Library Digital Collections

Cell Centered Database

View Collection Items

Collections »

Cell Centered Database

About this collection


471 digital objects.

Cite This Work

Martone, Maryann E.; Ellisman, Mark H.; Sosinsky, Gina E.; Gupta, Amarnath; Tran, Joshua; Wong, Willy; Cone, Angela C.; Fong, Lisa; Maynard, Sarah (2017). Cell Centered Database. UC San Diego Library Digital Collections.


The Cell Centered Database (CCDB) project was started in 1998 under the auspices of the Human Brain Project to provide a venue for sharing and mining cellular and subcellular data derived from light and electron microscopy, including correlated imaging. It was one of the first web databases devoted to the then emerging technique of electron tomography. The CCDB ( went online in 2014 and its contents are currently available at Cell Image Library ( The complete database was deposited for long-term preservation and access at UC San Diego Library and is therefore also available through this collection.

The goals of the CCDB project included:

Providing access for the biomedical community to primary and derived imaging 2D, 3D and 4D data from light and electron microscopy.

Developing advanced database capabilities for storing and mining complex cellular and subcellular imaging data.

Creating the necessary infrastructure for managing and sharing light and electron microscopic data securely within and between laboratories.

Developing tools and strategies for integrating data across scales and modalities and federating databases through the use of ontologies and shared spatial frameworks.

The CCDB models the entire process of reconstruction, from specimen preparation to segmentation and analysis. This collection provides the raw data, reconstruction, and segmented data for download, and includes 2D images, animations and image maps for online visualization.

Scope And Content

The CCDB collection, as archived here, is a digital collection of high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. The database was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. Within the CCDB, the “Microscopy product” refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. It is possible for a set of images to be both a mosaic and a tilt series, and thus contribute to more than one product. The Microscopy product ID serves as the accession number for the CCDB. Each microscopy product represents a unique dataset which belongs to an experiment within a project and is stored along with key specimen preparation details. Each project has a unique Project ID that groups together related microscopy products. Within this collection, each item, or digital object, contains all of the data associated with a single microscopy product. While many of the products are derived from the nervous system, the CCDB contains data from many systems. For each product, the CCDB makes available the raw data, reconstructions derived from the raw data and any segmentations and analyses performed on the data.

Date Collected
  • 1986 to 2012
Date Issued
  • 2017
Principal Investigators
Co Principal Investigators
Data Managers


View formats within this collection

  • English


Related Resources

    Primary associated publication

    • Martone, M. E., Gupta, A., Wong, M., Qian, X., Sosinsky, G., Ludӓscher, B., and Ellisman, M. H. 2002. A cell centered database for electron tomographic data. Journal of Structural Biology 138: 145-155.
    • Maryann E. Martone, Joshua Tran, Willy W. Wong, Joy Sargis, Lisa Fong, Stephen Larson, Stephan P. Lamont, Amarnath Gupta, Mark H. Ellisman, The Cell Centered Database project: An update on building community resources for managing and sharing 3D imaging data, In Journal of Structural Biology, Volume 161, Issue 3, 2008, Pages 220-231, ISSN 1047-8477.

    Other resource