Center for Scientific Computation in Imaging


Digital Fish Library

Project Description

The Digital Fish Library (DFL) at UCSD is a collaborative project 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's mission is to digitize the soft tissue anatomy of fishes preserved in SIO's Marine Vertebrates Collection using magnetic resonance imaging (MRI) and 3D image segmentation methods, and archive this data in an online database for research and education. While MRI is typically used for biomedical imaging of soft tissue injuries or brain function in people, the novel application of these non-invasive methods for studying the anatomy and morphology of natural history collection specimens helps secure the long-term integrity of these valuable resources. Furthermore, storing specimen image data and metadata in an online archival database means it can be shared with anyone with an internet connection, greatly enhancing the accessibility of natural history collections and their contribution to scientific discovery.

Visit the Digital Fish Library.


    Berquist RM, Galinsky VL, Kajiura SM, Frank LR. The coelacanth rostral organ is a low-resolution electro-detector that facilitates the strike. Scientific Reports, 5: 8962 2015.

    Graham JB, Wegner NC, Miller LA, Jew CJ, Lai NC, Berquist RM, Frank LR, Long JA. Spiracular air breathing in polypterid fishes and its implications for aerial respiration in stem tetrapods. Nature Communications, 5: e3022, 2014.

    Berquist RM, Gledhill KM, Peterson MW, Doan AH, Baxter GT, Yopak KE, Kang N, Walker NJ, Hastings PA, Frank LR. The Digital Fish Library: Using MRI to digitize, database, and document the morphological diversity of fish. PLOS ONE, 7: e34499, 2012.

    Chakrabarty P, Davis MP, Smith WL, Berquist R, Gledhill KM, Frank LR, Sparks JS. Evolution of the light organ system in ponyfishes (Teleostei: Leiognathidae). J Morphol, 272: 704-721, 2011.

    Rowe T, Frank LR. The disappearing third dimension. Science, 331: 712-714, 2011.

    Yopak KE, Frank LR. Brain size and brain organization of the whale shark, Rhincodon typus, using magnetic resonance imaging. Brain Behav Evol, 74: 121-142, 2009.

    Rogers BL, Lowe CG, Fernandez-Juricic E, Frank LR. Utilizing magnetic resonance imaging (MRI) to assess the effects of angling-induced barotraumas on rockfish (Sebastes). Can J Fish Aquat Sci, 65: 1245-1249, 2008.

    Perry CN, Cartamil DC, Bernal D, Sepulveda CA, Theilmann RJ, Graham JB, Frank LR. Quantification of red myotomal muscle volume and geometry in the shortfin mako shark (Isurus oxyrinchus) and the salmon shark (Lamna ditropis), using T1-weighted magnetic resonance imaging. J Morphol, 268: 284-292, 2007.