Why do the images look the way they do?

As you may know by now, the In Situ Ichthyoplankton Imaging system (ISIIS) is the instrument we used to obtain the images of plankton for Plankton Portal.  It captures images as it travels through the water column.  The idea behind this imaging system was to film a large volume of water in order to detect and image relatively rare zooplankton, like larval fish and small jellies.

So why are the images are black and white, very contrasted and almost like a line drawing? Our challenge in designing this instrument was to be able to employ macro-photography at a fast speed, obtain a large depth of field (large volume sampled), while minimizing motion blur. After researching for a few months we settled on an imaging technique that could answer our demands: Shadow imaging or focus shadowgraphy!

Gary setlles

a) prehistoric shadowgraphy, b) sunlight shadowgram of a martini glass, c) “focused” shadowgram of a common firecracker explosion, d) “Edgerton” shadowgram of the firing of an AK-47 assault rifle
Gary S. Settles

This technique is actually not new and was used extensively for the study of shockwaves as well as ballistic. The idea is to cast a shadow onto a sensor or film instead of trying to directly record the imaged object. Let me explain: since most plankton are small and quite transparent, imaging using a traditional camera must rely on ambient sunlight. In this scenario, you won’t see much because the organisms blend into the surrounding water. Imaging a shadow cast by ISIIS reveals their distinct shape and location. It’s like looking at the shadows at the bottom of a swimming pool created by the sun going through the water! In this case, we do not use the ambient sunlight, but create our own light beam using a blue LED light and a set of mirror and lenses. The light is collimated, meaning that the light beam travels in a tight, parallel direction like that of a laser thus ensuring that even over long distances, we can create a very good shadow. We then use a specific set of lenses aligned with the camera to capture this shadowgraph image. Since the light beam is directed toward the camera sensor, it allows for very high speed imaging and avoids motion blur when moving through the water. Lastly, we invert the images for aesthetic purposes on the site, and voila! Now you have a beautiful set of black and white images of plankton for the world to see!

isiis optics

This schematic shows the optical alignment inside ISIIS. A bean of light is collimated by a large lens and the refocused after going through the water. The camera records the shadows casted by the plankton as the moves behind the ship

So for all the people who asked about why some of the ctenophores (like lobates, beroids, and cydippids) were so ‘overexposed,’ now you know. These animals are dense and not very transparent, thus casting a hard shadow onto the lens. Instead of appearing black as a typical shadow, we have inverted the image and now they appear white.

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Lobate ctenophore

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Why use images to study plankton?

Although ocean science has made many great advances, many biological processes are still poorly understood. In the sciences generally, a common theme is using new technology to examine patterns on smaller, more fundamental scales (e.g., DNA technology in biology, nanoparticle physics), with the goal of revealing underlying mechanisms. Plankton imaging is a method to examine patterns of organisms on a smaller scale, giving insight into how these organisms live and interact with each other. In addition, many planktonic animals are fragile and easily destroyed by plankton nets: the traditional tool to study plankton distributions. These plankton nets also suffer from the problem of having to sample over large portions of the water column, so an oceanographer might use a single net to capture copepods and shrimps and assume that these organisms co-occur if they appear in the same sample. However, it is entirely possible that the organisms are confined to discrete thin layers that do not overlap spatially. An imaging system can distinguish between these two scenarios, while a plankton net cannot. Images also provide information about the natural orientation of plankton, which can allow us to make predictions about their movement and feeding strategies.

 The bongo net is a traditional tool of biological oceanographers but is biased toward plankton with a hard exoskeleton (crustaceans) (Image source: NOAA Cruise DE 10-09 Report).

The bongo net is a traditional tool of biological oceanographers but is biased toward plankton with a hard exoskeleton (crustaceans) (Image source: NOAA Cruise DE 10-09 Report).

When we think about the future of our planet, climate change and predicting its effects are of great concern. In order to make meaningful predictions about a system, you need to create a mathematical model. One of the most important aspects of any model is the initial conditions and baseline variability. For many planktonic animals, especially jellyfish, we do not know their abundance, variation, or how they interact within the oceanic food web, which is all crucial information for predicting the future of our oceans under climate change conditions. Using an imaging system like ISIIS can lead to better population estimates of many different plankton types, and this information can complement many types of oceanographic studies. Fine-scale data can improve estimates of feeding and encounter rates for planktonic organisms, which is critical to our understanding of the oceanic food web.

A colony of salps such as this one would be destroyed or broken up into individuals if sampled with a net system. The in situ image in this situation gives information on the asexual budding of this fast reproducing phytoplankton grazer.

A colony of salps such as this one would be destroyed or broken up into individuals if sampled with a net system. The in situ image in this situation gives information on the asexual budding of this fast reproducing phytoplankton grazer.

