Element Calcium Imaging

DataJoint Element for functional calcium imaging with ScanImage, Scanbox, Nikon NIS-Elements, and Bruker Prairie View acquisition software; and Suite2p, CaImAn, and EXTRACT analysis software. DataJoint Elements collectively standardize and automate data collection and analysis for neuroscience experiments. Each Element is a modular pipeline for data storage and processing with corresponding database tables that can be combined with other Elements to assemble a fully functional pipeline.

Experiment Flowchart

Data Pipeline Diagram

• We have designed three variations of the pipeline to handle different use cases. Displayed above is the default imaging schema. Details on all of the imaging schemas can be found in the Data Pipeline documentation page.

Getting Started

• Please fork the repository

• Clone the repository to your computer

  git clone https://github.com/<enter_github_username>/element-calcium-imaging
  

• Install with pip

  pip install -e .
  

• Data Pipeline - Pipeline and table descriptions

• Tutorials - Start building your data pipeline

• Code Repository

Support

• If you need help getting started or run into any errors, please contact our team by email at support@datajoint.com.