![]() Whether in kinematic analyses (e.g., ), in functional genetics (e.g., ), in cell biology (e.g., ), and in computational modeling (e.g., ), quantifying cell contours during growth is thus crucial to understand plant development as a whole. From a geometric perspective, this means that plant morphogenesis mainly depends on the cell growth rate and growth anisotropy. Because plant cells do not migrate, and usually do not go through apoptosis in young tissues, plant morphogenesis primarily relies on cell elongation and cell division. The combination of these two methods thus provides an ideal suite of tools for cell contour extraction in most biological samples, whether 3D precision or high-throughput analysis is the main priority.Ĭell shape is a primary variable in morphogenesis in all kingdoms, either as a building block for multicellular shape or because cell shape in turn biases the behavior of structural elements (e.g., cytoskeleton) or morphogens. SurfCut and MGX have complementary advantages: MGX is well suited for curvy samples and more complex analyses, up to computational cell-based modeling on real templates SurfCut is well suited for rather flat samples, is simple to use, and has the advantage to be easily automated for batch analysis of images in ImageJ. We provide a new ImageJ pipeline, SurfCut, that allows the extraction of cell contours from 3D confocal stacks. SurfCut was however not appropriate for cell or tissue samples with high curvature, as evidenced by a significant bias in shape and area quantification. ![]() While both methods differ in the approach used to extract the layer of signal, they output comparable results for tissues with shallow curvature, such as pavement cell shape in cotyledon epidermis (as quantified with PaCeQuant). As a reference point, we compared our output to that obtained with MorphoGraphX (MGX). We developed a macro in ImageJ, SurfCut, with the goal to provide a user-friendly pipeline specifically designed to extract epidermal cell contour signals, segment cells in 2D and analyze cell shape. However, proper extraction of 2D cell contours from 3D confocal stacks for such analysis can be problematic. For instance, the analysis of epithelial cells in Drosophila embryogenesis or jigsaw puzzle-shaped pavement cells in plant epidermis has led to the development of numerous quantification methods that are applied to 2D images. Many methods have been developed to quantify cell shape in 2D in tissues.
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