MorphoGraphX 2.0: Providing context for biological image analysis with positional information
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
Abstract Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially-coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here we present recent advances in the MorphoGraphX software (Barbier de Reuille et al. eLife 2015;4:e05864) that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.
Authors 22
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Max Planck Institute for Plant Breeding Research
Affiliation as printed
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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University of Calgary · Max Planck Institute for Plant Breeding Research
Affiliation as printed
Department of Computer Science, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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John Innes Centre · Norwich Research Park · Max Planck Institute for Plant Breeding Research
Affiliation as printed
John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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Affiliation as printed
Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
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Max Planck Institute for Plant Breeding Research
Affiliation as printed
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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John Innes Centre · Norwich Research Park · Max Planck Institute for Plant Breeding Research
Affiliation as printed
John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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Affiliation as printed
MIRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montréal H1X 2B2, QC, Canada
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Max Planck Institute for Plant Breeding Research
Affiliation as printed
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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Affiliation as printed
MIRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montréal H1X 2B2, QC, Canada
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Technical University of Munich
Affiliation as printed
Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Technical University of Munich
Affiliation as printed
Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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John Innes Centre · Norwich Research Park · Max Planck Institute for Plant Breeding Research
Affiliation as printed
John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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Affiliation as printed
MIRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montréal H1X 2B2, QC, Canada
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Affiliation as printed
MIRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montréal H1X 2B2, QC, Canada
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Affiliation as printed
MIRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montréal H1X 2B2, QC, Canada
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Max Planck Institute for Plant Breeding Research
Affiliation as printed
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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Technical University of Munich
Affiliation as printed
Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Affiliation as printed
School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Affiliation as printed
MIRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montréal H1X 2B2, QC, Canada
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Affiliation as printed
Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
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Max Planck Institute for Plant Breeding Research
Affiliation as printed
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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Richard S. Smith corresponding
John Innes Centre · Norwich Research Park · Max Planck Institute for Plant Breeding Research
Affiliation as printed
John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 50829, Germany
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne 5089, Germany
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