gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/pylabrobot/references/analytical-equipment.md

Analytical Equipment in PyLabRobot

Overview

PyLabRobot integrates with analytical equipment including plate readers, scales, and other measurement devices. This allows automated workflows that combine liquid handling with analytical measurements.

Plate Readers

BMG CLARIOstar (Plus)

The BMG Labtech CLARIOstar and CLARIOstar Plus are microplate readers that measure absorbance, luminescence, and fluorescence.

Hardware Setup

Physical Connections:

1. IEC C13 power cord to mains power
2. USB-B cable to computer (with security screws on device end)
3. Optional: RS-232 port for plate stacking units

Communication:

• Serial connection through FTDI/USB-A at firmware level
• Cross-platform support (Windows, macOS, Linux)

Software Setup

from pylabrobot.plate_reading import PlateReader
from pylabrobot.plate_reading.clario_star_backend import CLARIOstarBackend

# Create backend
backend = CLARIOstarBackend()

# Initialize plate reader
pr = PlateReader(
    name="CLARIOstar",
    backend=backend,
    size_x=0.0,    # Physical dimensions not critical for plate readers
    size_y=0.0,
    size_z=0.0
)

# Setup (initializes device)
await pr.setup()

# When done
await pr.stop()

Basic Operations

Opening and Closing:

# Open loading tray
await pr.open()

# (Load plate manually or robotically)

# Close loading tray
await pr.close()

Temperature Control:

# Set temperature (in Celsius)
await pr.set_temperature(37)

# Note: Reaching temperature is slow
# Set temperature early in protocol

Reading Measurements:

# Absorbance reading
data = await pr.read_absorbance(wavelength=450)  # nm

# Luminescence reading
data = await pr.read_luminescence()

# Fluorescence reading
data = await pr.read_fluorescence(
    excitation_wavelength=485,  # nm
    emission_wavelength=535     # nm
)

Data Format

Plate reader methods return array data:

import numpy as np

# Read absorbance
data = await pr.read_absorbance(wavelength=450)

# data is typically a 2D array (8x12 for 96-well plate)
print(f"Data shape: {data.shape}")
print(f"Well A1: {data[0][0]}")
print(f"Well H12: {data[7][11]}")

# Convert to DataFrame for easier handling
import pandas as pd
df = pd.DataFrame(data)

Integration with Liquid Handler

Combine plate reading with liquid handling:

from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.liquid_handling.backends import STAR
from pylabrobot.resources import STARLetDeck
from pylabrobot.plate_reading import PlateReader
from pylabrobot.plate_reading.clario_star_backend import CLARIOstarBackend

# Initialize liquid handler
lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
await lh.setup()

# Initialize plate reader
pr = PlateReader(name="CLARIOstar", backend=CLARIOstarBackend())
await pr.setup()

# Set temperature early
await pr.set_temperature(37)

try:
    # Prepare samples with liquid handler
    tip_rack = TIP_CAR_480_A00(name="tips")
    reagent_plate = Cos_96_DW_1mL(name="reagents")
    assay_plate = Cos_96_DW_1mL(name="assay")

    lh.deck.assign_child_resource(tip_rack, rails=1)
    lh.deck.assign_child_resource(reagent_plate, rails=10)
    lh.deck.assign_child_resource(assay_plate, rails=15)

    # Transfer samples
    await lh.pick_up_tips(tip_rack["A1:H1"])
    await lh.transfer(
        reagent_plate["A1:H12"],
        assay_plate["A1:H12"],
        vols=100
    )
    await lh.drop_tips()

    # Move plate to reader (manual or robotic arm)
    print("Move assay plate to plate reader")
    input("Press Enter when plate is loaded...")

    # Read plate
    await pr.open()
    # (plate loaded here)
    await pr.close()

    data = await pr.read_absorbance(wavelength=450)
    print(f"Absorbance data: {data}")

finally:
    await lh.stop()
    await pr.stop()

Advanced Features

Development Status:

Some CLARIOstar features are under development:

• Spectral scanning
• Injector needle control
• Detailed measurement parameter configuration
• Well-specific reading patterns

Check current documentation for latest feature support.

Best Practices

1. Temperature Control: Set temperature early as heating is slow
2. Plate Loading: Ensure plate is properly seated before closing
3. Measurement Selection: Choose appropriate wavelengths for your assay
4. Data Validation: Check measurement quality and expected ranges
5. Error Handling: Handle timeout and communication errors
6. Maintenance: Keep optics clean per manufacturer guidelines

Example: Complete Plate Reading Workflow

async def run_plate_reading_assay():
    """Complete workflow with sample prep and reading"""

    # Initialize equipment
    lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
    pr = PlateReader(name="CLARIOstar", backend=CLARIOstarBackend())

    await lh.setup()
    await pr.setup()

    # Set plate reader temperature
    await pr.set_temperature(37)

    try:
        # Define resources
        tip_rack = TIP_CAR_480_A00(name="tips")
        samples = Cos_96_DW_1mL(name="samples")
        assay_plate = Cos_96_DW_1mL(name="assay")
        substrate = Trough_100ml(name="substrate")

        lh.deck.assign_child_resource(tip_rack, rails=1)
        lh.deck.assign_child_resource(substrate, rails=5)
        lh.deck.assign_child_resource(samples, rails=10)
        lh.deck.assign_child_resource(assay_plate, rails=15)

        # Transfer samples
        await lh.pick_up_tips(tip_rack["A1:H1"])
        await lh.transfer(
            samples["A1:H12"],
            assay_plate["A1:H12"],
            vols=50
        )
        await lh.drop_tips()

