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, Maria Samsonova

Research output

35 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)58-66
Number of pages9
JournalFly
Volume2
Issue number2
DOIs
Publication statusPublished - 1 Jan 2008

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gene expression
Drosophila

Scopus subject areas

  • Insect Science

Cite this

Surkova, S., Myasnikova, E., Janssens, H., Kozlov, K. N., Samsonova, A. A., Reinitz, J., & Samsonova, M. (2008). Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images. Fly, 2(2), 58-66. https://doi.org/10.4161/fly.6060
Surkova, Svetlana ; Myasnikova, Ekaterina ; Janssens, Hilde ; Kozlov, Konstantin N. ; Samsonova, Anastasia A. ; Reinitz, John ; Samsonova, Maria. / Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images. In: Fly. 2008 ; Vol. 2, No. 2. pp. 58-66.
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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.",
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Surkova, S, Myasnikova, E, Janssens, H, Kozlov, KN, Samsonova, AA, Reinitz, J & Samsonova, M 2008, 'Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images', Fly, vol. 2, no. 2, pp. 58-66. https://doi.org/10.4161/fly.6060

Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images. / Surkova, Svetlana; Myasnikova, Ekaterina; Janssens, Hilde; Kozlov, Konstantin N.; Samsonova, Anastasia A.; Reinitz, John; Samsonova, Maria.

In: Fly, Vol. 2, No. 2, 01.01.2008, p. 58-66.

Research output

TY - JOUR

T1 - Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images

AU - Surkova, Svetlana

AU - Myasnikova, Ekaterina

AU - Janssens, Hilde

AU - Kozlov, Konstantin N.

AU - Samsonova, Anastasia A.

AU - Reinitz, John

AU - Samsonova, Maria

PY - 2008/1/1

Y1 - 2008/1/1

N2 - 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.

AB - 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.

KW - Background removal

KW - Confocal microscopy

KW - Gene expression

KW - Image processing

KW - Image segmentation

KW - Spatial registration

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U2 - 10.4161/fly.6060

DO - 10.4161/fly.6060

M3 - Review article

C2 - 18820476

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VL - 2

SP - 58

EP - 66

JO - Fly

JF - Fly

SN - 1933-6934

IS - 2

ER -