct? The main problem you’re facing is that this step only intends to deliver one aliquot to one location at a time. I’ve never actually used it before, but you might want to try the “Multiple Liquids” transfer for this supernatant removal step.

Do not do anything else with Multiple Liquids, as I hear that its not the most straightforward step.

The second problem you’re facing is the iteration of labware positions within the transfer steps themselves. Once you set up your “Multiple Liquids” transfer step, go to:

Dispense → Advanced → Increment the location every: and select “None”

By default, the Janus thinks that once you’ve performed a transfer step on a well, it needs to increment, and in most cases this is true. It has a hard time with understanding use cases with reagents and troughs, so you need to select this when doing something relatively unconventional for the Janus such as this.

You’ll run into an issue where you’ll need to do some if:then condition where if you have a certain amount of samples, use the next trough, as if this goes on indefinitely, you risk overflowing the first and only trough. Using a bigger trough to the maximum use case of supernatant volume will help you avoid the pain of trying to program that part.

  1. Labware Additions

Yes, the labware definition when you first create the labware should be in mm, however there are a number of painful inefficiencies you have to look out for. The first is that your plate adapter needs to be “Plate Support Tile” instead of “Plate Support Med Tile” or whichever it defaults to. Idk why PKI decided that the medium support tile should be the default but whatever. If you’re trying to do your alignment and measuring that way, it will throw you off.

The second that the Janus doesn’t really care about definitions in the normal sense, it basically measures everything relative to how it sits within the plate adapter. Its worth it to get a caliper and do the measurements for each one of the well details in the labware and get it super precise. If you select the value you want to edit within the “Details” tab of the labware properties, it will give you a little description below of what exactly is bein measured.

That being said, you HAVE TO use the “var evaluate tab” per labware to do the measurements relative to your instrument. There’s a whole walkthrough on how to do this by incrementally moving the probe of choice using the software to align to the labware, and its a lot easier than guessing the values. I’d go through that in the manual if you haven’t already and take it from there.

Good luck with everything, and let me know if you have further questions.



Thanks Doug for your super thorough response! Will get on it!

Update: Just tried it out and it works y’all!! Thanks a million

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