Syringe

Description

A Syringe tool class representing a motorized liquid handler mounted on the Jubilee system.

Handles aspiration, dispensing, and transfer of milliliter-scale liquid volumes, with built-in configuration checking to ensure movements stay within safe physical limits.

Constructor

Syringe(index: int, name: str, config: str)

Parameter	Type	Description
index	int	Tool index on the machine.
name	str	Human-readable name of the syringe.
config	str	Name of the configuration file (JSON format) that defines the syringe parameters.

Key Attributes

Attribute	Type	Description
min_range	float	Minimum allowed extrusion position.
max_range	float	Maximum allowed extrusion position.
mm_to_ml	float	Conversion factor from motor mm to milliliters.
e_drive	str	Extruder axis letter associated with the syringe. Default "E".

Important Methods

Method	Returns	Description
load_config(config: str)	None	Loads syringe configuration from a JSON file.
post_load()	None	Automatically queries the extruder drive assignment after tool is loaded.
aspirate(vol: float, location: Well/Location/Tuple, s: int = 2000)	None	Move to a well and aspirate a specified volume.
dispense(vol: float, location: Well/Location/Tuple, s: int = 2000)	None	Move to a well and dispense a specified volume.
transfer(vol: float, source: Well, destination: Well, s: int = 2000, mix_before: tuple = None, mix_after: tuple = None)	None	Perform aspiration from a source well and dispense into a destination well.
check_bounds(pos: float)	None	Check if the intended position is within min/max limits.
_aspirate(vol: float, s: int = 2000)	None	Internal method to aspirate without movement.
_dispense(vol: float, s: int = 2000)	None	Internal method to dispense without movement.

Method Details

Load Configuration

load_config(config)

• Reads .json configuration file from /tools/configs.
• Loads key parameters: min_range, max_range, and mm_to_ml.

Post Load

post_load()

• Queries machine firmware for the extruder axis (e.g., E0, E1) corresponding to the tool.

Aspirate

aspirate(vol, location, s=2000)

• Moves to a specific labware location and aspirates the requested volume.
• Raises error if volume would exceed syringe bounds.

Dispense

dispense(vol, location, s=2000)

• Moves to a specific labware location and dispenses the requested volume.
• Checks bounds similarly to aspirate.

Transfer

transfer(vol, s=2000, source, destination, mix_before=None, mix_after=None)

• Supports 1-to-1, 1-to-many, many-to-1, or many-to-many source/destination liquid transfers.
• Handles uneven source/destination list lengths by auto-repeating wells (with warnings).

Usage Example

syringe = Syringe(index=2, name="BigSyringe", config="big_syringe")
syringe.post_load()

# Aspirate 5 mL from Well A1
syringe.aspirate(vol=5.0, location=well_A1)

# Dispense 5 mL into Well B1
syringe.dispense(vol=5.0, location=well_B1)

# Transfer 5 mL from A1 to B1
syringe.transfer(vol=5.0, source=well_A1, destination=well_B1)

Configuration Options

Liquid Handling

• Volume range: 0.1 - 10 mL
• Mixing capabilities
• Multiple well transfer support
• Aspirate/dispense control

Gel Printing

• Pressure control
• Flow rate control
• Temperature control (if equipped)
• Nozzle size options

Usage Notes

• Always calibrate Z-offset before use
• Use appropriate syringe tips for application
• Clean and maintain regularly
• Monitor pressure and flow rates during gel printing
• Follow safety guidelines for liquid handling