Fast determination of coarse-grained cell anisotropy and size in epithelial tissue images using Fourier transform
Fast determination of coarse-grained cell anisotropy and size in epithelial tissue images using Fourier transform
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DOI：
10.1103/physreve.99.062401
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发表时间：
2019-06-04
影响因子：
2.4
通讯作者：
Delanoe-Ayari, H.
中科院分区：
文献类型：
--
作者：
Durande, M.;Tlili, S.;Delanoe-Ayari, H.
机械应变和应力在伤口愈合或形态发生等生物过程中发挥着重要作用。为了定量评估这一作用，需要在大视场中以细胞精度获取组织的固定或实时图像。为了利用这些数据，必须分析大量细胞以提取细胞形状各向异性和细胞大小。最常见的是，这是通过使用所谓的分割计算机程序详细确定单个细胞轮廓来执行的，如有必要，还可以通过手动检测和纠错进行补充。然而，至少在三种情况下可以推荐粗粒度且更快的技术：首先，当不需要单个细胞轮廓的详细信息时；例如，在仅需要细胞各向异性的粗粒度平均信息的研究中。其次，作为确定完全分割是否可能有用的探索性步骤。第三，当分割太困难时，例如由于图像质量差或细胞数量太大。我们开发了一种用户友好的、基于傅里叶变换的图像分析管道。它速度很快（当前笔记本电脑通常每分钟 10(4) 个单元）并且适合时间、空间或整体平均值。我们在一组人工图像和两组完全分割的图像上验证了它，一组来自果蝇蛹，另一组来自鸡胚胎；管道结果是稳健的。视角包括体外组织、非生物细胞图案，例如泡沫和 xyz 堆栈。
Mechanical strain and stress play a major role in biological processes such as wound healing or morphogenesis. To assess this role quantitatively, fixed or live images of tissues are acquired at a cellular precision in large fields of views. To exploit these data, large numbers of cells have to be analyzed to extract cell shape anisotropy and cell size. Most frequently, this is performed through detailed individual cell contour determination, using so-called segmentation computer programs, complemented if necessary by manual detection and error corrections. However, a coarse-grained and faster technique can be recommended in at least three situations: first, when detailed information on individual cell contours is not required; for instance, in studies which require only coarse-grained average information on cell anisotropy. Second, as an exploratory step to determine whether full segmentation can be potentially useful. Third, when segmentation is too difficult, for instance due to poor image quality or too large a cell number. We developed a user-friendly, Fourier-transform-based image analysis pipeline. It is fast (typically 10(4) cells per minute with a current laptop computer) and suitable for time, space, or ensemble averages. We validate it on one set of artificial images and on two sets of fully segmented images, one from a Drosophila pupa and the other from a chicken embryo; the pipeline results are robust. Perspectives include in vitro tissues, nonbiological cellular patterns such as foams and xyz stacks.