Database Commons

a catalog of worldwide biological databases

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: (http://mousecochlea.umn.edu). 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.

The Mouse Cochlea Database (MCD) is a collection of resources that include digital images and bibliographic information on the mouse cochlea and is available at: http://mousecochlea.ccgb.umn.edu. The purpose of this communication is to report on the development of one MCD resource: the Digital Cytocochleogram. A cytocochleogram is a graphic representation of the anatomical state of the hair cells along the complete width and length of the organ of Corti. The Digital Cytocochleogram provides Internet users with a complete collection of digital images of one or more surface preparations of the mouse organ of Corti from which morphometric information can be obtained. By moving a mouse driven, screen cursor over a digital image, the location and approximate frequency region of the anatomical structure is displayed. Users can also measure the straight-line distance between any two structures on the image. The Digital Cytocochleogram resource uses two software programs, the Coordinate Finder and Viewer, which are written as CGI scripts. The Coordinate Finder program maps each digital image to an X,Y coordinate system. The total length of the organ of Corti from all tissue segments is computed using an arc-distance approximation formula, with the lateral border of the inner pillar cell headplates serving as a trace line or reference location. After all of the digital images of the tissue segments are mapped, they are placed on the MCD Website where users can use the Viewer program to view and morphometrically assess structures using a web browser. A single, complete surface preparation from a normal mouse is presently available on the MCD website. As the MCD grows, additional images of surface preparations at different magnifications from normal, mutant, and experimentally altered mouse cochleas will become available.