Week 3 HW: Lab Automation

Python Script for Opentrons Artwork

I have created Space Invaders with green and red because my node Designer Cells mentioned they have only red (mrfp1) and green (sfGFP) right now. I have evil plans to create also text “Designer Cells” down the Space Invaders logo:) - done!-

Space Invaders - Opentrons Bio Art

Designer: Beyza Batır
Design: Space Invaders [mrfp1(red)+sfGFP(green)]

Google Colab

Simulation

Protocol Code

from opentrons import types

metadata = {
    'author': 'Beyza Batır',
    'protocolName': 'HTGAA Opentrons Lab',
    'description': 'SpaceInvaders',
    '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',
}

def run(protocol):
    # --- Load labware ---
    tips_20ul = protocol.load_labware('opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips')
    pipette_20ul = protocol.load_instrument("p20_single_gen2", "right", [tips_20ul])
    temperature_module = protocol.load_module('temperature module gen2', COLORS_DECK_SLOT)
    temperature_plate = temperature_module.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul', 'Cold Plate')
    color_plate = temperature_plate
    agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate')
    center_location = agar_plate['A1'].top()
    pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL)

    # --- Helper functions ---
    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}")

    def dispense_and_detach(pipette, volume, location):
        above_location = location.move(types.Point(z=5))
        pipette.move_to(above_location)
        pipette.dispense(volume, location)
        pipette.move_to(above_location)

    # --- Coordinates from GUI ---
