Shedding light on the diverse plankton universe of the Northern California Current

Moritz S Schmid* and Margaret E Martinez


The northern California Current (NCC) is a dynamic, highly productive region within the broader California Current Large Marine Ecosystem (CCLME), that exhibits strong ecosystem variability on seasonal, interannual, and decadal time scales. Along the California, Oregon, and Washington coasts, wind blowing alongshore the US coast can create upwelling and downwelling events. Wind blowing Southward pushes surface water away at a 90-degree angle (through the Coriolis force, see more info here). Surface waters moving away are then replaced by the deeper water underneath. This deeper water coming to the surface has more nutrients than the surface water (because the nutrient-using phytoplankton doesn’t grow as good at depth – without sunlight), and thus this upwelled, nutrient-rich water can now sustain new phytoplankton growth, which in turn can then support more zooplankton growth, and so on. Downwelling on the other hand occurs when the alongshore wind is blowing Northward. The same Coriolis effect now pushes water into the landmass at a 90-degree angle from the Northward blowing wind. Because the water has nowhere to go, the least resistance for the water is to push downward. Thus, surface water is forced deeper, and no upwelling effect occurs. Along the CA, OR, and WA coasts, wind patterns differ, and while most of the California coast experiences Southward blowing winds year-round, and subsequent upwelling also occurring year-round, Oregon and Washington experience a mix of North-, and Southward winds in summer, and predominantly Northward winds winter. The mix of South-, and Northward wind means the coast gets some upwelling and some downwelling, also referred to as intermittent upwelling, while Northward winds in winter mean that the coast gets less new nutrients from depth during that time. Ultimately, this means that the California coast experiences continuous new nutrient input from deep water that can be used by the organisms, while along the OR and WA coasts this input is more inconsistent. Nonetheless, also OR and WA coastal waters provide a unique and productive environment for plankton and fishes that sustains the livelihood of many communities on the Pacific Northwest coast.

In May and early June 2021, we joined the National Oceanic and Atmospheric Administration’s (NOAA) Northern California Current (NCC) cruise aboard NOAAS Bell M. Shimada. NOAA’s NCC cruises occur on a regular basis and are designed to characterize the planktonic ecosystem ranging from northern California to Washington, with a focus on the Newport Hydrographic Line. Our aim was to collect zooplankton imagery for the NCC Marine Biodiversity Observation Network (MBON, see more info here and here) funded by NASA, as well as the Belmont Forum-funded project ‘World Wide Web of Plankton Image Curation’ (wPIC, see more info here and here), using the In Situ Ichthyoplankton Imaging System (ISIIS, Figs. 1-4).

The MBON project’s focus is on seascapes. Similar to different landscapes on land, the surface ocean can be classified into different categories based on environmental variables such as phytoplankton abundance and temperature. While seascapes are currently classified using data from the surface ocean (i.e., the first 10 m of the ocean) largely due to heavily relying on satellite data, we collect data using ISIIS to inform seascapes also using information from deeper waters (e.g., data on plankton and temperature down to 100 m). wPIC is aiming at very different things – it is largely a project focused on underwater imaging methods. The idea is that all around the world laboratories use different instruments for imaging aquatic animals, and these instruments also come with different methodologies of processing the images and ancillary data. wPIC’s aim is to streamline these efforts more and to better exploit synergies between different projects and instruments. wPIC includes project partners from France, Japan, Brazil, and the US.

Figure 1. Deploying ISIIS on a gray day off the Oregon Coast.
Figure 2. ISIIS is secured to the aft deck of NOAAS Bell M. Shimada as it heads out past the bar in Newport, Oregon, for the start of the Spring 2021 NCC cruise.
Figure 3. Moritz and Margaret posing with ISIIS after a successful nighttime recovery.
Figure 4. “Flying” ISIIS means observing multiple monitors, each tracking several variables, ranging from ship and ISIIS speeds, communication with the winch operator outside who hauls-in and pays-out oceanographic wire, raising and lowering the ISIIS, to making sure all cameras are recording, and looking for interesting ecological features in the live imagery coming through the fiber optic data stream.

