ImageJ SurfCut: a user-friendly pipeline for high-throughput extraction of cell contours from 3D image stacks

BMC Biology

Olivier Hamant¹  Özer Erguvan²  Marion Louveaux³  Stéphane Verger⁴ 

[1] Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d’Italie, 69364, Lyon Cedex 07, France;Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d’Italie, 69364, Lyon Cedex 07, France;Department of Biology, Graduate School of Natural and Applied Sciences, Bursa Uludağ University, Bursa, Turkey;Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d’Italie, 69364, Lyon Cedex 07, France;Present Address: Center for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany;Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, UCB Lyon 1, ENS de Lyon, INRA, CNRS, 46 Allée d’Italie, 69364, Lyon Cedex 07, France;Present Address: Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden;

关键词: Cell shape;    Cell contour;    Segmentation;    Confocal microscopy;    Cell wall;    MorphoGraphX;    ImageJ;    R;   

DOI  :  10.1186/s12915-019-0657-1

来源: Springer

【 摘 要 】

BackgroundMany methods have been developed to quantify cell shape in 2D in tissues. 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. However, proper extraction of 2D cell contours from 3D confocal stacks for such analysis can be problematic.ResultsWe 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. As a reference point, we compared our output to that obtained with MorphoGraphX (MGX). 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). SurfCut was however not appropriate for cell or tissue samples with high curvature, as evidenced by a significant bias in shape and area quantification.ConclusionWe provide a new ImageJ pipeline, SurfCut, that allows the extraction of cell contours from 3D confocal stacks. 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. 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.

【 授权许可】

CC BY