用于从共聚焦图像中获取分割基因表达定量数据的流程。
Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images.
作者信息
Surkova Svetlana, Myasnikova Ekaterina, Janssens Hilde, Kozlov Konstantin N, Samsonova Anastasia A, Reinitz John, Samsonova Maria
机构信息
Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, St. Petersburg, Russia.
出版信息
Fly (Austin). 2008 Mar-Apr;2(2):58-66. doi: 10.4161/fly.6060. Epub 2008 Mar 8.
Abstract
We describe a data pipeline developed to extract the quantitative data on segmentation gene expression from confocal images of gene expression patterns in Drosophila. The pipeline consists of five steps: image segmentation, background removal, temporal characterization of an embryo, data registration and data averaging. This pipeline was successfully applied to obtain quantitative gene expression data at cellular resolution in space and at the 6.5-minute resolution in time, as well as to construct a spatiotemporal atlas of segmentation gene expression. Each data pipeline step can be easily adapted to process a wide range of images of gene expression patterns.
摘要
我们描述了一种开发的数据管道，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。该管道由五个步骤组成：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。此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分钟分辨率获取定量基因表达数据，以及构建分割基因表达的时空图谱。数据管道的每个步骤都可以轻松调整，以处理各种基因表达模式的图像。
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