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kabilar committed May 12, 2023
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DataJoint Element for functional calcium imaging data acquired with the
[UCLA Miniscope](https://github.com/Aharoni-Lab/Miniscope-v4) and
[Miniscope DAQ](https://github.com/Aharoni-Lab/Miniscope-DAQ-QT-Software)
acquisition system, and analyzed 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.
[Miniscope DAQ](https://github.com/Aharoni-Lab/Miniscope-DAQ-QT-Software) acquisition
system, and analyzed 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.

![diagram](https://raw.githubusercontent.com/datajoint/element-miniscope/main/images/diagram_flowchart.svg)
## Experiment Flowchart

Installation and usage instructions can be found at the
[Element documentation](https://datajoint.com/docs/elements/element-miniscope).
![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.svg)

## Getting Started

+ Install from PyPI

```bash
pip install element-miniscope
```

+ [Interactive tutorial on GitHub Codespaces](https://github.com/datajoint/workflow-miniscope#interactive-tutorial)

+ [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 [email protected].

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