PS Seminar Series (LEAPS Seminar) - ANU Plant Phenomics at the Australian Plant Phenomics Facility - Open source tools for high throughput Phenomics, NextGen data visualization and Deep Learning

Date & time

3.30–4.30pm 13 April 2018


Eucalyptus Room (S2.05), Level 2, RN Robertson Building (46), ANU


Dr Timothy Brown, Dr Richard Poire and Alyssa Weirman, APPF, ANU


 Gagan Bhardwaj
 02 6125 9395



Addressing environmental management and food production challenges of the 21st century requires exponential increases in our ability to understand and model ecosystems and agricultural processes. Lab approaches enable accurate measurement of the genetic and environmental basis of yield and fitness traits. Field data enables modelling of how genotype/environment interactions scale from plot to ecosystem.

High-throughput lab phenomics can precisely phenotype thousands of plants under simulated climates. In the field, new technologies (UAVs, sensor networks, etc.) and cloud computation enable 3D time-series monitoring of crops, forests and the environment at unprecedented resolutions. Such high-density data is extremely hard to manage, visualize and analyse.

The Australian Plant Phenomics Facility (APPF) provides growth and phenotyping services from seeds through to analysis in a range of growth environment and conditions. Including High-throughput phenotyping combining multispectral lighting and environmental controls for simulating regional and climate-shifted conditions in growth chambers for phenotyping up to 2,000 plants continuously. We are also using neural networks and deep learning to develop novel methods for phenotype detection in Arabidopsis


Tim Brown has a PhD (2006) from the University of Utah in the US, combining complexity theory, field work and modeling of self-organized swarming behavior in New World army ants. From 2006 to 2012 he founded and ran an environmental consulting business in the US (TimeScience) developing phenocams and billion-pixel resolution timelapse cameras. In 2012, Tim moved to the Australian National University as a postdoc, to develop high throughput phenotyping systems for the the Borevitz Phenomics Lab at the Research School of Biology, Plant Sciences. He is currently the Director of the ANU node of the Australian Plant Phenomics Facility and a Postdoctoral Fellow at the Center for Excellence in Plant Energy Biology. His work focuses on developing open source hardware and software pipelines for enabling high throughput phenotyping, high resolution monitoring and visualization of environmental and research data. He is a co-founder of the Australian Phenocam Network and creator of EcoVR, a software package for modelling research sites and visualizing time-series environmental data in virtual reality using computer game engine technology. Other projects include Augmented and Virtual reality applications for visualizing time-series point cloud data and exploring new technologies for enhancing agriculture and food security such as robotic gardening and vertical agricultural.

Richard Poiré holds an MSc in plant ecophysiology from Montpellier (France) and was working at INRA on modelling light interception, photosynthesis and biomass allocation. Richard then completed his PhD at Forschungszentrum Jülich (Germany) focussing on the diurnal effects of light and temperature on plant canopy growth. Richard has since worked at the APPF CSIRO to expand his plant phenomics skills and gained expertise with a wide range of plant phenomics platforms. He has extensive experience with PAM chlorophyll fluorescence, gas exchange, time-lapse imaging and even contributed to the development of various phenotyping platforms. Richard also worked for IRRI to transfer his plant phenomics skills to a new team of users of the platform and he has at heart to educate the scientific community. Richard is now back at APPF ANU to make those tools more accessible.

Alyssa Weirman has worked as a business manager with the ANU Node since 2016 and the APPF since 2010. Alyssa holds a Bachelor of Science (Hons) (1st Class) and a Diploma of Management, Business Administration combined with over ten years’ experience working in administrative positions within the public sector for the NSW State Government and CSIRO, following eight years working in the private sector.

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