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Published November 2015 | public
Journal Article Open

The Caltech Tomography Database and Automatic Processing Pipeline


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.

Additional Information

© 2015 Elsevier B.V. Received Date: 20 March 2015; Revised Date: 11 June 2015; Accepted Date: 13 June 2015; Available online 15 June 2015. We thank David Mastronarde for assisting with the "Grab with Note" plugin and integrating it into the IMOD software. This work was supported in part by NIH grant 2P50GM082545 to GJJ and the Beckman Institute at Caltech. This project/publication was made possible through the support of a grant from the John Templeton Foundation as part of the Boundaries of Life project. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation.

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Accepted Version - nihms708068.pdf


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August 22, 2023
August 22, 2023