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NEWSLETTER

(Q4 2020)
 

EDITORIAL


 

A Welcome from the Industry Section Chairs
 

As some of you may recall, the IPPN has structured itself into two sections, one focused on academia and one focused on industry. As the Inaugural Chairs of the Industry Section, we would like to take this opportunity to welcome all members of the IPPN and to explain more about our vision for the Industry Section.  

The goal of the IPPN is to increase the visibility and impact of plant phenotyping research and enable cooperation by fostering communication between stakeholders in academia, industry and governments. The Industry Section of the IPPN wants to represent all the companies that are active in phenotyping. From start-up companies up to big breeders and technology companies. Also, we want to bridge the gap between industry and academia and work closely together to bring the phenotyping world to a higher level. The following examples will show how we want to do this:

  • Create a (online / physical) environment where academia and industry can meet.
  • Organize events where industry can market themselves to researchers. 
  • Show-off the latest technology that is produced within the companies that are member of the IPPN.
  • Get input from Industry members to determine the direction we want to go as a group.
  • Get input from the Academia Section what the big hurdles are in current phenotyping and try to develop solutions within the industry section.  

We would love to welcome more companies into the IPPN because in this way a lot of expertise will be in one location. This information will then be easily accessible for over 40 universities and 1000+researchers.   
Do you have input or you want to join the IPPN please send us an email! We hope to see you soon at the next IPPS in Wageningen (October 2021)!






Vincent Jalink     &     David Han
(Chair & Vice-Chair IPPN Academia Section)
 

 

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NEWS

Your participation needed: Global Plant Phenotyping Survey 2020/21


For the past six years, IPPN and EMPHASIS have carried out their bi-annual "Plant Phenotyping Surveys". They cover basic and advanced questions related to plant phenotyping for the purpose of assessing the status of global plant phenotyping and emerging fields. The surveys address participants from all geographic regions and in all professional disciplines in any way related to plant phenotyping.

The survey data provide the primary source of information for our plant phenotyping knowledge base, informing us about the topics and issues inherent to the international and regional (sub-)communities, in academia and industry. This also helps us to identify potential gaps and understand the demands of the community in terms of required services and tools.

Results are being made available on the IPPN homepage & in the past, survey results have been extensively used for analysing the global status of plant phenotyping (such as in this review by Yang et.al.).

Participating in these surveys empowers everyone who contributes to add to the big picture of how plant phenotyping is being applied & viewed.

The Plant Phenotyping Survey 2020/21 is published with the release of this newsletter and will hopefully find its way from here to all relevant stakeholders around the world.

Please disseminate the link to this survey among any relevant audiences, and please feel free to use it in any reasonable context. The more people take part in this survey, the more relevant the obtained results will become.

Industry x Academia: International collaboration targets plant-based vaccine development


Plant phenomics is helping optimize biotechnology for plant-based vaccine development in a new research collaboration between Australia’s Australian National University (ANU) and Canadian biopharmaceutical company, Medicago R&D Inc.
Medicago uses a proprietary plant-based technology to develop vaccines and protein-based therapeutics, producing Virus-Like Particles (VLPs). VLPs mimic the structure of viruses and induce an immune response without causing an infection. When purified, VLPs can be used as vaccines for a range of viruses, such as influenza, rotavirus, and norovirus.
This research aims to develop new methods and tools to non-invasively monitor the growth and performance of plants used in the production of VLPs.
In the first phase of the project, the APPF group at the ANU is contributing facilities and expertise in phenomics, bioinformatics, and data visualization, as well as access to equipment and infrastructure including hyperspectral scanning and controlled environment growth chambers.
“This collaboration highlights the value of university-based, interdisciplinary teams working with an industry partner to help address complex challenges of global significance – in this case, the urgent need to improve global access to vaccines,” said Professor Owen Atkin, Director, Centre for Entrepreneurial Agri-Technology (CEAT) at ANU.
Medicago recently received $CAD173M in funding to supply up to 76M doses of their plant-derived, made in Canada COVID19 vaccine candidate to the Government of Canada, subject to Health Canada approval.
 

