DataJoint Workflow for ZStack Imaging

The DataJoint Workflow for ZStack Imaging combines five DataJoint Elements for volume cell segmentation - Elements Lab, Animal, Session, Calcium Imaging, and ZStack. 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 environment and notebook to learn the pipeline.

Experiment Flowchart

Data Pipeline Diagram

Getting Started

• Interactive tutorial

• Install Element ZStack from PyPI

  pip install element-zstack

• Documentation

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
  • 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 volume_root_data_dir. See User Guide for details.
  • Add your example data to the volume_root_data_dir.

Instructions

1. To upload data to BossDB, create an account to access the BossDB API and generate an API token. Please contact the team at BossDB to ensure you have resource-manager permissions for your account.
2. Follow the instructions below to set up the intern REST API locally.
   • Create a new folder .intern in your user directory.
   • Create a configuration file intern.cfg within the .intern folder. The path to this file should be ~/.intern/intern.cfg.
   • The intern.cfg file should contain the following exactly as shown below:

    # ~/.intern/intern.cfg
    [Default]
    protocol = https
    host = api.bossdb.io
    token = <your-api-key>

3. Use the instructions above to set up a local environment.
4. Navigate to the notebooks directory. Execute the cells in the notebooks to begin your walk through of the tutorial.