Week 3 HW: Lab Automation

Week 3 – Lab Automation

✨ Week 3 - Homework ✨

You can view my Automation Art design here: Opentrons Art Link

After creating this shell pattern using Opentrons Art, I duplicated the provided Colab notebook to develop a Python protocol. To program the Opentrons robot to physically recreate the artwork on a plate, I systematically entered the coordinate data from my design step-by-step into the script. Once the protocol was complete, it successfully generated the images shown below.

Digital Shell Design

✨ Post-Lab Questions ✨

1) Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

Article Title: An Automation Workflow for High-Throughput Manufacturing and Analysis of Scaffold-Supported 3D Tissue Arrays

Authors: Ruonan Cao, Nancy T. Li, Simon Latour, Jose L. Cadavid, Cassidy M. Tan, Ari Forman, Hartland W. Jackson, Alison P. McGuigan

Year: 2023

DOI: 10.1002/adhm.202202422

Article 1

This paper tackles a real bottleneck in advanced 3D culture: patient-derived organoids and complex co-cultures are powerful, but hard to scale and hard to analyze at single-cell resolution when manufacturing and handling are manual. The authors focus on the SPOT platform (Scaffold-supported Platform for Organoid-based Tissues), which generates flat, thin, dimensionally controlled microtissues in 96- and 384-well plate formats compatible with longitudinal imaging—yet historically limited by manual fabrication.

What’s automated with Opentrons OT-2 (and what makes it novel):

Automated 3D microtissue manufacturing (seeding): They use the Opentrons OT-2 to dispense a cell–gel mixture into 96/384-SPOT plates and optimize the process so automated manufacturing is comparable to manual consistency.
Temperature control + custom hardware for reliability: Two temperature modules set to 4 °C keep the SPOT plate and cell-gel cold during seeding, and a custom aluminum plate improves support and heat conduction for the thin plate—showing how automation often needs small mechanical/thermal design choices to work well.
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Automation beyond seeding (screening + single-cell endpoints): The OT-2 also supports drug/reagent addition and culture maintenance, and it automates gel digestion to recover single cells for high-throughput flow cytometry.
Multiplexed CyTOF enablement: A particularly strong “novel application” angle is that OT-2 is used to generate a barcode master plate and automate parts of the barcoding/washing/pooling workflow to reduce manual errors—enabling scalable CyTOF proteomic readouts.
Proof-of-value biology: They generate 3D complex tissues with different tumor/stromal ratios and show the workflow can incorporate primary patient-derived organoids, supporting scalable, patient-relevant screening and analysis.

2) Write a description about what you intend to do with automation tools for your final project.

Across all three ideas, the Opentrons OT-2 is my core “execution engine” for repeatable, programmable liquid handling—reducing variability, scaling to multi-sample workflows, and producing clean run logs/plate maps. Where formats aren’t standard labware, I’d use custom 3D-printed holders.

Idea 1 — Automated Seeding of Patient-Specific Bone Scaffolds

Goal: Improve cell distribution and viability deep inside porous bone scaffolds by replacing static pipetting with automated, repeatable dynamic “drip-seeding.”

What I would automate on the OT-2

A custom 3D-printed scaffold holder mounting multiple scaffolds on the OT-2 deck.
A timed protocol dispensing cell suspension (e.g., MSCs) + osteogenic media cues across scaffolds in multi-pass patterns.
Optional scheduled media refresh + standardized sampling for assays.

Example pseudocode (conceptual)

# Conceptual workflow: dynamic drip-seeding across multiple scaffolds
scaffolds = load_custom_holder(num_scaffolds=8)
cell_source = reservoir("MSC_suspension")
media_source = reservoir("osteogenic_media")

for round in range(N_seed_rounds):
    for scaf in scaffolds:
        drip_dispense(cell_source, scaf, volume=V_cell, pattern="multi-point")
    wait(minutes=settle_time)

for day in culture_days:
    for scaf in scaffolds:
        exchange_media(scaf, media_source, volume=V_media)
    log_run(day)

Idea 2 — Anti-Biofilm “Guardian Bacteria” (high-throughput screening)

Goal: Run a high-throughput anti-biofilm screen on titanium-relevant surfaces using a plate-based assay format.

What I would automate on the OT-2

A 96-well screening layout (controls + variants + replicates).
Automated mixing, dispensing, wash steps, and readout reagent handling.
Standardized timing + plate map + run log for comparability.

Example pseudocode (conceptual)

# Conceptual workflow: plate-based biofilm screen automation
plate = load_labware("96_well_plate")
variants = load_conditions("variant_plate_map.csv")

for well, condition in variants.items():
    dispense_inoculum(plate[well], condition)

incubate(plate, hours=incubation_time)

for wash in range(n_washes):
    wash_plate(plate)

apply_readout_reagent(plate)   # e.g., stain
final_wash_and_dispense(plate)
export_plate_map_and_log()

Idea 3 — Bioprinted Tooth-on-a-Chip Biosensor (automated long-term culture + exposure)

Goal: Improve dental material testing realism using a chip that includes a dentin barrier + engineered reporter pulp cells for real-time toxicity/biocompatibility readouts.

What I would automate on the OT-2

Daily/recurring media exchange across multiple chips.
Controlled dosing/exposure scheduling for different materials.
Optional sampling workflow into plates for downstream measurements.

Example pseudocode (conceptual)

# Conceptual workflow: chip maintenance + condition dosing
chips = load_custom_chip_holder(n=6)
media = reservoir("pulp_media")
test_conditions = load_conditions("cement_conditions.csv")

for day in range(total_days):
    for chip in chips:
        media_exchange(chip, media)

    if day in dosing_days:
        for chip in chips:
            condition = test_conditions[chip.id]
            dispense_condition(chip, condition)

    log_run(day)

✨ Final Project Ideas ✨

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