Image analysis of Arabidopsis trichome patterning in 4D confocal datasets

In this article, we present an approach for the automated extraction of quantitative information about trichome patterning on leaves of Arabidopsis thaliana. Time series of growing rosette leaves (4D confocal datasets, 3D + time) are used for this work. At first, significant anatomical structures, i.e. leaf surface and midplane are extracted robustly. Using the extracted anatomical structures, a biological reference coordinate system is registered to the leaves. The performed registration allows to determine intra- as well as inter-series spatiotemporal correspondences. Trichomes are localized by first detecting candidates using Hough transform. Then, local 3D invariants are extracted and the candidates are validated using a Support Vector Machine (SVM).