Video bioinformatics analysis of human embryonic stem cell colony growth.
Video bioinformatics analysis of human embryonic stem cell colony growth.
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DOI：
10.3791/1933
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发表时间：
2010-05-20
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影响因子：
--
通讯作者：
Talbot, Prue
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文献类型：
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作者：
Lin, Sabrina;Fonteno, Shawn;Talbot, Prue
由于视频数据是复杂的，由许多图像组成，没有计算机软件的帮助，很难从视频材料中挖掘信息。视频生物信息学是一种利用计算机软件从视频图像中提取时空数据进行年代挖掘和分析的强有力的定量方法。在这篇文章中，我们介绍了一种视频生物信息学方法，通过分析在配备视频成像摄像头的尼康生物站CT孵化器中收集的延时视频来量化人类胚胎干细胞(HESC)的生长。在我们的实验中，将附着在Matrigel上的hESC克隆在BioStation CT中拍摄了48小时。为了确定这些菌落的生长速度，使用CL-Quant软件开发了食谱，使用户能够从视频图像中提取各种类型的数据。为了准确地评估菌落生长，我们创建了三个食谱。第一种方法将图像分割为蜂群和背景，第二种方法增强图像以准确地定义整个视频序列中的殖民地，第三种方法测量随着时间的推移群体中的像素数。这三种食谱在BioStation CT中收集的视频数据上按顺序运行，以分析单个hESC菌落在48小时内的生长速度。为了验证CL-Quant配方的真实性，使用Adobe Photoshop软件对相同的数据进行了手动分析。将CL-Quant配方和Photoshop得到的数据进行比较，结果基本一致，表明CL-Quant配方是真实的。这里描述的方法可以应用于任何视频数据，以测量hESC或其他集落生长的细胞的生长速度。此外，未来还可以开发其他视频生物信息学配方，用于其他细胞过程，如迁移、凋亡和细胞黏附。
Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion.