electrophysiology

Metadata for electrophysiology experiments.

The following methods are currently supported:

• patch clamp recording in brain slices
• sharp electrode intracellular recording in brain slices

Coming soon:

• patch clamp recordings in cultured neurons
• extracellular electrode recording, including tetrodes and multi-electrode arrays

class fairgraph.electrophysiology.Sensor(name, coordinate_system=None, coordinate_units=None, description=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Object specific to sensors used in electrode array experiments

Parameters:

• name (str) –
• coordinate_system (Distribution) –
• coordinate_units (str) –
• description (str) –

class fairgraph.electrophysiology.Trace(name, data_location, generated_by, generation_metadata, channel, data_unit, time_step, part_of=None, retrieval_date=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Single time series recorded during an experiment or simulation.

Trace represents a single recording from a single channel. If you have a file containing recordings from multiple channels, or multiple recordings from a single channel, use MultiChannelMultiTrialRecording.

Parameters:

• name (str) –
• data_location (Distribution) –
• generated_by (PatchClampExperiment) –
• generation_metadata (QualifiedTraceGeneration) –
• channel (int) –
• data_unit (str) –
• time_step (QuantitativeValue) –
• part_of (Dataset) –
• retrieval_date (datetime) –

class fairgraph.electrophysiology.MultiChannelMultiTrialRecording(name, data_location, generated_by, generation_metadata, channel_names, data_unit, time_step, channel_type=None, part_of=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.Trace

Multiple time series recorded during an experiment or simulation.

Time series may be recorded from multiple channels. If you have a file containing only a single recording from a single channel, you may instead use Trace.

Parameters:

• name (str) –
• data_location (Distribution) –
• generated_by (PatchClampExperiment, ExtracellularElectrodeExperiment, ElectrodeArrayExperiment, EEGExperiment, ECoGExperiment) –
• generation_metadata (QualifiedMultiTraceGeneration) –
• channel_names (str) –
• data_unit (str) –
• time_step (QuantitativeValue) –
• channel_type (ChannelType) –
• part_of (Dataset) –

class fairgraph.electrophysiology.PatchedCell(name, brain_location, collection=None, putative_cell_type=None, cell_type=None, morphology_type=None, experiments=None, pipette_id=None, seal_resistance=None, pipette_resistance=None, start_membrane_potential=None, end_membrane_potential=None, pipette_solution=None, liquid_junction_potential=None, labeling_compound=None, reversal_potential_cl=None, description=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A cell recorded in patch clamp.

Parameters:

• name (str) –
• brain_location (BrainRegion) –
• collection (PatchedCellCollection) –
• cell_type (CellType) –
• experiments (PatchClampExperiment) –
• pipette_id (str, int) –
• seal_resistance (QuantitativeValue) –
• pipette_resistance (QuantitativeValue) –
• liquid_junction_potential (QuantitativeValue) –
• start_membrane_potential (QuantitativeValue) –
• end_membrane_potential (QuantitativeValue) –
• pipette_solution (str) –
• labeling_compound (str) –
• reversal_potential_cl (QuantitativeValue) –
• description (str) –

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)

List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.PatchedSlice(name, slice, recorded_cells, recording_activity=None, brain_location=None, bath_solution=None, description=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A slice that has been recorded from using patch clamp.

Parameters:

• name (str) –
• slice (Slice) –
• recorded_cells (PatchedCellCollection) –
• recording_activity (PatchClampActivity) –
• brain_location (BrainRegion) –
• bath_solution (QuantitativeValue) –
• description (str) –

class fairgraph.electrophysiology.PatchedCellCollection(name, cells, slice=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A collection of patched cells.

Parameters:

• name (str) –
• cells (PatchedCell) –
• slice (PatchedSlice) –

class fairgraph.electrophysiology.CellCulture(name, subject, cells, culturing_activity=None, experiment=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A cell culture.

Parameters:

• name (str) –
• subject (Subject) –
• cells (PatchedCell) –
• culturing_activity (CellCulturingActivity) –
• experiment (PatchClampActivity) –

class fairgraph.electrophysiology.PatchClampActivity(name, recorded_tissue, recorded_slice=None, protocol=None, people=None, start_time=None, end_time=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A patch clamp recording session.

Parameters:

• name (str) –
• recorded_tissue (CellCulture, Slice, CranialWindow) –
• recorded_slice (PatchedSlice) –
• protocol (str) –
• people (Person) –
• start_time (datetime) –
• end_time (datetime) –

class fairgraph.electrophysiology.PatchClampExperiment(name, recorded_cell, acquisition_device=None, stimulation=None, traces=None, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Stimulation of the neural tissue and recording of the responses during a patch clamp

recording session.

