title: Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images.
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.
authors.affiliation: Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, St. Petersburg, Russia.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Surkova
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Myasnikova
authors.forename: Hilde
authors.initials: H
authors.lastname: Janssens
authors.forename: Konstantin N
authors.initials: KN
authors.lastname: Kozlov
authors.forename: Anastasia A
authors.initials: AA
authors.lastname: Samsonova
authors.forename: John
authors.initials: J
authors.lastname: Reinitz
authors.forename: Maria
authors.initials: M
authors.lastname: Samsonova
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000639:trends; D004330:Drosophila / Q000196:embryology* / Q000235:genetics*; D015870:Gene Expression; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D018613:Microscopy, Confocal