element-array-ephys 0.1.0b0

DataJoint Element for Extracellular Array Electrophysiology

DataJoint Element - Array Electrophysiology Element

DataJoint Element for array electrophysiology.

This repository features DataJoint pipeline design for extracellular array electrophysiology, with Neuropixels probe and kilosort spike sorting method.

The pipeline presented here is not a complete pipeline by itself, but rather a modular design of tables and dependencies specific to the extracellular electrophysiology workflow.

This modular pipeline element can be flexibly attached downstream to any particular design of experiment session, thus assembling a fully functional ephys pipeline.

See Background for the background information and development timeline.

The Pipeline Architecture

As the diagram depicts, the array ephys element starts immediately downstream from Session, and also requires some notion of Location as a dependency for InsertionLocation.

The design of probe

• ProbeType - a lookup table specifying the type of Neuropixels probe (e.g. "neuropixels 1.0", "neuropixels 2.0 single-shank")
• ProbeType.Electrode - all electrode and their properties for a particular probe type
  • An electrode here refers to one recordable electrode site on the Neuropixels probe (e.g. for Neuropixels 1.0, there are 960 sites per shank)
• Probe - record of an actual physical probe, identifiable by some unique ID (e.g. probe's serial number)
• ElectrodeConfig - particular electrode configuration to be used for ephys recording
• ElectrodeConfig.Electrode - corresponding electrodes in ProbeType.Electrode that are used for recording in this electrode configuration (e.g. for Neuropixels 1.0 or 2.0, there can be at most 384 electrodes usable for recording per probe)

Extracellular ephys recording

• ProbeInsertion - a surgical insertion of a probe in the brain. Every experimental session consists of one or more entries in ProbeInsertion with a corresponding InsertionLocation each
• EphysRecording - each ProbeInsertion is accompanied by a corresponding EphysRecording, specifying the ElectrodeConfig used for the recording from the Probe defined in such ProbeInsertion

Clusters and spikes

This ephys element features automatic ingestion for spike sorting results from the kilosort method.

• Clustering - specify instance(s) of clustering on an EphysRecording, by some ClusteringMethod
• Curation - specify instance(s) of curations performed on the output of a given Clustering
• CuratedClustering - set of results from a particular round of clustering/curation
  • CuratedClustering.Unit - Identified unit(s) from one Curation, and the associated properties (e.g. cluster quality, spike times, spike depths, etc.)
  • WaveformSet - A set of spike waveforms for units from a given CuratedClustering

Installation

pip install element-array-ephys

If you already have an older version of element-array-ephys installed using pip, upgrade with

pip install --upgrade element-array-ephys

Usage

Element activation

To activate the element-array-ephys, ones need to provide:

1. Schema names

   • schema name for the probe module
   • schema name for the ephys module

2. Upstream tables

   • Session table
   • SkullReference table (Reference table for InsertionLocation, specifying the skull reference)

3. Utility functions

   • get_ephys_root_data_dir()
   • get_session_directory()

For more detail, check the docstring of the element-array-ephys:

help(probe.activate)
help(ephys.activate)

Example usage

See this project for an example usage of this Array Electrophysiology Element.