Tutorials

• Element Calcium Imaging includes an interactive tutorial on GitHub Codespaces, which is configured for users to run the pipeline.

• DataJoint Elements are modular and can be connected into a complete pipeline. In the interactive tutorial are example Jupyter notebooks that combine five DataJoint Elements - Lab, Animal, Session, Event, and Calcium Imaging. The notebooks describe the pipeline and provide instructions for running the pipeline. For convenience, these notebooks are also rendered on this website:
  • Tutorial notebook
  • Quality metrics notebook

Installation Instructions for Active Projects

• The Element Calcium Imaging described above can be modified for a user's specific experimental requirements and thereby used in active projects.

• The GitHub Codespace and Dev Container is configured for tutorials and prototyping.
  We recommend users to configure a database specifically for production pipelines. Instructions for a local installation of the integrated development environment with a database can be found on the User Guide page.

Videos

• The YouTube tutorial gives an overview of the workflow files and notebooks, as well as core concepts related to calcium imaging analysis.

EXTRACT

• Analysis with the EXTRACT package is currently supported for single channel, single plane scans using Suite2p for motion correction. For processing with EXTRACT, please set processing_method="extract" in the ProcessingParamSet table, and provide the params attribute of the ProcessingParamSet table in the {'suite2p': {...}, 'extract': {...}} dictionary format. Please also install the MATLAB engine API for Python.