Globally optimal stitching of tiled 3D microscopic image acquisitions.
Globally optimal stitching of tiled 3D microscopic image acquisitions.
复制标题
平铺 3D 显微图像采集的全局最佳拼接。
DOI：
10.1093/bioinformatics/btp184
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发表时间：
2009-06-01
期刊：
影响因子：
--
通讯作者：
Tomancak P
中科院分区：
文献类型：
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作者：
Preibisch S;Saalfeld S;Tomancak P
动机：现代解剖学和发展研究通常需要在三个维度（3D）中对大型标本进行高分辨率成像。共聚焦显微镜会产生高分辨率的3D图像，但与大型生物样品的大小相比，相对较小的视野受到限制。因此，移动样品的电动阶段用于创建整个样品的瓷砖扫描。显微镜阶段提供的物理坐标不够精确，无法从各个图像堆栈中直接重建（缝合）。
结果：为了最佳地缝合大量的3D共聚焦图像，我们开发了一种方法，该方法基于傅立叶移位定理，计算出3D图像对之间的所有可能翻译，从找到整个3D图像组的全球最佳配置。该方法通过连续的注册步骤避免了错误传播。此外，为了补偿瓷砖之间的亮度差异，我们在重叠图像之间应用平滑的非线性强度过渡。我们的缝合方法很快，可用于2D和3D图像，对于小图像集，不需要有关瓷砖配置的先验知识。
可用性：该方法的实现可作为imagej插件作为斐济项目的一部分（fiji只是ImageJ：http：//pacific.mpi-cbg.de/）提供。
联系人：tomancak@mpi-cbg.de
Motivation: Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks. Results: To optimally stitch a large collection of 3D confocal images, we developed a method that, based on the Fourier Shift Theorem, computes all possible translations between pairs of 3D images, yielding the best overlap in terms of the cross-correlation measure and subsequently finds the globally optimal configuration of the whole group of 3D images. This method avoids the propagation of errors by consecutive registration steps. Additionally, to compensate the brightness differences between tiles, we apply a smooth, non-linear intensity transition between the overlapping images. Our stitching approach is fast, works on 2D and 3D images, and for small image sets does not require prior knowledge about the tile configuration. Availability: The implementation of this method is available as an ImageJ plugin distributed as a part of the Fiji project (Fiji is just ImageJ: http://pacific.mpi-cbg.de/). Contact: tomancak@mpi-cbg.de
影响因子：
19.5
作者：
Brown, Matthew;Lowe, David G.
通讯作者：
Lowe, David G.