ArticleBMC biology2019
ImageJ SurfCut: a user-friendly pipeline for high-throughput extraction of cell contours from 3D image stacks.
Article in BMC biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- A drought stress-induced MYB transcription factor regulates pavement cell shape in leaves of European aspen (Populus tremula).The New phytologist · 2026Article
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- Dynamic interactions between epithelial skin cells and a sensory cavity sculpt the growing olfactory orifice.Nature communications · 2026Article
- A Guide to Reproducible Cellulose Synthase Density and Speed Measurements inBio-protocol · 2026Article
- Rho GTPase overexpression impacts leaf internal architecture and mesophyll conductance in Arabidopsis.The New phytologist · 2025Article
- Behind phyllotaxis, within the meristem: a REM-ARF complex shapes inflorescence in Arabidopsis thaliana.The Plant journal : for cell and molecular biology · 2025Article
- OrgaMapper: a robust and easy-to-use workflow for analyzing organelle positioning.BMC biology · 2024Article
- Large-volume fully automated cell reconstruction generates a cell atlas of plant tissues.The Plant cell · 2024Article
- Increased basal fibronectin is sufficient to promote excess endothelial cell matrix assembly causing localized barrier dysfunction.Molecular biology of the cell · 2024Article
- A transient radial cortical microtubule array primes cell division inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Spatiotemporally distinct responses to mechanical forces shape the developing seed of Arabidopsis.The EMBO journal · 2024Article
- Community-developed checklists for publishing images and image analyses.Nature methods · 2024Review
- Article
- High-throughput characterization of cortical microtubule arrays response to anisotropic tensile stress.BMC biology · 2023Article
- Assessing CaMPARI as new approach methodology for evaluating neurotoxicity.Neurotoxicology · 2023Article
- Actomyosin contractility in olfactory placode neurons opens the skin epithelium to form the zebrafish nostril.Developmental cell · 2023Article
- Mechano-chemical regulation of complex cell shape formation: Epidermal pavement cells-A case study.Quantitative plant biology · 2023Review
- DeepProjection: specific and robust projection of curved 2D tissue sheets from 3D microscopy using deep learning.Development (Cambridge, England) · 2022Article
- LeafNet: a tool for segmenting and quantifying stomata and pavement cells.The Plant cell · 2022Article
- Misregulation of MYB16 expression causes stomatal cluster formation by disrupting polarity during asymmetric cell divisions.The Plant cell · 2022Article
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4 authors.
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Abstract
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.
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