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Cell segmentation is a fundamental task in microscopy image analysis. Several foundation models for cell segmentation have been introduced, virtually all of them are extensions of Segment Anything Model (SAM), improving it for microscopy…
Vascular and non-vascular cells often form an interconnected network in vitro, similar to the early vascular bed of warm blooded embryos. Our time-lapse recordings show that the network forms by extending sprouts, i.e., multicellular linear…
Plants have developed different tropisms: in particular, they re-orient the growth of their branches towards light (phototropism) or upwards (gravitropism). How these tropisms affect the shape of a tree crown remains unanswered. We address…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
In the past 50 years, the formalism of L-systems has been successfully used and developed to model the growth of filamentous and branching biological forms. These simulations take place in classical 2-D or 3-D Euclidean spaces. However,…
The rheological properties of biological tissues are core to processes such as cancer metastasis, wound healing and embryo development. The emergence of tissue and organ structures during morphogenesis requires the precise formation of…
Stem cells are characterized by their ability to self-renew, as well as to differentiate and give rise to new populations of cells. Stem cell divisions are crucial for generative processes that occur during early development, and later in…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal,…
In densely-packed two-dimensional systems of growing cells, such as rod-shaped bacteria, a number of experimental and numerical studies report distinct patterns of nematic orientational order in the presence of confinement. So far, these…
Developmental processes in multicellular organisms occur far from equilibrium, yet produce complex patterns with astonishing reproducibility. We measure the precision and reproducibility of bilaterally symmetric fly wings across the natural…
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. We investigate this phenomenon using gastruloids, an in vitro model for early mammalian…
Thermal fluctuations in cell membranes manifest as an excess area (${\cal A}_{\rm ex}$) which governs a multitude of physical process at the sub-micron scale. We present a theoretical framework, based on an in silico tether pulling method,…
Metastable vaterite crystals were synthesized by increasing the pH and consequently the saturation states of Ca and CO3 containing solutions using an ammonia diffusion method. SEM and TEM analyses indicate that vaterite grains produced by…
Arabidopsis thaliana is a plant species widely utilized by scientists to estimate the impact of genetic differences in root morphological features. For this purpose, images of this plant after genetic modifications are taken to study…
We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring…
The original Hardenberg's model of biomass patterns in arid and semi-arid regions is revisited to extend it to more general non flat regions. It is proposed a technique to study these more generalized (non-flat) regions using both a…
The growth of bacterial flagellar filaments is a self-assembly process where flagellin molecules are transported through the narrow core of the flagellum and are added at the distal end. To model this situation, we generalize a growth…
Cell neighbor exchanges play a critical role in regulating tissue fluidity during epithelial morphogenesis and repair. In vivo, these neighbor exchanges are often hindered by the formation of transiently stable four-fold vertices, which can…
We use laser hole-drilling to assess the mechanics of an embryonic epithelium during development - in vivo and with subcellular resolution. We ablate a subcellular cylindrical hole clean through the epithelium, and track the subsequent…