Studying the Ocean’s Microscopic World With the AUTOHOLO

Off the west coast of Florida, recurring toxic, harmful algal blooms (HABs) of microscopic algae—Florida’s so-called red tide—can kill and widely impact fish, dolphins, seabirds, manatees, and can cause severe health issues in humans. In Florida’s freshwater lakes and estuaries, nutrient pollution, and other environmental factors produce recurring cyanobacteria blooms, which can coat the water’s surface with toxic green sludge. To better understand why these HABs are occurring and under what environmental conditions, researchers at Florida Atlantic University Harbor Branch Oceanographic Institute (FAU Harbor Branch) developed the AUTOHOLO, a novel autonomous underwater holographic microscope.

“We have improved upon a known technology to expand our capabilities in HAB research,” said Malcolm McFarland, Research Scientist at FAU Harbor Branch. “This device allows us to image the underwater microscopic world in its natural and undisturbed state.”


The AUTOHOLO installed within its towed enclosure before deployment from an FAU Harbor Branch Oceanographic Institute small RV Ocean Power. (Image credit: FAU HBOI)

In an underwater holographic microscope like the AUTOHOLO, a laser light illuminates a natural and undisturbed volume of water, and a camera records the light which is scattered by the particles within that volume. This process results in a 3D image (or hologram) of all the microscopic organisms in the volume of water, precise enough to allow scientists to determine the different types of plankton/algae species present, how they are distributed, and at what concentrations.

Compared to traditional lab-based microscopes, the AUTOHOLO takes underwater holographic images in the field rather than needing to take water samples back to the lab for analysis. It can also capture images in the field for extended periods of time rather than just a single snapshot, which is one of its main advantages. “We’re using these new technologies and techniques to look at the microscopic world in a novel way and to see things that we were never able to see before with the old techniques,” he said, “and this will really open up a whole new view of HAB ecology, by directly looking at what's going on in the water.”


Researchers deploy the AUTOHOLO in Lake Erie, Mich., in August 2022, during an ongoing cyanobacterial bloom. (Image credit: Steve Ruberg)

Microscopic plant-like organisms, called phytoplankton (or more commonly called algae), are the base of aquatic food webs and responsible for almost half of the world’s primary production of carbon ‘foods’ through photosynthesis. Most are not harmful. “Marine algae are a critical piece of aquatic ecosystems and are essential to life,” said McFarland, “adding tools like the AUTOHOLO can answer basic questions in aquatic science that haven't yet been answered with standard microscopes. Algae are very dynamic. They're always changing. There are always different species growing and others dying; it is very complex in an ecological sense.”

Versatile Use

“We have made the AUTOHOLO as versatile as possible for deployment in almost any imaginable condition,” said Dr. Aditya Nayak, Assistant Professor, FAU Harbor Branch, “from spending weeks deployed on stationary platforms in shallow water to collect continuous samples, or towed behind a boat, to being deployed at varying depth profiles for a few hours in the open ocean.” By keeping the design flexible, it allows for a modifiable optical mechanism to record organisms from just a few micrometers to a few centimeters. Additionally, the optics can look through cloudy water as well as clear water.


An image of cells of the toxic, bioluminescent dinoflagellate Pyrodinium bahamense acquired during a bloom in the northern Indian River Lagoon in South Florida. (Image credit: FAU)

In a recent study published in the journal Harmful Algae, Nayak and other FAU Harbor Branch scientists employed the AUTOHOLO for the rapid detection of ‘red tides’ caused by the toxic marine algae Karenia brevis and highlighted the benefits of the AUTOHOLO over current ‘red tide’ monitoring methods. They used the AUTOHOLO to take field measurements in the coastal Gulf of Mexico during an active K. brevis bloom. To analyze the data, Nayak and the team trained a convolutional neural network to detect different algae species and identify them automatically, which Nayak says, “requires a lot of legwork.”

In the Past

The AUTOHOLO builds on prior research conducted by Jim Sullivan, Ph.D., Executive Director of FAU Harbor Branch, who developed and used an earlier generation of the instrument to document how algae horizontally orient in the ocean, likely to maximize their photosynthesizing abilities.

“That was something that no one had ever been able to really see before,” McFarland said. “And it's because of the holographic imaging technique that we were able to visualize this because you can look at an undisturbed volume of water.”

McFarland said an earlier holographic system was deployed by FAU Harbor Branch in the Gulf of Maine in 2000 and was mounted atop the Johnson Sea Link submersible. “These older systems were very ungainly and big pieces of equipment to manage,” he said. “So, we've gotten it down to something that's relatively small, and we can now easily deploy it over the side of a small boat to get in the water.”

Public Benefit

Currently, images collected by the AUTOHOLO are taken to the lab for processing. Using machine-learning techniques, the data can be rapidly analyzed overnight with automated classification tools, which would take weeks or longer if done manually, McFarland said.

The next goal for Nayak, McFarland and other FAU Harbor Branch scientists, is to develop more AUTOHOLO imaging systems and integrate them with existing real-time monitoring systems to help detect HABs in advance. The real-time data would serve to inform the public regarding water management and recreation, ultimately keeping people safe from toxic HABs.


The AUTOHOLO submersible holographic microscope on a bench in the laboratory at FAU Harbor Branch Oceanographic Institute. (Image credit: FAU)

For now, Nayak said they have made their database of plankton/algae publicly available for other scientists to use and develop detection algorithms. A few publications have already come from the data. “It’s unique; there's no other holographic plankton database right now in the world,” he said. “So, we've made that available, generally to the science community and whoever wants it upon request. Time will tell what more we can learn from these data.”

To discover more of the holographic microscope world, visit: https://rb.gy/zdxaht

This feature appeared in Environment, Coastal & Offshore (ECO) Magazine's 2023 Deep Dive I special edition Ocean Observation, to read more access the magazine here.

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