element-array-ephys 0.1.2

DataJoint Element for Extracellular Array Electrophysiology

DataJoint Element - Array Electrophysiology Element

• 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 the Element Array Electrophysiology documentation for the background information and development timeline.

• For more information on the DataJoint Elements project, please visit https://elements.datajoint.org. This work is supported by the National Institutes of Health.

Element architecture

element-array-ephys is comprised of two schemas, probe and ephys. To handle several use cases of this pipeline, we have designed several ephys schemas, including ephys_acute, ephys_chronic, and ephys_precluster.

• ephys_acute - A probe(s) is inserted into a new location during each session.

• ephys_chronic - A probe(s) is inserted once and used to record across multiple sessions.

• ephys_precluster - A probe(s) is inserted into a new location during each session.
  And pre-clustering steps (e.g. CatGT) are performed on the data from each probe prior to Kilosort analysis.

ephys_acute module

ephys_chronic module

ephys_precluster module

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. We provide an example workflow with a pipeline script that models (a) combining this Element with the corresponding Element-Session , and (b) declaring a SkullReference table to provide Location.

Table descriptions

Probe & electrodes

The probe schema contains information regarding the Neuropixels probe and electrode configuration.

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• 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 electrophysiology recording

The ephys schema stores information regarding the recording from a probe for a given session.

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• 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

The ephys schema features automatic ingestion of spike sorting results from the Kilosort analysis method.

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• 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

Click to expand details

• Install element-array-ephys

  pip install element-array-ephys
  

• Upgrade element-array-ephys previously installed with pip

  pip install --upgrade element-array-ephys
  

• Install element-interface

  • element-interface is a dependency of element-array-ephys, however it is not contained within requirements.txt.

  pip install "element-interface @ git+https://github.com/datajoint/element-interface"
  

Usage

Element activation

When using this Element, one needs to run ephys.activate to declare the schemas and tables on the database.

Click to expand details

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: A set of keys identifying a recording session (see Element-Session).
   • SkullReference table: A reference table for InsertionLocation, specifying the skull reference (see example pipeline).

3. Utility functions. See example definitions here

   • get_ephys_root_data_dir(): Returns your root data directory.
   • get_session_directory(): Returns the path of the session data relative to the root.

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.

Citation

• If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.

• DataJoint for Python or MATLAB

  • Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658

  • DataJoint (RRID:SCR_014543) - DataJoint for <Select Python or MATLAB> (version <Enter version number>)

• DataJoint Elements

  • Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358

  • DataJoint Elements (RRID:SCR_021894) - Element Array Electrophysiology (version <Enter version number>)