Sonicator

Description

Represents a Qsonica Sonicator tool integrated with the Jubilee system. Controls ultrasonic sonication operations through either a Raspberry Pi Pico (via serial) or a Raspberry Pi Hat (via GPIO + DAC).

Supports precision-controlled sonication at specified power levels, duty cycles, and pulse intervals, including well-based targeting and cleaning protocols.

Constructor

Sonicator(index, name, mode, port=None)

Parameter	Type	Description
index	int	Tool index for the sonicator.
name	str	Tool name.
mode	str	'Pico' or 'Hat' depending on control hardware.
port	str, optional	Required for 'Pico' mode: serial port path to connect to microcontroller.

Assertion: mode must be 'Pico' or 'Hat'. Assertion: port must be specified if using 'Pico'.

Key Properties

Property	Type	Description
interface_mode	str	Hardware mode for sonicator control ('Pico' or 'Hat').
serial_interface	Serial	Serial interface for Pico communication (if applicable).
plunge_depth	float	Last used plunge depth into well.
cleaning	dict	Cleaning protocol settings.

Important Methods

Method	Returns	Description
_raspberrypi_hat()	None	Initializes DAC and GPIO for Raspberry Pi Hat control.
_raspberrypi_pico(port)	None	Sets up serial connection to Pico microcontroller.
_set_sonication_power(power)	None	Set sonication power level (0.4–1.0).
_sonication_on()	None	Start sonication.
_sonication_off()	None	Stop sonication.
_sonicate(exposure_time, power, pulse_duty_cycle, pulse_interval, verbose)	None	Execute a complete sonication sequence.
sonicate_well(location, plunge_depth, sonication_time, ...)	None	Sonicate a specific well at controlled depth and timing.
set_cleaning_protocol(wells, power, time, plunge_depth=None)	None	Define a reusable cleaning sequence.
perform_cleanining_protocol(plunge_depth=None)	None	Run the defined cleaning sequence across multiple wells.

Method Details

Set Sonication Power

_set_sonication_power(power)

Set the sonication amplitude. Valid range: 0.4 (minimum effective) to 1.0 (maximum).

Perform Sonication

_sonicate(exposure_time, power, pulse_duty_cycle, pulse_interval, verbose)

Perform sonication with defined exposure time, pulse frequency, and power level. Handles both continuous and pulsed sonication modes.

Sonicate a Specific Well

sonicate_well(location, plunge_depth, sonication_time, ...)

Move to a target well and sonicate at a controlled depth for a specified time.

• Checks if plunge depth is valid.
• Supports autocleaning after sonication.

Set Cleaning Protocol

set_cleaning_protocol(wells, power, time, plunge_depth=None)

Define a sequence of cleaning sonications across multiple wells.

Perform Cleaning Protocol

perform_cleanining_protocol(plunge_depth=None)

Automatically sonicate across specified wells following the cleaning protocol.

• If plunge_depth is not specified at call time, uses the preset depth.

Usage Flow Example

# Initialize Sonicator with Pico connection
sonicator = Sonicator(index=1, name="qsonica_tool", mode="Pico", port="/dev/ttyUSB0")

# Sonicate a well at 10 mm depth for 5 seconds
sonicator.sonicate_well(my_target_well, plunge_depth=10, sonication_time=5.0)

# Set a cleaning protocol
sonicator.set_cleaning_protocol(
    wells=[well1, well2],
    power=[0.5, 0.6],
    time=[5, 7],
    plunge_depth=10
)

# Run the cleaning sequence
sonicator.perform_cleanining_protocol()

Important Notes

• Minimum effective power: 0.4. Below this, the sonicator will not engage.
• Always validate that the plunge depth is appropriate for the target labware.
• Communication latency may occur with serial-controlled sonicators (Pico mode); small wait times are built-in.
• Autocleaning protocols are strongly recommended after heavy sonication use to prevent contamination.

Related Concepts

• Tool
• Labware
• Well