eprintid: 26416
rev_number: 13
eprint_status: archive
userid: 1589
dir: disk0/00/02/64/16
datestamp: 2019-07-25 15:35:22
lastmod: 2019-08-20 12:41:22
status_changed: 2019-07-25 15:35:22
type: article
metadata_visibility: show
creators_name: Erguvan, Özer
creators_name: Louveaux, Marion
creators_name: Hamant, Olivier
creators_name: Verger, Stéphane
title: ImageJ SurfCut: a user-friendly pipeline for high-throughput extraction of cell contours from 3D image stacks
subjects: ddc-610
divisions: i-910100
keywords: Cell shape, Cell contour, Segmentation, Confocal microscopy, Cell wall, MorphoGraphX, ImageJ, R
abstract: Background: Many 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.

Results: 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. 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.

Conclusion: We 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.
date: 2019
publisher: Springer
id_scheme: DOI
ppn_swb: 1671264401
own_urn: urn:nbn:de:bsz:16-heidok-264167
language: eng
bibsort: ERGUVANOZEIMAGEJSURF2019
full_text_status: public
publication: BMC Biology
volume: 17
number: 38
place_of_pub: Berlin ; Heidelberg
pagerange: 1-12
issn: 1741-7007
citation:   Erguvan, Özer ; Louveaux, Marion ; Hamant, Olivier ; Verger, Stéphane  (2019) ImageJ SurfCut: a user-friendly pipeline for high-throughput extraction of cell contours from 3D image stacks.  BMC Biology, 17 (38).  pp. 1-12.  ISSN 1741-7007     
document_url: https://archiv.ub.uni-heidelberg.de/volltextserver/26416/1/12915_2019_Article_657.pdf