ISIIS is a line-scan and shadowgraph imager that records the shadows of organisms swimming through the beam of light projected by a LED (Fig. 5). With this setup, a water parcel measuring 13 cm x 13 cm x 45 cm is recorded by the camera system, ultimately leading to 180 L of seawater imaged per second. Compared to other imaging systems, this is a very large volume of imaged water, which gives us the ability to look at rather rare larval fishes (Fig. 6) as well as fragile jellies and the ubiquitous crustacean zooplankton (Figs 7-8).

Figure 5. A schematic of the lower pods of ISIIS (compare with Fig. 1) housing the LED and camera setup.

Figure 6. A myctophid (lanternfish, left), and an engrauliid (anchovy, right).


A dense layer of doliolids.
A chaetognath (arrow worm).
A cydippid ctenophore.
Eutonina indicans, a leptomedusae, with gonads visible in the radial canals.


Figure 7. Key gelatinous zooplankton in the NCC includes doliolids, chaetognaths, ctenophores, and hydromedusae*.


Several euphausiids having a dance party.
Mitrocoma cellularia.

A large euphausiid dwarfs a calanoid copepod.
A lobate ctenophore showing off its auricles (red arrow).


Figure 8. Key crustaceans include euphausiids and calanoid copepods. ISIIS’s ability to image fragile jellyfish without disturbance is clearly visible in the images of Mitrocoma and its many tentacles, as well as a ctenophore with its auricles clearly visible*.

*All images except the doliolids (Crescent City line, 5/26/2021), were taken from Newport Hydrographic Line imagery (5/23/2021).

Using a sophisticated image processing pipeline (Luo et al. 2018, Schmid et al. 2021), based on artificial intelligence, we can quickly identify all plankton in the images, and also get their sizes. These ecological data can then be used in a diversity of ecological studies. As ISIIS produces vast quantities of data (ca. 75-100 million images for a 7-hr ISIIS transect) we collaborate with the National Science Foundation’s Extreme Science and Engineering Discovery Environment (XSEDE), a nationwide supercomputing cluster. Controlling the processing from Oregon State University’s (OSU) Center for Genomics and Biocomputing (CGRB), but utilizing hardware at XSEDE (Fig. 9), we are able to get through the data blazingly fast. The resulting data enables us to tackle ecological questions that wouldn’t be possible with more traditional net systems (e.g., Briseño-Avena et al. 2020, Schmid et al. 2020, Swieca et al. 2020).

Figure 9. The Plankton Ecology Lab’s image processing pipeline deployed at OSU’s CGRB and using resources on NSF XSEDE. The orange panel shows components at the CGRB, while components in the lower panel (i.e., the cloud) are deployed on NSF’s XSEDE supercomputing cluster.

At this point we want to give a big shout out to all our citizen scientists at Plankton Portal who help with making these studies possible by volunteering to classify plankton. This effort helps us to fine-tune plankton classification image libraries and models, and provides insight into how automated plankton classifications differ from human annotations (Robinson et al. 2017). We hope that you enjoyed this little glimpse into collecting the images that you get to look at. We also thank Jennifer Fisher, the Chief Scientist on NOAA’s NCC cruise on NOAAS Bell M. Shimada, as well as Bell M. Shimada’s CO Amanda Goeller, and crew, as well as all scientists who helped with manning the ISIIS winch.


Briseño-Avena C, Schmid M, Swieca K, Sponaugle S, Brodeur R, Cowen RK. 2020. Three dimensional cross-shelf zooplankton distributions off the central Oregon coast during anomalous oceanographic conditions. Progr Oceanogr 188:102436

Luo JY, Irisson J-O, Graham B, Guigand C, Sarafraz A, Mader C, Cowen RK. 2018. Automated plankton image analysis using convolutional neural networks. Limnol Oceanogr Methods 16: 814-827

Robinson KL, Luo JY, Sponaugle S, Guigand C, Cowen RK. 2017. A tale of two crowds: Public engagement in plankton classification. Frontiers Mar Sci 4:82

Swieca K, Sponaugle S, Briseño-Avena C, Schmid M, Brodeur R, Cowen RK. 2020. Changing with the tides: fine-scale larval fish prey availability and predation pressure near a tidally-modulated river plume. Mar Ecol Progr Ser 650:217-238

Schmid MS, Daprano D, Jacobson KM, Sullivan CM, Briseño-Avena C, Luo JY, Cowen RK. 2021. A Convolutional Neural Network based high-throughput image classification pipeline – code and documentation to process plankton underwater imagery using local HPC infrastructure and NSF’s XSEDE. [Software]. Zenodo.

