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   NEWSLETTER

           (Q1 2020)
 

EDITORIAL



Dear Recipient,                       

This newsletter is the first in its new form since the realignment of the IPPN Office at the end of 2019.
IPPN is the association gathering the world's leading experts and institutions in the discipline of plant phenotyping on a global level.

To continuously provide you with high-quality content (besides all the off-line activities IPPN does), we use tools such as our website, social media accounts, video platforms and email lists to channel information delivered by IPPN members & affiliates to the phenotyping community.

To streamline the list of information services going out from IPPN into the world, we decided to renew our e-strategy in face of all the Social Media platforms and mailing lists to be complementary across all these channels.


IPPN Office presents the new IPPN Newsletter:

  • The IPPN Newsletter will be released on a quarterly basis (four times a year), to avoid spam & redundancy with information presented in other IPPN media channels
  • Featured are news, announcements, publications, projects, etc. connected to plant phenotyping which can be send to the IPPN Office from IPPN members & non-members, -from academia & industry
  • Dedicated sections with specific content (e.g. publications, symposia, workshops, jobs, research spotlight & expert interviews) will be added for the future
  • Feedback & content input is welcome & can be directed to IPPN@fz-juelich.de (subject: Newsletter)



Best regards,


               
Philipp von Gillhaussen
(IPPN Operations Manager)


 

Information on Data Privacy for this Newsletter


While for most of the above mentioned tools Privacy Policies can be accessed on the respective channels themselves, we always want to make underlying policies transparent wherever this is not as obviously displayed: 

  • This Newsletter is brought to you by IPPN Office using the 3rd party software MailChimp. To be fully informed on MailChimp’s Privacy Policy, please read here.
  • Only for the IPPN newsletters we are using (anonymous) “Click Tracking” to see which content/link is most interesting to our community. Any related information is used only used internally by IPPN.
  • You -of course- always have the option to unsubscribe via the link at the bottom of this newsletter.
 

NEWS

IPPS 2019


End of October 2019, The 6th International Plant Phenotyping Symposium (IPPS) took place in Nanjing, China. It was co-organized by IPPN member Agricultural University of Nanjing, one of Chinas most rapidly developing AgTech hot-spots.

The IPPS gathered 300 participants from all over the world, for 5 days to give or listen to over 45 talks & over 70 posters, sorted into 9 different session topics in reference to IPPNs Expert Working Groups (Yield Improvement, Abiotic stress tolerance, Image analysis, Forest- and Root phenotyping). The scientific program was supplemented by a framework program intended to further foster the interaction of scientists with related industry representatives and field trips to the city of Nanjing.

Digital Twin project “Virtual Tomato Crop


Wageningen University & Research has launched the project Digital Twin “Virtual Tomato Crop” with the aim to develop a digital twin of a tomato crop in a greenhouse: a 3D simulation model that is fed in real-time with sensor information from a real greenhouse, to be tested in the (new) Netherlands Plant Eco-phenotyping Center (NPEC) on the campus together with WUR researchers in the fields of greenhouse horticulture, economics, agrotechnology, statistics and breeding. 

New IPPN Logo


End of 2019, the IPPN Executive Board (2019) & the IPPN Office, in conjunction with the Munich-based designers FriedlHampen worked out a design revision for the old IPPN logo. The result can be seen above.

The new Logo will replace the old logo soon on the IPPN website and shall be used from now on in any IPPN related communications.

 

WHAT WE READ 

Youtube Originals: The Age of A.I.


IPPN members from WUR (Leo Marcelis and Rick van de Zedde) are featured in "The Age of A.I." documentary, episode 5 The 'Space Architects' of Mars describing their research incl. phenotyping tools and robots.

NPEC under Construction: A Progress report


The Netherlands Plant Eco-phenotyping Centre (NPEC) is a joint, 22Mio.-Euro-heavy national infrastructure of Wageningen University & Research and Utrecht University and is co-funded by The Netherlands Organisation for Scientific Research (NWO).

New HTPPS @VCBF Vienna


 

IPPN member & top-tier developer of phenotyping systems, PSI has just been selected to build a large phenotyping system inside a controlled environment for Vienna BioCenter Core Facilities (VBCF) (...)

