Center for Scientific Computation in Imaging


Rachel Berquist


Staff Scientist, Digital Fish Library Curator


Ph.D. (Zoology), University of Otago, New Zealand
M.Sc. (Marine Biology), University of Auckland, NZ
B.Sc. (Biological and Marine Sciences), University of Auckland, NZ

Research Interests

My primary research interests are the anatomy and physiology of sensory systems in fish and how these relate to behavior and ecology, with a particular emphasis on prey localization and orientation. Some of the tools I use to investigate this include magnetic resonance imaging (MRI), behavioral observation, neurophysiological recording, histology, 3D graphical modeling, and computational modeling. I have previously applied combinations of these tools to investigate the morphology and function of electrosensory systems in sharks and primitive fishes, sound localization in toadfish, and temporal patterns of feeding and movement behavior in reef fish. My current research at CSCI focuses on the application of MRI methods to investigate the comparative morphology and evolution of fishes.

Research Projects

As a staff scientist in Professor Lawrence Frank's CSCI group, I am the Research Coordinator for many collaborative research projects involving the application of a range of high-field anatomical MRI, functional MRI (FMRI) and diffusion tensor imaging (DTI) methods in fish and other marine organisms. I am also responsible for facilitating the work of students, post-docs, and visiting researchers, and provide support to the CSCI Director in essential grant and research administrative functions. Some of the projects I presently work on include: neuromorphology of the olfactory system in fishes, in collaboration with Dr Steve Kajiura at FAU; the comparative morphology of auditory accessory structures in cichlid fish, led by Dr John Sparks at AMNH; the application of FMRI methods to study sensory system integration in elasmobranch fishes, in collaboration with Dr Steve Kajiura at FAU and Dr Nick Wegner at SWFSC; and the application of shape analysis methods for comparative morphological analysis of brain and body tissues in fishes and other animals, led by Dr Frank.

I am also the Curator of the Digital Fish Library (DFL), a National Science Foundation (NSF) sponsored project at UCSD that uses MRI to map the morphological diversity of the world's fishes at the family level. This has involved working in conjunction with ichthyologists at the Marine Vertebrate Collection at Scripps Institute of Oceanography (SIO) and elsewhere, Earthguide educators at SIO, MR specialists at both the Center for Functional MRI and our local Veteran's Affairs Medical Center, and also web developers and science writers. Some of my responsibilities are the selection and preparation of specimens for imaging, acquisition of high-resolution MR image data using the 7-Teslar small animal magnet at CFMRI, image data processing and analysis, archiving and curating data, and overseeing of development of the DFL database and web-site content.