Schmid MS, Cowen RK, Robinson KL, Luo JL, Briseño-Avena C, Sponaugle S. 2020. Prey and predator overlap at the edge of a mesoscale eddy: fine-scale, in-situ distributions to inform our understanding of oceanographic processes. Sci Rep 10:921

Upcoming cruise to collect California Current (summer) data

We are gearing up for another cruise! These data will augment our California Current (summer) dataset that you all have been diligently sorting for the last few weeks. 

Yesterday PI Bob Cowen, post-doc Moritz Schmid, and graduate students Kelsey Swieca and Margaret Martinez began cruise mobilization by moving the plankton imager (In situ Ichthyoplankton Imaging System) from the lab to the marine center’s loading dock.  It was a tight squeeze, but we made it! Today we will check all of the nuts and bolts on the imager then transport it to the ship staging area before beginning a 7 day shelter in place prior to cruise departure (a COVID precaution). 

Keep an eye out for an at-sea blog post over the next few weeks.

Plankton Portal Publication: Thank you!

“The archetypal approach of a single research group processing and analyzing large datasets in isolation is becoming increasingly infeasible — particularly given the need for the data to be promptly incorporated into ocean health assessments and marine ecosystem management. An effective, alternative approach is citizen science.” 

This was a main finding of Robinson and colleagues’ recent paper examining how citizen scientists, including those from Plankton Portal, can help researchers chip away at their ‘big data’ processing goals. The authors of this article, including many of Plankton Portal‘s Science Team members, explain that with the advent of high resolution sampling technologies, it has become essential for biological oceanographers to develop innovative ways to process their data in a timely matter. One approach to this problem is citizen science.

Excitingly, this paper also found that Plankton Portal and its sister citizen science project, Kaggle, where data scientists competed to develop computer algorithms for automated image processing, are effective tools for engaging, educating, and promoting public engagement in plankton classification.

Citizen science has proven invaluable to Plankton Portal‘s Science Team. Check out our paper and be sure to read the Acknowledgements section were we give a special thanks to our most active volunteers. Thank you for your contributions and we look forward to continuing to work with you!



Paper link:

Citation: Robinson KL, Luo JY, Sponaugle S, Guigand C, Cowen RK (2017) A tale of two crowds: public engagement in plankton classification. Front Mar Sci 4: 82. doi: 10.3389/fmars.2017.00082


innovative citizen sailing oceanography

Just discovered this, after reading the Tara Expedition news periodical while visiting Tara in Miami! This is a very interesting Citizen Science project inspired from the Tara Expeditions. The idea is to “recruit” the help of volunteer sailors across the world and have them collect plankton using a very simple method of sample preservation. The sample is then sent to a lab for DNA barcoding to look at the different species present in the sample. A very elegant way to do oceanography.



go visit:

OSTRICH cruise leg 2 almost done!

We have been zigzagging up and down the Florida Straits for the last two weeks. This photo, from two days ago, shows our ship track (in blue) and drifter track (in red).

RV Walton Smith Tracks

Our first study was the Spatial Study, where we deployed a drifter at the beginning of the day, and then followed it, sampling with ISIIS and MOCNESS in a zig-zag track for the whole day. We started our cruise sampling near Miami and Bimini, Bahamas, and finished up the Spatial Study in the FL Keys.

Photo by Cedric Guigand, taken with a Phantom DJI drone

Research Vessel F.G. Walton Smith during the OSTRICH Cruise, June 2014. Photo by Cedric Guigand, taken with a Phantom DJI drone.


In the second leg of our cruise (which concludes tonight), we have been sampling in the Lagrangian Study, which lasted a total of 4 days. We deployed a drifter in the Lower Keys at the beginning of the study and have been following it continuously, sampling with ISIIS and MOCNESS.

