MowJoe: a method for automated-high throughput dissected leaf phenotyping

BACKGROUND: Accurate and automated phenotyping of leaf images is necessary for high throughput studies of leaf form like genome-wide association analysis and other forms of quantitative trait locus mapping. Dissected leaves (also referred to as compound) that are subdivided into individual units are an attractive system to study diversification of form. However, there are only few software tools for their automated analysis. Thus, high-throughput image processing algorithms are needed that can partition these leaves in their phenotypically relevant units and calculate morphological features based on these units. RESULTS: We have developed MowJoe, an image processing algorithm that dissects a dissected leaf into leaflets, petiolule, rachis and petioles. It employs image skeletonization to convert leaves into graphs, and thereafter applies algorithms operating on graph structures. This partitioning of a leaf allows the derivation of morphological features such as leaf size, or eccentricity of leaflets. Furthermore, MowJoe automatically places landmarks onto the terminal leaflet that can be used for further leaf shape analysis. It generates specific output files that can directly be imported into downstream shape analysis tools. We applied the algorithm to two accessions of Cardamine hirsuta and show that our features are able to robustly discriminate between these accessions. CONCLUSION: MowJoe is a tool for the semi-automated, quantitative high throughput shape analysis of dissected leaf images. It provides the statistical power for the detection of the genetic basis of quantitative morphological variations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13007-018-0290-y) contains supplementary material, which is available to authorized users.