Design of a Low-cost, Submersible, Digital Holographic Microscope for in Situ Microbial Imaging

Abstract

The methodologies for studying marine microbiology typically consist of utilizing instrumentation within a laboratory. This typically requires extracting a sample from its place of origin prior to examination, which may be days after collection. Oftentimes, the solution is to bring the lab to the ocean, which may be costly and provide further limitations for a sterile and stable laboratory environment. Here we present a low-cost, submersible, digital holographic microscope (DHM) designed to image marine microorganisms (such as bacteria and plankton) in their natural underwater environment. Our instrument eliminates the need to transport samples and allows for instantaneous data collection of microbes in-situ. The DHM achieves sub-micron spatial resolution and is paired with artificial intelligence for the detection and tracking of specimens to reduce the overall collected data. This instrument also aims to reduce the cost of manufacturing and field expenses relative to marine micro-biological research. “Off the shelf” components were selected in the design process of this instrument which allows us to achieve precise results without sacrificing data quality. The DHM itself costs under one thousand dollars and features a low-cost high-resolution camera, the Arducam MT9J001. Included in the design were five main subsystems: optical, mechanical, electrical, power, and machine learning. Our on board computer and artificial intelligence consist of a Raspberry Pi 4 (8 Gb) and Google Coral USB Tensorflow accelerator. Instrument testing has successfully proven our abilities of data acquisition for at least two hours in depths of at least forty meters below sea level. Additionally, our artificial intelligence system is currently capable of tracking up to ten areas of interest in a fraction of a second with over ninety percent confidence via the neural net driven by the tensor cores on the Google Coral. Furthermore, we have demonstrated the versatility of our instrument by mounting it on an ocean-going ROV, the BlueRov2 by Blue Robotics. Our tests on the BlueRov2 exemplified the cost-effective nature of a submersible and reusable instrument that can be implemented in moderate environments and on most vessels.