PSI will install a climate chamber with two precisely controlled compartments & state of the art features like online control of environmental parameters through external weather station that can be deployed anywhere in the world or multi-spectral LED illumination.

The climate chamber will contain the PlantScreen Modular high-throughput phenotyping system utilizing cutting edge multi-excitation PAM kinetic chlorophyll fluorescence imager (first of its kind in whole Europe and Asia) and other imaging modalities such as RGB, VNIR/SWIR hyperspectral, thermal & 3D units.

Link to post: here
 

 

FROM OTHER PP-NETWORKS

Heads up: Last Call of EPPN2020 coming soon...!


EPPN2020 is a research infrastructure project funded by Horizon 2020 providing transnational access to 31 European state-of-the-art plant phenotyping facilities for public and private users to apply and perform experiments with either scientific or technological objectives. Currently nearly 100 experiments have been enabled within 4 calls. The 5th call is being evaluated and the 6th (final) call will be released in March – do not miss the last chance to apply for access.

More information on access

Did you know?: Some basics for you about EMPHASIS


EMPHASIS is a pan-European research infrastructure currently in preparation that will enable researchers to use facilities, resources and services for plant phenotyping across Europe.
EMPHASIS will to that end develop and provide access to facilities and services that address multi-scale plant phenotyping in different agro-climatic scenarios in Europe.
EMPHASIS preparation has started in 2017 with a participatory, open and transparent process mapping the European plant phenotyping landscape, including the concrete demands of its wide stakeholder community. The results form a basis for the EMPHASIS business plan, describing how EMPHASIS will be implemented starting 2020 and operated afterwards.

Scientists interested in EMPHASIS have multiple opportunities to get involved:

  • Find an overview of the rich plant phenotyping landscape in Europe within the EMPHASIS plant phenotyping landscape map.
  • Make use of our modelling pilot Quantitative Plant via the EMPHASIS homepage, which offers image analysis software tools and models for plants.
  • If you work in Europe, get in touch with the Support Group members of your country. They form the link between national communities and EMPHASIS, providing input towards on the respective country’s expectations and informing the community about EMPHASIS developments.
  • Subscribe to our newsletter, Twitter, LinkedIn or Facebook pages via the EMPHASIS homepage.
  • Make use of the services of our partner projects, i.e., trans-national access via EPPN2020 or find joint activities on a global level via IPPN.
  • If you would like further information or have any questions, please don’t hesitate to get in touch with the EMPHASIS Coordination and Support Office: emphasis@fz-juelich.de.
 

IPPN SERVICES

IPPN Website:  Infrastructure DB & -Map updated


IPPN Office updated & re-released the global plant phenotyping installations database (“Infrastructure Database”) & connected it to the “Infrastructure Map”. With close to 100 entries (status: Feb 2020) now being properly mapped via an embedded GIS based on Open StreetMap, accessible on the IPPN Website.
Additionally, many other properties like the possibilities for Environmental Manipulation, High-/Low throughput, measurable plant traits and references connected to this installation, as well as contact information can be found.
For interested operators/responsibles of plant phenotyping installations, who want to expose their infrastructure onto the global plant phenotyping community, the database is open for registrations, here.

Two new IPPN Expert Working Groups


End of 2019, two new Expert Working Groups were officially administered by the IPPN Executive Board. They are open also towards non-IPPN members:

1) Advanced Sensor Applications (ASA)
The primary goal of the working group is to further exploit sensor technologies for application in plant phenotyping & establish best practices. Over this, the working group will actively discuss existing and emerging technologies and associated issues within plant science, including other scientific disciplines and industry. 

Executive Board:

Chair: Stefan Gerth, Fraunhofer (ILS), Germany

Co-Chair: Robert Koller, Forschungszentrum Juelich (IBG-2), Germany

SecretaryJennifer Clarke , University Nebraska-Lincoln (UNL), USA

More information & subscription


2) Working Group on Forest Phenotyping  
The goals of  the Forest Phenotyping Working Group is to improve the understanding of multiple scale forest dynamics through its phenotypes. The development of tools, platforms, methodologies and an international community will bring together experts from silvilculture, forest management, genetic, computer & data science, experimental design, and forest biometrics and geomatics, to tackle the emerging challenges related to climate changes, sustainable forest management, the need for healthier forests and the manufacture of sustainable and cleaner products.

