A deep learning-based toolkit for 3D nuclei segmentation and quantitative analysis in cellular and tissue context.

We present a new set of computational tools that enable accurate and widely applicable 3D segmentation of nuclei in various 3D digital organs. We have developed an approach for ground truth generation and iterative training of 3D nuclear segmentation models, which we applied to popular CellPose, PlantSeg and StarDist algorithms. We provide two high-quality models trained on plant nuclei that enable 3D segmentation of nuclei in datasets obtained from fixed or live samples, acquired from different plant and animal tissues, and stained with various nuclear stains or fluorescent protein-based nuclear reporters.

Twin Embryos in Mutants.

Regulation of microtubule dynamics is crucial during key developmental transitions such as gametogenesis, fertilization, embryogenesis, and seed formation, where cells undergo rapid changes in shape and function. In plants, katanin plays an essential role in microtubule dynamics. This study investigates two seed developmental mutants in , named (, ) and (), which are characterized by round seeds, dwarfism, and fertility defects.

Topological analysis of 3D digital ovules identifies cellular patterns associated with ovule shape diversity.

Tissue morphogenesis remains poorly understood. In plants, a central problem is how the 3D cellular architecture of a developing organ contributes to its final shape. We address this question through a comparative analysis of ovule morphogenesis, taking advantage of the diversity in ovule shape across angiosperms.

The 1991 review by Coen and Meyerowitz on the war of the whorls and the ABC model of floral organ identity.

The 1991 review paper by Coen and Meyerowitz on the control of floral organ development set out the evidence available at that time, which led to the now famous ABC model of floral organ identity control. The authors summarised the genetic and molecular analyses that had been carried out in a relatively short time by several laboratories, mainly in and . The work was a successful example of how systematic genetic and molecular analysis can decipher the mechanism that controls a developmental process in plants.

Arabidopsis MCTP family member QUIRKY regulates the formation of the STRUBBELIG receptor kinase complex.

Intercellular communication plays a central role in organogenesis. Tissue morphogenesis in Arabidopsis (Arabidopsis thaliana) requires signaling mediated by a cell surface complex containing the atypical receptor kinase STRUBBELIG (SUB) and the multiple C2 domains and transmembrane region protein QUIRKY (QKY). QKY is required to stabilize SUB at the plasma membrane.

Pivotal role of STIP in ovule pattern formation and female germline development in Arabidopsis thaliana.

In spermatophytes the sporophytic (diploid) and the gametophytic (haploid) generations co-exist in ovules, and the coordination of their developmental programs is of pivotal importance for plant reproduction. To achieve efficient fertilization, the haploid female gametophyte and the diploid ovule structures must coordinate their development to form a functional and correctly shaped ovule. WUSCHEL-RELATED HOMEOBOX (WOX) genes encode a family of transcription factors that share important roles in a wide range of processes throughout plant development.

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.

Using Steady-State Fluorescence Anisotropy to Study Protein Clustering.

Signaling pathways rely on the precise control of protein-protein interactions. Therefore, it is essential to be able to investigate such interactions with spatiotemporal resolution and in live cells. Here we describe a microscope-based fluorescence spectrometry technique to investigate homotypic interactions between GFP-labeled fusion proteins in a rapid and reproducible fashion using fluorescence anisotropy.

The annotation and analysis of complex 3D plant organs using 3DCoordX.

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ.

Cell wall damage attenuates root hair patterning and tissue morphogenesis mediated by the receptor kinase STRUBBELIG.

Cell wall remodeling is essential for the control of growth and development as well as the regulation of stress responses. However, the underlying cell wall monitoring mechanisms remain poorly understood. Regulation of root hair fate and flower development in Arabidopsis thaliana requires signaling mediated by the atypical receptor kinase STRUBBELIG (SUB).

A digital 3D reference atlas reveals cellular growth patterns shaping the ovule.

A fundamental question in biology is how morphogenesis integrates the multitude of processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Using machine-learning-based digital image analysis, we generated a three-dimensional atlas of ovule development in , enabling the quantitative spatio-temporal analysis of cellular and gene expression patterns with cell and tissue resolution. We discovered novel morphological manifestations of ovule polarity, a new mode of cell layer formation, and previously unrecognized subepidermal cell populations that initiate ovule curvature.

Accurate and versatile 3D segmentation of plant tissues at cellular resolution.

Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio-image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells.

Shaping the genome of plants.

Fertilization of an egg cell by more than one sperm cell can produce viable progeny in a flowering plant.

The Arabidopsis receptor kinase STRUBBELIG regulates the response to cellulose deficiency.

Plant cells are encased in a semi-rigid cell wall of complex build. As a consequence, cell wall remodeling is essential for the control of growth and development as well as the regulation of abiotic and biotic stress responses. Plant cells actively sense physico-chemical changes in the cell wall and initiate corresponding cellular responses.

Protocol for rapid clearing and staining of fixed Arabidopsis ovules for improved imaging by confocal laser scanning microscopy.

Background: A salient topic in developmental biology relates to the molecular and genetic mechanisms that underlie tissue morphogenesis. Modern quantitative approaches to this central question frequently involve digital cellular models of the organ or tissue under study. The ovules of the model species have long been established as a model system for the study of organogenesis in plants.

Asymmetric Redundancy of and in Different Accessions of .

Divergence among duplicate genes is one of the important sources of evolutionary innovation. But, the contribution of duplicate divergence to variation in Arabidopsis accessions is sparsely known. Recently, we studied the role of a cell wall localized protein, ZERZAUST (ZET), in Landsberg (L) accession, lack of which results in aberrant plant morphology.

The Arabidopsis receptor kinase STRUBBELIG undergoes clathrin-dependent endocytosis.

Signaling mediated by cell surface receptor kinases is central to the coordination of growth patterns during organogenesis. Receptor kinase signaling is in part controlled through endocytosis and subcellular distribution of the respective receptor kinase. For the majority of plant cell surface receptors, the underlying trafficking mechanisms are not characterized.

Correction: The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana.

[This corrects the article DOI: 10.1371/journal.pgen.

The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana.

Tissue morphogenesis critically depends on the coordination of cellular growth patterns. In plants, many organs consist of clonally distinct cell layers, such as the epidermis, whose cells undergo divisions that are oriented along the plane of the layer. The developmental control of such planar growth is poorly understood.

The role of KDEL-tailed cysteine endopeptidases of Arabidopsis (AtCEP2 and AtCEP1) in root development.

Plants encode a unique group of papain-type cysteine endopeptidases (CysEP) characterized by a C-terminal KDEL endoplasmic reticulum retention signal (KDEL-CysEP) and an unusually broad substrate specificity. The three Arabidopsis KDEL-CysEPs (AtCEP1, AtCEP2, and AtCEP3) are differentially expressed in vegetative and generative tissues undergoing programmed cell death (PCD). While KDEL-CysEPs have been shown to be implicated in the collapse of tissues during PCD, roles of these peptidases in processes other than PCD are unknown.

The cell wall-localized atypical β-1,3 glucanase ZERZAUST controls tissue morphogenesis in .

Orchestration of cellular behavior in plant organogenesis requires integration of intercellular communication and cell wall dynamics. The underlying signaling mechanisms are poorly understood. Tissue morphogenesis in depends on the receptor-like kinase STRUBBELIG.

Pattern formation during early floral development.

Flowers are central to sexual reproduction in plants. The study of floral development proved tremendously successful in obtaining key insight into processes, such as fate determination, pattern formation, and growth regulation. Recent advances relate to the complex mechanisms underlying the crosstalk between phytohormone signaling, cell and tissue mechanics, and regulatory gene networks that positions floral buds at the apex and directs floral specification, initiation and outgrowth.

The C2-domain protein QUIRKY and the receptor-like kinase STRUBBELIG localize to plasmodesmata and mediate tissue morphogenesis in Arabidopsis thaliana.

Tissue morphogenesis in plants requires communication between cells, a process involving the trafficking of molecules through plasmodesmata (PD). PD conductivity is regulated by endogenous and exogenous signals. However, the underlying signaling mechanisms remain enigmatic.

Detection of mRNA expression patterns by nonradioactive in situ hybridization on histological sections of floral tissue.

Analysis of gene activity with high spatial resolution is a prerequisite for deciphering regulatory networks which underlie developmental programs. Over many years, in situ hybridization has become the gold standard for the identification of in vivo expression patterns of endogenous mRNAs. Nonetheless, the method has several limitations, and the detection of lowly expressed transcripts is still a challenge.