Week 3 HW: Lab Automation

My Design on https://opentrons-art.rcdonovan.com/

My Design on Opentrons Colab

My Opentrons instructions

from opentrons import types

metadata = { # see https://docs.opentrons.com/v2/tutorial.html#tutorial-metadata

‘author’: ‘’,

‘protocolName’: ‘HTGAA 2026 Creeper Face’,

‘description’: ‘Draw a Creeper face pixel art on agar using Green background and Red features.’,

‘source’: ‘HTGAA 2026 Opentrons Lab’,

‘apiLevel’: ‘2.20’

}

TIP_RACK_DECK_SLOT = 9

COLORS_DECK_SLOT = 6

AGAR_DECK_SLOT = 5

PIPETTE_STARTING_TIP_WELL = ‘A1’

well_colors = {

‘A1’ : ‘Red’,

‘B1’ : ‘Green’,

‘C1’ : ‘Orange’

}

def run(protocol):

Load labware, modules and pipettes

Tips

tips_20ul = protocol.load_labware(‘opentrons_96_tiprack_20ul’, TIP_RACK_DECK_SLOT, ‘Opentrons 20uL Tips’)

Pipettes

pipette_20ul = protocol.load_instrument(“p20_single_gen2”, “right”, [tips_20ul])

Modules

temperature_module = protocol.load_module(’temperature module gen2’, COLORS_DECK_SLOT)

Temperature Module Plate

temperature_plate = temperature_module.load_labware(‘opentrons_96_aluminumblock_generic_pcr_strip_200ul’,

‘Cold Plate’)

Choose where to take the colors from

color_plate = temperature_plate

Agar Plate

agar_plate = protocol.load_labware(‘htgaa_agar_plate’, AGAR_DECK_SLOT, ‘Agar Plate’) ## TA MUST CALIBRATE EACH PLATE!

Get the top-center of the plate, make sure the plate was calibrated before running this

center_location = agar_plate[‘A1’].top()

pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

Patterning

pass this e.g. ‘Red’ and get back a Location which can be passed to aspirate()

def location_of_color(color_string):

for well,color in well_colors.items():

if color.lower() == color_string.lower():

return color_plate[well]

raise ValueError(f"No well found with color {color_string}")

For this lab, instead of calling pipette.dispense(1, loc) use this: dispense_and_detach(pipette, 1, loc)

def dispense_and_detach(pipette, volume, location):

"""

Move laterally 5mm above the plate (to avoid smearing a drop); then drop down to the plate,

dispense, move back up 5mm to detach drop, and stay high to be ready for next lateral move.

"""

assert(isinstance(volume, (int, float)))

above_location = location.move(types.Point(z=location.point.z + 5)) # 5mm above

pipette.move_to(above_location) # Go to 5mm above the dispensing location

pipette.dispense(volume, location) # Go straight downwards and dispense

pipette.move_to(above_location) # Go straight up to detach drop and stay high

YOUR CODE HERE to create your design: CREEPER FACE (8x8)

Pixel settings (keep same style as your example)

pitch = 5 # mm between pixel centers

vol = 1 # uL per pixel dot

Creeper face mask: 0 = background (Green), 1 = feature (Red)

creeper = [

[0,0,0,0,0,0,0,0],

[0,1,1,0,0,1,1,0],

[0,0,0,1,1,0,0,0],

[0,0,1,1,1,1,0,0],

[0,0,1,0,0,1,0,0],

]

Center the 8x8 grid around center_location

(0..7) -> offsets (-3.5..+3.5)*pitch

def pixel_location(i, j):

x = (j - 3.5) * pitch

y = (3.5 - i) * pitch

return center_location.move(types.Point(x=x, y=y))

————————-

PASS 1: GREEN background

————————-

pipette_20ul.pick_up_tip()

pipette_20ul.aspirate(16, location_of_color(‘Green’))

remaining = 16

for i in range(8):

for j in range(8):

if creeper[i][j] == 0:

if remaining < vol:

pipette_20ul.aspirate(16, location_of_color(‘Green’))

remaining = 16

dispense_and_detach(pipette_20ul, vol, pixel_location(i, j))

remaining -= vol

pipette_20ul.drop_tip()

————————-

PASS 2: RED features

————————-

pipette_20ul.pick_up_tip()

pipette_20ul.aspirate(16, location_of_color(‘Red’))

remaining = 16

for i in range(8):

for j in range(8):

if creeper[i][j] == 1:

if remaining < vol:

pipette_20ul.aspirate(16, location_of_color(‘Red’))

remaining = 16

dispense_and_detach(pipette_20ul, vol, pixel_location(i, j))

remaining -= vol

Don’t forget to end with a drop_tip()

pipette_20ul.drop_tip()