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Using BossDB Tools to Access, Visualize, and Share Volumetric Neuroscience Data.

Hannah Martinez1, Nicole Guittari1, Timothy Gion1

  • 1Johns Hopkins Applied Physics Laboratory, Laurel, Maryland.

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PubMed
Summary
This summary is machine-generated.

BossDB provides a free, cloud-based archive for petascale neuroimaging data, focusing on FAIR principles. It offers tools and protocols for researchers to access, analyze, and share electron microscopy and connectomics datasets.

Keywords:
BossDBconnectomicselectron microscopyneuroglancerneuroscience

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Area of Science:

  • Neuroscience
  • Data Science
  • Bioinformatics

Background:

  • Petascale neuroimaging data presents significant storage and accessibility challenges.
  • Sharing and analyzing large-scale neuroimaging datasets is crucial for advancing neuroscience research.
  • Existing data archives may not fully adhere to FAIR (Findable, Accessible, Interoperable, Reusable) principles.

Purpose of the Study:

  • To introduce BossDB, a free and publicly accessible archive for petascale neuroimaging data.
  • To provide detailed protocols for utilizing BossDB's interfaces and tools for data management and analysis.
  • To facilitate the sharing and accessibility of electron microscopy (EM) and X-ray microtomography (XRM) imaging data.

Main Methods:

  • BossDB utilizes cloud-based infrastructure and software tools to ensure data accessibility and analysis.
  • The archive supports volumetric EM and XRM imaging data, including segmentations, annotations, meshes, and connectomes.
  • Users can interact with BossDB via a website, Python SDK, and web API for various data operations.

Main Results:

  • Step-by-step protocols are presented for browsing, accessing, downloading, visualizing, analyzing, and uploading data.
  • Specific protocols cover data access using Python SDK and data API, metadata querying, and creating visualizations.
  • Protocols for account creation and data uploading (public and private) are also detailed.

Conclusions:

  • BossDB offers a comprehensive solution for managing and analyzing large-scale neuroimaging datasets.
  • The provided protocols empower researchers to effectively use BossDB for data exploration and contribution.
  • BossDB promotes FAIR data principles, enhancing the collaborative potential within the neuroscience community.