1. High Resolution Plant Phenomics Centre http://www.plantphenomics.org.au/hrppc

2. High Resolution Plant Phenomics Centre From growth cabinet to the field ‘Deep phenotyping’ technology - development, validation and deployment Model Plant Module (HTP) Crop Plant Shoot Module (MTP) Crop Plant Root Module (MTP) Crop Plant Field Module (HTP)  1500 m 2 lab space and ‘research hotel’  Imaging modules interfaced with 245 m 2 greenhouse, 260 m 2 growth cabinets  Large field site with distributed sensor networks portable ‘phenomobile’ and 15m imaging tower

3. Measuring systems and traits to be measured – model plants to crops –Colour images Plant area, volume, mass, structure, phenology Senescence, relative chlorophyll content, pathogenic lesions Seed yield, agronomic traits –Near IR imaging Tissue water content Soil water content –Far IR imaging Canopy / leaf temperature / water use / salt tolerance –Chl Fluorescence imaging Physiological state of photosynthetic machinery – Hyperspectral imaging  Carbohydrates, pigments and protein – Carbon isotope ratio Transpiration efficiency, photosynthetic pathway (TDL/MS) – FTIR Imaging Spectroscopy Cellular localisation of metabolites (sugars, protein, aromatics) Key technologies

4. Model plant module Growth and morphology Photosynthetic performance (Chl Fluor) under defined environmental conditions Fluorogro-scan TrayScanRGB / FIR in-Cabinet IR screening for leaf temperature Automated destructive sampling for metabolites, protein, DNA and RNA, delta 13 C Target plants : Arabidopsis, Tobacco, Brachypodium and seedling screens

5. Data Analysis: non-destructive Growth Analysis and morphological clustering Leaf area / growth analysis (eg heterosis and drought stress) Photosynthetic mutants Lesions / pathogen attack Architecture / morphology Morphological clustering Interfaced to PODD phenotypic dBase Conveyor Tray Scan: 3000 plants per day Phenome / Genome Database at last!

6. Isolating Photosynthetic and Photorespiratory Mutants Fv/FmNPQ Badger et al., 2009

7. In Cabinet HTP FIR Tray Screens 30cm X 25cm trays Defined grids and automatic regions of interest defined

8. Brachypodium distachyon as a model for wheat and biofuel feedstocks (USDA / DOE) Small cereal (can be grown in trays of 20, as for Arabidopsis, 10cm high at maturity) 6-8 week lifecycle Small sequenced genome (50Mb) High synteny with wheat Phenotyping 2000 genome wide KO’s and 100 accessions for growth, biomass and yield, photosynthesis, abiotic stress tolerance and lignin / cell wall properties Mapping traits to genomic regions and genes Cloning homologues in wheat and C4 grasses

9. Crop Shoot Module :Growth imaging, 3D reconstruction and overlay of signals in controlled environments Whole of lifecycle photosynthesis and growth Dynamic growth and carbon allocation to plants organs Transpiration and water use Hyperspectral detection of leaf protein and CHO Max ETR=0.2 Max NPQ=1.25

10. Full 3-D Models with mesh overlay Plant Scan and Imaging Arch HRPPC, ADFA and CMIS collaboration

11. Digital estimation of biomass validated for a range of species Wheat Rice Barley Cotton Chickpea Cowpea Flaveria Arabidopsis 3-D Volume and In silico Dissection

12. Array multiplication (element by element) to separate background from leaves and to apportion temperature data to leaf area control 297.84 o K 296.91 o K ∆ = 0.93 o C 100 mM 297.84 o K 296.91 o K Temperature data averaged for each plant and saved in EXCEL spreadsheet Automated analysis protocol for IR thermography Thermograph: matrix of temperature [640x480] (8-bit false colour image for visualisation) Automatic threshold detection (Otsu method, 1979) Use threshold limit to set binary mask

13. Crop Plant Root Module : NIR imaging of soil /roots Results of NIR monitoring allow measurement of spatial distribution water content in soil We have shown it can be made quantitative 0h 2h 4h 6h 8h R 2 = 0.9943 R 2 = 0.9932 0 50 100 150 200 250 0.000.020.040.060.080.100.120.14 Gravimetric water content (g/g) Mean pixel value 100mm diameter 45mm diameter

14. Ground-based : Phenomobile, Imaging tower and Distributed Sensors Variable span buggy 3M boom IR Camera + Hyperspec Radiometer / camera Stereo camera / Lidar 2cm Hi Res GPS registers all data Porometer / SPAD Licor 6400 Fits on a trailer Gives 1m 2 area coverage at 2M boom height

15. What Next ? : Cropatron

16. The Challenges at HRPPC Variety of non-commercial imaging systems and sensors Need to link experiments across platforms Metadata may have genotype, experimental and growth conditions plus GIS data Users must be able to retrieve calculated and raw data Requirements to preserve large data sets for later reanalysis or for “probity” in publication Long term desire to link to public databases