Using positional information to provide context for biological image analysis with MorphoGraphX 2.0

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

Towards an integrated understanding of leaf form development and diversity

Leaves of eudicots show tremendous morphological diversity. Remarkably different leaf morphologies may occur between closely-related species, as within-species variants, or even in the same plant. Diverse leaf shapes also emerge in molecular-level studies of reference plants including Arabidopsis thaliana, Cardamine hirsuta and tomato, where small genetic or hormonal changes yield significantly different forms. This lability of shapes, juxtaposed with similar molecular mechanisms underlying leaf development in reference plants, suggests that the striking diversity of eudicot leaves results from variations of a common generative program. Notably, this mechanism acts jointly on leaf shape and vasculature, patterning both marginal protrusions and corresponding veins in the blade. Inspired by this perspective, we propose a geometric model of leaf development and diversity. It simulates development as a feedback between two processes: the dynamic patterning of growth centers at the leaf margin, and control of growth directions by veins associated with these points. Our models show that the spatial separation of the processes patterning and directing growth facilitates the generation of a wide range of leaf forms, from simple to lobed and compound. Additionally, transitions between different forms can be controlled in a continuous manner. These transitions reproduce frequently observed, and often drastic, changes in leaf form within the same plant or between closely related species. Our results highlight the flexible and self-organizing nature of leaf development, and provide a path towards an integrated understanding of their development and diversity.Non UBCUnreviewedAuthor affiliation: Max Planck Institute for Plant Breeding ResearchPostdoctora

Modeling Biological Patterns using the Space Colonization Algorithm

This thesis introduces a class of algorithms for modeling biological patterns with branching (tree-like) and network (with loops) topologies. The key idea behind these algorithms is the marking and subsequent colonization of empty space. Models are formulated in terms of iterative geometric operations on sets of points representing the elements of the pattern and markers of free space. This concept is formalized as the space colonization algorithm. The practical value of this approach is demonstrated by modeling the architecture of trees and vasculature in plants. Trees are modeled using markers of empty space to mediate competition between branches. When vascular patterns are modeled, the markers of empty space represent sources of a vein inducing signal (auxin). Several algorithms are introduced to simulate vein development in a growing leaf blade. Additionally, a model simulating vasculature patterning in the stem is proposed and used to examine the relation between phylotaxis and stem vasculature The applications explored in this thesis demonstrate that a common mechanism

Modeling Trees with a Space Colonization Algorithm

We extend the open leaf venation model by Runions et al. [RFL*05] to three dimensions and show that it generates surprisingly realistic tree structures. Model parameters correspond to visually relevant tree characteristics identified in landscaping, offering convenient control of tree shape and structure.Eurographics Workshop on Natural Phenomen