    mrfp1_points = [(-9.9, 38.5),(-7.7, 38.5),(-5.5, 38.5),(-3.3, 38.5),(-1.1, 38.5),(1.1, 38.5),(3.3, 38.5),(5.5, 38.5),(7.7, 38.5),(9.9, 38.5),(-16.5, 36.3),(-14.3, 36.3),(-12.1, 36.3),(-9.9, 36.3),(-7.7, 36.3),(-5.5, 36.3),(-3.3, 36.3),(-1.1, 36.3),(1.1, 36.3),(3.3, 36.3),(5.5, 36.3),(7.7, 36.3),(9.9, 36.3),(12.1, 36.3),(14.3, 36.3),(16.5, 36.3),(-20.9, 34.1),(-18.7, 34.1),(-16.5, 34.1),(-14.3, 34.1),(-12.1, 34.1),(-9.9, 34.1),(-7.7, 34.1),(-5.5, 34.1),(-3.3, 34.1),(-1.1, 34.1),(1.1, 34.1),(3.3, 34.1),(5.5, 34.1),(7.7, 34.1),(9.9, 34.1),(12.1, 34.1),(14.3, 34.1),(16.5, 34.1),(18.7, 34.1),(20.9, 34.1),(-23.1, 31.9),(-20.9, 31.9),(-18.7, 31.9),(-16.5, 31.9),(-14.3, 31.9),(-12.1, 31.9),(-9.9, 31.9),(-7.7, 31.9),(-5.5, 31.9),(-3.3, 31.9),(-1.1, 31.9),(1.1, 31.9),(3.3, 31.9),(5.5, 31.9),(7.7, 31.9),(9.9, 31.9),(12.1, 31.9),(14.3, 31.9),(16.5, 31.9),(18.7, 31.9),(20.9, 31.9),(23.1, 31.9),(-25.3, 29.7),(-23.1, 29.7),(-20.9, 29.7),(-18.7, 29.7),(-16.5, 29.7),(-14.3, 29.7),(-12.1, 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-29.7),(-7.7, -29.7),(-5.5, -29.7),(-3.3, -29.7),(-1.1, -29.7),(1.1, -29.7),(3.3, -29.7),(5.5, -29.7),(7.7, -29.7),(9.9, -29.7),(12.1, -29.7),(14.3, -29.7),(16.5, -29.7),(18.7, -29.7),(20.9, -29.7),(23.1, -29.7),(25.3, -29.7),(-23.1, -31.9),(-20.9, -31.9),(-18.7, -31.9),(-16.5, -31.9),(-14.3, -31.9),(-12.1, -31.9),(-9.9, -31.9),(-7.7, -31.9),(-5.5, -31.9),(-3.3, -31.9),(-1.1, -31.9),(1.1, -31.9),(3.3, -31.9),(5.5, -31.9),(7.7, -31.9),(9.9, -31.9),(12.1, -31.9),(14.3, -31.9),(16.5, -31.9),(18.7, -31.9),(20.9, -31.9),(23.1, -31.9),(-20.9, -34.1),(-18.7, -34.1),(-16.5, -34.1),(-14.3, -34.1),(-12.1, -34.1),(-9.9, -34.1),(-7.7, -34.1),(-5.5, -34.1),(-3.3, -34.1),(-1.1, -34.1),(1.1, -34.1),(3.3, -34.1),(5.5, -34.1),(7.7, -34.1),(9.9, -34.1),(12.1, -34.1),(14.3, -34.1),(16.5, -34.1),(18.7, -34.1),(20.9, -34.1),(-16.5, -36.3),(-14.3, -36.3),(-12.1, -36.3),(-9.9, -36.3),(-7.7, -36.3),(-5.5, -36.3),(-3.3, -36.3),(-1.1, -36.3),(1.1, -36.3),(3.3, -36.3),(5.5, -36.3),(7.7, -36.3),(9.9, -36.3),(12.1, -36.3),(14.3, -36.3),(16.5, -36.3),(-9.9, -38.5),(-7.7, -38.5),(-5.5, -38.5),(-3.3, -38.5),(-1.1, -38.5),(1.1, -38.5),(3.3, -38.5),(5.5, -38.5),(7.7, -38.5),(9.9, -38.5)]

