Automated stitching of microtubule centerlines across serial electron tomograms.
Automated stitching of microtubule centerlines across serial electron tomograms.
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DOI：
10.1371/journal.pone.0113222
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Prohaska S
中科院分区：
文献类型：
--
作者：
Weber B;Tranfield EM;Höög JL;Baum D;Antony C;Hyman T;Verbavatz JM;Prohaska S
在连续切片电子断层扫描中追踪微管中心线需要跨切片缝合微管，即来自不同切片的线需要对齐，端点需要在切片边界处匹配以建立相邻切片之间的对应关系，并且对应的线需要跨多个切片连接。我们提出了这些任务的计算方法：1）使用距离相容性图计算初始对齐。2)一个精细的对齐，然后计算的概率变化的迭代最近点算法，我们扩展到处理线的方向，通过引入一个周期性的随机变量的概率公式。3)端点对应关系的建立是通过制定一个匹配问题的马尔可夫随机场和计算最佳匹配与信念传播。置信传播通常不能保证收敛到最小值。尽管如此，我们展示了如何以最少的手动输入实现收敛。除了对微管中心线进行拼接外，还将对应关系应用于电子断层图像的变换和合并。我们将所提出的方法应用于C. elegans，X. laevis和T.布鲁塞。该方法能够缝合微管跨越截面边界，与专家对纺锤体样品的意见非常一致。然而，结果并不令人满意的微管阵列。对于某些实验，例如纺锤体的分析，所提出的方法可以取代手动专家追踪，从而能够以合理的手动努力长距离地分析微管。
Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.
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作者：
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