Recent Posts

Review: Deep learning on image-based plant phenotyping (Trends Plant Sci)

The development of deep learning brings opportunities to train computers to solve complex questions. Self-driving vehicles are classic examples of an application of deep learning in the real world. However, the large amounts of data that are required for building accurate models and avoiding overfitting…

Special Issue: Genome to Phenome (Plant Journal)

It’s January, which seems to be a month of weather extremes for many “temperate” parts of the globe. Here’s an excellent collection to curl up with as you try to stay warm or cool and out of the elements. The issue includes free-to-access reviews focused on using genomic data (e.g., genome-wide…

Review: How to analyse plant phenotypic plasticity in response to a changing climate

Phenotypic plasticity, or the ability to change in response to the environment, is one of the most characteristic (and to me, endearing) qualities of plants. As Arnold et al. observe, it is also one of the most important in terms of future climate change; phenotypic plasticity will mean the difference…

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…