The Caltech Tomography Database and Automatic Processing Pipeline
The Caltech Tomography Database and Automatic Processing Pipeline
复制标题
DOI：
10.1016/j.jsb.2015.06.016
复制
发表时间：
2015-11-01
影响因子：
3
通讯作者：
Jensen, Grant J.
中科院分区：
文献类型：
--
作者：
Ding, H. Jane;Oikonomou, Catherine M.;Jensen, Grant J.
在这里，我们描述了加州理工学院断层扫描数据库和自动图像处理管道，旨在处理，存储，显示和分发电子断层扫描数据，包括倾斜系列，样本信息，数据收集参数，3D重建，相关的光学显微镜图像，快照，分割，电影和其他相关文件。倾斜系列通常在收集期间自动上传到用户的“数据库”并自动处理，但也可以通过脚本或通过互联网接口逐文件批量输入和处理。与视频网站YouTube一样，每个倾斜系列在浏览页面上都有一个指向完整记录的链接、一个缩略图和一个视频图标，该图标在弹出窗口中提供断层图像的电影。注释工具允许用户添加注释和快照。该数据库是完全可搜索的，倾斜系列集可以选择和重新处理，编辑，或下载到个人工作站。进一步处理的结果和关键结果的快照可以记录在数据库中，并自动链接到适当的倾斜系列。虽然数据库受密码保护，可供本地浏览和搜索，但数据集可以公开，单个文件可以通过互联网与合作者共享。这些工具共同促进了个人和团体的高通量断层扫描工作。(C)2015 Elsevier Inc. All rights reserved.
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. (C) 2015 Elsevier Inc. All rights reserved.