https://github.com/datajoint/workflow-miniscope

Example DataJoint workflow for miniscope calcium imaging analysis with CaImAn
https://github.com/datajoint/workflow-miniscope

Last synced: 7 months ago
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Example DataJoint workflow for miniscope calcium imaging analysis with CaImAn

• Host: GitHub
• URL: https://github.com/datajoint/workflow-miniscope
• Owner: datajoint
• License: mit
• Created: 2021-03-22T21:48:13.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2023-05-18T16:14:54.000Z (over 2 years ago)
• Last Synced: 2025-04-29T22:36:23.382Z (10 months ago)
• Language: Jupyter Notebook
• Homepage: https://datajoint.com/docs
• Size: 1.1 MB
• Stars: 2
• Watchers: 10
• Forks: 9
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

          
# DataJoint Workflow for Miniscope Calcium Imaging

The DataJoint Workflow for miniscope calcium imaging data acquired with miniature

microscopes (e.g. [UCLA Miniscope](https://github.com/Aharoni-Lab/Miniscope-v4)) using

the [Miniscope-DAQ](https://github.com/Aharoni-Lab/Miniscope-DAQ-QT-Software)

acquisition software and processed with

[CaImAn](https://github.com/flatironinstitute/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](https://raw.githubusercontent.com/datajoint/element-miniscope/main/images/flowchart.svg)

## Data Pipeline Diagram

![pipeline](https://raw.githubusercontent.com/datajoint/element-miniscope/main/images/pipeline_imaging.svg)

## Getting Started

+ [Interactive tutorial](#interactive-tutorial)

+ Install Element Miniscope from PyPI

     ```bash

     pip install element-miniscope

     ```

+ [Documentation](https://datajoint.com/docs/elements/element-miniscope)

## 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](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)

  + Install [VSCode](https://code.visualstudio.com/)

  + Install [Conda](https://docs.conda.io/en/latest/miniconda.html)

  + Install [Mamba](https://mamba.readthedocs.io/en/latest/installation.html)

  + Install [CaImAn](https://caiman.readthedocs.io/en/master/Installation.html)

  + Configure a database.  See [here](https://tutorials.datajoint.org/setting-up/local-database.html) 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](https://datajoint.com/docs/elements/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.