Launch of New Omics and Precision Agriculture Laboratory


The Global Institute for Food Security (GIFS) at the University of Saskatchewan (USask) in Canada has launched the Omics and Precision Agriculture Laboratory (OPAL) technology platform, a one-stop-shop for plant analyses at the molecular level. Offering genomics, phenomics and bioinformatics services, combined with the latest precision agriculture technology, OPAL provides a complete profile of plant samples for researchers, industry, producers and other clients. The first-of-its-kind in Canada is an enabler for the GIFS-managed Plant Imaging and Imaging Research Centre (P2IRC) at the University of Saskatchewan in Canada.
Using some of the latest in agtech, OPAL combines global positioning systems, remote aerial imaging, unmanned aerial vehicles and in-field environmental monitoring—with digital DNA sequence information—to provide a complete profile of plant samples. The versatile equipment can also analyze animal and human samples.
OPAL’s detailed plant analyses will help farmers target their crops with the right amounts of water, fertilizers and pesticides, rather than uniformly spraying these products across their fields. This precision in agriculture means a more efficient use of resources and reduced environmental impact, leading to accelerated crop breeding, less waste, and increased efficiency for breeders, agronomists, producers and other stakeholders.
OPAL was founded by Agriculture and Agri-Food Canada, the National Research Council of Canada and USask, with a strategic investment from Western Economic Diversification Canada.

 

What we read... 


 

TechnoHouse by Rijk Zwaan: Digital Twins, the future in plant phenotyping


Rijk Zwaan, a major vegetable breeder hosts a regular online show called Techno House that addresses hot topics around plant breeding and horticulture. Seeing that the show has great content for the phenotyping community we gathered the content here for you.

The topic of this episode: “Digital Twins”. Three experts were invited to share thoughts and vision on digital twins but from different perspectives.

  1. Grégoire HummelPhenospex
  2. Ben ScheresRijk Zwaan
  3. Gert KootstraUniversity of Wageningen

Rijk Zwaan produced some short and crispy videos introducing the different experts which are definitely worth to watch.

New Project: Agricultural Genome to Phenome Initiative


A new research initiative has formed around PIs from University of Arizona, Iowa State University, University of Idaho & the University of Nebraska Lincoln. The overall objective of the Agriculture Genome to Phenome Initiative (AG2PI) is to assemble and prepare a transdisciplinary community to conduct AG2P research.

First approaches & goals include:

  • Develop a vision for AG2P research
  • Identify research gaps and opportunities
  • Foster early community solutions to these challenges and gaps
  • Rapidly disseminate findings to the broader community

The recording of the AG2PI launch event is available on the AG2PI Youtube-channel. More information on anything around the project is made available via the project website.

Recordings now available: 5th Annual Plant Phenotyping and Imaging Research Centre Symposium


The 5th Annual Plant Phenotyping and Imaging Research Centre (P2IRC) Symposium took place from October 21-22, 2020. Taking place fully online for the first time, the theme of the Symposium was collaboration, innovation and results, and it featured a slate of speakers from Canada and international, discussing:

  • Field Imaging for Phenotyping in Plant Breeding and Precision Agriculture.
  • Deep Learning for Phenomics.
  • Genomic and Physiological Selection for Yield Stability; and
  • Mobilizing Root-Soil-Microbiome Interactions.

The entire symposium is now available online and registration will remain open for a year. Visit the platform to view recordings.
The P2IRC Symposium is an annual conference hosted by P2IRC, a digital agriculture program created to develop innovative technologies that will accelerate plant breeding, leading to new crops that are more resilient to climate change.
Managed by the Global Institute for Food Security (GIFS) at the University of Saskatchewan (USask) in Canada, the multidisciplinary and multi-sector P2IRC program involves researchers from various fields, including biology, computer science, engineering and the social sciences. The outcome will be sustainable solutions to accelerate plant breeding and to address food production challenges of limited land, water, energy and the COVID-19 pandemic.

P2IRC was established at USask in 2015 with a $37.2 million award from the Canada First Research Excellence Fund (CFREF).

