Mobile autonomous cytometer

Small tool, big impact

A traditional flow cytometer that attaches to a mooring.

Approximately a million microbes can be found in a single milliliter of seawater, which leaves scientists with a vast and complicated array of these single celled organisms to study. Our understanding of the distribution and abundance of marine microbes is largely due to the use of cytometry, which allows scientists to count and characterize microbes.

In a flow cytometer, water is constantly run past a laser or other specifically tuned light source. The way the light reflects off of individual cells reveals cell size and the presence of fluorescent pigments, which together allow the cells to be identified.

When an autonomous camera is added to a cytometer, it automatically takes pictures as water flows through the cytometer. In this way, it functions like an autonomous microscope and produces a large gallery of images for scientists to review.

Why is a mobile cytometer necessary?

Although single-celled microbes are quite small, cytometers themselves are often large, power-hungry, and complex, making them difficult to bring aboard research vessels. Cytometers also require a human operator, which is costly in terms of time and money. Until recently, marine cytometry studies have usually been limited to widely-spaced and discrete samples collected from ships.

A cytometer that was smaller and able to run without human intervention would be less expensive and could be mounted on a variety of autonomous platforms, ranging from mobile gliders to stationary locations. A mobile cytometer would be able to access previously unavailable locations and stay for longer periods of time to take samples, providing an insight into how marine microbe populations change over location and time, and how they respond to climate change and human influence.

Better understanding of marine microbial communities is important because phytoplankton, just one type of microbe, produce 50 percent of the atmosphere’s breathable oxygen. Phytoplankton also regulate atmospheric carbon dioxide, and are the base of the marine food web. Some marine microbes, such as toxic algae can cause red tides, which can have major effects on the health of humans, coastal ecosystems, and fisheries.

How will we get there?

Participants in the “Mobile cytometer-microscope workshop” hosted by MBARI, June 1-3 2016, who formed three working groups to identify and solve obstacles to using a mobile cytometer

MBARI’s Cytometer Technology for Autonomous Platforms Feasibility Study (2013-2016) surveyed existing and emerging technologies for small autonomous cytometers and microscopes that could potentially be integrated with autonomous underwater and surface vehicles. After the team borrowed and evaluated several commercially available instruments, they published a review article in the Marine Technology Society Journal. Three working groups were organized to troubleshoot the existing obstacles to a mobile cytometer:

Image processing and identification:

Using a machine-learning approach, this group is investigating ways to automatically process cytometer images and identify present species. The group is also exploring open-source technology to allow both software and image databases to be shared, which will assist in calibrating and validating newly developed software.

Adaptive sampling:

A mobile cytometer would benefit from adaptive sampling, which means certain base-measurements taken could then trigger other, more specific measurements.

For example, after a species of interest is identified by the cytometer, its vehicle or device may take additional water samples, measure water temperature, or look for specific chemical signals. One application could be a sensor to detect domoic acid, the harmful neurotoxin linked to red tides. The team will first design and implement simple adaptive sampling experiments where information from one sensor can trigger another. Over time, these experiments will evolve in complexity to include multiple vehicles and sensors/samplers.

Onboard processing power:

Adaptive sampling and image processing and identification would require the mobile cytometer to have significant graphical processing units (GPUs), which could be used for both image processing and non-graphical applications. This working group is identifying various GPUs and software developments that could result in useful software that could be shared among instrument development teams.


This project has also led to collaboration with colleagues at the Jupiter Research Foundation (JRF) in their development of an autonomous microscope carried by a Wave Glider. MBARI project engineers offered expertise and advice on microscope design and calibration, which then joined the CANON Fall 2014 and CANON Spring 2015 expeditions.



Solving challenges
Taking the laboratory into the ocean
Environmental Sample Processor (ESP)
In Situ Ultraviolet Spectrophotometer
Midwater Respirometer System
Mobile flow cytometer
Enabling targeted sampling
Automated Video Event Detection
Environmental Sample Processor (ESP)
Gulper autonomous underwater vehicle
Advancing a persistent presence
Aerostat hotspot
Benthic event detectors
Benthic rover
Fault Prognostication
Long-range autonomous underwater vehicle Tethys
MARS hydrophone for passive acoustic monitoring
Monterey Ocean-Bottom Broadband Seismometer
Shark Café camera
Vehicle Persistence
Wave Glider-based communications hotspot
Emerging and current tools
Aerostat hotspot
Wave Glider-based communications hotspot
Data management
Oceanographic Decision Support System
Spatial Temporal Oceanographic Query System (STOQS) Data
Video Annotation and Reference System
Apex profiling floats
Benthic event detectors
Deep particle image velocimetry
Environmental Sample Processor (ESP)
Persistent presence—2G ESP
How does the 2G ESP work?
Arrays on the 2G ESP
Printing probe arrays
Expeditions and deployments
In Situ Ultraviolet Spectrophotometer
Investigations of imaging for midwater autonomous platforms
Lagrangian sediment traps
Midwater Respirometer System
Mobile flow cytometer
SeeStar Imaging System
Shark Café camera
Smart underwater connector
Wave-Power Buoy
Vehicle technology
Benthic Rover
Gulper autonomous underwater vehicle
Imaging autonomous underwater vehicle
Seafloor mapping AUV
Long-range autonomous underwater vehicle Tethys
Mini remotely operated vehicle
ROV Doc Ricketts
ROV Ventana
Automated Video Event Detection
Deep learning
Video Annotation and Reference System
Technology publications
Technology transfer