AgreenSkills session, year: 1st session, 2013
Receiving laboratory: LEPSE Ecophysiology of Plants under Environmental Stresses Montpellier, France
Country of origin : Switzerland
A software pipeline for model-assisted image analysis for the phenotyping of plant architectural development
Image-based phenotyping platforms in semi-controlled conditions offer enormous possibilities to perform genetic analyses of plant growth, architecture, light interception and biomass accumulation over large time series for thousands of plants in well-defined environmental scenarios. The objective of this project is to develop an integrated pipeline inside the OpenAlea framework, allowing assessment of growths of individual organs, plant geometry and derived variables such as light interception. The project involves (i) Plant image segmentation allowing computing growths of individual organs under different environmental conditions. (ii) Assessment of architectural variables, their change with time and environment, allowing genetic analysis of these traits (iii) Interfacing the resulting 3D image reconstructions with canopy-level models of light interception, allowing calculation of intercepted light and radiation use efficiency. The challenge of this project is to develop a parsimonious pipeline in which a lesser amount of pictures is compensated by the use of prior knowledge on plant development, which improves the efficiency of the process. Segmentation of the plant into individual organs is a key process for calculating architectural and growth properties. Because plants have a complex architecture, we combine image analysis routines with a model of plant development that informs the image analysis routine on the expected number and size of organs. This improves efficiency of the process and also reduces the number of images per plant, a necessary condition for high throughput phenotyping. We believe that this method will greatly improve the capability of the Plant Science community for genetic analyses at high throughput of variables hardly accessible in the field such as architecture, response of organ growth to environmental conditions or radiation use efficiency. This will in turn improve our ability for the modeling of genetic variability of plant responses to environmental cues associated for example with climate change.
Michael Mielewczick obtained a Diploma in Biology from Heinrich-Heine-University Düsseldorf, Germany, in 2007. After working as a Scientific Assistant at Forschungszentrum Jülich GmbH, Institute of Chemistry and Dynamics of the Geosphere (Phytosphere), Germany, for one and a half years, he proceeded to obtain his PhD at ETH Zürich, Institute of Agricultural Sciences, Switzerland on the, “Optimization and application of image based phenotyping approaches with a focus on plant phenotyping and near infrared imaging.” His research interests include (i) high-throughput and high-resolution monitoring by using computer-assisted image-based phenotyping to investigate the influence of environment effects and metabolism on plant growth and architecture, and (ii) the optimization of image-acquisition, processing and analysis in the framework of image-based phenotyping platforms.
Mielewczik M, Friedli M, Kirchgessner N, Walter A (2013): Diel leaf growth of soybean: a novel method to analyze two-dimensional leaf expansion in high temporal resolution based on a marker tracking approach (Martrack Leaf). Plant Methods 9(1):
Fernie AR, Bauwe H, Eisenhut M, Florian A, Hanson DT, Hagemann M, Keech O, Mielewczik M, Nikoloski Z, Peterhänsel C, Roje S, Sage R, Timm S, Cammerer S, Weber APM, Westhoff P (2013): Perspectives on plant photorespiratory metabolism. Plant Biology 15(4):748-753
Peterhänsel C, Krause K, Braun H‐P, Espie GS, Fernie AR, Hanson DT, Keech O, Maurino VG, Mielewczik M, Sage RF (2013): Engineering photorespiration: current state and future possibilities. Plant Biology 15(4):754-758
Timm S, Mielewczik M, Florian A, Frankenbach S, Dreissen A, Hocken N, Fernie AR, Walter A, Bauwe H (2012): High-to-low CO2 acclimation reveals plasticity of the photorespiratory pathway and indicates regulatory links to cellular metabolism of Arabidopsis. PloS one 7(8): e42809
Mielewczik M, Liebisch F, Walter A, Greven H (2012) Near-Infrared (NIR)-Reflectance in Insects–Phenetic Studies of 181 Species. Entomologie heute 24:183-215
Rosar C, Kanonenberg K, Nanda AM, Mielewczik M, Bräutigam A, Novák O, Strnad M, Walter A, Weber APM (2012): The leaf reticulate mutant dov1 is impaired in the first step of purine metabolism. Molecular Plant 5(6):1227-1241
Poiré R, Wiese-Klinkenberg A, Parent B, Mielewczik M, Schurr U, Tardieu F, Walter A (2010): Diel time-courses of leaf growth in monocot and dicot species: endogenous rhythms and temperature effects. J. Exp. Bot. 61(6):1751-1759
Mielewczik M, Mehlhorn H, Al-Quraishy S, Grabensteiner E, Hess M (2008): Transmission electron microscopic studies of stages of Histomonas meleagridis from clonal cultures. Parasitology Research 103(4):745-750