A cell-centered database for electron tomographic data

Maryann E. Martone, Amarnath Gupta, Mona Wong, Xufei Qian, Gina Sosinsky, Bertram Ludäscher, Mark H. Ellisman

Research output: Contribution to journalArticlepeer-review


Electron tomography is providing a wealth of 3D structural data on biological components ranging from molecules to cells. We are developing a web-accessible database tailored to high-resolution cellular level structural and protein localization data derived from electron tomography. The Cell Centered Database or CCDB is built on an object-relational framework using Oracle 8i and is housed on a server at the San Diego Supercomputer Center at the University of California, San Diego. Data can be deposited and accessed via a web interface. Each volume reconstruction is stored with a full set of descriptors along with tilt images and any derived products such as segmented objects and animations. Tomographic data are supplemented by high-resolution light microscopic data in order to provide correlated data on higher-order cellular and tissue structure. Every object segmented from a reconstruction is included as a distinct entity in the database along with measurements such as volume, surface area, diameter, and length and amount of protein labeling, allowing the querying of image-specific attributes. Data sets obtained in response to a CCDB query are retrieved via the Storage Resource Broker, a data management system for transparent access to local and distributed data collections. The CCDB is designed to provide a resource for structural biologists and to make tomographic data sets available to the scientific community at large.

Original languageEnglish (US)
Pages (from-to)145-155
Number of pages11
JournalJournal of Structural Biology
Issue number1-2
StatePublished - 2002
Externally publishedYes


  • 3D reconstruction
  • Electron tomography
  • High-voltage electron microscopy
  • Neuroinformatics

ASJC Scopus subject areas

  • Structural Biology


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