Web tools for large-scale 3D biological images and atlases.
Web tools for large-scale 3D biological images and atlases.
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DOI：
10.1186/1471-2105-13-122
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发表时间：
2012-06-07
影响因子：
3
通讯作者：
Baldock RA
中科院分区：
文献类型：
--
作者：
Husz ZL;Burton N;Hill B;Milyaev N;Baldock RA
三维或三维以上的大规模体积生物医学图像数据是分布式浏览和可视化的一个重大挑战。许多图像现在超过10 GB，这对于大多数用户来说太大了，无法处理计算机RAM和网络带宽。当用户需要从存档中访问数十或数百个此类图像时，情况会恶化。在这里，我们通过提供压缩平铺图像的存档数据来解决2D截面视图的问题，使用户能够在标准Web浏览器的上下文中浏览非常大的体积数据。该系统为灰度级和彩色3D图像提供交互式可视化，包括多个图像层和空间数据叠加。标准的互联网成像协议（IIP）已被扩展，以实现3D数据的任意2D切片以及多层图像和索引覆盖。扩展的协议被称为IIP 3D，我们已经实现了一个匹配的服务器提供的协议和一系列的Ajax/JavaScript客户端代码，将在互联网浏览器中运行。我们已经在一个低成本的基于Linux的服务器上测试了服务器软件，其映像容量高达135 GB，同时有64个用户。截面视图的响应时间与比例和方向无关。示例客户端提供了用户控制的颜色过滤和覆盖的多层图像视图。通过使用扩展的互联网协议和高效的基于服务器的图像平铺，可以通过大型生物医学图像卷交互式浏览任意部分。这些工具提供了快速访问大型图像存档的可能性，而无需下载整个图像和具有非常大内存配置的客户端计算机。该系统使用一系列医学和生物医学图像数据进行了演示，单个图像体积最高可达135 GB。
Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay. The standard Internet Imaging Protocol (IIP) has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays. Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume.
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影响因子：
64.8
作者：
Bock, Davi D.;Lee, Wei-Chung Allen;Kerlin, Aaron M.;Andermann, Mark L.;Hood, Greg;Wetzel, Arthur W.;Yurgenson, Sergey;Soucy, Edward R.;Kim, Hyon Suk;Reid, R. Clay
通讯作者：
Reid, R. Clay
影响因子：
--
作者：
DeLaurier, April;Burton, Nicholas;Logan, Malcolm P. O.
通讯作者：
Logan, Malcolm P. O.
影响因子：
5.1
作者：
JI, L;PIPER, J;TANG, JY
通讯作者：
TANG, JY
影响因子：
48
作者：
Walter, Thomas;Shattuck, David W.;Baldock, Richard;Bastin, Mark E.;Carpenter, Anne E.;Duce, Suzanne;Ellenberg, Jan;Fraser, Adam;Hamilton, Nicholas;Pieper, Steve;Ragan, Mark A.;Schneider, Jurgen E.;Tomancak, Pavel;Heriche, Jean-Karim
通讯作者：
Heriche, Jean-Karim
影响因子：
5.1
作者：
PIPER, J;RUTOVITZ, D
通讯作者：
RUTOVITZ, D