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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

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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

Purchase article for $19

Subscribe to this journal for $79/year