Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images

Fly
Svetlana SurkovaMaria Samsonova

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.

Citations

May 7, 2013·Biochimica Et Biophysica Acta·Jacqueline M DreschAhmet Ay
Oct 12, 2010·Cellular and Molecular Life Sciences : CMLS·Johannes Jaeger
Dec 22, 2009·Molecular BioSystems·Johannes Jaeger
Jan 22, 2013·Developmental Biology·Hilde JanssensJohannes Jaeger
Apr 16, 2014·Methods : a Companion to Methods in Enzymology·Florian JugPavel Tomancak
Aug 29, 2012·PLoS Computational Biology·Konstantin KozlovMaria Samsonova
Oct 31, 2009·PLoS Computational Biology·Maksat AshyraliyevJohannes Jaeger
Nov 10, 2013·PLoS Computational Biology·Kolja BeckerJohannes Jaeger
Jan 11, 2014·PloS One·Karl R WottonJohannes Jaeger
Jan 11, 2014·PloS One·Eva Jiménez-GuriJohannes Jaeger
Jul 19, 2012·PLoS Computational Biology·Anton CrombachJohannes Jaeger
Mar 4, 2010·BMC Systems Biology·Luke Jostins, Johannes Jaeger
Nov 16, 2019·PLoS Computational Biology·Kenneth A BarrOvidiu Radulescu
Mar 18, 2016·Physical Review. E·Guilherme N PrataAlexandre F Ramos

Related Concepts

Metazoa
Drosophila
Optical Image Reconstruction
Gene Expression
Laser Scanning Microscopy
Computational Molecular Biology
Drosophila
Embryo
Gene Expression
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