PatchPipette

class acq4.devices.PatchPipette.PatchPipette(deviceManager, config, name)[source]

Bases: Device

Represents a single patch pipette, manipulator, and headstage.

This class extends from the Pipette device class to provide automation and visual feedback on the status of the patch:

Whether a cell is currently patched

Input resistance, access resistance, and holding levels

This is also a good place to implement pressure control, autopatching, slow voltage clamp, etc.

If you intend this for use with the MultiPatch module, the device name in the configuration needs to end in a number.

breakIn()[source]

Rupture the cell membrane using negative current pulses.

-2 psi for 3 sec or until rupture
-4, -6, -8 psi if needed
longer wait time if needed

clampStateChanged(state)[source]

defaultStateManagerClass: alias of PatchPipetteStateManager

deviceInterface(win)[source]: Return a widget with a UI to put in the device rack

emitFullTestPulseData(emit: bool)[source]

emitNewEvent(eventType, eventData=None)[source]

finishPatchRecord()[source]

focusOnTarget(speed, raiseErrors=False)[source]

focusOnTip(speed, raiseErrors=False)[source]

getState()[source]

goHome(speed, **kwds)[source]

imagingDevice() → Camera[source]

isTipBroken()[source]

isTipClean()[source]

listStates()[source]: Return a list of all known state names this pipette can be set to.

newCell()[source]

newPatchAttempt()[source]: Ready to begin a new patch attempt; reset TP history and patch record.

newPipette()[source]: A new physical pipette has been attached; reset any per-pipette state.

patchRecord()[source]

pipetteRecord()[source]

pressureChanged(dev, source, pressure)[source]

quit()[source]

requestNewPipette()[source]: Call to emit a signal requesting a new pipette.

scopeDevice()[source]

setActive(active)[source]

setCell(cell, target=True)[source]

setSelected()[source]

setState(state, setActive=True, **config)[source]

Attempt to set the state (out, bath, seal, whole cell, etc.) of this patch pipette.

The actual resulting state is returned.

setTipBroken(broken)[source]

setTipClean(clean)[source]

sigActiveChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigMoveFinished

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigMoveStarted

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigNewEvent

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigNewPipetteRequested

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigPatchAttemptFinished

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigPressureChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigStateChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigTargetChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigTipBrokenChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sigTipCleanChanged

pyqtSignal(*types, name: str = …, revision: int = …, arguments: Sequence = …) -> PYQT_SIGNAL

types is normally a sequence of individual types. Each type is either a type object or a string that is the name of a C++ type. Alternatively each type could itself be a sequence of types each describing a different overloaded signal. name is the optional C++ name of the signal. If it is not specified then the name of the class attribute that is bound to the signal is used. revision is the optional revision of the signal that is exported to QML. If it is not specified then 0 is used. arguments is the optional sequence of the names of the signal’s arguments.

sonicationChanged(state: str)[source]

stateManager()[source]

The PatchPipette device represents a single patch pipette, manipulator, and headstage combination with automated patching capabilities. It extends the Pipette device to provide automation and visual feedback on patch status.

Features

Automated Patching: State-based patch automation with configurable parameters
Real-time Monitoring: Input resistance, access resistance, and holding level tracking
Visual Feedback: Integration with camera systems for visual pipette control
Pressure Control: Automated pressure regulation during patching procedures
State Management: Comprehensive state tracking (bath, approach, seal, break-in, etc.)

Configuration

The PatchPipette device requires careful configuration of multiple components:

parentDevice: The manipulator/stage device controlling pipette position
clampDevice: The patch clamp amplifier device
pressureDevice: The pressure control device
cameraDevice: Camera for visual feedback (optional)

Example configuration:

PatchPipette1:
    driver: 'PatchPipette'
    parentDevice: 'Manipulator1'
    clampDevice: 'Clamp1'
    pressureDevice: 'PressureController1'
    cameraDevice: 'Camera1'

    # Approach parameters
    approachDistance: 100e-6  # meters
    approachSpeed: 10e-6      # m/s

    # Seal parameters
    sealThreshold: 1e9        # ohms
    sealVoltage: -70e-3       # volts

    # Break-in parameters
    breakInVoltage: -1.0      # volts
    breakInDuration: 0.1      # seconds

State Management

The PatchPipette uses a comprehensive state management system with the following states:

Basic States:

Out: Pipette is withdrawn from solution and not actively patching - Test pulse disabled, atmospheric pressure - Finishes current patch record
Bath: Pipette is immersed in bath solution - Monitors resistance for bath entry detection - Auto pipette offset and initial resistance recording - Detects pipette breaks or clogs - Parameters: bathThreshold (50 MΩ), bathPressure (1.5 kPa)
Approach: Pipette is approaching target cell - Moves to approach position with auto pipette offset - Resets test pulse history - Default next state: cell detect

Detection and Attachment:

Cell Detect: Pipette monitors for cell contact - Real-time resistance analysis for obstacle/cell detection - Fast and slow detection algorithms - Parameters: Various thresholds for detection sensitivity
Seal: Pipette is forming gigaseal - Monitors resistance increase toward gigaseal formation - Pressure and voltage control for seal optimization - Success/failure analysis with configurable thresholds - Parameters: sealThreshold, pressure protocols
Cell Attached: Pipette in cell-attached configuration - Monitors for spontaneous break-in or cell loss - Optional automatic transition to break-in after delay - Parameters: autoBreakInDelay, capacitanceThreshold (10 pF), minimumBreakInResistance (1 GΩ)

Whole Cell Recording:

Break In: Active membrane rupture for whole-cell access - Applies sequence of pressure pulses with increasing strength - Monitors capacitance for successful break-in - Parameters: nPulses, pulseDurations, pulsePressures, capacitanceThreshold
Whole Cell: Successful whole-cell recording configuration - Voltage clamp mode with auto bias enabled - Continuous monitoring for cell health - Records whole-cell start time and position - Default settings: -70 mV holding, auto bias to -70 mV
Reseal: Attempting to reseal from whole-cell to cell-attached - Monitors resistance recovery - Stretch and tearing threshold analysis

Error and Maintenance States:

Broken: Pipette tip is physically damaged - Sets tip broken flag, disables patching - Atmospheric pressure, 0 mV holding - Finishes current patch record
Fouled: Pipette tip is blocked/contaminated - Sets tip clean flag to false - Maintains test pulse for resistance monitoring - Next action: Usually transition to cleaning
Blowout: High-pressure cleaning attempt - Retracts from surface and applies high pressure pulse - Parameters: blowoutPressure (65 kPa), blowoutDuration (2.0 s)

Specialized States:

Clean: Automated pipette cleaning protocol - Cycles positive/negative pressure in cleaning bath - Optional rinse sequence and sonication - Parameters: cleanSequence, rinseSequence, sonicationProtocol
Collect: Nucleus collection protocol - Pressure cycling for nucleus extraction - Specialized for single-cell nuclear collection - Parameters: pressureSequence, approachDistance, sonicationProtocol
Move Nucleus to Home: Returns nucleus to home position after collection

Integration with MultiPatch

For use with the MultiPatch module, the device name must end with a number (e.g., ‘PatchPipette1’, ‘PatchPipette2’).

Dependencies

PatchClamp device (amplifier)
Stage device (manipulator)
PressureControl device (optional but recommended)
Camera device (optional, for visual feedback)
Sonicator device (optional, for tip cleaning)