Fast determination of coarse grained cell anisotropy and size in epithelial tissue images using Fourier transform

TL;DR

This paper introduces a rapid Fourier transform-based method for estimating cell shape anisotropy and size in epithelial tissues, providing a coarse-grained alternative to detailed segmentation for large datasets.

Contribution

The authors developed a fast, user-friendly Fourier transform pipeline for analyzing cell anisotropy and size, suitable for large-scale and low-quality images, validated on biological tissue images.

Findings

Achieves analysis of 10^4 cells per minute on a laptop

Robust results validated on artificial and biological images

Applicable to various tissue types and imaging conditions

Abstract

Mechanical strain and stress play a major role in biological processes such as wound healing or morphogenesis. To assess this role quantitatively, fixed or live images of tissues are acquired at a cellular precision in large fields of views. To exploit these data, large numbers of cells have to be analyzed to extract cell shape anisotropy and cell size. Most frequently, this is performed through detailed individual cell contour determination, using so-called segmentation computer programs, complemented if necessary by manual detection and error corrections. However, a coarse grained and faster technique can be recommended in at least three situations. First, when detailed information on individual cell contours is not required, for instance in studies which require only coarse-grained average information on cell anisotropy. Second, as an exploratory step to determine whether full segmentation can be potentially useful. Third, when segmentation is too difficult, for instance due to poor image quality or too large a cell number. We developed a user-friendly, Fourier transform-based image analysis pipeline. It is fast (typically $10^4$ cells per minute with a current laptop computer) and suitable for time, space or ensemble averages. We validate it on one set of artificial images and on two sets of fully segmented images, one from a Drosophila pupa and the other from a chicken embryo; the pipeline results are robust. Perspectives include \textit{in vitro} tissues, non-biological cellular patterns such as foams, and $xyz$ stacks.