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Liquid handling

skills/pylabrobot/references/liquid-handling.md

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Liquid handling

Verified against PyLabRobot 0.2.1 on 2026-07-23. Examples in this reference are planning or chatterbox-only. They are not authorization to connect to a robot.

Stable frontend and backend

python
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import LiquidHandlerChatterboxBackend
from pylabrobot.resources.hamilton import STARLetDeck

lh = LiquidHandler(
    backend=LiquidHandlerChatterboxBackend(num_channels=8),
    deck=STARLetDeck(),
)
await lh.setup()  # prints operations; no hardware transport

For 0.2.1, the important frontend signatures are:

text
pick_up_tips(tip_spots, use_channels=None, offsets=None, **backend_kwargs)
drop_tips(tip_spots, use_channels=None, offsets=None,
          allow_nonzero_volume=False, **backend_kwargs)
return_tips(use_channels=None, allow_nonzero_volume=False, offsets=None,
            **backend_kwargs)
aspirate(resources, vols, use_channels=None, flow_rates=None, offsets=None,
         liquid_height=None, blow_out_air_volume=None, spread="wide",
         mix=None, **backend_kwargs)
dispense(resources, vols, use_channels=None, flow_rates=None, offsets=None,
         liquid_height=None, blow_out_air_volume=None, spread="wide",
         mix=None, **backend_kwargs)

Volumes are microlitres (uL), coordinates/heights are millimetres (mm), and flow rates are uL/s unless the exact backend page says otherwise. Use lists whose lengths agree with selected resources/channels; do not rely on scalar broadcasting copied from an older example.

Safe operation shape

With the software-only backend and already assigned resources:

python
source.get_well("A1").tracker.set_volume(100.0)  # bookkeeping only

await lh.pick_up_tips(tips["A1"])
await lh.aspirate(
    source["A1"],
    vols=[25.0],
    use_channels=[0],
    flow_rates=[50.0],
    liquid_height=[1.0],
)
await lh.dispense(
    destination["A1"],
    vols=[25.0],
    use_channels=[0],
    flow_rates=[75.0],
    liquid_height=[2.0],
)
await lh.return_tips()

Before translating this to any physical system, verify:

  • resource and well identity, actual position, orientation, dimensions, and reachability;
  • source fill volume and dead volume; destination capacity and headspace;
  • tip model, fitting, filter, capacity, rack state, liquid compatibility, and channel compatibility;
  • 0-based use_channels mapping against the physical head and mounted tools;
  • volume, length, rate, and time units;
  • aspiration/dispense height, offset, rate, settling, blowout, mixing, air gaps, surface behavior, and validated liquid class;
  • contamination grouping, filtered-tip requirement, tip reuse prohibition or validated policy, waste route, and carryover controls.

The bundled transfer planner makes the conservative choice of one new tip per CSV row.

transfer() is not the old plate-copy API

In 0.2.1 the verified signature is:

text
transfer(source: Well, targets: List[Well], source_vol=None, ratios=None,
         target_vols=None, aspiration_flow_rate=None,
         dispense_flow_rates=None, **backend_kwargs)

It represents distribution from one source to multiple targets. Old examples that pass parallel source=source_plate["A1:H12"], dest=..., and vols=... do not match this stable signature. For one-to-one transfers, plan explicit aspirate/dispense pairs and validate channel/tip state.

Tip tracking

Enable tracking before operations:

python
from pylabrobot.resources import set_tip_tracking

set_tip_tracking(True)

Tip racks normally start populated; supported factories accept with_tips=False, and TipRack.fill(), empty(), and set_tip_state(...) modify planned state. return_tips() depends on operation history. Tip tracking can catch inconsistent planned operations, but it cannot detect whether a tip is physically present, seated, blocked, damaged, or the expected type.

Never disable tracking merely to bypass NoTipError or HasTipError. Reconcile the physical deck and planned state instead.

Volume tracking is bookkeeping

python
from pylabrobot.resources import set_volume_tracking

set_volume_tracking(True)
well.tracker.set_volume(200.0)
used_uL = well.tracker.get_used_volume()
free_uL = well.tracker.get_free_volume()

The VolumeTracker updates planned volumes and can reject under-aspiration, tip overfill, or well overfill. It does not measure a meniscus or confirm liquid identity. Initial state must come from a trusted preparation record and human reconciliation.

Keep dead volume separate from geometric capacity. The tracker may allow a withdrawal that is physically unreliable because of vessel shape, tilt, surface tension, foam, viscosity, or required submersion.

Physical liquid detection is backend-specific

Hamilton STAR liquid-level detection is a separate physical feature. Stable STAR docs expose backend kwargs such as lld_mode, immersion_depth, and surface_following_distance. It is not portable to all backends and is not enabled by volume tracking. Validate the model, sensors, consumables, conductive properties, firmware behavior, failure handling, and channel-specific values before considering it.

Liquid classes

There is no stable generic import:

python
# Invalid in 0.2.1:
# from pylabrobot.liquid_handling import LiquidClass

Hamilton liquid classes are vendor-specific:

python
from pylabrobot.liquid_handling.liquid_classes.hamilton import HamiltonLiquidClass
from pylabrobot.liquid_handling.liquid_classes.hamilton.star import (
    HighVolumeFilter_Water_DispenseSurface_Part,
)

await lh.aspirate(
    source["A1"],
    vols=[100.0],
    hamilton_liquid_classes=[
        HighVolumeFilter_Water_DispenseSurface_Part
    ],
)

The keyword above is a STAR backend kwarg, not a universal frontend contract. TecanLiquidClass and get_liquid_class exist under pylabrobot.liquid_handling.liquid_classes.tecan, but are a different vendor-specific system.

Do not select a class from its name alone. Review liquid, tip, head, volume range, jet/surface mode, vessel geometry, calibration curve, flow, settling, transport air, blowout, and firmware/model applicability. Custom classes need documented gravimetric or assay validation and operator approval.

Mixing, serial dilution, and multichannel work

  • Make every aspirate/dispense pair explicit in the plan.
  • Check the tip's current planned volume before mixing.
  • Keep the mix volume below both tip capacity and usable well volume.
  • For serial dilutions, define where a tip may be reused and where a fresh tip is mandatory; do not infer contamination safety from row order.
  • Confirm well order and channel order. A plate slice is not proof that the physical channels align with those wells.
  • Include residual volume, pre-wet cycles, adsorption, foaming, and carryover in the acceptance criteria.

Deterministic preflight

bash
python3 skills/pylabrobot/scripts/plan_transfers.py \
  --manifest skills/pylabrobot/tests/fixtures/protocol_manifest.json \
  --transfers skills/pylabrobot/tests/fixtures/transfers.csv

The CSV header is exact and fixed. Unknown columns, duplicate IDs, unsupported tip policies, missing source volumes, non-finite numbers, out-of-grid wells, unallowlisted liquid classes/tips, excess rates/heights/volumes, channel mismatches, dead-volume violations, destination overflow, and insufficient tips fail closed.

Sources

Checked 2026-07-23: