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2021

An Integrated Toolkit for Extensible and Reproducible Neuroscience


Abstract

As neuroimagery datasets continue to grow in size, the complexity of data analyses can require a detailed understanding and implementation of systems computer science for storage, access, processing, and sharing. Currently, several general data standards (e.g., Zarr, HDF5, precomputed) and purpose-built ecosystems (e.g., BossDB, CloudVolume, DVID, and Knossos) exist. Each of these systems has advantages and limitations and is most appropriate for different use cases. Using datasets that don’t fit into RAM in this heterogeneous environment is challenging, and significant barriers exist to leverage underlying research investments. In this manuscript, we outline our perspective for how to approach this challenge through the use of community provided, standardized interfaces that unify various computational backends and abstract computer science challenges from the scientist. We introduce desirable design patterns and share our reference implementation called intern.


Citation

@INPROCEEDINGS9630199 author=Matelsky Jordan K and Rodriguez Luis M and Xenes Daniel and Gion Timothy and Hider Robert and Wester Brock A and Gray-Roncal William booktitle=2021 43rd Annual International Conference of the IEEE Engineering in Medicine Biology Society (EMBC) An Integrated Toolkit for Extensible and Reproducible Neuroscience

Citation

@INPROCEEDINGS9630199 author=Matelsky Jordan K and Rodriguez Luis M and Xenes Daniel and Gion Timothy and Hider Robert and Wester Brock A and Gray-Roncal William booktitle=2021 43rd Annual International Conference of the IEEE Engineering in Medicine Biology Society (EMBC) An Integrated Toolkit for Extensible and Reproducible Neuroscience