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OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience πŸπŸ§ πŸ”¬πŸ–₯οΈπŸ“ˆ

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OpenScope Databook

The Deployed Databook can be found here: https://alleninstitute.github.io/openscope_databook

The citeable DOI page on Zenodo can be found here: https://zenodo.org/records/12614664

The OpenScope Databook is meant to store code and documentation used for reproducible brain data analysis and visualization, primarily working with NWB files and the DANDI archive. It is provided by the Allen Institute's OpenScope Project, a component of The Allen Institute for Neural Dynamics. OpenScope is a platform for high-throughput and reproducible neurophysiology open to external scientists to test theories of brain function. Through Jupyter Book, this code is structured as a series of documented Jupyter notebooks intended to explain and educate users on how to work with brain data.

We are releasing this code to the public as a tool we expect others to use and are actively updating and maintaining this project. Issue submissions are encouraged. Questions can be directed to @rcpeene or @jeromelecoq. Below, you can see a working list of the content goals for this databook. We are open to hearing input from users about what types of analysis and visualization might be useful for reproducible neuroscience, particularly when working with the NWB file standard.

Content Goals

Chapter 1: Using DANDI/getting data

Chapter 2: Data visualization

Chapter 3: First-order analysis

Chapter 4: Higher-order analysis

Chapter 5: Replicating figures

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OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience πŸπŸ§ πŸ”¬πŸ–₯οΈπŸ“ˆ

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