1. What is the Digital Fish Library?
2. Why build the Digital Fish Library?
3. How are the digital images made?
4. How does the Digital Fish Library Work?
5. Contributors to the Library

What is the Digital Fish Library?

A baby Great White specimen from the Marine
Vertebrates Collection The Digital Fish Library (DFL) is a collaborative project at the University of California, San Diego between the Center for Scientific Computation in Imaging (CSCI), the Center for functional Magnetic Resonance Imaging (CfMRI) and the Scripps Institution of Oceanography (SIO), including the Birch Aquarium at Scripps.

The DFL mission is to catalog the anatomical magnetic resonance imaging (MRI) data of fishes from most major saltwater, and many freshwater genera to provide a resource for research and education.

While MRI is typically used to image injuries or brain activity, this novel application of the imaging technology preserves the long-term integrity of specimens and allows anyone to access and gather data from high-resolution, 3D images of the fishes.

Since its inception in June 2005 through a grant from the National Science Foundation, the DFL library of scanned fishes continues to grow. It will soon include over 1000 specimens that represent each of the 515 known fish families.

Why build the Digital Fish Library?

The DFL catalogs fishes from the SIO Marine Vertebrate Collection - one of the most comprehensive assemblages of its kind with more than 2 million specimens from around the world. The collection represents over 5,700 species, including deep-sea, pelagic, and marine shore fishes. These specimens, some of which represent the only record of the species, provide a valuable resource for research and education.

Normally fishes are studied by cutting specimens into slices (cross sections), so direct measurements, such as muscle locations and volumes can be made. Such dissections can only be studied by a limited number of researchers, and often destroy the integrity of the fish specimen. This is a serious concern with valuable specimens like those in the SIO Marine Vertebrate Collection.

However, MRI is non-invasive and allows for more detailed measurements, so it is a scientifically valuable way to collect detailed 3D scanned images of fishes that can be digitally dissected over and over again by anyone visiting the DFL.

How are the digital images made?

Each fish specimen in the DFL is transported from the Scripps Institution of Oceanography (SIO) Marine Vertebrate Collection and scanned at the UCSD Center for functional Magnetic Resonance Imaging (CfMRI), a research facility with three MRI systems where animals are routinely scanned for a wide variety of research projects, including the anatomical magnetic resonance imaging used in the DFL project.

Magnetic resonance imaging works by reading magnetic resonance signals from the protons in hydrogen atoms, which are present in the water of soft tissue. These atoms have magnetic properties that cause the protons to spin. When placed in a large magnet, like an MRI scanner, the hydrogen protons spin in line with the direction of the external magnetic field. This magnetic movement of the protons can be manipulated, recorded and translated into a high resolution, 3D image.

MR signals differ depending on the type of soft tissue and the shape of the specimen being scanned. Because fishes are not typically used for MRI study, special imaging parameters that accurately read signals in fish soft tissue have been established to scan fishes for the DFL.

The specialized coil used to image fish As part of the project, a special oval-shaped radio frequency (RF) coil, which reads the MR signal, has been built to accommodate the unique shapes of fish bodies that are laterally compressed (more tall than broad). Standard RF coils are circular to scan mammals like humans and mice with cylindrical-shaped bodies; however, the optimal design for an RF coil is one that fits snugly around the specimen, minimizing the difference in volumes between the specimen and the coil.

This new coil and the unique imaging parameters developed to scan the fish serve to create accurate MR images of fishes for research and education in the Digital Fish Library. These new methods and equipment also advance MRI technology by providing new tools to image varied shapes, sizes and tissue types.

How does the Digital Fish Library work?

Visitors can browse the DFL collection or search for a specific genus, family, or species of fish. Once a specimen is accessed, basic data like classification, habitat, and behavior will appear, along with links to MR images of the fish. Visitors will be able to access these MR images and examine the internal anatomy of the specimen by using the Digital Dissection Tool.

This is a visualization tool visitors will be able to access so they can manipulate the 3D image and examine the fish's muscles, tissues, skeleton and organs. More than simply viewing the image, visitors can measure and collect quantitative data, analyze fish anatomy and compare this anatomy to other fishes. For example, a DFL visitor could analyze the differences between the brain of a coral reef fish that relies on vision with one from the deep sea that relies mainly on smell, or compare the muscles of deep-sea fishes that regularly migrate to the surface with those that stay in the deep.

Contributors

Special thanks to the photographers and institutions that have generously donated their underwater images or have otherwise contributed resources to the Digital Fish Library. If you are a photographer and have underwater photos you would like to contribute, please email our web content developer, Elise Sbarbori (esbarbor@ucsd.edu).

Photography Credits:

• FishBase.org
• Dr. John E. Randall
• Mary Rose, Birch Aquarium at Scripps
• University of Delaware College of Marine and Earth Studies
• University of Delaware Sea Grant College Program (Anoplogaster cornuta)
• Randy Wilder, Monterey Bay Aquarium (Carcharodon carcharias)
• Tanya Dewey, Animal Diversity Web (Hemilepidotus hemilepidotus)