Executive Board:

Chair: Maxime Bombrun, Scion, NZ

Co-Chair: Lin Cao, Nanjing Forestry University, China

Co-Chair: David Pont, Scion, NZ

More information & subscription

New Member Institution: Northeast Agricultural University


We are happy to welcome Northeast Agricultural University as IPPN's first new member institution in the new decade 2020!

Short Introduction:
NEAU is one of the key universities under the scope of China's ‘National 211 Project and Mid-west basic competence of higher education Project. In addition, NEAU is one of A-level universities in undergraduate education granted by Ministry of Education. Over the past years, NEAU developed into a comprehensive university with 16 schools and one department in the areas of agriculture, engineering, science, economy and management and art.


NEAU's representative withinin IPPN will be Prof. Qingshan Chen, Director of the College of Agriculture.
His group's research focus is on soybean breeding and recently moved towards the phenotypic description & 3D reconstruction of soybean phenotypes via UAVs in the field & in the greenhouse.

For direct contact please refer to the IPPN Office.

 

UPCOMING 

CONFERENCES 

The fourth annual Phenome 2020 conference represents a multidisciplinary community comprising plant biologists, ecologists, engineers, agronomists, computational scientists, and representatives from U.S. federal agencies who come together in a rich and diverse networking environment to foster collaboration, innovation, and the initiation of multi-investigator and multi-institution projects.

In accordance with the decisions made by the General Assembly in 2019, Phenome2020 will be host to IPPN's General Assembly 2020, as the partnering national conference.

The General Assembly will take place during the conference, on Thursday 27.02. 6pm-7:30pm (local time).
The Rooting 2020 conference aims to bring together scientists in plant developmental biology, agriculture, horticulture, forestry, ecophysiology and biotechnology, with a shared interest in root development. This year the symposium features a new ‘hands on’ style session on Root phenomics where delegates can experience new technologies for characterising root growth and development in controlled and field environments.

Thanks to support from IPPN and KWS Seeds 9 bursaries are given out to support students wanting to attend the conference. Apply here!
The fourth annual Phenome 2020 conference represents a multidisciplinary community comprising plant biologists, ecologists, engineers, agronomists, computational scientists, and representatives from U.S. federal agencies who come together in a rich and diverse networking environment to foster collaboration, innovation, and the initiation of multi-investigator and multi-institution projects.
The conference will focus on the rapidly expanding field of high throughput plant and algal phenotyping with a program that includes challenges and solutions to field studies, novel approaches to root phenotyping and the application of machine learning and big data computation for predictive modelling. The application of metaphenomic data analysis and trait elucidation will be considered in relation to acceleration of breeding programs for agronomically important crops, and the selection of algal strains for high yielding commercial culture.

IPPN's Controlled Environment Plant Phenotyping (CePPG) Working Group will organize a Workshop/Session during the conference. Details will be available soon.
 

CALLS &

SPECIAL ISSUES

Special Issue in Plant Phenomics: DEADLINE EXTENDED to March 31st


We invite contributions on the advancement and impact of plant phenotyping as an open call for publications initiated by the IPPS2019 -The 6th International Plant Phenotyping Symposium, held in Nanjing, China, on the 22nd-26th, October 2019.

Within this Special Issue, we want to outline the current status of plant phenotyping collecting studies on technological advancement, understanding the diverse plant environment interactions above or belowground, under controlled or field conditions and, translating this knowledge into application.

Link to manuscript submission 

Special Issue in Sensors: Low-Cost Sensors and Vectors for Plant Phenotyping DEADLINE EXTENDED to May 10th


 

IPPN's Affordable Phenotyping Working Group in cooperation with Sensors MDPI launches a Special Issue on "Low-Cost Sensors and Vectors for Plant Phenotyping". 

This Special Issue aims to collect manuscripts (review and original research articles) associated with low-cost sensor and vector technologies for plant phenotyping in controlled or field conditions. Among others, original and innovative contributions that involve widely accessible and reproducible plant phenotyping technologies, such as smartphone-embedded sensors, Internet of Things technologies, credit card mini-computer systems, associated with low-cost vectors made available under 3D printable objects, do-it-yourself item lists, together with embedded artificial intelligence under open sources, are encouraged. 

