Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions.
Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions.
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DOI：
10.1093/bioinformatics/bts404
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发表时间：
2012-09-15
期刊：
影响因子：
--
通讯作者：
Roeder I
中科院分区：
文献类型：
--
作者：
Scherf N;Herberg M;Thierbach K;Zerjatke T;Kalkan T;Humphreys P;Smith A;Glauche I;Roeder I
动机：小鼠胚胎干细胞 (mESC) 已发展成为研究稳定细胞系中多能性调节的主要系统。众所周知，用于维持 mESC 多能性的不同的既定方案支持形态和功能上不同的细胞培养。然而，目前尚不清楚细胞集落的特性如何随着时间的推移而发展，以及它们在细胞传代后如何根据培养条件重新建立。此外，细胞集落似乎具有关于细胞大小、标记表达或生物力学特性的内部结构，但这一点尚未得到充分理解。这些表型特性的分析对于全面了解 mESC 的发育至关重要，最终需要生物信息学方法来保证可重复性和高通量数据分析。结果：我们开发了一种自动图像分析和集落跟踪框架，以获得细胞集落在空间和时间上演化时的结构特性的客观且可重复的量化。特别是，我们建立了一种使用流体图像配准和图像分割来量化菌落形状和（内部）运动变化的方法。该方法还允许在一系列图像上稳健地跟踪菌落的运动、分裂和合并。我们的结果提供了对时间性 mESC 集落形成的首次定量评估，并估计了不同培养条件下集落生长之间的结构差异。此外，我们提供了整个实验中各个菌落随时间的结构特征的基于流的可视化，促进对实验条件之间差异的视觉理解。因此，所提出的方法为基于模型的 mESC 集落发育分析奠定了基础。它可以轻松扩展以使用荧光信号和分化标记来集成更多功能信息。可用性：该分析工具采用 C++ 和 Mathematica 8.0 实现（Wolfram Research Inc.，美国伊利诺伊州尚佩恩）。该工具可以从作者那里免费获得。我们还将根据要求提供源代码。联系方式：nico.scherf@tu-dresden.de
Motivation: Mouse embryonic stem cells (mESCs) have developed into a prime system to study the regulation of pluripotency in stable cell lines. It is well recognized that different, established protocols for the maintenance of mESC pluripotency support morphologically and functionally different cell cultures. However, it is unclear how characteristic properties of cell colonies develop over time and how they are re-established after cell passage depending on the culture conditions. Furthermore, it appears that cell colonies have an internal structure with respect to cell size, marker expression or biomechanical properties, which is not sufficiently understood. The analysis of these phenotypic properties is essential for a comprehensive understanding of mESC development and ultimately requires a bioinformatics approach to guarantee reproducibility and high-throughput data analysis. Results: We developed an automated image analysis and colony tracking framework to obtain an objective and reproducible quantification of structural properties of cell colonies as they evolve in space and time. In particular, we established a method that quantifies changes in colony shape and (internal) motion using fluid image registration and image segmentation. The methodology also allows to robustly track motion, splitting and merging of colonies over a sequence of images. Our results provide a first quantitative assessment of temporal mESC colony formation and estimates of structural differences between colony growth under different culture conditions. Furthermore, we provide a stream-based visualization of structural features of individual colonies over time for the whole experiment, facilitating visual comprehension of differences between experimental conditions. Thus, the presented method establishes the basis for the model-based analysis of mESC colony development. It can be easily extended to integrate further functional information using fluorescence signals and differentiation markers. Availability: The analysis tool is implemented C++ and Mathematica 8.0 (Wolfram Research Inc., Champaign, IL, USA). The tool is freely available from the authors. We will also provide the source code upon request. Contact: nico.scherf@tu-dresden.de
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