autoprotocol.liquid_handle¶

liquid_handle.liquid_handle_method¶

LiquidHandleMethod

Base class for generating complex liquid handling behavior.

Summary¶

LiquidHandleMethods are passed as arguments to Protocol methods along with LiquidClasses to specify complex series of liquid handling behaviors.

Notes

Methods in this file should not be used directly, but are intended to be extended by other methods depending on desired behavior.

When creating a vendor-specific library it’s likely desirable to monkey patch LiquidHandleMethod._get_tip_types to reference TipTypes that the vendor supports.

class autoprotocol.liquid_handle.liquid_handle_method.LiquidHandleMethod(tip_type=None, blowout=True)¶

Base LiquidHandleMethod

General framework for liquid handling abstractions and helpers for building a series of liquid_handle transports.

_shape¶: dict – the SBS shape and number of rows and columns of the liquid_handle

_transports¶: list – tracks transports to be added to the LiquidHandle instruction

Notes

There is a hierarchy of logic to all LiquidHandleMethods that abstracts a complex set of liquid handling behavior into smaller, discrete steps.

For step x (aspirate, dispense, mix) and parameter y (e.g. blowout):

Protocol method:
- calls LiquidHandleMethod._`x`_transports
LiquidHandleMethod._`x`_transports method:
- clears the _transports list
- walks through all _transport methods including _transport_`y`
- returns the _transports lists
LiquidHandleMethod._transport_`y` method:
- checks parameter y in addition to the default_`y` method
- possibly generates a series of transports based on the two values
- calls lower level helper methods
LiquidHandleMethod lower level helper methods:
- generate transports and append them to _transports

Examples

For specifying a single, global liquid handling behavior across all volumes the easiest way is to specify parameters when instantiating a LiquidHandleMethod.

from autoprotocol import Unit
from autoprotocol.instruction import LiquidHandle
from autoprotocol.liquid_handle import LiquidHandleMethod

lhm = LiquidHandleMethod(
    blowout=LiquidHandle.builders.blowout(volume=Unit(10, "uL"))
)

For behavior that relies on more liquid handling parameters or even defines new behavior you can define your own LiquidHandleMethod.

from autoprotocol import Unit
from autoprotocol.instruction import LiquidHandle
from autoprotocol.liquid_handle import LiquidHandleMethod

class NewLHM(LiquidHandleMethod):
    def default_blowout(self, volume):
        if volume < Unit(10, "uL"):
            blowout_volume = Unit(1, "uL")
        else:
            blowout_volume = Unit(10, "uL")
        return LiquidHandle.builders.blowout(
            volume=blowout_volume
        )

See also

Transfer: method for handling liquid between two locations
Mix: method for handling liquid within locations
LiquidClass: contain properties that are intrinsic to specific liquids
Protocol: contains methods that accept LiquidHandleMethods as arguments

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__format__()¶: default object formatter

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__hash__¶

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

default_blowout(volume)¶

Default blowout behavior

Parameters:	volume (Unit) –
Returns:	blowout_params
Return type:	dict

See also

blowout(): holds any user specified blowout parameters
_transport_blowout(): generates the actual blowout transports

static default_lld_position_z(liquid)¶

Default lld position_z

Returns:	position_z for sensing the liquid surface
Return type:	dict

static default_tracked_position_z()¶

Default tracked position_z

Returns:	position_z for tracking the liquid surface
Return type:	dict

static default_well_bottom_position_z()¶

Default well bottom position_z

Returns:	position_z for the well bottom
Return type:	dict

static default_well_top_position_z()¶

Default well top position_z

Returns:	position_z for the well top
Return type:	dict

liquid_handle.liquid_class¶

LiquidClass

Base class for defining the portions of liquid handling behavior that are intrinsic to specific types of liquids.

class autoprotocol.liquid_handle.liquid_class.LiquidClass(calibrated_volume=None, aspirate_flowrate=None, dispense_flowrate=None, delay_time=None, clld_threshold=None, plld_threshold=None)¶