Visit the Symposium’s platform to register and view conference recordings from the 5th Annual P2IRc Symposium.

Nordic Plant Phenotyping: NordPlant Prolonged for Three Years


The Nordic network NordPlant has been prolonged until 2023 with funding from NordForsk.

NordPlant is a climate and plant phenomics university hub for sustainable agriculture and forest production in future Nordic climates. The goal of NordPlant is to promote education and research mobility, and strengthen collaboration between researchers interested in plant phenotyping. ​NordPlant is one out of a total of six Nordic University Hubs funded by NordForsk.

Initially, NordPlant was funded for three years, with the possibility of a three year prolongation. In June, NordForsk decided to extend the funding for another three years, which means that activities will continue 2021-2023.​

 

IPPN SERVICE


 

New open source tool for root phenotyping: RhizoVision Explorer


RhizoVision Explorer is a new free and open-source software developed at IPPN member organization, Noble Research Institute, in the lab of Dr. Larry York. The software estimates root traits from images acquired from a flatbed scanner or camera. Root images are expected to have a high contrast of roots with the background, homogenous lighting, and minimal overlapping of roots. The software is built in C++ for speed and stability, using QT for the graphical user interface and OpenCV for image processing. Traits extracted by RhizoVision Explorer have been extensively validated using a physical copper wire ground truth image set, thousands of simulated roots, and comparisons with other image analysis software. The default “Broken Roots” mode is meant for roots washed out from soil cores or pots that are disconnected and provides length, volume, branching frequency, among other features, with the ability to bin measurements based on diameter thresholds. The “Whole Root” mode extracts additional root system architecture features of more intact root systems, especially excavated root crowns or rhizoboxes, such as the convex hull, angles, and holes. The software supports multiple regions of interest, batch mode, and user-defined export of processed images with overlaid features for use in reports.

Download now!

EMPHASIS Photo Competition: And the winner is ...


Congratulations to Biswabiplab Singh, PhD student at the Indian Agricultural Research Institute (ICAR), for winning the EMPHASIS Photo Competition in collaboration with IPPN!
His winning picture shows plants prior to phenotyping at the Nanaji Deshmukh Plant Phenomics Centre in New Delhi (left). After Biswabiplab won the competition, the whole Phenomics Group sent a photo to express their gratitude towards the organizers, sponsors & the jury (right). 

"The photographer has captured an interesting motif that everyone immediately associates with research. The evening atmosphere is aesthetically pleasing, the air-conditioned greenhouse demonstrates the technical commitment, but given the plant pots set up outdoors, it is also clear that different plant species are directly exposed to the climatic conditions. Another aspect that ultimately tipped the scales in favor of this picture: The storm clouds are brewing in the background expressing an almost symbolic urgency in the face of climate change. But there are also silver linings," comments Gero von der Stein, Deputy Head of Communication at the Klaus Tschira Foundation and judge of the EMPHASIS Photo Competition.

Biswabiplab Singh received a high-end camera and equipment sponsored by LemnaTec and DPPN.

Coming soon: IPPN Forest Phenotyping Working Group Newsletter in the making


The Forest Phenotyping Working Group is a community sharing the ambition to understand forest dynamics through its phenotypes. We will bring experts from multiple fields such as biology, genetics, computer science and remote sensing to tackle the emerging challenges related, inter alia, to climate change, healthier forests, and the manufacture of more sustainable products. Thanks to IPPN, we can use resources, tools and a platform to communicate science and participate in active workshops to progress towards these goals.
If you want to join force with us, share your research and follow the latest innovation and challenges of the Forest Phenotyping community, you can become a member and subscribe e.g. to the general IPPN newsletter on the IPPN website or send an email to WGForestPhenotyping@fz-juelich.de to join the working group or enlist for the WGs newsletter. You will automatically receive the first newsletter and also be informed of the future webinars (#1 to be around April 2021 in partnership with our new 2020 members).
We are excited to announce that the first WG newsletter will be under your Christmas tree with a special highlight on the novel research developed by Scion, the forest research institute in New Zealand.

