Development of the mouse cochlea database (MCD)

Peter A. Santi, Ian Rapson, Arne Voie

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


The mouse cochlea database (MCD) provides an interactive, image database of the mouse cochlea for learning its anatomy and data mining of its resources. The MCD website is hosted on a centrally maintained, high-speed server at the following URL: The MCD contains two types of image resources, serial 2D image stacks and 3D reconstructions of cochlear structures. Complete image stacks of the cochlea from two different mouse strains were obtained using orthogonal plane fluorescence optical microscopy (OPFOS). 2D images of the cochlea are presented on the MCD website as: viewable images within a stack, 2D atlas of the cochlea, orthogonal sections, and direct volume renderings combined with isosurface reconstructions. In order to assess cochlear structures quantitatively, "true" cross-sections of the scala media along the length of the basilar membrane were generated by virtual resectioning of a cochlea orthogonal to a cochlear structure, such as the centroid of the basilar membrane or the scala media. 3D images are presented on the MCD website as: direct volume renderings, movies, interactive QuickTime VRs, flythrough, and isosurface 3D reconstructions of different cochlear structures. 3D computer models can also be used for solid model fabrication by rapid prototyping and models from different cochleas can be combined to produce an average 3D model. The MCD is the first comprehensive image resource on the mouse cochlea and is a new paradigm for understanding the anatomy of the cochlea, and establishing morphometric parameters of cochlear structures in normal and mutant mice.

Original languageEnglish (US)
Pages (from-to)11-17
Number of pages7
JournalHearing Research
Issue number1-2
StatePublished - Sep 2008

Bibliographical note

Funding Information:
The authors thank the following students who have worked on the initial development of the MCD: Viet Pham, Jodi Lukkes, and Ann Schrafnagle, who did a great deal of structure segmentation. We also thank Tom Forsythe for work on the Stack Viewer program, and John Purdy for his excellent work on preliminary development of the 3D coordinate system of the cochlea. We also thank Dr. Douglas B. Webster of Louisiana State University the celloidin sections of the mouse cochlea and Dave Hultman for assistance with the rapid prototyping. Authorship credit follows ICMJE guidelines ( ). Funding for this research has been provided by the: NIDCD (R21 DC005482 ; R01 DC007588 ), Capita Foundation, and University of Minnesota resources including the: Digital Technology Center, Supercomputing Institute, and Biomedical Engineering Institute. P.S. designed the MCD, wrote grants to fund the project, prepared the images, and wrote the manuscript. A.V. performed the OPFOS imaging and reviewed the manuscript. A.V. is an employee of Spencer Technologies ( ).


  • 3D reconstruction
  • Atlas
  • Cochlea
  • Mice


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