    sfgfp_points = [(-20.9, 23.1),(-18.7, 23.1),(18.7, 23.1),(20.9, 23.1),(-20.9, 20.9),(-18.7, 20.9),(18.7, 20.9),(20.9, 20.9),(-20.9, 18.7),(-18.7, 18.7),(18.7, 18.7),(20.9, 18.7),(-16.5, 16.5),(-14.3, 16.5),(-12.1, 16.5),(12.1, 16.5),(14.3, 16.5),(16.5, 16.5),(-16.5, 14.3),(-14.3, 14.3),(-12.1, 14.3),(12.1, 14.3),(14.3, 14.3),(16.5, 14.3),(-20.9, 12.1),(-18.7, 12.1),(-16.5, 12.1),(-14.3, 12.1),(-12.1, 12.1),(-9.9, 12.1),(-7.7, 12.1),(-5.5, 12.1),(-3.3, 12.1),(-1.1, 12.1),(1.1, 12.1),(3.3, 12.1),(5.5, 12.1),(7.7, 12.1),(9.9, 12.1),(12.1, 12.1),(14.3, 12.1),(16.5, 12.1),(18.7, 12.1),(20.9, 12.1),(-20.9, 9.9),(-18.7, 9.9),(-16.5, 9.9),(-14.3, 9.9),(-12.1, 9.9),(-9.9, 9.9),(-7.7, 9.9),(-5.5, 9.9),(-3.3, 9.9),(-1.1, 9.9),(1.1, 9.9),(3.3, 9.9),(5.5, 9.9),(7.7, 9.9),(9.9, 9.9),(12.1, 9.9),(14.3, 9.9),(16.5, 9.9),(18.7, 9.9),(20.9, 9.9),(-20.9, 7.7),(-18.7, 7.7),(-16.5, 7.7),(-14.3, 7.7),(-12.1, 7.7),(-9.9, 7.7),(-7.7, 7.7),(-5.5, 7.7),(-3.3, 7.7),(-1.1, 7.7),(1.1, 7.7),(3.3, 7.7),(5.5, 7.7),(7.7, 7.7),(9.9, 7.7),(12.1, 7.7),(14.3, 7.7),(16.5, 7.7),(18.7, 7.7),(20.9, 7.7),(-29.7, 5.5),(-27.5, 5.5),(-25.3, 5.5),(-23.1, 5.5),(-20.9, 5.5),(-18.7, 5.5),(-9.9, 5.5),(-7.7, 5.5),(-5.5, 5.5),(-3.3, 5.5),(-1.1, 5.5),(1.1, 5.5),(3.3, 5.5),(5.5, 5.5),(7.7, 5.5),(9.9, 5.5),(18.7, 5.5),(20.9, 5.5),(23.1, 5.5),(25.3, 5.5),(27.5, 5.5),(29.7, 5.5),(-29.7, 3.3),(-27.5, 3.3),(-25.3, 3.3),(-23.1, 3.3),(-20.9, 3.3),(-18.7, 3.3),(-9.9, 3.3),(-7.7, 3.3),(-5.5, 3.3),(-3.3, 3.3),(-1.1, 3.3),(1.1, 3.3),(3.3, 3.3),(5.5, 3.3),(7.7, 3.3),(9.9, 3.3),(18.7, 3.3),(20.9, 3.3),(23.1, 3.3),(25.3, 3.3),(27.5, 3.3),(29.7, 3.3),(-29.7, 1.1),(-27.5, 1.1),(-25.3, 1.1),(-23.1, 1.1),(-20.9, 1.1),(-18.7, 1.1),(-9.9, 1.1),(-7.7, 1.1),(-5.5, 1.1),(-3.3, 1.1),(-1.1, 1.1),(1.1, 1.1),(3.3, 1.1),(5.5, 1.1),(7.7, 1.1),(9.9, 1.1),(18.7, 1.1),(20.9, 1.1),(23.1, 1.1),(25.3, 1.1),(27.5, 1.1),(29.7, 1.1),(-36.3, -1.1),(-34.1, -1.1),(-31.9, -1.1),(-29.7, -1.1),(-27.5, -1.1),(-25.3, -1.1),(-23.1, -1.1),(-20.9, -1.1),(-18.7, -1.1),(-16.5, -1.1),(-14.3, -1.1),(-12.1, -1.1),(-9.9, -1.1),(-7.7, -1.1),(-5.5, -1.1),(-3.3, -1.1),(-1.1, -1.1),(1.1, -1.1),(3.3, -1.1),(5.5, -1.1),(7.7, -1.1),(9.9, -1.1),(12.1, -1.1),(14.3, -1.1),(16.5, -1.1),(18.7, -1.1),(20.9, -1.1),(23.1, -1.1),(25.3, -1.1),(27.5, -1.1),(29.7, -1.1),(31.9, -1.1),(34.1, -1.1),(36.3, -1.1),(-36.3, -3.3),(-34.1, -3.3),(-31.9, -3.3),(-29.7, -3.3),(-27.5, -3.3),(-25.3, -3.3),