New Animation: Plant Phenotyping Explained


The European Infrastructure for Plant Phenotyping, EMPHASIS, has produced a series of films: three short animated videos produced in scribble style illustrate not only what research infrastructures are and what EMPHASIS is all about but also explain in a simple way & for a broad audience what plant phenotyping is & what researchers use it for.

Anyone is free to use and share the scribble films wherever suitable to explain these concepts.

 

Upcoming (E-)vents 
 

Mark the date: 1st North American Plant Phenotyping Network Conference


The 1st NAPPN Annual Conference will be held virtually, & highlight the most recent advances in the rapidly developing field of Plant Phenomics.  Join us for exciting scientific content, the NAPPN General Assembly meeting, hands on workshops, virtual tours, and more!  
The planning of this event is currently in progress. First versions of the conference agenda, speakers & registration fees are already displayed on the conference website. As the planning moves on you will find all relevant updates there.

Submission deadline for talks (no registration needed): December 2nd 2020 

Want to have a talk? Submit your talk here!

FIRA goes Virtual: 8 - 10 December 2020


Since 2016, FIRA has managed to establish itself as the leading event for professionals in the agricultural robotics sector. Launched and organized since then by Naïo Technologies, FIRA evolves today and will be carried out from now on by the association GOFAR – Global Organization for Agricultural Robotics.

This year is marked by the Covid-19 pandemic and the global confinement it has led to and we have all faced. This unprecedented situation impacts the agricultural production and further conveys the difficulties of a sector that is demanding but undergoes labor shortage. In that light, how can robotics provide an appropriate and alternative response, without neglecting its integration into an unusual social, economic and environmental context? The international speakers selected for their expertise will be featured to share their vision and exchange with the participants.

Link to brochure

PhenomUK Webinar: "Ubiquitous & Synchronous 'Roots & Shoots' imaging for Phenotyping & Controlled Environment agriculture"


Ubiquitous & Synchronous ‘Roots & Shoots’ imaging for Phenotyping & Controlled Environment agriculture Seminar November 24th 2020.
FREE ONLINE EVENT!!

The Link to the webinar will be published close to the webinar date, on the PhenomUK website.

New Date: Wageningen Summer School on Image Analysis for Plant Phenotyping


Are you looking for a complete overview of image analysis techniques for automatic plant phenotyping?
This Summer School will provide a mixture of underlying theory and practical hands-on training. You will have the opportunity to work on real plant image analysis problems to challenge you to directly apply and combine the theory in practice.
This program is primarily intended for researchers working on automatic phenotyping and technical experts in breeding companies who use, or plan to use, image analysis.

Registration deadline: 1 June 2021: Register directly or download the flyer

International Undergraduate Summer School


The Undergraduate Summer School is a unique opportunity for undergraduates from all corners of the world to spend eight weeks at our internationally renowned research centre, partnering with fellow Norwich Research Park institutes; The Sainsbury Laboratory and the Earlham Institute.
Students experience plant and microbial science, interacting with some of our world-leading scientists and gain an unrivalled insight into research.

Subject to the ongoing Covid-19 pandemic, we are hoping to run the 2021 International Undergraduate Summer School from 27 June to 21 August 2021.

Applications for 2021 are now open – closing on Monday 18 January 2021

More information

 

CALLS &

SPECIAL ISSUES


 

Ongoing: Plant Physiology Focus Issue on "Digital Agriculture":
Submission deadline December 1st 2021; Publication date: June 2021 

The Plant Phenome Journal Special Issue "Belowground Phenotyping": Submission deadline: 1st March 2021


This special section will be published in The Plant Phenome Journal (TPPJ), a trans-disciplinary, gold open access journal that focuses on original research, interpretations, and datasets investigating all aspects of plant phenomics. TPPJ is a forum that combines engineering, remote sensing, computer or data science with plant science, breeding, genetics, or agronomy.  

Scope: 
This special issue will focus on belowground phenotyping technologies and efforts to understand the function and variation of plant root systems. Root phenotyping is the high hanging fruit, and the purpose of this special section is to feature pioneering work in this area. 
 

