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Review
Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images
Svetlana Surkova, Ekaterina Myasnikova, Hilde Janssens, Konstantin N. Kozlov, Anastasia A. Samsonova, John Reinitz and Maria Samsonova
volume 2 | issue 2
March/April 2008Subscribe to this journal for $129/year
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 5 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
Svetlana Surkova
St. Petersburg State Polytechnical University
Ekaterina Myasnikova
St. Petersburg State Polytechnical University
Hilde Janssens
University of Cambridge
Konstantin N. Kozlov
St. Petersburg State Polytechnical University
Anastasia A. Samsonova
Harvard Medical School
John Reinitz
Stony Brook University
Maria Samsonova
St. Petersburg State Polytechnical University