Actin-mediated avoidance of tricellular junction influences global topology at the Arabidopsis shoot apical meristem.

Division plane orientation contributes to cell shape and topological organization, playing a key role in morphogenesis, but the precise physical and molecular mechanism influencing these processes remains largely obscure in plants. In particular, it is less clear how the placement of the new walls occurs in relation to the walls of neighboring cells. Here, we show that genetic perturbation of the actin cytoskeleton results in more rectangular cell shapes and higher incidences of four-way junctions, perturbing the global topology of cells in the shoot apical meristem of Arabidopsis thaliana.

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.

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.

Robust organ size requires robust timing of initiation orchestrated by focused auxin and cytokinin signalling.

Organ size and shape are precisely regulated to ensure proper function. The four sepals in each Arabidopsis thaliana flower must maintain the same size throughout their growth to continuously enclose and protect the developing bud. Here we show that DEVELOPMENT RELATED MYB-LIKE 1 (DRMY1) is required for both timing of organ initiation and proper growth, leading to robust sepal size in Arabidopsis.

From Stained Plant Tissues to Quantitative Cell Segmentation Analysis with MorphoGraphX.

Development and growth of plant organs is determined by a myriad of molecular processes that occur in each individual cell. As a direct consequence of these processes, cells alter in size and shape. They therefore serve as excellent parameters to thoroughly understand gene function.

Quantifying Plant Growth and Cell Proliferation with MorphoGraphX.

Confocal microscopy is widely used to live-image plant tissue. Cell outlines can be visualized using fluorescent probes that mark the cell wall or plasma membrane, enabling the confocal microscope to be used as a 3D scanner with submicron precision. After imaging, the data needs to be analyzed by specialized software to quantify the features of interest, such as cell size and shape, growth rates and anisotropy, and gene expression.

3DCellAtlas Meristem: a tool for the global cellular annotation of shoot apical meristems.

Modern imaging approaches enable the acquisition of 3D and 4D datasets capturing plant organ development at cellular resolution. Computational analyses of these data enable the digitization and analysis of individual cells. In order to fully harness the information encoded within these datasets, annotation of the cell types within organs may be performed.

Global Topological Order Emerges through Local Mechanical Control of Cell Divisions in the Arabidopsis Shoot Apical Meristem.

The control of cell position and division act in concert to dictate multicellular organization in tissues and organs. How these processes shape global order and molecular movement across organs is an outstanding problem in biology. Using live 3D imaging and computational analyses, we extracted networks capturing cellular connectivity dynamics across the Arabidopsis shoot apical meristem (SAM) and topologically analyzed the local and global properties of cellular architecture.

On the micro-indentation of plant cells in a tissue context.

The effect of geometry on cell stiffness measured with micro-indentation techniques has been explored in single cells, however it is unclear if results on single cells can be readily transferred to indentation experiments performed on a tissue in vivo. Here we explored this question by using simulation models of osmotic treatments and micro-indentation experiments on 3D multicellular tissues with the finite element method. We found that the cellular context does affect measured cell stiffness, and that several cells of context in each direction are required for optimal results.

In Silico Methods for Cell Annotation, Quantification of Gene Expression, and Cell Geometry at Single-Cell Resolution Using 3DCellAtlas.

A comprehensive understanding of plant growth and development requires the integration of the spatial and temporal dynamics of gene regulatory networks with changes in cellular geometry during 3D organ growth. 3DCellAtlas is an integrative computational pipeline that semi-automatically identifies cell type and position within radially symmetric plant organs, and simultaneously quantifies 3D cell anisotropy and reporter abundance at single-cell resolution. It is a powerful tool that generates digital single-cell cellular atlases of plant organs and enables 3D cell geometry and reporter abundance (gene/protein/biosensor) from multiple samples to be integrated at single-cell resolution across whole organs.

Choice reaching with a LEGO arm robot (CoRLEGO): The motor system guides visual attention to movement-relevant information.

We present an extension of a neurobiologically inspired robotics model, termed CoRLEGO (Choice reaching with a LEGO arm robot). CoRLEGO models experimental evidence from choice reaching tasks (CRT). In a CRT participants are asked to rapidly reach and touch an item presented on the screen.

Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas.

Diverse molecular networks underlying plant growth and development are rapidly being uncovered. Integrating these data into the spatial and temporal context of dynamic organ growth remains a technical challenge. We developed 3DCellAtlas, an integrative computational pipeline that semiautomatically identifies cell types and quantifies both 3D cellular anisotropy and reporter abundance at single-cell resolution across whole plant organs.

Motor cortex guides selection of predictable movement targets.

The present paper asks whether the motor cortex contributes to prediction-based guidance of target selection. This question was inspired by recent evidence that suggests (i) recurrent connections from the motor system into the attentional system may extract movement-relevant perceptual information and (ii) that the motor cortex cannot only generate predictions of the sensory consequences of movements but may also operate as predictor of perceptual events in general. To test this idea we employed a choice reaching task requiring participants to rapidly reach and touch a predictable or unpredictable colour target.

A robotics-based approach to modeling of choice reaching experiments on visual attention.

The paper presents a robotics-based model for choice reaching experiments on visual attention. In these experiments participants were asked to make rapid reach movements toward a target in an odd-color search task, i.e.