We encourage contributions on the following topics:  

  • Phenotyping technologies used to understand the function and variation of plant root systems 
  • Work with novel sensors aimed at translating medical and defense imaging technologies into greenhouses and into the field to gather root traits  
  • Other indirect methods to observe root systems based on aboveground correlates 

Remote Sensing Special Issue: "Remote and Proximal Assessment of Plant Traits": Submission deadline: 31st March 2021


Plants are optically sensed by a variety of sensors and at different scales to answer diverse research questions and to meet practical challenges. Research in quantitative remote sensing starts at the organ scale moving to the entire plant, population, field, or biotope, up to data obtained from entire continents to explore global phenomena. This Special Issue strongly encourages contributions aimed at estimating the morpho-physiological and biochemical plant traits from Earth Observation data in agricultural and ecological contexts. This Special Issue aims to cover a vast range of spatial resolutions and spectral resolutions. Besides diverse empirical and physically based retrieval approaches, “hybrid approaches” combining the generic properties of radiative transfer models with the flexibility and efficiency of nonlinear nonparametric methods are welcome. Moreover, time-series analysis related to plant traits assessment can be exploited. This Special Issue is expected to demonstrate recent progress and to discuss future perspectives in plant traits sensing.

Link to Special Issue Flyer

Agronomy Special Issue "Improving Nutrient Use Efficiency from Lab to Field": Submission deadline: 30 July 2021


This special issue in Agronomy will primarily focus on the macro nutrients N and P, the study of all essential nutrients is welcomed. We are interested in latest studies that untangle plant uptake, nutrient allocation, and nutrient sensing and signalling in the plant. Furthermore, we welcome manuscripts on novel strategies for improving plant performance at limiting nutrient levels (at the molecular level or through the identification of novel root traits/phenotypes that facilitate uptake), and agricultural practices including but not limiting to the use of microorganisms.

Link to Special Issue Flyer

 

PUBLICATIONS


 

PNAS Inner Workings: Crop researchers harness artificial intelligence to breed crops for the changing climate. Carolyn Beans, Proceedings of the National Academy of Sciences Nov 2020, 117 (44) 27066-27069; DOI: 10.1073/pnas.2018732117


October this year, PNAS released an „Inner Workings” article summarizing the development that crop research has been undergoing since the first Green Revolution up to the successful application of artificial intelligence for crop improvement nowadays. Among others, the research group of Prof Achim Walter of the Institute of Agricultural Sciences at ETH Zürich in Switzerland (IPPN member) has been featured with their application of drones & the cable-suspended high-throughput phenotyping system FIPS which deliver the necessary image data to obtain data for crop growth models to indentify stress adapted crop lines.

Mariam Awlia, Nouf Alshareef, Noha Saber, Arthur Korte, Helena Oakey, Klára Panzarová, Martin Trtílek, Sónia Negrão, Mark Tester, Magdalena M. Julkowska (2020) Genetic mapping of the early responses to salt stress in Arabidopsis thalianabioRxiv 2020.10.02.324178; https://doi.org/10.1101/2020.10.02.324178

Ball KR, Power SA, Brien C, Woodin S, Jewell N, et al. (2020) High-throughput, image-based phenotyping reveals nutrient-dependent growth facilitation in a grass-legume mixture. PLOS ONE 15(10): e0239673. https://doi.org/10.1371/journal.pone.0239673


John N. Ferguson, Samuel B. Fernandes, Brandon Monier et. al. (2020) Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. bioRxiv 2020.11.02.365213; doi: https://doi.org/10.1101/2020.11.02.365213

Freschet, G.T., Roumet, C., Comas, L.H., Weemstra, M., Bengough, A.G., Rewald, B., Bardgett, R.D., De Deyn, G.B., Johnson, D., Klimešová, J., Lukac, M., McCormack, M.L., Meier, I.C., Pagès, L., Poorter, H., Prieto, I., Wurzburger, N., Zadworny, M., Bagniewska‐Zadworna, A., Blancaflor, E.B., Brunner, I., Gessler, A., Hobbie, S.E., Iversen, C.M., Mommer, L., Picon‐Cochard, C., Postma, J.A., Rose, L., Ryser, P., Scherer‐Lorenzen, M., Soudzilovskaia, N.A., Sun, T., Valverde‐Barrantes, O.J., Weigelt, A., York, L.M. and Stokes, A. (2020), Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs. New Phytol. Accepted Author Manuscript. https://doi.org/10.1111/nph.17072