Parameters:

• name (str) –
• recorded_cell (PatchedCell) –
• acquisition_device (Device) –
• stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
• traces (Trace, MultiChannelMultiTrialRecording) –
• start_time (datetime) –
• end_time (datetime) –
• people (Person) –
• protocol (Protocol) –

classmethod from_kg_instance(instance, client, resolved=False)

docstring

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)

List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.QualifiedTraceGeneration(name, stimulus_experiment, sweep, repetition=None, at_time=None, provider_experiment_id=None, provider_experiment_name=None, holding_potential=None, measured_holding_potential=None, input_resistance=None, series_resistance=None, compensation_current=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Additional information about the generation of a single-channel electrophysiology trace.

Parameters:

• name (str) –
• stimulus_experiment (PatchClampExperiment, IntraCellularSharpElectrodeExperiment) –
• sweep (int) –
• repetition (int) –
• at_time (datetime) –
• provider_experiment_id (str) –
• provider_experiment_name (str) –
• holding_potential (QuantitativeValue) –
• measured_holding_potential (QuantitativeValue) –
• input_resistance (QuantitativeValue) –
• series_resistance (QuantitativeValue) –
• compensation_current (QuantitativeValue) –

class fairgraph.electrophysiology.ImplantedBrainTissue(name, subject, implantation_activity=None, experiment=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Brain tissue in which extracellular electrode was implanted.

Parameters:

• name (str) –
• subject (Subject) –
• implantation_activity (ElectrodeImplantationActivity) –
• experiment (ExtracellularElectrodeExperiment) –

resolve(client, api='query', use_cache=True)

To avoid having to check if a child attribute is a proxy or a real object, a real object resolves to itself.

class fairgraph.electrophysiology.ElectrodeArrayExperiment(name, device=None, implanted_brain_tissues=None, stimulation=None, sensors=None, digitized_head_points_coordinates=None, head_localization_coils_coordinates=None, digitized_head_points=False, digitized_landmarks=False, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Electrode array experiment (EEG, ECoG, MEG, ERP).

Parameters:

• name (str) –
• device (Device) –
• implanted_brain_tissues (ImplantedBrainTissue) –
• stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
• sensors (Sensor) –
• digitized_head_points_coordinates (Sensor) –
• head_localization_coils_coordinates (Sensor) –
• digitized_head_points (bool) –
• digitized_landmarks (bool) –
• start_time (datetime) –
• end_time (datetime) –
• people (Person) –
• protocol (Protocol) –

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)

List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.ECoGExperiment(name, device=None, implanted_brain_tissues=None, stimulation=None, sensors=None, digitized_head_points_coordinates=None, head_localization_coils_coordinates=None, digitized_head_points=False, digitized_landmarks=False, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.ElectrodeArrayExperiment

Electrocorticography experiment.

Parameters:

• name (str) –
• device (Device) –
• implanted_brain_tissues (ImplantedBrainTissue) –
• stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
• sensors (Sensor) –
• digitized_head_points_coordinates (Sensor) –
• head_localization_coils_coordinates (Sensor) –
• digitized_head_points (bool) –
• digitized_landmarks (bool) –
• start_time (datetime) –
• end_time (datetime) –
• people (Person) –
• protocol (Protocol) –

class fairgraph.electrophysiology.EEGExperiment(name, device=None, implanted_brain_tissues=None, stimulation=None, sensors=None, digitized_head_points_coordinates=None, head_localization_coils_coordinates=None, digitized_head_points=False, digitized_landmarks=False, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.ElectrodeArrayExperiment

Electroencephalography experiment.

Parameters:

• name (str) –
• device (Device) –
• implanted_brain_tissues (ImplantedBrainTissue) –
• stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
• sensors (Sensor) –
• digitized_head_points_coordinates (Sensor) –
• head_localization_coils_coordinates (Sensor) –
• digitized_head_points (bool) –
• digitized_landmarks (bool) –
• start_time (datetime) –
• end_time (datetime) –
• people (Person) –
• protocol (Protocol) –

class fairgraph.electrophysiology.ElectrodePlacementActivity(name, subject, brain_location, device=None, protocol=None, people=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

docstring

Parameters:

• name (str) –
• subject (Subject) –
• brain_location (BrainRegion) –
• device (Device) –
• protocol (Protocol) –
• people (Person) –

class fairgraph.electrophysiology.ElectrodeImplantationActivity(name, subject, brain_location, implanted_brain_tissues=None, device=None, cranial_window=None, protocol=None, anesthesia=None, start_time=None, end_time=None, people=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.ElectrodePlacementActivity

docstring

Parameters:

• name (str) –
• subject (Subject) –
• brain_location (BrainRegion) –
• implanted_brain_tissues (ImplantedBrainTissue) –
• device (Device) –
• cranial_window (CranialWindow) –
• protocol (Protocol) –
• anesthesia (str) –
• start_time (datetime) –
• end_time (datetime) –
• people (Person) –

class fairgraph.electrophysiology.ExtracellularElectrodeExperiment(name, stimulation=None, recorded_cell=None, traces=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.PatchClampExperiment

Stimulation of the neural tissue and recording of the responses with

an extracellular electrode.