Link to manuscript submission 

PlosOne Collection on "Plant Phenomics and Precision Agriculture": DEADLINE June 5


PLOS ONE invites submissions that focus on advancements in plant phenomic and precious agriculture research. Articles in this Collection will be specially selected by a panel of Guest Editors.
 

Topics of interest include:
Sensor design
Robotic systems
Machine/computer vision tools
Data visualisation and integration
Digital soil mapping
In-field phenomic applications
Distributed research infrastructure
Multi-environment networks
Farmer support services

Link to manuscript submission

Special Issue "Remote Sensing of Plant-Climate Interactions": DEADLINE September 30th


This Special Issue invites studies focused on improving estimates of all plant–climate interface interactions, including but not limited to evapotranspiration and other assessments of water and heat stress from remote sensing platforms (satellite, UAV, or proximal sensing) under varying hydroclimates and land-cover conditions. We especially encourage studies that: 

(1) provide guidelines for improved parameterizations of different existing algorithms for remote sensing data under different hydroclimates, seasons, and land cover conditions, 

(2) use advanced techniques like machine learning, data assimilation, data fusion for utilizing various sources of ground-based data or multiple remote sensing platforms for estimating, calibrating, and validating remote sensing data and 

(3) assess the accuracy of different plant–climate interface algorithms with varying space–time scale remote sensing inputs. Multimodel comparisons and feedback mechanisms under different land-use land cover, seasons, and hydroclimates are also encouraged.

Link to manuscript submission

 

PUBLICATIONS

Research Spotlight: A meta‐analysis of plant responses to light intensity for 70 traits ranging from molecules to whole plant performance


Poorter et al. (2019) published a meta-analysis on the effect of light intensity on plants. Based on the data of 500 publications, they established dose-response curves for 70 plant traits from xanthophyll and nitrate concentrations up to plant growth and reproduction and established plasticity indices for different functional groups of species. A knowledge sheet with all the direct and indirect responses to light is added to quickly bring you up to date.



Albrecht, H. ; Fiorani, F. ; Pieruschka, R. ; Müller-Linow, M. ; Jedmowski, C. ; Schreiber, L. ; Schurr, U. ; Rascher, U. (2020) Quantitative Estimation of Leaf Heat Transfer Coefficients by Active Thermography at Varying Boundary Layer Conditions. Frontiers in plant science 10. https://doi.org/10.3389/fpls.2019.01684

Arouisse, Korte, van Eeuwijk, Kruijer (2019): Imputation of 3 million SNPs in the Arabidopsis regional mapping population. The Plant Journal. https://DOI: 10.1111/tpj.14659

Bateman, C.J., Fourie, J., Hsiao, J., Iire, K., Heslop, A., Hilditch, A., Hagedorn, M., Jessep, B., Gebbie, S. and Ghamkhar, K.. 2020 (in press), Assessment of Mixed Sward using Context Sensitive Convolutional Neural Networks. Frontiers in Plant Science.

Belachew K.Y., Nagel K.A., Poorter H., Stoddard F.L. (2019) Association of Shoot and Root Responses to Water Deficit in Young Faba Bean (Vicia faba L.) Plants. Front. Plant Sci. 10:1063. https://doi.org/10.3389/fpls.2019.01063

Boudiar R., Casas A.M., Gioia T., Fiorani F., Nagel K.A., Igartua E. (2020) Effects of low water availability on root placement and shoot development in landraces and modern barley cultivars. Agronomy, 10(1), 134. https://doi:10.3390/agronomy10010134

Dodic et al (2019) Image-Derived Traits Related to Mid-Season Growth Performance of Maize under Nitrogen and Water Stress. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.00814

George, R.M., Barrett, B.A. and Ghamkhar, K., 2019. Evaluation of LiDAR scanning for measurement of yield in perennial ryegrass. Journal of New Zealand Grasslands, 81, pp.55-60. https://doi.org/10.1186/s13007-019-0456-2

Ghamkhar, K., Irie, K., Hagedorn, M., Hsiao, J., Fourie, J., Gebbie, S., Hoyos-Villegas, V., George, R., Stewart, A., Inch, C. and Werner, A., 2019. Real-time, non-destructive and in-field foliage yield and growth rate measurement in perennial ryegrass (Lolium perenne L.). Plant methods, 15(1), p.72.https://doi.org/10.1186/s13007-019-0456-2

