DataJoint Workflow - Array Electrophysiology

Workflow for extracellular array electrophysiology data acquired with a polytrode probe (e.g. Neuropixels, Neuralynx) using the SpikeGLX or OpenEphys acquisition software and processed with MATLAB- or python-based Kilosort spike sorting software.

A complete electrophysiology workflow can be built using the DataJoint Elements.

• element-lab
• element-animal
• element-session
• element-array-ephys

This repository provides demonstrations for:

1. Set up a workflow using DataJoint Elements (see workflow_array_ephys/pipeline.py)
2. Ingestion of data/metadata based on a predefined file structure, file naming convention, and directory lookup methods (see workflow_array_ephys/paths.py).
3. Ingestion of clustering results.

Workflow architecture

The electrophysiology workflow presented here uses components from 4 DataJoint Elements (element-lab, element-animal, element-session, element-array-ephys) assembled together to form a fully functional workflow.

element-lab

element-animal

assembled with element-array-ephys

Installation instructions

• The installation instructions can be found at the datajoint-elements repository.

Interacting with the DataJoint workflow

• Please refer to the following workflow-specific Jupyter notebooks for an in-depth explanation of how to run the workflow (03-process.ipynb) and explore the data (05-explore.ipynb).