opentrons-integration

# Opentrons Integration — Lab Automation

## Overview

Opentrons provides a Python-based Protocol API (v2) for programming OT-2 and Flex liquid handling robots. Protocols are structured Python files with metadata and a `run()` function that controls pipettes, labware, and hardware modules. All protocols can be simulated locally before running on physical hardware.

## When to Use

- Automating liquid handling workflows (pipetting, mixing, distributing)
- Writing PCR setup protocols with thermocycler control
- Performing serial dilutions across plates
- Replicating plates or reformatting between plate types
- Controlling hardware modules (temperature, magnetic, heater-shaker, thermocycler)
- Setting up multi-channel pipetting for 96-well plate operations
- Simulating protocols before running on the robot
- For **multi-vendor automation** (Hamilton, Beckman, etc.), use pylabrobot instead
- For **flow cytometry analysis** of automated experiment results, use flowio/flowkit

## Prerequisites

```bash
pip install opentrons
# Simulate protocols locally (no robot needed)
opentrons_simulate my_protocol.py
```

**Protocol API Version**: Always use the latest stable API level (currently `2.19`). Set `apiLevel` in protocol metadata. Protocols are forward-compatible within major versions.

**Robot Types**: Flex (newer, larger deck, 96-channel pipette) vs OT-2 (smaller, 8-channel max). Key differences: deck slot naming (Flex: A1-D3, OT-2: 1-11), available pipettes, and module support.

## Quick Start

```python
from opentrons import protocol_api

metadata = {"protocolName": "Quick Transfer", "apiLevel": "2.19"}

def run(protocol: protocol_api.ProtocolContext):
    tips = protocol.load_labware("opentrons_96_tiprack_300ul", "1")
    source = protocol.load_labware("nest_12_reservoir_15ml", "2")
    plate = protocol.load_labware("corning_96_wellplate_360ul_flat", "3")
    pipette = protocol.load_instrument("p300_single_gen2", "left", tip_racks=[tips])

    pipette.distribute(50, source["A1"], plate.wells()[:12], new_tip="once")
```

## Core API

### 1. Protocol Structure

Every Opentrons protocol follows a required structure: metadata dict + `run()` function.

```python
from opentrons import protocol_api

metadata = {
    "protocolName": "My Protocol",
    "author": "Name <email>",
    "description": "Protocol description",
    "apiLevel": "2.19",
}

# Optional: specify robot type
requirements = {"robotType": "Flex", "apiLevel": "2.19"}

def run(protocol: protocol_api.ProtocolContext):
    # All protocol logic goes here
    protocol.comment("Protocol started")
```

### 2. Labware and Deck Layout

Load labware (plates, reservoirs, tip racks) onto deck slots and optionally onto adapters.

```python
def run(protocol: protocol_api.ProtocolContext):
    # Tip racks
    tips_300 = protocol.load_labware("opentrons_96_tiprack_300ul", "1")
    tips_20 = protocol.load_labware("opentrons_96_tiprack_20ul", "4")

    # Plates and reservoirs
    plate = protocol.load_labware("corning_96_wellplate_360ul_flat", "2", label="Sample Plate")
    reservoir = protocol.load_labware("nest_12_reservoir_15ml", "3")

    # Labware on adapter (Flex)
    adapter = protocol.load_adapter("opentrons_flex_96_tiprack_adapter", "B1")
    tips_on_adapter = adapter.load_labware("opentrons_flex_96_tiprack_200ul")

    # Pipettes
    p300 = protocol.load_instrument("p300_single_gen2", "left", tip_racks=[tips_300])
    p20 = protocol.load_instrument("p20_single_gen2", "right", tip_racks=[tips_20])
```

**Common pipette names**:
- OT-2: `p20_single_gen2`, `p300_single_gen2`, `p1000_single_gen2`, `p20_multi_gen2`, `p300_multi_gen2`
- Flex: `p50_single_flex`, `p1000_single_flex`, `p50_multi_flex`, `p1000_multi_flex`

### 3. Pipette Operations

Basic, compound, and advanced liquid handling operations.

```python
def run(protocol: protocol_api.ProtocolContext):
    # ... (labware loaded above)

    # === Basic operations ===
    p300.pick_up_tip()
    p300.aspirate(100, source["A1"])        # Draw 100 µL
    p300.dispense(100, dest["B1"])          # Expel 100 µL
    p300.drop_tip()

    # === Compound operations (auto tip management) ===
    # Transfer: single source → single dest
    p300.transfer(100, source["A1"], dest["B1"], new_tip="always")

    # Distribute: one source → many dests
    p300.distribute(50, reservoir["A1"],
                    [plate["A1"], plate["A2"], plate["A3"]], new_tip="once")

    # Consolidate: many sources → one dest
    p300.consolidate(50, [plate["A1"], plate["A2"]], reservoir["A1"])

    # === Advanced techniques ===
    p300.pick_up_tip()
    p300.mix(repetitions=3, volume=50, location=plate["A1"])  # Mix in place
    p300.aspirate(100, source["A1"])
    p300.air_gap(20)                        # Prevent dripping
    p300.dispense(120, dest["A1"])
    p300.blow_out(dest["A1"].top())          # Expel residual
    p300.touch_tip(plate["A1"])              # Remove exterior drops
    p300.drop_tip()
```

### 4. Well Access and Locations

Navigate wells by name, index, row, or column. Control vertical position within wells.

```python
def run(protocol: protocol_api.ProtocolContext):
    plate = protocol.load_labware("corning_96_wellplate_360ul_flat", "1")

    # Access by name or index
    well = plate["A1"]
    first = plate.wells()[0]           # Same as plate["A1"]

    # Iterate rows/columns
    row_a = plate.rows()[0]            # [A1, A2, ..., A12]
    col_1 = plate.columns()[0]         # [A1, B1, ..., H1]

    # Vertical positions
    pipette.aspirate(100, well.top())          # 1mm below top
    pipette.aspirate(100, well.bottom(z=2))    # 2mm above bottom
    pipette.aspirate(100, well.center())       # Center of well
    pipette.dispense(100, well.top(z=5))       # 5mm above top
```

### 5. Hardware Modules

Control temperature, magnetic, heater-shaker, and thermocycler modules.

```python
def run(protocol: protocol_api.ProtocolContext):
    # Temperature module
    temp_mod = protocol.load_module("temperatur