Nicolás Gaggion, Federico Ariel, Vladimir Daric, Éric Lambert et. al. (2020) ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture. bioRxiv 2020.10.27.350553; https://doi.org/10.1101/2020.10.27.350553

Gaillard M, Miao C, Schnable JC, Benes B. (2020) Voxel carving-based 3D reconstruction of sorghum identifies genetic determinants of light interception efficiency. Plant Direct. 2020;00:1–16. https://doi. org/10.1002/pld3.255

Galli, G, Horne, DW, Collins, SD, et al. (2020) Optimization of UAS‐based high‐throughput phenotyping to estimate plant health and grain yield in sorghum. The Plant Phenome J. 2020; 3:e20010. 
https://doi.org/10.1002/ppj2.20010


Kronenberg L, Yates S, Boer MP, Kirchgessner N, Walter A, Hund A. (2020) Temperature response of wheat affects final height and the timing of stem elongation under field conditions. Journal of Experimental Botany, in press. https://doi.org/10.1093/jxb/eraa471

Roth L, Camenzind M, Aasen H, Kronenberg L, Barendregt C, Camp KH, Walter A, Kirchgessner N, Hund A. (2020) Repeated multiview imaging for estimating seedling tiller counts of wheat genotypes using drones. Plant Phenomics. https://doi.org/10.34133/2020/3729715

Saint Cast, C., Meredieu, C., Défossez, P. et al. (2020) Clustering of Pinus pinaster coarse roots, from juvenile to mature stagePlant Soil. https://doi.org/10.1007/s11104-020-04736-5

Trevisan, R.; Pérez, O.; Schmitz, N.; Diers, B.; Martin, N. (2020) High-Throughput Phenotyping of Soybean Maturity Using Time Series UAV Imagery and Convolutional Neural Networks. Remote Sens.12, 3617. https://doi.org/10.3390/rs12213617

Underhill, A., Hirsch, C., & Clark, M. (2020). Image-based Phenotyping Identifies Quantitative Trait Loci for Cluster Compactness in GrapeJournal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci.145(6), 363-373. Retrieved Nov 12, 2020, doi.org/10.21273/JASHS04932-20

van der Plas, F., Schröder-Georgi, T., Weigelt, A. et al. (2020) Plant traits alone are poor predictors of ecosystem properties and long-term ecosystem functioning. Nat Ecol Evol. https://doi.org/10.1038/s41559-020-01316-9
 

PLANT

PHENOTYPING

JOBS


 

Open Positions

 

Research Assistant/Associate in Plant Phenotyping, Newcastle University, UK

Phenotypic Insights Lead, Bayer, Missouri , USA

Full Professorship (W3), Data Science in Crop Production Phenorob Cluster, Bonn, Germany

Head of Phenomics, Bayer, St. Louis, USA

Graduate Research Assistantship, Phenomics Lab, Washington State University, USA

 

 

Postdoctoral Positions

 

ANU/CSIRO Post-doc, Innovation in Synthetic Biology, Canberra , AUS

Post-doc in Phenotyping nutritional status of crops using remote sensing technologies, Mohammed VI Polytechnic University (UM6P), AgroBioSciences program (AgBS), Marocco

Post-doc position in Precision Agriculture Lab, Washington State University, USA

Postdoc on the computing side of high-throughput phenotyping systems, Univesity of Georgia, USA

 

 

PhD positions

 

Research associate / Doctoral position (m/f/d): Optimizing Nitrogen use efficiency in agricultural production systems, KIT, Germany

35 PhD international fellowships for early-stage researchers  in the fields technology, engineering, physics, mathematics, life and health sciences, Spain/Portugal

 

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