Recent Posts

Transforming Pixels to Millimeters: Geometric Camera Calibration

About This Seminar The affordability and ubiquity of cameras have led to their increasing use in many disciplines. In plant phenomics, it is common to see experimental data based on image-derived measurements. This seminar will explain geometric camera calibration, whereby pixel measurements are mapped…

Review. Review. Functional phenomics: An emerging field integrating high-throughput phenotyping, physiology, and bioinformatics (J. Exp. Bot)

Understanding the processes contributing to plant productivity will help to secure food production in the future. Larry York proposes how this can be achieved using functional phenomics. First the ideotype needs to be constructed; the ideotype is a set of phene states that are hypothesized to enhance…

Lights, Camera, Action! Detecting crop biomass traits with low-cost photography (Plant Direct)

Maximizing and improving biomass productivity is essential for grower profitability, to protect natural resources, and to meet global population needs. Unfortunately, assessing biomass usually requires destructive sampling which delays the process for breeding high biomass germplasm. Remote sensing is…

CRootBox: a structural – functional modeling framework for root systems (Ann Bot)

Root architecture is important to understand the response of plants during biotic and abiotic stress conditions. Root growth is mostly under soil, which deprives us of the ability to observe its development and growth pattern. In this paper, Schnepf et al. present CRootBox, a framework developed based…

Review: Plant phenomics, from sensors to knowledge ($)

Plants adapt their form, function and metabolism to the surrounding environment. According to Tardieu et al., understanding the plant phenome requires that plant phenotypes to be studied on different spatial and temporal scales. High precision platforms are instrumental for discovery of new physiological…

Measures of interoperability of phenotypic data: minimum information requirements and formatting

If you ever tried to compare the results from two different experiments, you probably realized that small variations in the environment have big impact on how the plants grow. There is a lot to be learned from how the variation in the environment affects plant phenotypes, but currently the description…

Chlorophyll can be reduced in crop canopies with little penalty to photosynthesis

The effect of reducing leaf chlorophyll content on canopy CO2 assimilation (Acan) is somewhat contentious.  Walker et al. obtained data from 67 soybean accessions to parameterise a canopy-root-soil model (MLCan) in order to simulate the effect of altering chlorophyll levels on Acan.  There was no increase…

Deep learning for multi-task plant phenotyping

Despite the significant developments in computational biology and modern plant breeding, crop phenotyping poses challenges for automation. Previous machine learning approaches of plant phenotyping have mainly focused on leaf counting in rosette forms or leaf segmentation, and rely on large datasets not…

ePlant: Visualizing and exploring multiple levels of data for hypothesis generation ($)

The application of systems biology is quite phenomenal these days for prediction-based modeling and interactive data visualization. Along with the genome sequencing of the model plant Arabidopsis thaliana, there has been a parallel increase in systems biology tools. Unfortunately, these tools have been…