Web portal to an image database for high-resolution three-dimensional reconstruction

Dai, Wei; Liang, Yao Jen; Zhou, Z.H.

doi:10.1016/j.jsb.2003.09.035

Cited by 3 publications

(2 citation statements)

References 28 publications

(25 reference statements)

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“…One approach to organizing parameters in a workflow is to have a relational database accessed through the processing programs (Dai et al, 2003;Ludtke et al, 2003;Metoz et al, 2001). The disadvantage of this approach is the need for database management experience in the user.…”

Section: A Parameter Exchange Mechanismmentioning

confidence: 99%

Bsoft: Image processing and molecular modeling for electron microscopy

Heymann

Belnap

2007

Journal of Structural Biology

506

460

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Section: A Parameter Exchange Mechanismmentioning

confidence: 99%

Bsoft: Image processing and molecular modeling for electron microscopy

Heymann

Belnap

2007

Journal of Structural Biology

506

460

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“…the BioImage database (Carazo et al, 1999; Lindek et al, 1999), EMEN2 (Ludtke et al, 2003; Rees et al, 2013), the Carragher Lab database (Fellmann et al, 2002), IMIRS (Dai et al, 2003), E-MSD (Boutselakis et al, 2003), PDB (Berman et al, 2003; Bernstein et al, 1977), and the EMDB (Henrick et al, 2003; Lawson et al, 2011; Tagari et al, 2002)), and we first explored whether an existing program might meet our needs. We installed and tested the Cell Centered Database developed at UC San Diego, a sophisticated and complex tool designed to house microscopy data of many different types in a distributed fashion across disk drives spread across the world (Martone et al, 2002; Martone et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

The Caltech Tomography Database and Automatic Processing Pipeline

Ding

Oikonomou

Jensen

2015

Journal of Structural Biology

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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.

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