title: The Caltech Tomography Database and Automatic Processing Pipeline.
abstract: Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user's "Inbox" and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups.
authors.affiliation: Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States.
authors.forename: H Jane
authors.initials: HJ
authors.lastname: Ding
authors.affiliation: Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Oikonomou
authors.affiliation: Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States; Howard Hughes Medical Institute, United States. Electronic address: jensen@caltech.edu.
authors.forename: Grant J
authors.initials: GJ
authors.lastname: Jensen
mesh_terms: D016208:Databases, Factual; D055032:Electron Microscope Tomography / Q000379:methods; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D007256:Information Systems
keywords: Automatic processing; Caltech Tomography Database; Electron tomography; Image database; Structural biology database