12Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most 13 important agronomic traits are lacking. To address this problem, we developed an automated analysis 14 platform that extracts components of size and shape for carrot shoots and roots, which are necessary 15 to advance carrot breeding and genetics. This method reliably measured variation in shoot size and 16 shape, leaf number, petiole length, and petiole width as evidenced by high correlations with hundreds 17 of manual measurements. Similarly, root length and biomass were accurately measured from the 18 images. This platform quantified shoot and root shapes in terms of principal components, which do 19 not have traditional, manually-measurable equivalents. We applied the pipeline in a study of a six-20 parent diallel population and an F 2 mapping population consisting of 316 individuals. We found high 21 levels of repeatability within a growing environment, with low to moderate repeatability across 22 environments. We also observed co-localization of quantitative trait loci for shoot and root 23 characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage 24 and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably 25 quantified, the development of a high-throughput image analysis pipeline to measure carrot shoot and 26 root morphology will expand the scope and scale of breeding and genetic studies. 27All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.