PlantCV is an open-source open-development image analysis software package for plant phenotyping written in Python that has been actively developed since 2014. A new version of PlantCV was recently released. Major goals of the version 4 release were to 1) simplify the process of developing workflows by reducing the amount of coding needed; 2) broadening the set of supported data types; and 3) introducing interactive annotation tools that can be used directly in PlantCV workflow notebooks. Here we highlight the use of point annotations that can be used to quickly collect sets of points for parameterization of functions such as regions of interest or the identification of landmark points. Another application of point annotations this for image annotation, which is a major bottleneck in plant phenomics. For example, we have used point annotations to analyze microscopy images aimed at measurement of quinoa salt bladders, the number and size of stomata, and scoring of pollen germination. These tasks have traditionally been low throughput and have required manual scoring, but our point annotation tools can be used along with traditional segmentation methods to semi-automatically detect and annotate images. The PlantCV point annotation tools also allow users to correct semi-automated detection results before classification (e.g., germinated vs non-germinated pollen) and extraction of size & color traits per object. Once images are annotated, results can be analyzed directly or potentially can be used as labeled data in supervised learning methods.

Chenopodium quinoa is an important crop known for its salt tolerance. Salinity is an osmotic stress and ions accumulation in the root zone causes a reduction in soil water availability, affecting the uptake of essential nutrients, changing seed composition, and reducing biomass. Hence, the need for high-yield crops in poor soils. This research examines the effect of salt stress on quinoa photosynthetic efficiency and salt bladder development. Sensitive and tolerant quinoa lines were examined under salt stress conditions when a concentration of 155mM NaCl was applied. Soil conductivity was monitored for salt stress during the experiment. At approximately two months old, CropReporter images were taken and analyzed using PlantCV to estimate photosystem II efficiency, non-photochemical quenching (NPQ), chlorophyll content, and anthocyanin content. The analysis showed that the salt treatment did not negatively affect the plant photosynthetic efficiency (no changes in Fv/Fm, NPQ, Fq’/Fm’) but leaf area and chlorophyll content was statistically negatively affected by the treatment when comparing genotypes. Live tissue was also analyzed using reflection and fluorescence confocal microscopy, where epidermal salt bladders images were acquired, visualized and analyzed in 3-D and the salt tolerant line showed bigger bladder volumes compared with control conditions. A more high-throughput approach using PlantCV, an open-source image analysis software package targeted for plant phenotyping. This software helped count epidermal salt bladders using stereoscope images. A comprehensive understanding of the quinoa salt tolerant mechanisms by employing multidisciplinary approaches is necessary for their effective incorporation into salt-sensitive crops for better crop yields under stressful environments.

Chenopodium quinoa is an important crop that is known for its salt tolerance. Salinity is an osmotic stress and accumulation of ions in the root zone causes a reduction in soil water availability, which negatively affects the uptake of essential nutrients, changes seed composition, and reduces biomass. Therefore, there is a need to develop crops that are highly productive under poor soils. This research examines the effect of salt stress on quinoa photosynthetic efficiency and chloroplast development. Sensitive and tolerant quinoa lines were examined under salt stress conditions when a concentration of 155mM NaCl was applied. Electrical soil conductivity was monitored during the experiment to assure salt stress and at approximately two months old, CropReporter images, which are used to estimate photosystem II efficiency, non-photochemical quenching (NPQ), chlorophyll content, and anthocyanin content were captured and analyzed using PlantCV. The analysis showed that the salt treatment did not negatively affect the plant photosynthetic efficiency (no changes in Fv/Fm, NPQ, Fq'/Fm') but leaf area and chlorophyll content was statistically negatively affected by the treatment when comparing genotypes. Leaf tissue was sampled and chloroplasts were imaged using super-resolution microscopy. Salt-sensitive lines showed swelling of the chloroplast lamellae, starch accumulation, and unrecognizable grana structure. A comprehensive understanding of the quinoa salt tolerant mechanisms by employing multidisciplinary approaches is necessary for their effective incorporation into salt-sensitive crops for better crop yields under stressful environments.