Surkova Svetlana, Myasnikova Ekaterina, Kozlov Konstantin N, Pisarev Andrei, Reinitz John, Samsonova Maria
Cold Spring Harb Protoc. 2013 Jun 1;2013(6):488-97. doi: 10.1101/pdb.top075101.
Quantitative measurements derived using sophisticated microscopy techniques are essential for understanding the basic principles that control the behavior of biological systems. Here we describe a data pipeline developed to extract quantitative data on segmentation gene expression from confocal images of gene expression patterns in Drosophila. The pipeline consists of image segmentation, background removal, temporal characterization of an embryo, data registration, and data averaging. This pipeline has been successfully applied to obtain quantitative gene expression data at cellular resolution in space and at 6.5-min resolution in time. It has also enabled the construction of a spatiotemporal atlas of segmentation gene expression. We describe the software used to construct a workflow for extracting quantitative data on segmentation gene expression and the BREReA package, which implements the methods for background removal and registration of segmentation gene expression patterns.
使用复杂的显微镜技术获得的定量测量对于理解控制生物系统行为的基本原理至关重要。在这里，我们描述了一个开发的数据管道，用于从果蝇基因表达模式的共聚焦图像中提取关于分割基因表达的定量数据。该管道包括图像分割、背景去除、胚胎的时间特征分析、数据配准和数据平均。该管道已成功应用于在空间上以细胞分辨率和在时间上以6.5分钟分辨率获得定量基因表达数据。它还使得能够构建一个分割基因表达的时空图谱。我们描述了用于构建提取分割基因表达定量数据工作流程的软件以及BREReA软件包，该软件包实现了背景去除和分割基因表达模式配准的方法。
