In Vitro Whole Cell Patch Clamp Recording

Use case


This specification describes the metadata collected for in vitro intracellular electrophysiology recordings using the whole cell patch clamp configuration. Whole cell patch clamp is a type of electrophysiological recording used to measure ionic currents over the membrane of an entire cell. Suction is applied to rupture the cell membrane which provides access to the intracellular space of the patched cell. Metadata is collected on the subject used in the experiment, the slice, the patched cell which was recorded as well as the recording traces and protocols. Additionally, metadata for the brain slicing, the whole cell patch clamp and the stimulus (including protocols and agents) involved in the generation of the recording traces are captured.

Supported Data Queries

The following points describe an example subset of questions supported by the data provenance pattern:

  • Retrieve all recording traces generated from rat somatosensory cortex using selected stimuli.
  • Retrieve recording traces by recording day and experimenter.
  • Retrieve all response traces from a specific patched cell.
  • Get the holding potential for an individual recording trace.

Data Provenance pattern

In Vitro Whole Cell Patch Clamp Recording



The different entity types involved in the experiment are listed below.

Type Description
Subject Subject that was used in the experiment
Slice Brain slice obtained from the subject
PatchedSlice Brain slice containing patched cells
PatchedCellCollection Collection of patched cells in a single slice (e.g. for multi-patch recordings)
PatchedCell Cell that was patched in the slice
Trace Individual recording trace of the patched cell (stimulation/input and response/output trace)
Protocol Protocol that describes the method used in the design and execution of the experiment


The different activity types involved in the experiment are listed below.

Type Description
BrainSlicing Technique used to obtain a brain slice for patching
WholeCellPatchClamp Technique used to study electrical activity of individual living cells
StimulusExperiment Technique used to obtain the electrical signature of cells through injection of a defined current pattern


The different agent types involved in the experiment are listed below.

Type Description
Person Person associated with an activity
SoftwareAgent Software associated with an activity
Organization Organization associated with an activity