The idea is that by following a drifter, we will be continuously sampling the same body of water. Consider this analogy: you are sampling a fast moving stream. If you stand at a fixed point on land and continuously sample, you sample different parts of the stream because it is constantly flowing in front of you. However, if you build a raft and float down the stream with it, sampling along the way, then you are actually sampling the same part of the stream at different points in time. The latter case is what we are doing. The Gulf Stream / Florida Current is our fast moving “stream” and we are drifting with the stream in a fancy raft, sampling along the way.

R/V F.G. Walton Smith, aerial view of the back deck, with ISIIS on board. Photo by Cedric Guigand

Continue following our updates on the ISIIS Facebook page as we conclude our 18-day cruise this week.

Polychaetes: ocean “crawlers”

The name for these worms literally means “many bristles,” which refers to the “legs” that they use to move through the water. These surprisingly fast animals are predators of copepods, appendicularians, and even small larval fishes. Most polychaetes are meroplankton, meaning that they are plankton only for their egg and larval stages. When they reach a certain size, they settle out of the water column and spend their adult lives associated with some kind of substrate (e.g., reefs, sand, mud, rock, etc.). A few species are holoplanktonic, spending their entire lives drifting in the ocean currents.

One genus of holoplanktonic polychaete that we have encountered in the ISIIS images is Tomopteris. These 2-5 cm polychaetes feature several adaptations that are favorable for life in water column. First, they are highly transparent, allowing them to blend into the surrounding water. If they could be easily seen, polychaetes would be tasty little snacks for fish. One thing that limits their transparency is a gut that runs down the middle of the body. When this gut is full, the polychaete is easier to see because it cannot hide a stomach full of food! Someone might hypothesize that polychaetes that have recently eaten might be more susceptible to visual predators, such as fish, but to date, no one has explored this question. Second, their “legs” have paddle-shaped ends with two lobes, which improve their swimming ability compared to other groups of polychaetes (Todd et al. 1996).


Many of these polychaetes (Tomopteris spp.) are actively swimming. The gut runs down the center of the animal between the legs, but it is difficult to see in these images.

Although polychaetes are relatively rare plankton, we did manage to see a good number of them near Stellwagen Bank, Massachusetts, USA. The graph shows the vertical distribution of the Tomopteris polychaetes along two ISIIS transects. As you can see, Tomopteris polychaetes were predominantly found in deeper waters. In the images taken, it is difficult to see the gut, which would show up as a white line running down the middle of the body. This means that these individuals had not eaten recently, so what are they doing in the deep waters? Possibly hiding from predators in waters with less light? Or could this behavior be related to mating? Only with further research can we find out what influences the distributions of these and other planktonic animals.


Near Stellwagen Bank, Massachusetts, USA, many of the polychaetes tended to reside deeper in the water column. They are virtually absent from the top 20 m.

Unidentified polychaete larvae imaged by ISIIS in the Gulf of Mexico

Unidentified polychaete larvae imaged by ISIIS in the Gulf of Mexico.


Todd CD, Laverack MS, Boxshall GA (1996) Coastal Marine Zooplankton: A practical manual for students (2nd ed.) Cambridge University Press, New York.

Great plankton pictures taken offshore Miami

Here is a nice collection of plankton underwater shot  by Dr. Evan D’alessandro while conducting research offshore Miami

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the Portuguese Man of War is not a Jellyfish but a Siphonophore!

The Portuguese Man of War or Physalia is a siphonophore floating at the surface of the ocean like a drifting balloon with deadly tentacles waiting to capture careless preys. Its body looks like a sail that catches the ocean wind to propel itself.

More Information on Physalia

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Portuguese Man of War Fish

The Portuguese Man of War Fish or Nomeid seems to be immune to the powerful sting of the Physalia. It is actually a very agile swimmer that can avoid the stinging tentacles.It uses this deadly siphonophore for shelter against predators and can also feed on some of the smaller tentacles that do not seems to have a strong sting.

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Nice ctenophore

Our favorite, the Venus Belt! Nice to see this one in color!

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salp chain

If you click on the this amazing picture you will see a small fish larvae seeking shelter among the salps. very neat!

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ctenophore bloom

Beautiful bloom of lobate ctenohphores. The wall of death some smaller plankters:)