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DataJoint Workflow - Calcium Imaging

Workflow for calcium imaging data acquired with ScanImage,
Scanbox, or Nikon NIS software and processed with Suite2p or CaImAn.

A complete calcium imaging workflow can be built using the DataJoint Elements.

This repository provides demonstrations for:

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

See the Element Calcium Imaging 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.

Workflow architecture

The calcium imaging workflow presented here uses components from four DataJoint Elements (element-lab, element-animal, element-session, element-calcium-imaging) assembled together to form a fully functional workflow.

element_calcium_imaging

Installation instructions

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).

  • See our YouTube tutorial for a walkthrough of the schemas and functions:

    YouTube tutorial

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 Calcium Imaging (version <Enter version number>)