Versatile method for quantifying and analyzing morphological differences in experimentally obtained images

Analyzing high-resolution images to gain insight into anatomical properties is an essential tool for investigation in many scientific fields. In plant biology, studying plant phenotypes from micrographs is often used to build hypotheses on gene function. In this report, we discuss a bespoke method for inspecting the significance in the differences between the morphologies of several plant mutants at cellular level. By examining a specific example in the literature, we will detail the approach previously used to quantify the effects of two gene families on the vascular development of hypocotyls in Arabidopsis thaliana. The method incorporates a MATLAB algorithm and statistical tools which can be modified and enhanced to tailor to different research questions in future studies.