Contains properties intrinsic to individual LiquidClasses

name¶: str – the name of the liquid_class may be used by vendors to generate more sensible defaults for unspecified behavior

volume_calibration_curve¶: dict(str, VolumeCalibration) – a calibration curve describing the relationship between tip_type, volume bins, and volume calibration parameters See Also VolumeCalibration

aspirate_flowrate_calibration_curve¶: dict(str, VolumeCalibration) – a calibration curve describing the relationship between tip_type, volume bins, and aspirate flowrate calibration parameters See Also VolumeCalibration

dispense_flowrate_calibration_curve¶: dict(str, VolumeCalibration) – a calibration curve describing the relationship between tip_type, volume bins, and dispense flowrate calibration parameters See Also VolumeCalibration

_safe_volume_multiplier¶: Numeric – a multiplier used by LiquidHandleMethods to estimate safe pump buffers for volume calibration without any prior knowledge about tip_type See Also LiquidHandleMethod._estimate_calibrated_volume

Examples

For specifying a single, global liquid handling behavior across all volumes the easiest way is to specify parameters when instantiating a LiquidClass. If the following LiquidClass is specified then the pump_override_volume will always be set to 10:uL and the flowrate for all aspirate steps will have a target of 10:uL/s, regardless of the stated volume to be transferred.

from autoprotocol import Unit
from autoprotocol.instruction import LiquidHandle
from autoprotocol.liquid_handle import LiquidClass

lc = LiquidClass(
    aspirate_flowrate=LiquidHandle.builders.flowrate(
        target=Unit(10, "ul/s")
    ),
    calibrated_volume=Unit(10, "uL")
)

For behavior that differs between volumes you can define your own LiquidClass.

from autoprotocol import Unit
from autoprotocol.instruction import LiquidHandle
from autoprotocol.liquid_handle.liquid_class import (
    LiquidClass, VolumeCalibration, VolumeCalibrationBin
)

vol_curve = {
    "generic_1_50": VolumeCalibration(
        (Unit(5, "uL"), VolumeCalibrationBin(
            slope=1.1, intercept=Unit(0.1, "uL")
        )),
        (Unit(10, "uL"), VolumeCalibrationBin(
            slope=0.9, intercept=Unit(0.2, "uL")
        ))
    )
}
asp_flow_curve = {
    "generic_1_50": VolumeCalibration(
        (Unit(5, "uL"), LiquidHandle.builders.flowrate(
            target=Unit(50, "uL/s")
        )),
        (Unit(15, "uL"), LiquidHandle.builders.flowrate(
            target=Unit(200, "uL/s")
        ))
    )
}

class NewLC(LiquidClass):
    def __init__(self, *args, **kwargs):
        super(NewLC, self).__init__(*args, **kwargs)
        self.volume_calibration_curve = vol_curve
        self.aspirate_flowrate_calibration_curve = asp_flow_curve

See also

VolumeCalibration: used to specify calibration_curves
LiquidHandleMethod: used to specify liquid handling movement behavior
Protocol.transfer: accepts LiquidClass arguments to determine behavior
Protocol.mix: accepts a LiquidClass argument to determine behavior

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__format__()¶: default object formatter

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__hash__¶

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

class autoprotocol.liquid_handle.liquid_class.VolumeCalibration(*args)¶

Wrapper for a volume-binned calibration curve A data structure that represents a calibration curve for either volumes or flowrates that are binned by upper bounded volume ranges.

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__format__()¶: default object formatter

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__hash__¶

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

binned_calibration_for_volume(volume)¶

Gets the smallest suitable bin in the calibration curve Finds the smallest point on the calibration curve that has a bin that’s greater than or equal to the size of the specified value.

Parameters:	volume (Unit or int or float) – the value to be binned
Returns:	target_bin
Return type:	dict
Raises:	`RuntimeError` – No suitably large calibration bin

class autoprotocol.liquid_handle.liquid_class.VolumeCalibrationBin¶

Wrapper for slope and intercept parameters for linear fitting Holds information required to calibrate a volume for liquid handle step assuming a linear relationship between volume and calibrated volume.

