The Scripps Plankton Camera system: A framework and platform for in situ microscopy

Abstract

The large data sets provided by in situ optical microscopes are allowing us to answer longstanding questions about the dynamics of planktonic ecosystems. To deal with the influx of information, while facilitating ecological insights, the design of these instruments increasingly must consider the data: storage standards, human annotation, and automated classification. In that context, we detail the design of the Scripps Plankton Camera (SPC) system, an in situ microscopic imaging system. Broadly speaking, the SPC consists of three units: (1) an underwater, free-space, dark-field imaging microscope; (2) a server-based management system for data storage and analysis; and (3) a web-based user interface for real-time data browsing and annotation. Combined, these components facilitate observations and insights into the diverse planktonic ecosystem. Here, we detail the basic design of the SPC and briefly present several preliminary, machine-learning-enabled studies illustrating its utility and efficacy.