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README.md

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DataJoint Workflow for functional calcium imaging combines multiple DataJoint Elements to process data acquired with [ScanImage](http://scanimage.vidriotechnologies.com), [Scanbox](https://scanbox.org), `Nikon
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NIS`, or `PrairieView` acquisition software, using [Suite2p](https://github.com/MouseLand/suite2p) or [CaImAn](https://github.com/flatironinstitute/CaImAn) analysis software. 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.
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Installation and usage instructions can be found at the
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[Element documentation](https://datajoint.com/docs/elements/element-calcium-imaging).
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To get started, see below for an [interactive tutorial](#interactive-tutorial) on GitHub Codespaces. More information can be found at the
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[Element documentation page](https://datajoint.com/docs/elements/element-calcium-imaging).
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![diagram](https://raw.githubusercontent.com/datajoint/element-calcium-imaging/main/images/diagram_flowchart.svg)
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## Interactive tutorial
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The easiest way to learn about DataJoint Elements is to use the tutorial notebook within a [GitHub Codespace](https://docs.github.com/en/codespaces/overview). Please follow the steps below for the best experience:
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1. Fork this repository to your GitHub account.
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2. Select the green `Code` button.
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3. Within the dropdown menu, select the `Codespaces` tab.
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4. Select the green `Create codespace on main` button.
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5. The environment is ready when a Visual Studio Code window is rendered within your browser. This takes ~5 minutes the first time being launched, and ~1 minute if you revisit this Codespace.
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6. Navigate to the `notebooks` directory on the left panel and open the `tutorial.ipynb` Jupyter notebook. Execute the cells in this notebook to begin your walk through the tutorial.
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7. Once you are done, GitHub will automatically terminate the Codespace after 30 minutes of inactivity or you can manually terminate the Codespace.
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+ If you are new to GitHub and run into any errors, please contact us via email at [email protected]. If you are experienced with GitHub, please create an issue on the upstream repository or issue a pull request with a thorough explanantion of the error and proposed solution.
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**Please Note:**
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+ GitHub Codespaces are limited to 120 core-hours per month for free users. Once you exceed this limit, you will have to wait for the hours to reset or pay to use Codespaces.

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