__add__¶: x.__add__(y) <==> x+y

__contains__¶: x.__contains__(y) <==> y in x

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__eq__¶: x.__eq__(y) <==> x==y

__format__()¶: default object formatter

__ge__¶: x.__ge__(y) <==> x>=y

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__getitem__¶: x.__getitem__(y) <==> x[y]

__getslice__¶

x.__getslice__(i, j) <==> x[i – j]

Use of negative indices is not supported.

__gt__¶: x.__gt__(y) <==> x>y

__hash__¶

__iter__¶

__le__¶: x.__le__(y) <==> x<=y

__len__¶

__lt__¶: x.__lt__(y) <==> x<y

__mul__¶: x.__mul__(n) <==> x*n

__ne__¶: x.__ne__(y) <==> x!=y

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__rmul__¶: x.__rmul__(n) <==> n*x

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

calibrate_volume(volume)¶

Calibrates the volume using slope and intercept

Parameters:	volume (Unit) – the volume to be calibrated
Returns:	calibrated volume
Return type:	Unit

count(value) → integer -- return number of occurrences of value¶

index(value[, start[, stop]]) → integer -- return first index of value.¶: Raises ValueError if the value is not present.

intercept¶: Alias for field number 1

slope¶: Alias for field number 0

liquid_handle.transfer¶

Transfer LiquidHandleMethod

Base LiquidHandleMethod used by Protocol.transfer to generate a series of movements between pairs of wells.

class autoprotocol.liquid_handle.transfer.DryWellTransfer(tip_type=None, blowout=True, prime=True, transit=True, mix_before=False, mix_after=False, aspirate_z=None, dispense_z=None)¶

Dispenses while tracking liquid without mix_after

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__format__()¶: default object formatter

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__hash__¶

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

default_aspirate_z(volume)¶

Default aspirate_z parameters

Parameters:	volume (Unit) –
Returns:	aspirate position_z
Return type:	dict

See also

aspirate_z(): holds any user defined aspirate_z parameters
_transport_aspirate_target_volume(): generates actual aspirate transports

default_blowout(volume)¶

Default blowout behavior

Parameters:	volume (Unit) –
Returns:	blowout_params
Return type:	dict

See also

blowout(): holds any user specified blowout parameters
_transport_blowout(): generates the actual blowout transports

default_dispense_z(volume)¶

Default aspirate_z parameters

Parameters:	volume (Unit) –
Returns:	dispense position_z
Return type:	dict

See also

dispense_z(): holds any user defined dispense_z parameters
_transport_dispense_target_volume(): generates actual dispense transports

static default_lld_position_z(liquid)¶

Default lld position_z

Returns:	position_z for sensing the liquid surface
Return type:	dict

default_mix_after(volume)¶

Default mix_after parameters

Parameters:	volume (Unit) –
Returns:	mix_after params
Return type:	dict

See also

mix_after(): holds any user defined mix_after parameters
_transport_mix(): generates the actual mix_after transports

default_mix_before(volume)¶

Default mix_before parameters

Parameters:	volume (Unit) –
Returns:	mix_before params
Return type:	dict

See also

mix_before(): holds any user defined mix_before parameters
_transport_mix(): generates the actual mix_before transports

default_prime(volume)¶

Default prime volume

Parameters:	volume (Unit) –
Returns:	priming volume
Return type:	Unit

See also

prime(): holds any user defined prime volume
_transport_aspirate_target_volume(): generates actual aspirate transports

static default_tracked_position_z()¶

Default tracked position_z

Returns:	position_z for tracking the liquid surface
Return type:	dict

default_transit(volume)¶

Default transit volume

Parameters:	volume (Unit) –
Returns:	transit volume
Return type:	Unit

See also

transit(): holds any user defined transit volume
_transport_aspirate_transit(): generates the actual transit transports
_transport_dispense_transit(): generates the actual transit transports

static default_well_bottom_position_z()¶

Default well bottom position_z

Returns:	position_z for the well bottom
Return type:	dict

static default_well_top_position_z()¶

Default well top position_z

Returns:	position_z for the well top
Return type:	dict

class autoprotocol.liquid_handle.transfer.PreMixBlowoutTransfer(tip_type=None, blowout=True, prime=True, transit=True, mix_before=False, mix_after=True, aspirate_z=None, dispense_z=None, pre_mix_blowout=True)¶

