Hello everyone!
First off, thank you @MeghanFerzoco for the example partial tip pick up script in the other configure_nozzle thread! It’s been helpful for my troubleshooting with partial tip pickups. (Namely that I ought to have tip_racks defined when doing configure_nozzle_layout().
I’ve been writing a cell passaging protocol with a bunch of Partial Tip Pick Up actions, but I’m running into an issue where I have a reservoir plate (12 wells, each well is an entire column) and the Partial Pick Up is giving a PartialTipMovementNotAllowedError.
PartialTipMovementNotAllowedError [line 245]: Error 2004 MOTION_PLANNING_FAILURE (PartialTipMovementNotAllowedError): Moving to Reagent Reservoir in slot C1 with H1 nozzle partial configuration will result in collision with items in deck slot B1.
Is there a way to make partial tip pick up actions not overhang when going into reservoir plates, such that it doesn’t risk colliding with items in adjacent slots? (Since it shouldn’t need to overhang if the entire column in the plate is the same well)
I’m wondering because I have no more space to move my labware/modules! So I can’t move things out of the way for the partial pick up actions in the reservoir plate
The tall 1000 ul tip rack in B1 gets in the way of overhanging partial pick up related actions for the reservoir plate in C1. I can’t move the tip rack to A1 because PARTIAL_COLUMN partial tip pick ups don’t work there (because you can only do H1 as the starting nozzle for PARTIAL_COLUMN).
We’re doing lots of offset pipetting in our protocols and have run into this issue as well. I’ve found that you’ll need to put a good amount of thought into where each piece of labware lives on deck and be willing to get creative in adjusting the heights of your labware.
The biggest help for us has been 3D printing custom risers to adjust the height of tip racks. That way we can have two tip racks next to each other and do offset tip pickup on them without crashing into the neighbor. For example, we’d have a rack in B1 raised by 12mm and then a rack in C1 sitting flat on the deck, allowing for row-wise tip pickup starting from row H of rack 1. The catch here is that you have to chew through your tips from highest rack to lowest. It would also be a bit more difficult for you if you’re doing partial column pickup because you may end up with overhangs in the x and y direction simultaneously.
This approach has unlocked a lot of deck space for us and I’ve suggested to Opentrons that they offer tip rack risers in multiple heights as a first-party solution for this problem - maybe @MeghanFerzoco will have thoughts on this when she reads this thread.
The corollary to this is that you can also adjust the height of your labware - if the reagent reservoir was high enough up, the head wouldn’t crash into your tip racks while pipetting even with an overhang.
One final note - you mentioned you’re using PARTIAL_COLUMN pickup. How many tips are you actually picking up? If it’s just one, can you use the SINGLE nozzle configuration to avoid the H1 start nozzle requirement? If it’s all 8 tips, can you use COLUMN instead of PARTIAL_COLUMN for the same reason?
Hi osand317,
Thank you for the note about the tip rack heights, that’s GENIUS!! That would open up so many more labware configurations for me on the deck. e.g., I could put an adapter-less 1000 ul tip rack in C1 and put the reservoir in B1, which might fix everything! Do you make a custom labware definition for the tip rack with a lower height value? I see the regular tip rack’s definition/dimensions in the labware library so I could do that
Regarding PARTIAL_COLUMN, I’m doing 4 tip pick ups! And sometimes I do SINGLE and COLUMN/ALL . I’m culturing in 96 well plates where each column of 8 wells houses two n = 4 sample groups.
(Not randomizing the well positions I know , but I’m implementing some other measures to try and reduce variability from well positioning - 1) Adding a gas permeable membrane on top to make evaporation consistent and 2) leaving the well plates at RT for a while until the cells to attach so that the temperature gradient doesn’t mess with cell attachment)
We’ve used custom risers before to avoid this as well. I’ll bring this suggestion to productive this to our product development team!
We have had people also use the PCR lid holder for this purpose!
@hkjawn we weren’t lowering tip racks, only raising them. So we achieved that by creating new adapter labware definitions (based on the Opentrons PCR lid adapter definition) and then creating copies of the tip rack definitions that have stackingOffsetWithLabware tags to determine the final height of the tip rack sitting on the adapter:
Hey @hkjawn - are you using a custom labware def here or an Opentrons definition? Sometimes, we have some quirks on how we treat these, and I’m trying to get feedback from our internal team on this specific case.
@MeghanFerzoco Thank you! We considered the PCR lid holder but needed multiple different height risers to fully utilize the deck. We only needed 3 different heights (deck height/0mm, +12mm, and +24mm) but I could technically imagine someone needing a 4th option as well.
Thank you for the example! I’ll have to figure this out some time… I ended up removing the waste chute and opting to use the trash bin in A3, which frees up the slot above my reservoir plate!
. I’m culturing in 96 well plates where each column of 8 wells houses two n = 4 sample groups.
, but I’m implementing some other measures to try and reduce variability from well positioning - 1) Adding a gas permeable membrane on top to make evaporation consistent and 2) leaving the well plates at RT for a while until the cells to attach so that the 