Kattge, J,Bönisch, G,Díaz, S, et al. 2020. TRY plant trait database – enhanced coverage and open access. Glob Change Biol, 26: 119–188. https://doi.org/10.1111/gcb.14904
 
Millet et al (2019) Genomic prediction of maize yield across European environmental conditions. Nature Genetics. 51: 952-956. https://doi.org/10.1038/s41588-019-0414-y

Müller-Linow, M.; Wilhelm, J.; Briese, C.; Wojciechowski, T.; Schurr, U.; Fiorani, F. (2019) Plant Screen Mobile: an open-source mobile device app for plant trait analysis. Plant methods 15(1). https://doi.org/10.1186/s13007-019-0386-z

Roitsch, T., Cabrera-Bosquet, L., Fournier, A., Ghamkhar, K., Jiménez-Berni, J., Pinto, F. and Ober, E.S., 2019. New sensors and data-driven approaches—A path to next generation phenomics. Plant science, 282, pp.2-10. https://doi.org/10.1016/j.plantsci.2019.01.011

Sharifi, M., Sevier, S., Zhang H., Wood R., Jessep, B, Gebbie, S., Irie, K., Hagedorn, M., Barret, B. and Ghamkhar, K. (in press), Mechatronics for a LiDAR-based Mobile Robotic Platform for Pasture Biomass measurement – In: Mechatronics and Machine Vision in Practice. Springer.

Shorten, P.R., Leath, S.R., Schmidt, J. and Ghamkhar, K., 2019. Predicting the quality of ryegrass using hyperspectral imaging. Plant methods, 15(1), p.63. https://doi.org/10.1186/s13007-019-0448-2

Soares et al (2019) Preserving the nutritional quality of crop plants under a changing climate: importance and strategies. Plant and Soil. https://doi.org/10.1007/s11104-019-04229-0

Tracy S., Nagel K.A., Postma J.A., Fassbender H., Wasson A., Watt M. (2019) Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities. Trends in Plant Science. doi: 10.1016/j.tplants.2019.10.015

Van Oosten et al (2019) Omeprazole treatment enhances nitrogen use efficiency through increased nitrogen uptake and assimilation in corn. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01507

Wasson A.P., Nagel K.A., Tracy S., Watt M. (2019) Beyond digging: Noninvasive Root and Rhizosphere Phenotyping. Trends in Plant Science. doi: 10.1016/ j.tplants.2019.10.011
 

PLANT

PHENOTYPING

JOBS

Open Positions

Assistant or Associate Member, Danold Danforth Plant Science Center, MO, USA

University Academic Fellow, Rhizosphere Biology, University of Leeds, UK

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

Research assistant (m/w/d) - Didigitale Transformation im Pflanzenbau (Agro-Nordwest)“, Osnabrueck, Germany

Senior Scientist - Digital Phenotyping, Nunhem, Limburg Province, Netherlands

S&T-Assistant for Implementation of digital technology for plant protection (FarmerSpace), Goettingen, Germany

Group Leader (f/m/d) Plant Biotic Stress Biology @ KWS

4 Professorships-, 3 Junior Research Group Leader-, 2 Post-doc & 15 PhD Student Positions in the Excellence Cluster "PhenoRob"

 

Postdoctoral Positions

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

Post-doctoral researcher (scientific collaborator) in grapevine physiology and genomics, Nyon, Switzerland

Postdoc Position on Implementation of digital technology for plant protection (FarmerSpace), Goettingen, Germany

Postdoc Position: Open source plant phenotyping system

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

Postdoc to join the plant phenotyping facilities at Purdue University

 

PhD positions

PhD Student (w/m/d) - in the field of Plant Computational Biology/Bioinformatics, IPK Gartersleben, Germany

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

Pre-PhD Internship & PhD position Studying the phenotypic plasticity of Vitis vinifera to water deficit, INRA, Montpellier, France

PhD position Plant Metabolome Analysis (f/m/d), Munich, Germany

2 PhD positions  Townsend Lab, University of Wisconsin, USA

PhD position: Agricultural bioinformatics and modern data management and sharing, University of Nebraska-Lincoln, USA

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