Adds an additional blowout before the mix_after step

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__format__()¶: default object formatter

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__hash__¶

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

default_aspirate_z(volume)¶

Default aspirate_z parameters

Parameters:	volume (Unit) –
Returns:	aspirate position_z
Return type:	dict

See also

aspirate_z(): holds any user defined aspirate_z parameters
_transport_aspirate_target_volume(): generates actual aspirate transports

default_blowout(volume)¶

Default blowout behavior

Parameters:	volume (Unit) –
Returns:	blowout_params
Return type:	dict

See also

blowout(): holds any user specified blowout parameters
_transport_blowout(): generates the actual blowout transports

default_dispense_z(volume)¶

Default aspirate_z parameters

Parameters:	volume (Unit) –
Returns:	dispense position_z
Return type:	dict

See also

dispense_z(): holds any user defined dispense_z parameters
_transport_dispense_target_volume(): generates actual dispense transports

static default_lld_position_z(liquid)¶

Default lld position_z

Returns:	position_z for sensing the liquid surface
Return type:	dict

default_mix_after(volume)¶

Default mix_after parameters

Parameters:	volume (Unit) –
Returns:	mix_after params
Return type:	dict

See also

mix_after(): holds any user defined mix_after parameters
_transport_mix(): generates the actual mix_after transports

default_mix_before(volume)¶

Default mix_before parameters

Parameters:	volume (Unit) –
Returns:	mix_before params
Return type:	dict

See also

mix_before(): holds any user defined mix_before parameters
_transport_mix(): generates the actual mix_before transports

default_pre_mix_blowout(volume)¶

Default pre_mix_blowout parameters

Parameters:	volume (Unit) –
Returns:	pre_mix_blowout params
Return type:	dict

See also

pre_mix_blowout(): holds any user defined pre_mix_blowout parameters
_transport_pre_mix_blowout(): generates the actual blowout transports

default_prime(volume)¶

Default prime volume

Parameters:	volume (Unit) –
Returns:	priming volume
Return type:	Unit

See also

prime(): holds any user defined prime volume
_transport_aspirate_target_volume(): generates actual aspirate transports

static default_tracked_position_z()¶

Default tracked position_z

Returns:	position_z for tracking the liquid surface
Return type:	dict

default_transit(volume)¶

Default transit volume

Parameters:	volume (Unit) –
Returns:	transit volume
Return type:	Unit

See also

transit(): holds any user defined transit volume
_transport_aspirate_transit(): generates the actual transit transports
_transport_dispense_transit(): generates the actual transit transports

static default_well_bottom_position_z()¶

Default well bottom position_z

Returns:	position_z for the well bottom
Return type:	dict

static default_well_top_position_z()¶

Default well top position_z

Returns:	position_z for the well top
Return type:	dict

class autoprotocol.liquid_handle.transfer.Transfer(tip_type=None, blowout=True, prime=True, transit=True, mix_before=False, mix_after=True, aspirate_z=None, dispense_z=None)¶

LiquidHandleMethod for generating transfers between pairs of wells

LiquidHandleMethod for transferring volume from one well to another.

_source_liquid¶: LiquidClass – used to determine calibration, flowrates, and sensing thresholds

_destination_liquid¶: LiquidClass – used to determine calibration, flowrates, and sensing thresholds

Notes

The primary entry points that for this class are:

_aspirate_transports : generates transports for a source location
_dispense_transports : generates transports for a destination location

See also

LiquidHandleMethod: base LiquidHandleMethod with reused functionality
Protocol.transfer: the standard interface for interacting with Transfer

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__format__()¶: default object formatter

