Plant phenotyping is the identification of effects on the phenotype (i.e., the plant appearance and performance) as a result of genotype differences (i.e., differences in the genetic code) and the environmental conditions to which a plant has been exposed [1]?[3]. According to the Food and Agriculture Organization of the United Nations, large-scale experiments in plant phenotyping are a key factor in meeting the agricultural needs of the future to feed the world and provide biomass for energy, while using less water, land, and fertilizer under a constantly evolving environment due to climate change. Working on model plants (such as Arabidopsis), combined with remarkable advances in genotyping, has revolutionized our understanding of biology but has accelerated the need for precision and automation in phenotyping, favoring approaches that provide quantifiable phenotypic information that could be better used to link and find associations in the genotype [4]. While early on, the collection of phenotypes was manual, currently noninvasive, imaging-based methods are increasingly being utilized [5], [6]. However, the rate at which phenotypes are extracted in the field or in the lab is not matching the speed of genotyping and is creating a bottleneck [1].

We found the article by Singh et al. [1] extremely interesting because it introduces and showcases the utility of machine learning for high-throughput data-driven plant phenotyping. With this letter we aim to emphasize the role that image analysis and processing have in the phenotyping pipeline beyond what is suggested in [1], both in analyzing phenotyping data (e.g., to measure growth) and when providing effective feature extraction to be used by machine learning. Key recent reviews have shown that it is image analysis itself (what the authors of [1] consider as part of pre-processing) that has brought a renaissance in phenotyping [2]

Plant phenotyping investigates how a plant's genome, interacting with the environment, affects the observable traits of a plant (phenome). It is becoming increasingly important in our quest towards efficient and sustainable agriculture. While sequencing the genome is becoming increasingly efficient, acquiring phenotype information has remained largely of low throughput. Current solutions for automated image-based plant phenotyping, rely either on semi-automated or manual analysis of the imaging data, or on expensive and proprietary software which accompanies costly hardware infrastructure. While some attempts have been made to create software applications that enable the analysis of such images in an automated fashion, most solutions are tailored to particular acquisition scenarios and restrictions on experimental design. In this paper we propose and test, a method for the segmentation and the automated analysis of time-lapse plant images from phenotyping experiments in a general laboratory setting, that can adapt to scene variability. The method involves minimal user interaction, necessary to establish the statistical experiments that may follow. At every time instance (i.e., a digital photograph), it segments the plants in images that contain many specimens of the same species. For accurate plant segmentation we propose a vector valued level set formulation that incorporates features of color intensity, local texture, and prior knowledge. Prior knowledge is incorporated using a plant appearance model implemented with Gaussian mixture models, which utilizes incrementally information from previously segmented instances. The proposed approach is tested on Arabidopsis plant images acquired with a static camera capturing many subjects at the same time. Our validation with ground truth segmentations and comparisons with state-of-the-art methods in the literature shows that the proposed method is able to handle images with complicated and changing background in an automated fashion. An accuracy of 96.7% (dice similarity coefficient) was observed, which was higher than other methods used for comparison. While here it was tested on a single plant species, the fact that we do not employ shape driven models and we do not rely on fully supervised classification (trained on a large dataset) increases the ease of deployment of the proposed solution for the study of different plant species in a variety of laboratory settings. Our solution will be accompanied by an easy to use graphical user interface and, to facilitate adoption, we will make the software available to the scientific community

Summary: Phenotyping is important to understand plant biology, but current solutions are costly, not versatile or are difficult to deploy. To solve this problem, we present Phenotiki, an affordable system for plant phenotyping that, relying on off‐the‐shelf parts, provides an easy to install and maintain platform, offering an out‐of‐box experience for a well‐established phenotyping need: imaging rosette‐shaped plants. The accompanying software (with available source code) processes data originating from our device seamlessly and automatically. Our software relies on machine learning to devise robust algorithms, and includes an automated leaf count obtained from 2D images without the need of depth (3D). Our affordable device (~€200) can be deployed in growth chambers or greenhouse to acquire optical 2D images of approximately up to 60 adult Arabidopsis rosettes concurrently. Data from the device are processed remotely on a workstation or via a cloud application (based on CyVerse). In this paper, we present a proof‐of‐concept validation experiment on top‐view images of 24 Arabidopsis plants in a combination of genotypes that has not been compared previously. Phenotypic analysis with respect to morphology, growth, color and leaf count has not been performed comprehensively before now. We confirm the findings of others on some of the extracted traits, showing that we can phenotype at reduced cost. We also perform extensive validations with external measurements and with higher fidelity equipment, and find no loss in statistical accuracy when we use the affordable setting that we propose. Device set‐up instructions and analysis software are publicly available ( http://phenotiki.com).