3D time series analysis of cell shape using Laplacian approaches.
3D time series analysis of cell shape using Laplacian approaches.
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DOI：
10.1186/1471-2105-14-296
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发表时间：
2013-10-04
影响因子：
3
通讯作者：
Bretschneider T
中科院分区：
文献类型：
--
作者：
Du CJ;Hawkins PT;Stephens LR;Bretschneider T
基本的细胞过程，如细胞运动，分裂或食物摄取，关键取决于细胞能够改变形状。三维图像时间序列的快速采集现在已经成为可能，但我们缺乏有效的工具来分析形状变形，以了解形状变化的真实的三维性质。我们提出了一个3D+时间细胞形状分析的框架。主要贡献是三方面的：首先，我们开发了一个快速，自动随机步行者的细胞分割方法。其次，提出了一种新的拓扑固定方法来固定没有球形拓扑的分段二进制体。第三，我们表明，用于分析管道的每个单独步骤（细胞分割，拓扑固定，球形参数化和形状表示）的算法与拉普拉斯算子密切相关。该框架适用于中性粒细胞的形状分析。我们提出的细胞分割方法比传统的随机步行者方法或水平集方法更快，并且在中性粒细胞的3D时间序列上表现得更好，中性粒细胞的3D时间序列相对嘈杂，因为堆栈必须足够快地获取以考虑细胞运动。我们的拓扑修复方法优于SPHARM-MAT和SPHARM-PDM提供的工具，在他们的成功修复率。所提出的细胞3D+时间形状分析流水线中的不同任务可以使用拉普拉斯方法来解决，从而打开了最终组合各个步骤以加速计算的可能性。
Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations.
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DOI：
10.1083/jcb.200302097
发表时间：
2003-05-12
期刊：
The Journal of cell biology
影响因子：
--
作者：
Eils R;Athale C
通讯作者：
Athale C
影响因子：
10.6
作者：
Gu, XF;Wang, YL;Yau, ST
通讯作者：
Yau, ST
影响因子：
3.7
作者：
Eichorst JP;Lu S;Xu J;Wang Y
通讯作者：
Wang Y
影响因子：
--
作者：
Kherlopian AR;Song T;Duan Q;Neimark MA;Po MJ;Gohagan JK;Laine AF
通讯作者：
Laine AF
DOI：
10.1109/tpami.2006.233
发表时间：
2006-11-01
影响因子：
23.6
作者：
Grady, Leo
通讯作者：
Grady, Leo