DataJoint Workflow for Miniscope Calcium Imaging

The DataJoint Workflow for miniscope calcium imaging data acquired with miniature microscopes (e.g. UCLA Miniscope) using the Miniscope-DAQ acquisition software and processed with CaImAn. 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. This repository also provides a tutorial notebook to learn the pipeline.

Experiment Flowchart

Data Pipeline Diagram

Getting Started

• Interactive tutorial

• Install Element Miniscope from PyPI

  pip install element-miniscope

• Documentation

Support

• If you need help getting started or run into any errors, please contact our team by email at [email protected].

Interactive Tutorial

Launch Environment

• Local Environment
  • Install Git
  • Install VSCode
  • Install Conda
  • Install Mamba
  • Install CaImAn
  • Configure a database. See here for details.
  • git clone the code repository and open it in VSCode
  • Install the repository with pip install -e .
  • Setup a dj_local_conf.json with the database.prefix and miniscope_root_data_dir. See User Guide for details.
  • Add your example data to the miniscope_root_data_dir.

Instructions

1. We recommend you start by navigating to the notebooks directory. Execute the cells in the notebooks to begin your walk through of the tutorial.