science_jubilee.tools.Pipette

Module Contents

Classes

Pipette	A class representation of an Opentrons OT2 pipette.
TipTracker	A class to track the usage of pipette tips and their location in the tiprack

Functions

tip_check(func)

Decorator to check if the pipette has a tip attached before performing an action.

Attributes

logger

science_jubilee.tools.Pipette.logger

science_jubilee.tools.Pipette.tip_check(func)

Decorator to check if the pipette has a tip attached before performing an action.

class science_jubilee.tools.Pipette.Pipette(index, name, brand, model, max_volume, min_volume, zero_position, blowout_position, drop_tip_position, mm_to_ul)

Bases: science_jubilee.tools.Tool.Tool

A class representation of an Opentrons OT2 pipette.

classmethod from_config(index, name, config_file: str, path: str = os.path.join(os.path.dirname(__file__), 'configs'))

Initialize the pipette object from a config file

Parameters:

• index (int) – The tool index of the pipette on the machine

• name (str) – The tool name

• config_file (str) – The name of the config file containign the pipette parameters

• path – The path to the labware configuration .json files for the labware, defaults to the ‘labware_definition/’ in the science_jubilee/labware directory.

Returns:

A Pipette object

Return type:

Pipette

post_load()

Prime the Pipette after loading it onto the Machine sot hat it is ready to use

vol2move(vol)

Converts desired volume in uL to a movement of the pipette motor axis

Parameters:

vol (float) – The desired amount of liquid expressed in uL

Returns:

The corresponding motor movement in mm

Return type:

float

prime(s=2500)

Moves the plunger to the low-point on the pipette motor axis to prepare for further commands Note::This position should not engage the pipette tip plunger

Parameters:

s (int) – The speed of the plunger movement in mm/min

_aspirate(vol: float, s: int = 2000)

Moves the plunger upwards to aspirate liquid into the pipette tip

Parameters:

• vol (float) – The volume of liquid to aspirate in uL

• s (int) – The speed of the plunger movement in mm/min

aspirate(vol: float, location: science_jubilee.labware.Labware.Well | Tuple | science_jubilee.labware.Labware.Location, s: int = 2000)

Moves the pipette to the specified location and aspirates the desired volume of liquid

Parameters:

• vol (float) – The volume of liquid to aspirate in uL

• location (Union[Well, Tuple, Location]) – The location from where to aspirate the liquid from.

• s (int, optional) – The speed of the plunger movement in mm/min, defaults to 2000

Raises:

ToolStateError – If the pipette does not have a tip attached

_dispense(vol: float, s: int = 2000)

Moves the plunger downwards to dispense liquid out of the pipette tip

Parameters:

• vol (float) – The volume of liquid to dispense in uL

• s (int) – The speed of the plunger movement in mm/min

Note:: Ideally the user does not call this functions directly, but instead uses the :method:`dispense` method

dispense(vol: float, location: science_jubilee.labware.Labware.Well | Tuple | science_jubilee.labware.Labware.Location, s: int = 2000)

Moves the pipette to the specified location and dispenses the desired volume of liquid

Parameters:

• vol (float) – The volume of liquid to dispense in uL

• location (Union[Well, Tuple, Location]) – The location to dispense the liquid into.

• s (int, optional) – The speed of the plunger movement in mm/min, defaults to 2000

Raises:

ToolStateError – If the pipette does not have a tip attached

transfer(vol: float | list[float], source_well: science_jubilee.labware.Labware.Well | Tuple | science_jubilee.labware.Labware.Location, destination_well: science_jubilee.labware.Labware.Well | Tuple | science_jubilee.labware.Labware.Location, s: int = 3000, blowout=None, mix_before: tuple = None, mix_after: tuple = None, air_gap: float = 0, new_tip: str = 'always')

Transfers the desired volume of liquid from the source well to the destination well

This is a combination of the :method:`aspirate` and :method:`dispense` steps.

Parameters:

• vol (float) – The volume of liquid to transfer in uL

• source_well (Union[Well, Tuple, Location]) – The location from where to aspirate the liquid from.

• destination_well (Union[Well, Tuple, Location]) – The location to dispense the liquid into.