Parameters:

• name (str) –
• stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
• recorded_cell (ImplantedBrainTissue) –
• traces (Trace) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecordedCell(name, brain_location, collection=None, putative_cell_type=None, cell_type=None, morphology_type=None, experiments=None, pipette_id=None, seal_resistance=None, pipette_resistance=None, start_membrane_potential=None, end_membrane_potential=None, pipette_solution=None, liquid_junction_potential=None, labeling_compound=None, reversal_potential_cl=None, description=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.PatchedCell

A cell recorded intracellularly with a sharp electrode.

Parameters:

• name (str) –
• brain_location (BrainRegion) –
• collection (IntraCellularSharpElectrodeRecordedCellCollection) –
• cell_type (CellType) –
• experiments (IntraCellularSharpElectrodeExperiment) –
• pipette_id (str, int) –
• seal_resistance (QuantitativeValue) –
• pipette_resistance (QuantitativeValue) –
• liquid_junction_potential (QuantitativeValue) –
• labeling_compound (str) –
• reversal_potential_cl (QuantitativeValue) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecording(name, recorded_tissue, recorded_slice=None, protocol=None, people=None, start_time=None, end_time=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.PatchClampActivity

A sharp-electrode recording session.

Parameters:

• name (str) –
• recorded_tissue (CellCulture, Slice, CranialWindow) –
• recorded_slice (IntraCellularSharpElectrodeRecordedSlice) –
• protocol (str) –
• people (Person) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecordedCellCollection(name, cells, slice=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.PatchedCellCollection

A collection of cells recorded with a sharp electrode.

Parameters:

• name (str) –
• cells (IntraCellularSharpElectrodeRecordedCell) –
• slice (IntraCellularSharpElectrodeRecordedSlice) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeRecordedSlice(name, slice, recorded_cells, recording_activity=None, brain_location=None, bath_solution=None, description=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.PatchedSlice

A slice that has been recorded from using a sharp electrode.

Parameters:

• name (str) –
• slice (Slice) –
• recorded_cells (IntraCellularSharpElectrodeRecordedCellCollection) –
• recording_activity (IntraCellularSharpElectrodeRecording) –

class fairgraph.electrophysiology.IntraCellularSharpElectrodeExperiment(name, recorded_cell, acquisition_device=None, stimulation=None, traces=None, start_time=None, end_time=None, people=None, protocol=None, id=None, instance=None)

Bases: fairgraph.electrophysiology.PatchClampExperiment

Stimulation of the neural tissue and recording of the responses with

a sharp intracellular electrode.

Parameters:

• name (str) –
• recorded_cell (IntraCellularSharpElectrodeRecordedCell) –
• stimulation (VisualStimulation, BehavioralStimulation, ElectrophysiologicalStimulation) –
• traces (Trace) –
• people (Person) –

classmethod list(client, size=100, from_index=0, api='query', scope='released', resolved=False, **filters)

List all objects of this type in the Knowledge Graph

class fairgraph.electrophysiology.QualifiedMultiTraceGeneration(name, stimulus_experiment, sweeps, channel_type=None, holding_potential=None, sampling_frequency=None, power_line_frequency=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Parameters:

• name (str) –
• stimulus_experiment (ExtracellularElectrodeExperiment, IntraCellularSharpElectrodeExperiment, PatchClampExperiment, ElectrodeArrayExperiment) –
• sweeps (int) –
• channel_type (str) –
• holding_potential (QuantitativeValue) –
• sampling_frequency (QuantitativeValue) –
• power_line_frequency (QuantitativeValue) –

class fairgraph.electrophysiology.CellCulturingActivity(subject, cell_culture, brain_location=None, culture_type=None, culture_age=None, hemisphere=None, culture_solution=None, start_time=None, end_time=None, people=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

The activity of preparing a cell culture from whole brain.

Parameters:

• subject (Subject) –
• cell_culture (CellCulture) –
• brain_location (BrainRegion) –
• culture_type (CultureType) –
• culture_age (QuantitativeValueRange) –
• hemisphere (str) –
• culture_solution (str) –
• start_time (datetime) –
• end_time (datetime) –
• people (Person) –

resolve(client, api='query', use_cache=True)

To avoid having to check if a child attribute is a proxy or a real object, a real object resolves to itself.

fairgraph.electrophysiology.list_kg_classes()

List all KG classes defined in this module

fairgraph.electrophysiology.use_namespace(namespace)

Set the namespace for all classes in this module.