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

BossDB is a free and publicly accessible archive for storing and sharing petascale neuroimaging data. Focused on FAIR (i.e., findable, accessible, interoperable, and reusable) principles, it utilizes cloud-based infrastructure and software tools to facilitate data access and analysis. BossDB specializes in storing volumetric electron microscopy (EM) and X-ray microtomography (XRM) imaging data along with associated segmentations, annotations, meshes, and connectomes. Users can browse, access, download, visualize, analyze, and upload data through a variety of interfaces, including the BossDB website, Python software development kit (SDK), and web application programming interface (API). Here we present step-by-step protocols for using these interfaces and BossDB tools to perform each of these tasks. These protocols target any researcher who is interested in learning more about BossDB public datasets, analyzing high-resolution neuroimaging and connectomics data with software tools, or contributing a project to BossDB's catalog of public and private data. © 2025 The Johns Hopkins University Applied Physics Laboratory LLC. Current Protocols published by Wiley Periodicals LLC. Support Protocol 1: Browsing public data online Basic Protocol 1: Accessing data with Python Basic Protocol 2: Accessing data with data API Basic Protocol 3: Metadata querying via metadata API Basic Protocol 4: Creating a Neuroglancer visualization Support Protocol 2: Creating a BossDB account Basic Protocol 5: Uploading data and metadata Basic Protocol 6: Uploading a small dataset for private use.