(-23.1, -3.3),(-20.9, -3.3),(-18.7, -3.3),(-16.5, -3.3),(-14.3, -3.3),(-12.1, -3.3),(-9.9, -3.3),(-7.7, -3.3),(-5.5, -3.3),(-3.3, -3.3),(-1.1, -3.3),(1.1, -3.3),(3.3, -3.3),(5.5, -3.3),(7.7, -3.3),(9.9, -3.3),(12.1, -3.3),(14.3, -3.3),(16.5, -3.3),(18.7, -3.3),(20.9, -3.3),(23.1, -3.3),(25.3, -3.3),(27.5, -3.3),(29.7, -3.3),(31.9, -3.3),(34.1, -3.3),(36.3, -3.3),(-36.3, -5.5),(-34.1, -5.5),(-31.9, -5.5),(-29.7, -5.5),(-27.5, -5.5),(-25.3, -5.5),(-23.1, -5.5),(-20.9, -5.5),(-18.7, -5.5),(-16.5, -5.5),(-14.3, -5.5),(-12.1, -5.5),(-9.9, -5.5),(-7.7, -5.5),(-5.5, -5.5),(-3.3, -5.5),(-1.1, -5.5),(1.1, -5.5),(3.3, -5.5),(5.5, -5.5),(7.7, -5.5),(9.9, -5.5),(12.1, -5.5),(14.3, -5.5),(16.5, -5.5),(18.7, -5.5),(20.9, -5.5),(23.1, -5.5),(25.3, -5.5),(27.5, -5.5),(29.7, -5.5),(31.9, -5.5),(34.1, -5.5),(36.3, -5.5),(-36.3, -7.7),(-34.1, -7.7),(-31.9, -7.7),(-23.1, -7.7),(-20.9, -7.7),(-18.7, -7.7),(-16.5, -7.7),(-14.3, -7.7),(-12.1, -7.7),(-9.9, -7.7),(-7.7, -7.7),(-5.5, -7.7),(-3.3, -7.7),(-1.1, -7.7),(1.1, -7.7),(3.3, -7.7),(5.5, -7.7),(7.7, -7.7),(9.9, -7.7),(12.1, -7.7),(14.3, -7.7),(16.5, -7.7),(18.7, -7.7),(20.9, -7.7),(23.1, -7.7),(31.9, -7.7),(34.1, -7.7),(36.3, -7.7),(-36.3, -9.9),(-34.1, -9.9),(-31.9, -9.9),(-23.1, -9.9),(-20.9, -9.9),(-18.7, -9.9),(-16.5, -9.9),(-14.3, -9.9),(-12.1, -9.9),(-9.9, -9.9),(-7.7, -9.9),(-5.5, -9.9),(-3.3, -9.9),(-1.1, -9.9),(1.1, -9.9),(3.3, -9.9),(5.5, -9.9),(7.7, -9.9),(9.9, -9.9),(12.1, -9.9),(14.3, -9.9),(16.5, -9.9),(18.7, -9.9),(20.9, -9.9),(23.1, -9.9),(31.9, -9.9),(34.1, -9.9),(36.3, -9.9),(-36.3, -12.1),(-34.1, -12.1),(-31.9, -12.1),(-23.1, -12.1),(-20.9, -12.1),(-18.7, -12.1),(18.7, -12.1),(20.9, -12.1),(23.1, -12.1),(31.9, -12.1),(34.1, -12.1),(36.3, -12.1),(-36.3, -14.3),(-34.1, -14.3),(-31.9, -14.3),(-23.1, -14.3),(-20.9, -14.3),(-18.7, -14.3),(18.7, -14.3),(20.9, -14.3),(23.1, -14.3),(31.9, -14.3),(34.1, -14.3),(36.3, -14.3),(-36.3, -16.5),(-34.1, -16.5),(-31.9, -16.5),(-23.1, -16.5),(-20.9, -16.5),(-18.7, -16.5),(18.7, -16.5),(20.9, -16.5),(23.1, -16.5),(31.9, -16.5),(34.1, -16.5),(36.3, -16.5),(-16.5, -18.7),(-14.3, -18.7),(-12.1, -18.7),(-9.9, -18.7),(-7.7, -18.7),(-5.5, -18.7),(5.5, -18.7),(7.7, -18.7),(9.9, -18.7),(12.1, -18.7),(14.3, -18.7),(16.5, -18.7),(-16.5, -20.9),(-14.3, -20.9),(-12.1, -20.9),(-9.9, -20.9),(-7.7, -20.9),(-5.5, -20.9),(5.5, -20.9),(7.7, -20.9),(9.9, -20.9),(12.1, -20.9),(14.3, -20.9),(16.5, -20.9)]

