FathomNet Database: Deep-Sea Scientific Illustration
- Deanna Soper
- Jul 30
- 5 min read
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Art and science are sometimes viewed as distinct disciplines, but biologists often use art to visually explain many aspects of biology. From anatomical structures of newly discovered species to molecular processes that are difficult to conceptualize without an image, these diagrams are an important form of science communication. Increasingly, journals are requesting that their authors create a digital abstract to visually convey the story their data tell in the paper. All of this means that biologists need to understand and illustrate life. Here, we will begin learning how professional scientists might illustrate an organism using deep-sea images collected by remotely operated vehicles (ROVs).
To begin learning to illustrate, it is important to understand why we illustrate. Watch this introductory video by Planet Tuna called Scientific Illustration I: A Guided Tour: https://youtu.be/6hmbGg9rMWQ
What did you notice about her work? What skills do you think might be important to learn in order to illustrate for scientific purposes?
Next, you will choose an organism to illustrate. However, before you do, it might be important to learn about the environment in which your organism lives. The deep ocean is characterized by the absence of sunlight. Light does exist in the deep ocean, but it is generally created by the organisms themselves. From deep-sea worms that have anti-predation “green bombs” that are released when threatened to the lure on top of a long fishing pole-like structure on the head of an angler fish, organisms can create light for many reasons. Reminiscent of the familiar lightning bugs you might see in the Midwest on a warm summer evening, animals can use this light to communicate with each other. Beyond that, though, these organisms live in total darkness. Because of its depth, generally considered anything greater than 1,000 meters, it is also an environment of cold, dense saltwater. This depth also creates intense pressure, yet the deep ocean is teeming with life. Deep-sea coral and sponge reefs can be incredibly biodiverse, hosting fish and invertebrates such as crabs and shrimp.
Many organizations exist that help collect and manage data documenting these environments and the organisms that live in them. One such organization is the Monterey Bay Aquarium Research Institute (MBARI). Dr. Kakani Katija is the lead of the FathomNet Program, which hosts the FathomNet Database. The FathomNet Database is a library of expert-annotated ocean images that seeks to represent all underwater life and improve machine learning models. You will use this database to explore ROV from NOAA Ocean Exploration. Go to this link. (https://database.fathomnet.org/fathomnet/#/explorer?ownerInstitutions=NOAA+Ocean+Exploration) and search by animal name or location to find an image that you would like to illustrate.
Download the image file from the FathomNet Database. To do this, you will go to the page where the image is hosted, which is likely within a dive. Click the box in the upper right-hand corner, then right-click it, or, on a Mac, right-click the image and choose “Save as” to save the image. A pop-up menu will appear; choose “Save As,” and another menu will appear. You can rename your file if you wish, and make sure it downloads to the folder you want. Typically, the default is to go to your “Downloads” folder, and that is okay. It just needs to be saved to your local hard drive.
Note: When downloading images from the FathomNet Database, please note that contributors select from one of four Creative Commons licenses: CC0, CC-BY, CC-BY-NC, and CC-BY-NC-ND. Please follow the guidelines provided in the FathomNet Terms of Use.
The next step is to learn how to illustrate. There are many programs available for scientific illustration. Here, we will use Adobe Illustrator, but note that this program can be costly. If you are unable to access Adobe Illustrator, you can search for an alternative free, open-source vector graphics editor.
Adobe Illustrator
*This is a loose guide of steps. You might need to use different tools based on what is necessary to visualize your animal.
Import your image into Adobe Illustrator.
Make sure your image is at least 3” X 5” or larger. You can resize your image if necessary.
Add a new layer. For your drawing, you will want to add layers for each aspect of the diagram. You will want to do this because it lets you easily go back and change specific aspects of the diagram without affecting other parts of your drawing.
Click the space just to the left of the layer the image is on; you should see a lock icon appear. This will lock that layer, meaning you won’t be able to make changes to your original image. You can also hit the eye icon to make the image disappear to see what you have drawn.
Use the drawing tools to outline the organism. You will likely want to use the line-drawing tool that allows curved lines. It looks like this:
Have patience, and use the dots you lay down to create the organism's curves. You will spend a lot of time on this step!
Once you have an outline, start adding details like eyes, the center of a polyp, or fine hairs.
Finally, use the dot tool to create shadows on the organism using stippling. If your organism is translucent and you want to show internal organs, use a dashed line to indicate the internal structure. See below for an example!
When you finish your line drawing, you will arrange the organism into a “plate,” an arrangement similar to the one above. You will place your image next to your line drawing. You will then write a report about your organism using the instructions outlined in this PDF:
And, follow the outline below:
Deep Sea Organism & Illustration Project (Report will be Due) 100 points total
Students will use the FathomNet Portal to learn about deep-sea biodiversity and begin to identify organisms. During this interaction, students will learn how to scientifically illustrate one chosen organism. Each student will choose a different species to illustrate. The student will choose one high-quality image taken from ROV images/footage to illustrate. Research will be conducted on that organism (which may not be identifiable to the species level; as such, it might require students to choose a broader taxonomic category, such as family or order). Students will turn in their own final laboratory report that will mimic a scientific paper describing a species. You will write a report on that species, which will include the following details:
biological background of the species (or higher order of classification if necessary)
anatomical description of the organism, written in telegraphic format
discussion of any published studies on that species (or higher order of classification)
Your report should be 2,000 – 2,500 words and should include at least three peer-reviewed journal sources and at least two reputable website sources (i.e., a college webpage – if someone is researching that species; a governmental website like the Department of Natural Resources, etc.).
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