        # Add substrate
        await lh.pick_up_tips(tip_rack["A2:H2"])
        for col in range(1, 13):
            await lh.transfer(
                substrate["channel_1"],
                assay_plate[f"A{col}:H{col}"],
                vols=50
            )
        await lh.drop_tips()

        # Incubate (if needed)
        # await asyncio.sleep(300)  # 5 minutes

        # Move to plate reader
        print("Transfer assay plate to CLARIOstar")
        input("Press Enter when ready...")

        await pr.open()
        input("Press Enter when plate is loaded...")
        await pr.close()

        # Read absorbance
        data = await pr.read_absorbance(wavelength=450)

        # Process results
        import pandas as pd
        df = pd.DataFrame(
            data,
            index=[f"{r}" for r in "ABCDEFGH"],
            columns=[f"{c}" for c in range(1, 13)]
        )

        print("Absorbance Results:")
        print(df)

        # Save results
        df.to_csv("plate_reading_results.csv")

        return df

    finally:
        await lh.stop()
        await pr.stop()

# Run assay
results = await run_plate_reading_assay()

Scales

Mettler Toledo Scales

PyLabRobot supports Mettler Toledo scales for mass measurements.

Setup

from pylabrobot.scales import Scale
from pylabrobot.scales.mettler_toledo_backend import MettlerToledoBackend

# Create scale
scale = Scale(
    name="analytical_scale",
    backend=MettlerToledoBackend()
)

await scale.setup()

Operations

# Get weight measurement
weight = await scale.get_weight()  # Returns weight in grams
print(f"Weight: {weight} g")

# Tare (zero) the scale
await scale.tare()

# Get multiple measurements
weights = []
for i in range(5):
    w = await scale.get_weight()
    weights.append(w)
    await asyncio.sleep(1)

average_weight = sum(weights) / len(weights)
print(f"Average weight: {average_weight} g")

Integration with Liquid Handler

# Weigh samples during protocol
lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
scale = Scale(name="scale", backend=MettlerToledoBackend())

await lh.setup()
await scale.setup()

try:
    # Tare scale
    await scale.tare()

    # Dispense liquid
    await lh.pick_up_tips(tip_rack["A1"])
    await lh.aspirate(reagent["A1"], vols=1000)

    # (Move to scale position)

    # Dispense and weigh
    await lh.dispense(container, vols=1000)
    weight = await scale.get_weight()

    print(f"Dispensed weight: {weight} g")

    # Calculate actual volume (assuming density = 1 g/mL for water)
    actual_volume = weight * 1000  # Convert g to µL
    print(f"Actual volume: {actual_volume} µL")

    await lh.drop_tips()

finally:
    await lh.stop()
    await scale.stop()

Other Analytical Devices

Flow Cytometers

Some flow cytometer integrations are in development. Check current documentation for support status.

Spectrophotometers

Additional spectrophotometer models may be supported. Check documentation for current device compatibility.

Multi-Device Workflows

Coordinating Multiple Devices

async def multi_device_workflow():
    """Coordinate liquid handler, plate reader, and scale"""

    # Initialize all devices
    lh = LiquidHandler(backend=STAR(), deck=STARLetDeck())
    pr = PlateReader(name="CLARIOstar", backend=CLARIOstarBackend())
    scale = Scale(name="scale", backend=MettlerToledoBackend())

    await lh.setup()
    await pr.setup()
    await scale.setup()

    try:
        # 1. Weigh reagent
        await scale.tare()
        # (place container on scale)
        reagent_weight = await scale.get_weight()

        # 2. Prepare samples with liquid handler
        await lh.pick_up_tips(tip_rack["A1:H1"])
        await lh.transfer(source["A1:H12"], dest["A1:H12"], vols=100)
        await lh.drop_tips()

        # 3. Read plate
        await pr.open()
        # (load plate)
        await pr.close()
        data = await pr.read_absorbance(wavelength=450)

        return {
            "reagent_weight": reagent_weight,
            "absorbance_data": data
        }

    finally:
        await lh.stop()
        await pr.stop()
        await scale.stop()

Best Practices

1. Device Initialization: Setup all devices at start of protocol
2. Error Handling: Handle communication errors gracefully
3. Cleanup: Always call stop() on all devices
4. Timing: Account for device-specific timing (temperature equilibration, measurement time)
5. Calibration: Follow manufacturer calibration procedures
6. Data Validation: Verify measurements are within expected ranges
7. Documentation: Record device settings and parameters
8. Integration Testing: Test multi-device workflows thoroughly
9. Concurrent Operations: Use async to overlap operations when possible
10. Data Storage: Save raw data with metadata (timestamps, settings)

Common Patterns

Kinetic Plate Reading

async def kinetic_reading(num_reads: int, interval: int):
    """Perform kinetic plate reading"""

    pr = PlateReader(name="CLARIOstar", backend=CLARIOstarBackend())
    await pr.setup()

    try:
        await pr.set_temperature(37)
        await pr.open()
        # (load plate)
        await pr.close()

        results = []
        for i in range(num_reads):
            data = await pr.read_absorbance(wavelength=450)
            timestamp = time.time()
            results.append({
                "read_number": i + 1,
                "timestamp": timestamp,
                "data": data
            })

            if i < num_reads - 1:
                await asyncio.sleep(interval)

        return results

    finally:
        await pr.stop()

# Read every 30 seconds for 10 minutes
results = await kinetic_reading(num_reads=20, interval=30)

Additional Resources

• Plate Reading Documentation: https://docs.pylabrobot.org/user_guide/02_analytical/
• BMG CLARIOstar Guide: https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/bmg-clariostar.html
• API Reference: https://docs.pylabrobot.org/api/pylabrobot.plate_reading.html
• Supported Equipment: https://docs.pylabrobot.org/user_guide/machines.html