spyglass-neuro 0.3.0

Neuroscience data analysis framework for reproducible research

spyglass

spyglass is a data analysis framework that facilitates the storage, analysis, visualization, and sharing of neuroscience data to support reproducible research. It is designed to be interoperable with the NWB format and integrates open-source tools into a coherent framework.

Documentation can be found at - https://lorenfranklab.github.io/spyglass/

Installing from pip

Install spyglass

pip install spyglass-neuro

Some functions may take advantage of the latest changes to spike interface, which currently has a slow release cycle. To get the latest changes:

pip install git+https://github.com/SpikeInterface/spikeinterface.git

The Frank Lab typically uses mountainsort, although spyglass uses spikeinterface, which allows for any spike sorter. To install mountainsort:

pip install mountainsort4

Spyglass uses the package ghostipy for filtering of signals:

pip install ghostipy

WARNING: If you are on an M1 Mac, you need to install pyfftw via conda BEFORE installing ghostipy

conda install -c conda-forge pyfftw

Finally, if you want to decode on the GPU, you must install cupy:

conda install -c conda-forge cupy

Setup

See the documentation for setup instructions - https://lorenfranklab.github.io/spyglass/type/html/installation.html

Tutorials

The tutorials for spyglass is currently in the form of Jupyter Notebooks and can be found in the notebooks directory. We strongly recommend opening them in the context of jupyterlab.

Contributing

See the Developer's Note for contributing instructions found at - https://lorenfranklab.github.io/spyglass/type/html/how_to_contribute.html

License/Copyright

License and Copyright notice can be found at https://lorenfranklab.github.io/spyglass/type/html/copyright.html

Citation

Kyu Hyun Lee, Eric Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules, Alison Comrie, Jennifer Guidera, Rhino Nevers, Daniel Gramling, Philip Adenekan, Ji Hyun Bak, Emily Monroe, Andrew Tritt, Oliver Rübel, Thinh Nguyen, Dimitri Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia, Alessio Buccino, Emily Aery Jones, Lisa Giocomo, and Loren Frank. Spyglass: A Data Analysis Framework for Reproducible and Shareable Neuroscience Research. Neuroscience Meeting Planner. San Diego, CA: Society for Neuroscience, 2022.