Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.

In Arabidopsis thaliana, the stem cell population of the shoot system is controlled by regulatory circuitry involving the WUSCHEL (WUS) and CLAVATA (CLV1-3) genes. WUS signals from the organizing center (OC) to promote stem cell fate at the meristem apex. Stem cells express the secreted peptide CLV3 that activates a signal transduction cascade to restrict WUS expression, thus providing a feedback mechanism. Stem cell homeostasis is proposed to be achieved by balancing these signals. We tested the dynamics of CLV3 signaling using an inducible gene expression system. We show here that increasing the CLV3 signal can very rapidly repress WUS expression during development, which in turn causes a fast reduction of CLV3 expression. We demonstrate that increased CLV3 signaling restricts meristem growth and promotes allocation of peripheral meristem cells into organ primordia. In addition, we extend the current model for stem cell control by showing that meristem homeostasis tolerates variation in CLV3 levels over a 10-fold range and that high-level CLV3 signaling can be partially compensated with time, indicating that the level of CLV3 expression communicates only limited information on stem cell number to the underlying OC cells.

The shoot apical meristem generates stem, leaves, and lateral shoot meristems during the entire shoot ontogeny. Vegetative leaves are generated by the meristem in the vegetative developmental phase, while in the reproductive phase either bracts subtending lateral flower primordia (or paraclades), or perianth and strictly reproductive organs are formed. Meristem growth is fully characterized by the principal growth rates, directions, volumetric, and areal growth rates. Growth modelling or sequential in vivo methods of meristem observation complemented by growth quantification allow the above growth variables to be estimated. Indirectly, growth is assessed by cell division rates and other cell cycle parameters. Temporal and spatial changes of growth and geometry take place at the meristem during the transition from the vegetative to the reproductive phase. During the vegetative phase, meristem growth is generally indeterminate. In the reproductive phase it is almost always determinate, but the extent of determinacy depends on the inflorescence architecture. In the vegetative phase the central meristem zone is the slowest growing region. The transition from the vegetative to the reproductive phase is accompanied by an increase in mitotic activity in this zone. The more determinate is the meristem growth, the stronger is this mitotic activation. However, regardless of the extent of the activation, in angiosperms the tunica/corpus structure of the meristem is preserved and therefore the mitotic activity of germ line cells remains relatively low. In the case of the thoroughly studied model angiosperm plant Arabidopsis thaliana, it is important to recognize that the flower primordium develops in the axil of a rudimentary bract. Another important feature of growth of the inflorescence shoot apical meristem is the heterogeneity of the peripheral zone. Finally, the role of mechanical factors in growth and functioning of the meristem needs further investigation.

A non‐destructive replica method and a 3‐D reconstruction algorithm are used to analyse the geometry and expansion of the shoot apex surface. Surface expansion in the central zone of the apex is slow and nearly isotropic while surface expansion in the peripheral zone is more intense and more anisotropic. Within the peripheral zone, the expansion rate, expansion anisotropy, and the direction of maximal expansion vary according to the age of adjacent leaf primordia. For each plastochron, this pattern of expansion is rotated around the apex by the Fibonacci angle. Early leaf primordium development is divided into four stages: bulging, lateral expansion, separation, and bending. These stages differ in their geometry and expansion pattern. At the bulging stage, the site of primordium initiation shows an intensified expansion that is nearly isotropic. The following stages develop sharp meridional gradients of expansion rates and anisotropy. The adaxial primordium boundary inferred from the surface curvature is shifting until the separation stage, when a crease develops between the primordium and the apex dome. The cells forming the crease, i.e. the future leaf axil, expand along the axil and contract across it. Thus they are arrested in this unique position.