element-facemap 0.1.3

Facemap DataJoint element

DataJoint Element - Facemap

• This repository features DataJoint pipeline design for facial behavior tracking of head-fixed rodent with MouseLand's Facemap.

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

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

• See the Element Facemap 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

As the diagram depicts, the facemap element starts immediately downstream from Session and Device. We provide an example workflow with a pipeline script that models combining this Element with the corresponding Element-Session.

• VideoRecording: All recordings from a given session.
• RecordingInfo: Meta information of each video recording (number of frames, pixel lengths, fps, etc.)
• FacialSignal: Set of results from SVD of user defined regions.
• FacialSignal.Region: Information about each region (region name, pixel indices, etc)
• FacialSignal.MovieSVD: Principle components, projections, singular values for each movie region
• FacialSignal.MotionSVD: Principle components, projections, singular values for each motion region
• FacialSignal.Summary: Average frame, average motion, spatial binning factor

Installation

• Install element-facemap

  pip install element-facemap
  

• Upgrade element-facemap previously installed with pip

  pip install --upgrade element-facemap
  

Usage

Element activation

To activate the element-facemap, ones need to provide:

1. Schema names

   • schema name for the facial behavior estimation module

2. Upstream tables

   • Session table: A set of keys identifying a recording session (see Element-Session).
   • Device table: A Device table to specify a video recording.

3. Utility functions

   • get_facemap_root_data_dir(): Returns your root data directory.
   • get_facemap_processed_data_dir(): Returns your output root data directory
   • get_facemap_video_files(): Returns your video files

Example usage

See the workflow-facemap repository for an example usage of this Facemap 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 Facemap (version <Enter version number>)