When compared to plankton samples preserved in ethanol or formalin, image data provide distinct advantages in data processing and collaboration. For one, oceanographers can tackle age old questions like what are the biological and physical drivers of plankton aggregations and dispersal, and how do plankton aggregations impact the populations of wild fish, a multi-billion dollar global industry? The ‘digitization’ of biological data improves the ability to share data, fostering collaboration among ocean scientists with differing expertise. Having these images available on the internet (through a database server) increases the accessibility of biological oceanography to students, teachers, and the public. It is our hope to one day have these images available to the public, so everyone can gain an appreciation for the diversity of life in the ocean and perhaps use them to supplement science classes. The Zooniverse and Citizen Science is a great start to achieving these goals of making ocean science more “open access,” and we are so appreciative of your help!

How do we get the images?

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Since the 1800’s, plankton has been studied and collected using simple nets with very fine mesh. The process of analysis of these plankton ‘samples’ is tedious, labor intensive, confined to laboratory, and can only be done on relatively small areas of the ocean. By sampling in this manner, it is difficult to get a good understanding of how planktonic organisms are distributed and how they interact with each other. Yet plankton represents a very important part of a global system feeding larger animals like fish, whales and many others. The In Situ Ichthyoplankton Imaging System (ISIIS) is one of a few systems in the world capable of improving the way we study plankton to better understand their life and function in the marine environment. Instead of using an actual net to capture plankton, ISIIS captures the images of the organisms and information about their immediate surroundings. ISIIS samples continuously, resulting in a collection of digital images that record the exact location of the various plankton organisms in relation to each other and the environment in which they live. Further, the images are recorded onto a simple hard drive instead of slurry of plankton all mixed together in a sample jar with formaldehyde (yech!).

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ISIIS is an underwater imaging system developed to capture real time images of plankton that are relatively rare, small, and fragile such as fish larvae and delicate gelatinous organisms (like jelly fish). ISIIS is composed not only of a macro-camera system with its own illumination but it also is integrated into an underwater vehicle with a variety of additional sensors to measure the depth, salinity and temperature of the water, as well as such properties as dissolved oxygen, light level, and even how much chlorophyll a (measure of primary production) is present. Together, the camera and sensors provide detailed profiles and tracks of what plankton are where and what the ocean environment around them is like.

isiis schematic

The vehicle, and associated imaging system and sensors, moves up and down through the water column using side-mounted, user-controlled dive fins (like an underwater glider) while being towed behind an oceanographic ship moving at 5 knots. The vehicle frame is divided into four compartmentalized enclosures with imaging and optical equipment seamlessly integrated into ISIIS’s ventral housings and environmental sensors and electronics in the dorsal housings. ISIIS is designed to undulate in a zigzag fashion between the surface and a maximum depth of 200 meters.

isiis2

The ISIIS system utilizes imaging technology very similar to an office scanner flipped on its side. The imaged parcel of water passes between the forward portions of two streamlined pods where it is “scanned” and transformed into a continuous image. The resulting very high-resolution image is of plankton in their natural position and orientation. When a sufficient volume of water is imaged this way, quantification of concentration (individuals per unit volume) and fine scale distribution is possible. ISIIS is capable of imaging a maximum of 162 Liters (43 gallons) of water per second (when moving at 5 knots) with a pixel resolution of 70 µm (the thickness of a human hair).

The imaging data and associated oceanographic data are sent to the surface ship via a fiber optic cable and recorder onto a main computer for later viewing and analysis.

Team introductions

We thought you’d like to know who are the scientists behind this project. So – here are a few introductions.

My name is Jessica Luo, and I am starting my fourth year as a Ph.D student at the University of Miami’s Rosenstiel School of Marine and Atmospheric Sciences. My research is on small gelatinous zooplankton (jellyfish and relatives) around fronts, and their vertical migration patterns. The research from this dataset forms part of my dissertation, so I’m really excited for Plankton Portal and the Zooniverse team. I recently moved from Miami to Newport, Oregon to be part of the new lab at Oregon State University. Here I am on a recent research cruise in the Mediterranean Sea:

Jessica on the Resaerch Vessel Tethys II, off the coast of France

Jessica on the R/V Tethys II this summer in the Northern Mediterranean



Adam Greer is a senior Ph.D student in our lab who’s about to defend soon. His research focuses on thin layers of zooplankton in coastal environments. He studies aggregation and the spatial relationships of organisms using ISIIS. He just got a very nice article published by the Journal of Plankton Research and made the cover! Congrats on all these achievements.

Adam scuba diving in the Caribbean

Adam scuba diving in Belize, 2011



Cedric Guigand, senior research associate in University of Miami and Charles Cousin, ocean engineer and CEO of Bellamare are the designers and developers of ISIIS. Their main contribution is to invent and built the crazy instruments that the scientists (i.e. Bob) come up in their wildest dreams! Not always easy… but always exiting! They also spent quite a bit at time at sea all over the world to help the group collect data and make sure the instruments are working well.

