OT-2 Simulator with Visualizer

This notebook shows how to use the OpentronsOT2Simulator backend to test OT-2 protocols offline, with the visualizer for real-time feedback.

See the OT-2 hello world notebook for using the real hardware.

from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import OpentronsOT2Simulator
from pylabrobot.resources.opentrons import (
    OTDeck,
    opentrons_96_filtertiprack_20ul,
    opentrons_96_tiprack_300ul,
)
from pylabrobot.resources.celltreat import CellTreat_96_wellplate_350ul_Fb
from pylabrobot.resources import set_tip_tracking, set_volume_tracking
from pylabrobot.visualizer import Visualizer

set_tip_tracking(True)
set_volume_tracking(True)

Set up the simulator and visualizer

The simulator takes optional pipette names. Defaults are p300_single_gen2 (left) and p20_single_gen2 (right).

backend = OpentronsOT2Simulator()
deck = OTDeck()
lh = LiquidHandler(backend=backend, deck=deck)
await lh.setup()

2026-03-12 18:32:17,220 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - OpentronsOT2Simulator setup: left=p300_single_gen2, right=p20_single_gen2
2026-03-12 18:32:17,220 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Homing (simulated).

vis = Visualizer(resource=lh)
await vis.setup()

Websocket server started at http://127.0.0.1:2121
File server started at http://127.0.0.1:1337 . Open this URL in your browser.

Add labware to the deck

Assign tip racks and a plate. These will appear in the visualizer automatically.

tip_rack_20 = opentrons_96_filtertiprack_20ul(name="tip_rack_20")
deck.assign_child_at_slot(tip_rack_20, slot=1)

tip_rack_300 = opentrons_96_tiprack_300ul(name="tip_rack_300")
deck.assign_child_at_slot(tip_rack_300, slot=2)

plate = CellTreat_96_wellplate_350ul_Fb(name="plate")
deck.assign_child_at_slot(plate, slot=6)

Run a simple protocol

Pick up a 20 uL tip (right pipette = channel 1), aspirate from well A1, dispense into well B1, and return the tip.

await lh.pick_up_tips(tip_rack_20["A1"], use_channels=[1])

2026-03-12 18:32:17,371 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Picked up tip from tip_rack_20_A1 with pipette sim-right

plate.get_well("A1").tracker.set_volume(200)
await lh.aspirate(plate["A1"], vols=[15], use_channels=[1])

2026-03-12 18:32:17,377 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Aspirated 15.00 µL from plate_well_A1

await lh.dispense(plate["B1"], vols=[15], use_channels=[1])

2026-03-12 18:32:17,384 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dispensed 15.00 µL to plate_well_B1

await lh.return_tips()

2026-03-12 18:32:17,390 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dropped tip to tip_rack_20_A1 with pipette sim-right

Now try the left pipette (p300) with the 300 uL tip rack.

await lh.pick_up_tips(tip_rack_300["A1"])

2026-03-12 18:32:17,395 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Picked up tip from tip_rack_300_A1 with pipette sim-left

await lh.aspirate(plate["A1"], vols=[100])
await lh.dispense(plate["C1"], vols=[100])

2026-03-12 18:32:17,402 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Aspirated 100.00 µL from plate_well_A1
2026-03-12 18:32:17,404 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dispensed 100.00 µL to plate_well_C1

await lh.return_tips()

2026-03-12 18:32:17,417 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - Dropped tip to tip_rack_300_A1 with pipette sim-left

Clean up

await vis.stop()
await lh.stop()

2026-03-12 18:32:17,442 - pylabrobot.liquid_handling.backends.opentrons_simulator - INFO - OpentronsOT2Simulator stopped.