    # --- Patterning ---
    VOLUME = 1  # µL per dot

    # Red layer (mrfp1)
    pipette_20ul.pick_up_tip()
    for (x, y) in mrfp1_points:
        pipette_20ul.aspirate(VOLUME, location_of_color('Red'))
        target = center_location.move(types.Point(x=x, y=y, z=0))
        dispense_and_detach(pipette_20ul, VOLUME, target)
    pipette_20ul.drop_tip()

    # Green layer (sfgfp)
    pipette_20ul.pick_up_tip()
    for (x, y) in sfgfp_points:
        pipette_20ul.aspirate(VOLUME, location_of_color('Green'))
        target = center_location.move(types.Point(x=x, y=y, z=0))
        dispense_and_detach(pipette_20ul, VOLUME, target)
    pipette_20ul.drop_tip()
  ###

–

I am using Claude as a console for errors.
Submitted my Python file via Google form both HTGAA and Node.

Post-Lab Questions

One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention, and design and deploy experiments remotely.

Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. I would like to mention from this research:

This paper is particularly relevant because it addresses a critical but often overlooked problem in laboratory automation: the gap between intended and actual liquid deposition. As demonstrated in the images captured by Chen (2026), this discrepancy becomes strikingly clear when comparing the physical petri dish under normal lighting conditions with its UV-illuminated counterpart. Under standard light, the dish appears largely as expected, with the deposited pattern barely distinguishable to the naked eye (Chen, 20256, Figure 2). However, when the same plate is examined under UV light, small, unwanted droplets become clearly visible in places where they were not present in the original design (Chen, 2026, Figures 3-4). The computer vision algorithm developed in this study successfully detects and maps these deviations, marking the spots with color codes according to their size to highlight the extent of the error.

Figure 1-4: Images captured from the Opentrons OT-2 liquid handling experiments by Yanchen Chen. Credit: Yanchen Chen (24.02.2026).

These satellite droplets arise from well-known physical phenomena in liquid handling, such as surface tension-driven splashing or residual liquid remaining on pipette tips between transfers. What makes this finding biologically significant is that in high-precision applications such as drug screening, dose-response assays, or microbial growth experiments, even a small unintended deposit can introduce a compound or organism into a zone where it was never meant to be. This cross-contamination would silently corrupt experimental results, and without a real-time quality control system, the researcher would have no way of knowing the data was compromised.

The novel contribution of this work is therefore not purely engineering: by enabling the Opentrons OT-2 to detect and flag these errors autonomously using computer vision, the system directly protects the integrity of biological experiments. This transforms the robot from a simple liquid-dispensing tool into a self-monitoring platform capable of ensuring experimental validity; a meaningful advancement for any biological application that depends on precise, contamination-free liquid handling.

References:

Khan, S.U., Møller, V.K., Frandsen, R.J.N. et al. Real-time AI-driven quality control for laboratory automation: a novel computer vision solution for the opentrons OT-2 liquid handling robot. Appl Intell 55, 524 (2025). https://doi.org/10.1007/s10489-025-06334-3
Shen, Y. (2026). Week 3 Lab: Lab Automation :: 2026a-yanchen-shen. [online] Available at: https://pages.htgaa.org/2026a/yanchen-shen/labs/week-03-lab-opentrons-art/index.html [Accessed 26 Feb. 2026].

Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details. While your description/project idea doesn’t need to be set in stone, we would like to see core details of what you would automate. This is due at the start of lecture and does not need to be tested on the Opentrons yet.

Example 1: You are creating a custom fabric, and want to deposit art onto specific parts that need to be intertwined in odd ways. You can design a 3D printed holder to attach this fabric to it, and be able to deposit bio art on top. Check out the Opentrons 3D Printing Directory.
Example 2: You are using the cloud laboratory to screen an array of biosensor constructs that you design, synthesize, and express using cell-free protein synthesis.

Echo transfer biosensor constructs and any required cofactors into specified wells. Bravo stamp in CPFS reagent master mix into all wells of a 96-well / 384-well plate. Multiflo dispense the CFPS lysate to all wells to start protein expression. PlateLoc seal the plate. Inheco incubate the plate at 37°C while the biosensor proteins are synthesized. XPeel remove the seal. PHERAstar measure fluorescence to compare biosensor responses.

Final Project Ideas

As explained in this week’s recitation, add 1-3 slides in your Node’s section of this slide deck with 3 ideas you have for an Individual Final Project. Be sure to put your name, city, and country on your slide!

Embedded slide deck of 1-3 slides with 3 ideas you have for an Individual Final Project. by naming (Beyza Batır, Izmir, Turkey)

I will upload my slides on CL powerpoint in DC Labs Student#7 section.

Brief

Reading & Resources Opentrons API Documentation: https://docs.opentrons.com/python-api/ Opentrons Artwork GUI Website: http://opentrons-art.rcdonovan.com/ Opentrons Artwork Colab: HTGAA26 Opentrons Colab Automation Equipment: HTGAA 2026 Recitation: Lab Automation, Opentrons Art, Intro to Cloud Laboratories

Extras

These extra designs were created within the “Automation Art Interface” to explore possibilities with different weights, colors, and area usage. I also created Designer Cells artworks for our node and this time corrected my mistakes (size, spacing, safe canvas margin) that did not comply with the requirements announced on HTGAA Google Colab. If needed, I can prepare Google Colab for all designs.