Adam (left) and Cedric (right) on a random friday afternoon in the lab: playing trombone

Adam (left) and Cedric (right) on a random friday afternoon in the lab: playing trombone.

Charles Cousin

Charles Cousin



Ben Grassian is a senior thesis student in our lab. He recently graduated from the University of Miami and his senior thesis was on the temporal and spatial distribution of ctenophores in San Diego. He spent an enormous amount of time identifying plankton images that helped us design the benchmark library we provided you to analyze the Plankton Portal data.

Ben_Grassian

Dorothy Tang is a research technician working on the identification of organisms in ISIIS images. Her everyday life is surrounded by plankton–looking for them, identifying them, and charmed by them. In her words, “ISIIS opens my eyes on plankton (especially zooplankton). As I learned more about different kinds of zooplankton–jellyfish, siphonophore, appendicularians and their houses, ctenophores, larval fish, etc., I appreciate them more.”

Dorothy in the Lab

Dorothy in the Lab



And the head honcho – Bob Cowen is the mastermind behind the whole lab and the one who motivates, guides and keeps us all in line. He dreamed up the concept of ISIIS over a decade ago while trying to catch rare fish larvae with nets in the Caribbean. He is now the Director of Oregon State University‘s Hatfield Marine Science Center – and enjoying life on the west coast.

Bob on a recent cruise in the Mediterranean, examining a plankton net tow

Bob on a recent cruise in the Mediterranean, examining a plankton net tow

So that’s us! You can find Plankton Portal on Facebook, Twitter or Google Plus, or visit our Lab Facebook Page. Tweet us or message us any questions you may have, or even just to say hello!

Welcome to the Plankton Portal!

Plankton species are a beautiful and fascinating group of organisms. We can’t wait to show you what we have seen of these diverse and elusive critters.  Let us start from the beginning—the five W-questions:

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What is plankton?
The word Plankton comes from the Greek word planktos meaning “wanderer” or “drifter”.  They are a group of organisms that are too small or too fragile to swim against naturally occurring currents. Plankton inhabit both freshwater and marine environments, such as lakes, ponds, and oceans.  Plankton can be broadly divided into two main groups: phytoplankton (plants) and zooplankton (animals). Phytoplankton are one of the primary producers in the ocean; like plants, they carry out photosynthesis to covert inorganic nutrients and light energy into organic material. Zooplankton, on the other hand, graze on phytoplankton or consume other zooplankton smaller than themselves. While you might think that plankton are too small to be seen by unaided eyes; that is not entirely true. Planktonic organisms have a very wide range in sizes. Many of them are microscopic in size; but others, like jellyfish, could grow up to more than one meter long.

Why do we study plankton?
Plankton are crucial to the marine ecosystem.  As a group, plankton form the basis of many marine food webs in that they are an important food source to organisms ranging from larval fish to the largest animal on earth—the blue whale. In addition, plankton play an important role in nutrient cycling in the ocean; such as carbon and nitrogen cycle.  Even humans are affected by plankton. As plankton are a food source for many marine organisms, our fishery industries depend highly upon these planktonic organisms as a source of fish productivity. Beyond being food, some plankton can also create problems to the fishing industry and even tourists visiting the shore when forming noxious blooms such as red tides.

How do we study plankton?
There are several ways to sample plankton: bottles, nets, acoustics, imaging systems, etc. Nets are the most common way of plankton sampling. Nets of different size, shape and design are used depending on the type of plankton of interest. A net is towed behind a moving vessel at the desired depth in order to collect and concentrate the planktonic organisms. When the net moves through the water column, plankton is retained in the net. One on board, the plankton ‘slurry’ is removed from the net and then (usually) preserved for later viewing and analysis under a microscope in the laboratory.

In this project, we sampled plankton by using a plankton imaging system – In Situ Ichthyoplankton Imaging System (ISIIS). ISIIS acts as a “virtual net” which captures the images of the organisms and information about their immediate surroundings. By sampling continuously, the result is a collection of digital images that record the exact location of the various planktonic organisms in relation to each other and the environment in which they live.

Where and when
The images currently shown in the Plankton Portal were taken in the Southern California Bight approximately 30 miles south of San Nicolas Island on October 15-17, 2010, on board the NOAA Ship Bell M. Shimada. But we are continuously traveling the world to bring new images and better understand how these little guys make a living in the ocean! ISIIS has also been towed in the Atlantic off of Georges Bank and Stellwagen Bank, MA, Straits of Florida, Gulf of Mexico, and recently off southern France in the Mediterranean.

This current project is to study the aggregation (patchiness) and distribution of different plankton in a small-scale front (where two different water masses meet) in the SCB. We want to know which organisms are present at the front (vs. those that may avoid it), and what they are doing there (e.g. are they prey or predators?). We need your help in identifying the organisms captured by ISIIS.