Back Page Photo Series: An Interview with Stacy Farina

Interview by Natalie Sopinka




What species of fish is in this image?

This is a 3D volume rendering from a micro-computed tomography (CT) scan of a Scalyhead Sculpin skeleton. Computed tomography scanning is commonly used as a diagnostic tool in medicine, but it is also incredibly useful for studying the biology of animals.The resolution of micro-CT scans is much higher than that of medical scans of humans, making micro-CTs one of the best ways to visualize and measure structures on small animals (the fish in this image is only 8 cm long). This scan was visualized using the software OsiriX, with lighter colors indicating tissues of higher density.

What information is revealed through this type of imaging?

Micro-CT can be used to visualize and quantify a number of different aspects of anatomy. For example, in this study, I measured the dimensions of individual bones in 3D. Because CT scans rely on X-rays, denser materials like bone will show up best. You can use different staining techniques to visualize soft structures (e.g., muscles, organs, and blood vessels), but I focused on skeletons for my doctoral dissertation.

How was this image produced?

The specimen was scanned by Mark Riccio at the Cornell University Biotechnology Resource Center Imaging Facility. We used an Xradia Versa XRM-520 CT scanner, which produces extremely high -contrast and high-resolution tomograms. I collected this fish at Friday Harbor Laboratories as a part of my dissertation with Willy Bemis at Cornell University. I preserved the fish and shipped it back to the Cornell University Museum of Vertebrates for permanent storage. When it was time to scan the fish, we put it in a plastic bag and scanned it with a voxel size (resolution) of 25 μm. Scanning took about two hours. I then took measurements of different bones and created this 3D volume image using the OsiriX software. This project was completed with funding provided by an NSF Doctoral Dissertation Improvement Grant. Data for this image are available for download via Open Science Framework ( Adam Summers, a professor at the University of Washington and Friday Harbor Laboratories, is hosting (and encouraging others to host) CT data sets on this website in an effort to create an open access repository for CT scans of fishes.

What are you looking for in these CT scans?

For my dissertation, I investigated the evolution of the gill ventilation system in fishes. Fishes pump water over their gills by cyclically expanding and contracting their mouth and gill chambers, drawing water in through the mouth and forcing it out the gill openings. Because fishes also use their mouth for feeding, I was interested in investigating which structures of the fish skull respond to evolutionary pressures on feeding and ventilation. This required in-depth morphological data from closely related species of fishes with similar habitats and diets. We scanned 20 species of sculpins and their close relatives for our analyses.

What drew you to the gills of fish, versus other body parts?

I really like the complexity of gill ventilation in fishes. I didn’t study gills specifically for my dissertation (although I study them now as a postdoc). Rather, I studied the structures involved with pumping water over the gills. It turns out that the bones that make up the gill chamber-the operculum and the branchiostegal rays-are highly diverse among fishes. For example, in this image, you can see seven thin branchiostegal rays below and behind the lower jaw, but fishes can have anywhere from zero (e.g., telescope fishes) to more than 30 pairs of branchiostegal rays (e.g., some snake eel species). When you consider that the jaws and the bony tongue of fishes are also involved in ventilatory pumping, things get complicated very fast. Fishes use all of these structures to manipulate water pressure in the head, alternating between generating positive and negative pressures. There are very few functional systems in animal biology that are more complicated than gill ventilation in fishes, but its evolutionary diversity is poorly studied. This makes it a fascinating system to investigate!

Which species has your favorite gill morphology?

My favorite species by far is the Goosefish Lophius americanus. I studied the ventilatory behavior of Goosefish at Shoals Marine Laboratory (Farina and Bemis, in press). Goosefishes have what I believe to be the slowest ventilatory cycle of all fishes, with a single breath taking 1–3 minutes to complete. If you see a Goosefish in an aquarium, watch them carefully for a few minutes. Eventually, you will see them open up their gill opening (which is located behind their large pectoral fins-essentially their armpits) and exhale a large jet of water. They can breathe so slowly because of their enormous gill chamber and sedentary lifestyle. They are bottom-dwellers, like sculpins, but they take it to the extreme.


Farina, F. C., and W. E. Bemis. In press. Functional morphology of gill ventilation of the Goosefish, Lophius americanus (Lophiiformes:Lophiidae). Zoology. doi:10.1016/j.zool.2016.01.006.

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