Using positional information to provide context for biological image analysis with MorphoGraphX 2.0
- Max Planck Institute for Plant Breeding Research, Germany
- John Innes Centre, United Kingdom
- RWTH Aachen University, Germany
- Université de Montréal, Canada
- University of Montreal, Canada
- Technical University of Munich, Germany
- University of Warwick, United Kingdom
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., 2015) 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.
Data availability
Datasets and software are available at www.MorphoGraphX.org and Dryad
-
MorphoGraphX2: Datasets that demostrate how to create positional information with local coordinate systemsDryad Digital Repository, doi:10.5061/dryad.m905qfv1r.
Article and author information
Author details
Anne-Lise Routier-Kierzkowska
Constance Le Gloanec
Daniel Kierzkowski
Johannes Stegmaier
Funding
Deutsche Forschungsgemeinschaft (Forschunggruppe 2581)
- Kay Schneitz
- Miltos Tsiantis
- Richard S Smith
Human Frontiers Science Program (RGP0002/2020)
- George Bassel
Max Planck Society (Core grant)
- Miltos Tsiantis
Fonds Nature et Technologies (282285)
- Anne-Lise Routier-Kierzkowska
- Daniel Kierzkowski
Deutsche Forschungsgemeinschaft (ERA-CAPS V-Morph)
- Richard S Smith
Biotechnology and Biological Sciences Research Council (ISP to John Innes Centre)
- Richard S Smith
Bundesministerium für Bildung und Forschung (031A494 & 031A492)
- Richard S Smith
Deutsche Forschungsgemeinschaft (STE2802/2-1)
- Dennis Eschweiler
New Frontiers in Research Fund (2018-00953)
- Anne-Lise Routier-Kierzkowska
- Daniel Kierzkowski
Natural Sciences and Engineering Research Council of Canada (RGPIN-2018-04897)
- Daniel Kierzkowski
Natural Sciences and Engineering Research Council of Canada (RGPIN-2018-05762)
- Anne-Lise Routier-Kierzkowska
Leverhulme Trust (RPG-2019-267)
- George Bassel
Biotechnology and Biological Sciences Research Council (BB/S002804/1)
- George Bassel
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Dominique C Bergmann, Stanford University, United States
Version history
- Received: August 12, 2021
- Preprint posted: August 13, 2021 (view preprint)
- Accepted: May 3, 2022
- Accepted Manuscript published: May 5, 2022 (version 1)
- Version of Record published: June 1, 2022 (version 2)
Copyright
© 2022, Strauss et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 3,389
- Page views
-
- 572
- Downloads
-
- 25
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Using positional information to provide context for biological image analysis with MorphoGraphX 2.0
eLife 11:e72601.
https://doi.org/10.7554/eLife.72601
Further reading
-
- Developmental Biology
- Neuroscience
Human fetal development has been associated with brain health at later stages. It is unknown whether growth in utero, as indexed by birth weight (BW), relates consistently to lifespan brain characteristics and changes, and to what extent these influences are of a genetic or environmental nature. Here we show remarkably stable and lifelong positive associations between BW and cortical surface area and volume across and within developmental, aging and lifespan longitudinal samples (N = 5794, 4–82 y of age, w/386 monozygotic twins, followed for up to 8.3 y w/12,088 brain MRIs). In contrast, no consistent effect of BW on brain changes was observed. Partly environmental effects were indicated by analysis of twin BW discordance. In conclusion, the influence of prenatal growth on cortical topography is stable and reliable through the lifespan. This early-life factor appears to influence the brain by association of brain reserve, rather than brain maintenance. Thus, fetal influences appear omnipresent in the spacetime of the human brain throughout the human lifespan. Optimizing fetal growth may increase brain reserve for life, also in aging.
-
- Developmental Biology
- Immunology and Inflammation
During embryogenesis, the fetal liver becomes the main hematopoietic organ, where stem and progenitor cells as well as immature and mature immune cells form an intricate cellular network. Hematopoietic stem cells (HSCs) reside in a specialized niche, which is essential for their proliferation and differentiation. However, the cellular and molecular determinants contributing to this fetal HSC niche remain largely unknown. Macrophages are the first differentiated hematopoietic cells found in the developing liver, where they are important for fetal erythropoiesis by promoting erythrocyte maturation and phagocytosing expelled nuclei. Yet, whether macrophages play a role in fetal hematopoiesis beyond serving as a niche for maturing erythroblasts remains elusive. Here, we investigate the heterogeneity of macrophage populations in the murine fetal liver to define their specific roles during hematopoiesis. Using a single-cell omics approach combined with spatial proteomics and genetic fate-mapping models, we found that fetal liver macrophages cluster into distinct yolk sac-derived subpopulations and that long-term HSCs are interacting preferentially with one of the macrophage subpopulations. Fetal livers lacking macrophages show a delay in erythropoiesis and have an increased number of granulocytes, which can be attributed to transcriptional reprogramming and altered differentiation potential of long-term HSCs. Together, our data provide a detailed map of fetal liver macrophage subpopulations and implicate macrophages as part of the fetal HSC niche.
