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

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

SUBMITTER: Erguvan O 

PROVIDER: S-EPMC6509810 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature