element-electrode-localization 0.1.0

Electrode localization DataJoint element

DataJoint Element - Electrode Localization

• This repository features a DataJoint pipeline design for localizing the Neuropixels electrodes within the Allen Mouse Common Coordinate Framework (CCF).

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

• This modular pipeline element can be flexibly attached downstream to any particular design of an array electrophysiology pipeline, thus assembling a fully functional electrode localization pipeline.

• See the Element Electrode Localization 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

Installation

• Install element-electrode-localization

  pip install element-electrode-localization
  

• Upgrade element-electrode-localization previously installed with pip

  pip install --upgrade element-electrode-localization
  

• Install element-interface

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

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

Usage

Video Tutorial

Element activation

To activate the element-electrode-localization, ones need to provide:

1. Schema names

   • schema name for the electrode module

2. Upstream tables +

3. Utility functions. See example definitions.

   • 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 details, check the docstring of the element-electrode-localization:

    help(electrode.activate)

Example usage

See the workflow-array-ephys project for an example usage of this 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 Electrode Localization (version <Enter version number>)