TeraStitcher - a tool for fast automatic 3D-stitching of teravoxel-sized microscopy images.
TeraStitcher - a tool for fast automatic 3D-stitching of teravoxel-sized microscopy images.
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DOI：
10.1186/1471-2105-13-316
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发表时间：
2012-11-27
影响因子：
3
通讯作者：
Iannello G
中科院分区：
文献类型：
--
作者：
Bria A;Iannello G
现代显微镜的进一步发展导致了太体像素大小的高分辨率平铺3D图像，从而增加了至少两个数量级的拼接问题的维度。现有的软件解决方案似乎不足以满足这些数据集产生的额外要求，例如最大限度地减少内存使用和只需要处理一小部分数据。我们提出了一个免费的，全自动的3D拼接工具，旨在匹配的特殊要求出来的太体像素大小的平铺显微镜图像，能够缝合他们在一个合理的时间，即使在工作站资源有限。该工具在具有微米分辨率的太体积像素大小的全小鼠脑图像上进行了测试，并且还将其与最先进的拼接工具在兆体积像素大小的可用数据集上进行了比较。这种比较证实了我们采用的解决方案适合拼接非常大的图像，并且在具有不同特征的数据集上也表现良好。事实上，嵌入在其他拼接工具中的一些算法可以很容易地集成到我们的框架中，如果它们在其他类别的图像上更有效的话。为此，我们设计了一种软件架构，该架构将有效使用内存资源的策略与可能取决于所获取图像的特性的算法分开。TeraStitcher是一款免费工具，即使在内存资源（<8 GB）和处理能力相对有限的工作站上，也可以拼接Teravoxel大小的平铺显微镜图像。它利用近似瓦片位置的知识，并使用专为这种非常大的数据集设计的ad-hoc策略和算法。生成的图像可以保存到多分辨率表示中，以便有效地检索和处理。我们提供TeraStitcher作为独立的应用程序和免费软件Vaa 3D的插件。
Further advances in modern microscopy are leading to teravoxel-sized tiled 3D images at high resolution, thus increasing the dimension of the stitching problem of at least two orders of magnitude. The existing software solutions do not seem adequate to address the additional requirements arising from these datasets, such as the minimization of memory usage and the need to process just a small portion of data. We propose a free and fully automated 3D Stitching tool designed to match the special requirements coming out of teravoxel-sized tiled microscopy images that is able to stitch them in a reasonable time even on workstations with limited resources. The tool was tested on teravoxel-sized whole mouse brain images with micrometer resolution and it was also compared with the state-of-the-art stitching tools on megavoxel-sized publicy available datasets. This comparison confirmed that the solutions we adopted are suited for stitching very large images and also perform well on datasets with different characteristics. Indeed, some of the algorithms embedded in other stitching tools could be easily integrated in our framework if they turned out to be more effective on other classes of images. To this purpose, we designed a software architecture which separates the strategies that use efficiently memory resources from the algorithms which may depend on the characteristics of the acquired images. TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently retrieved and processed. We provide TeraStitcher both as standalone application and as plugin of the free software Vaa3D.
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影响因子：
46.9
作者：
通讯作者：
--
平铺 3D 显微图像采集的全局最佳拼接。
DOI：
10.1093/bioinformatics/btp184
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Preibisch S;Saalfeld S;Tomancak P
通讯作者：
Tomancak P
影响因子：
3.8
作者：
Silvestri, L.;Bria, A.;Pavone, F. S.
通讯作者：
Pavone, F. S.
影响因子：
48
作者：
Dodt, Hans-Ulrich;Leischner, Ulrich;Becker, Klaus
通讯作者：
Becker, Klaus
影响因子：
2
作者：
Emmenlauer, M.;Ronneberger, O.;Burkhardt, H.
通讯作者：
Burkhardt, H.