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

Svetlana SurkovaMaria Samsonova


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.


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

Optical Image Reconstruction
Gene Expression
Laser Scanning Microscopy
Computational Molecular Biology
Gene Expression
Airway Suction Location: Type: Point in Time: Respiratory System: Nominal

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

The Tendon Seed Network

Tendons are rich in the extracellular matrix and are abundant throughout the body providing essential roles including structure and mobility. The transcriptome of tendons is being compiled to understand the micro-anatomical functioning of tendons. Discover the latest research pertaining to the Tendon Seed Network here.

Myocardial Stunning

Myocardial stunning is a mechanical dysfunction that persists after reperfusion of previously ischemic tissue in the absence of irreversible damage including myocardial necrosis. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.


Incretins are metabolic hormones that stimulate a decrease in glucose levels in the blood and they have been implicated in glycemic regulation in the remission phase of type 1 diabetes. Here is the latest research.

Chromatin Regulation and Circadian Clocks

The circadian clock plays an important role in regulating transcriptional dynamics through changes in chromatin folding and remodelling. Discover the latest research on Chromatin Regulation and Circadian Clocks here.

Long COVID-19

“Long Covid-19” describes illness in patients who are reporting long-lasting effects of the SARS-CoV-19 infection, often long after they have recovered from acute Covid-19. Ongoing health issues often reported include low exercise tolerance and breathing difficulties, chronic tiredness, and mental health problems such as post-traumatic stress disorder and depression. This feed follows the latest research into Long Covid.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.