• s (int, optional) – The speed of the plunger movement in mm/min, defaults to 3000

• blowout (Union[Well, Tuple, Location], optional) – The location to blowout any remainign liquid in the pipette tip

• mix_before (tuple, optional) – The number of times to mix before dispensing and the volume to mix

• mix_after (tuple, optional) – The number of times to mix after dispensing and the volume to mix

• new_tip (str, optional) – Whether or not to use a new tip for the transfer. Can be ‘always’, ‘never’, or ‘once’

• air_gap (float, optional) – The volume of air to aspirate after aspirating the liquid, defaults to None

Note:: :param new_tip: still not implemented at the moment (2023-11-16)

_create_volume_list(volume, total_xfers)

Creates a list of volumes to transfer

Parameters:

• volume (Union[float, list[float]]) – The volume of liquid to transfer

• total_xfers (int) – The total number of transfer steps to perform

Returns:

A list of volumes to transfer

Note: This function was taken from the Opentrons API and modified to work with the Pipette class of Science_Jubilee

static _extend_source_target_lists(sources: List[science_jubilee.labware.Labware.Well | science_jubilee.labware.Labware.Location], targets: List[science_jubilee.labware.Labware.Well | science_jubilee.labware.Labware.Location])

Extend source or target list to match the length of the other

Parameters:

• sources (List[Union[Well, Location]]) – The list of source wells

• targets (List[Union[Well, Location]]) – The list of target wells

Returns:

The extended source and target lists

Return type:

Tuple[List[Union[Well, Location]], List[Union[Well, Location]]]

Note: This function was taken from the Opentrons API and modified to work with the Pipette class of Science_Jubilee

static _expand_for_volume_contraints(volumes: Iterator[float], targets: Iterator, max_volume: float)

Expands the volumes and targets to ensure that the volume does not exceed the maximum volume of the pipette

Parameters:

• volumes (Iterator[float]) – An iterator of the volumes to transfer

• targets (Iterator) – An iterator of the targets to transfer the volumes to

• max_volume (float) – The maximum volume of the pipette in uL

Returns:

An iterator of the volumes and targets to transfer

Return type:

Iterator

Note: This function was taken from the Opentrons API and modified to work with the Pipette class of Science_Jubilee

blowout(s: int = 6000)

Blows out any remaining liquid in the pipette tip

Parameters:

s (int, optional) – The speed of the plunger movement in mm/min, defaults to 3000

air_gap(vol)

Moves the plunger upwards to aspirate air into the pipette tip

Parameters:

vol (float) – The volume of air to aspirate in uL

mix(vol: float, n: int, s: int = 5500)

Mixes liquid by alternating aspirate and dispense steps for the specified number of times

Parameters:

• vol (float) – The volume of liquid to mix in uL

• n (int) – The number of times to mix

• s (int, optional) – The speed of the plunger movement in mm/min, defaults to 5000

stir(n_times: int = 1, height: float = None)

Stirs the liquid in the current well by moving the pipette tip in a circular motion

Parameters:

• n_times (int, optional) – The number of times to stir the liquid, defaults to 1

• height (float, optional) – The z-coordinate to move the tip to during the stir step, defaults to None

Raises:

ToolStateError – If the pipette does not have a tip attached before stirring or if the pipette is not in a well

update_z_offset(tip: bool = None)

Shift the z-offset of the tool to account for the tip length

Parameters:

tip (bool, optional) – Parameter to indicated whether to add or remove the tip offset, defaults to None

add_tiprack(tiprack: science_jubilee.labware.Labware.Labware | list)

Associate a tiprack with the pipette tool

Parameters:

tiprack (Union[Labware, list]) – The tiprack to associate with the pipette

_pickup_tip(z)

Moves the Jubilee Z-axis upwards to pick up a pipette tip and stops once the tip sensor is triggered

Parameters:

z (float) – The z-coordinate to move the pipette to

Raises:

ToolStateError – If the pipette already has a tip attached

pickup_tip(tip_: science_jubilee.labware.Labware.Well | Tuple = None)

Moves the pipette to the specified location and picks up a tip

This function can either take a specific tip or if not specified, will pick up the next available tip in the tiprack associated with the pipette.

Parameters:

tip (Union[Well, Tuple], optional) – The location of the pipette tip to pick up, defaults to None

return_tip(location: science_jubilee.labware.Labware.Well = None)

Returns the pipette tip to the either the specified location or to where the tip was picked up from

Parameters:

location (Well, optional) – The location to return the tip to, defaults to None (i.e. return to where the tip was picked up from)

_drop_tip()

Moves the plunger to eject the pipette tip

Raises:

ToolConfigurationError – If the pipette does not have a tip attached

drop_tip(location: science_jubilee.labware.Labware.Well | Tuple = None)

Moves the pipette to the specified location and drops the pipette tip

Parameters:

location (Union[Well, tuple]) – The location to drop the tip into

class science_jubilee.tools.Pipette.TipTracker(tips, start_well=None)

A class to track the usage of pipette tips and their location in the tiprack

Parameters:

• tips (list[Well]) – The list of tips in the tiprack

• start_well (Well, optional) – The starting well to begin tracking the tips from, defaults to None

Note: This function was taken from the Opentrons API and modified to work with the Pipette class of Science_Jubilee

next_tip(start_well=None)

use_tip(tip_well)

previous_tip()

return_tip(well=None)

assign_tip_to_stock(tip_well, stock_well)