/workflow-miniscope

Example DataJoint workflow for miniscope calcium imaging analysis with CaImAn

Primary LanguageJupyter NotebookMIT LicenseMIT

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

flowchart

Data Pipeline Diagram

pipeline

Getting Started

Support

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

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.