Digital Fish Library

University Of California-San Diego, La Jolla CA

Investigators

Abstract

The University of California at San Diego is awarded a grant to digitize a representative sample of the Marine Vertebrates Collection (MVC) at the Scripps Institution of Oceanography (SIO), among the largest and most comprehensive collections of its kind in the world. It is a significant research resource for many scientists and also holds great potential as an educational resource. However, long-term maintenance of specimen integrity is often in conflict with specimen usage (e.g., dissection) and transfer of specimens is costly and involves potential risk to specimens. Moreover, accessibility to the MVC is necessarily restricted, limiting the potential scope of educational uses. Magnetic resonance imaging (MRI) is unique in its ability to non-invasively acquire high-resolution 3- dimensional (3D) digital data from soft tissue structures. Recent collaborative work between the UCSD Center for Functional MRI (CFMRI) and researchers at SIO has shown that MRI can effectively be used to non-invasively visualize and quantify the internal anatomy of fishes, and can potentially increase the effectiveness of both the research and educational uses of the MVC. In this award Digital Fish Library (DFL) will be developed that includes 1. Collection of high-resolution 3D MRI images of specimens that cover the range of morphological diversity in fishes with special emphasis on the strengths of the MVC; 2. Development of a public DFL web site for data retrieval, visualization, and quantitative analysis of the MRI data from the MVC, including integration of the data with extant databases and with data collected from other methodologies; 3. Development, in collaboration with the Birch Aquarium at Scripps (BAS), of the Digital Dissection Tool (DDT), an educational program embedded within the DFL site. Aimed at high-school science students, it uses the MRI data from the MVC and the image analysis tools within the DFL, and is supplemented by educational modules on the basic scientific areas involved in the DFL. This tool will be tested in the Academic Connections Program (ACP), a college preparatory high school level curriculum run through UCSD. Successful completion of this project will establish a digital library of approximately 1000 MVC specimens available to researchers, students, and educators on the internet for quantitative analysis, visualization, or bioinformatics purposes. In addition, an educational tool will be produced that is appropriate for high school students and above for learning about fish anatomy, MRI, bioinformatics, and the application of digital image analysis methods to marine biology.