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__hash__¶

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

default_aspirate_z(volume)¶

Default aspirate_z parameters

Parameters:	volume (Unit) –
Returns:	aspirate position_z
Return type:	dict

See also

aspirate_z(): holds any user defined aspirate_z parameters
_transport_aspirate_target_volume(): generates actual aspirate transports

default_blowout(volume)¶

Default blowout behavior

Parameters:	volume (Unit) –
Returns:	blowout_params
Return type:	dict

See also

blowout(): holds any user specified blowout parameters
_transport_blowout(): generates the actual blowout transports

default_dispense_z(volume)¶

Default aspirate_z parameters

Parameters:	volume (Unit) –
Returns:	dispense position_z
Return type:	dict

See also

dispense_z(): holds any user defined dispense_z parameters
_transport_dispense_target_volume(): generates actual dispense transports

static default_lld_position_z(liquid)¶

Default lld position_z

Returns:	position_z for sensing the liquid surface
Return type:	dict

default_mix_after(volume)¶

Default mix_after parameters

Parameters:	volume (Unit) –
Returns:	mix_after params
Return type:	dict

See also

mix_after(): holds any user defined mix_after parameters
_transport_mix(): generates the actual mix_after transports

default_mix_before(volume)¶

Default mix_before parameters

Parameters:	volume (Unit) –
Returns:	mix_before params
Return type:	dict

See also

mix_before(): holds any user defined mix_before parameters
_transport_mix(): generates the actual mix_before transports

default_prime(volume)¶

Default prime volume

Parameters:	volume (Unit) –
Returns:	priming volume
Return type:	Unit

See also

prime(): holds any user defined prime volume
_transport_aspirate_target_volume(): generates actual aspirate transports

static default_tracked_position_z()¶

Default tracked position_z

Returns:	position_z for tracking the liquid surface
Return type:	dict

default_transit(volume)¶

Default transit volume

Parameters:	volume (Unit) –
Returns:	transit volume
Return type:	Unit

See also

transit(): holds any user defined transit volume
_transport_aspirate_transit(): generates the actual transit transports
_transport_dispense_transit(): generates the actual transit transports

static default_well_bottom_position_z()¶

Default well bottom position_z

Returns:	position_z for the well bottom
Return type:	dict

static default_well_top_position_z()¶

Default well top position_z

Returns:	position_z for the well top
Return type:	dict

liquid_handle.mix¶

Mix LiquidHandleMethod

Base LiquidHandleMethod used by Protocol.mix to generate a series of movements within individual wells.

class autoprotocol.liquid_handle.mix.Mix(tip_type=None, blowout=True, repetitions=None, position_z=None)¶

LiquidHandleMethod for generating transfers within wells

LiquidHandleMethod for moving volume within a single well.

_liquid¶: LiquidClass – used to determine calibration, flowrates, and sensing thresholds

Notes

The primary entry points that for this class are:

_mix_transports : generates transports within a single location

See also

LiquidHandleMethod: base LiquidHandleMethod with reused functionality
Protocol.mix: the standard interface for interacting with Mix

__delattr__¶: x.__delattr__(‘name’) <==> del x.name

__format__()¶: default object formatter

__getattribute__¶: x.__getattribute__(‘name’) <==> x.name

__hash__¶

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶

__setattr__¶: x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶

default_blowout(volume)¶

Default blowout behavior

Parameters:	volume (Unit) –
Returns:	blowout_params
Return type:	dict

See also

blowout(): holds any user specified blowout parameters
_transport_blowout(): generates the actual blowout transports

static default_lld_position_z(liquid)¶

Default lld position_z

Returns:	position_z for sensing the liquid surface
Return type:	dict

default_position_z(volume)¶

Default position_z

Parameters:	volume (Unit) –
Returns:	mix position_z
Return type:	dict

See also

position_z(): holds any user defined position_z parameters
_transport_mix(): generates the actual mix transports

default_repetitions(volume)¶

Default mix repetitions

Parameters:	volume (Unit) –
Returns:	number of mix repetitions
Return type:	int

See also

repetitions(): holds any user defined repetition parameters
_transport_mix(): generates the actual mix transports

static default_tracked_position_z()¶

Default tracked position_z

Returns:	position_z for tracking the liquid surface
Return type:	dict

static default_well_bottom_position_z()¶

Default well bottom position_z

Returns:	position_z for the well bottom
Return type:	dict

static default_well_top_position_z()¶

Default well top position_z

Returns:	position_z for the well top
Return type:	dict

liquid_handle.tip_type¶

Generic tip type and device class mappings for LiquidHandleMethods