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NEWSLETTER

(Q2 2020)
 

EDITORIAL

Plant phenotyping in the pandemic crisis

 
At present almost all societies face major challenges due to the COVID-19 crisis. Obviously, scientists and plant phenotyping activities all over the world are affected.
In the past weeks and months, many of us have seen a massive lockdown of institutes and companies, which has caused acute problems in research organisations and companies. For example, experiments that were planned had to be cancelled and travel restrictions have led to a severe reduction in opportunities to install phenotyping gear. These continue to cause immediate scientific and business issues, which also affect members of the IPPN.
IPPN would

  • be interested to hear from IPPN members about immediate effects of the lockdown to your science and business. This will allow us to provide news of recent developments in the plant phenotyping community globally and discuss options with members of how to potentially support members in critical situations.
At present, some countries still face massive shutdowns; others have started their route back towards a “somewhat normal” operation mode that often in itself has severe restrictions. There is no clear indication in many countries regarding how things will develop in the next months given the level of uncertainty about the pandemic. It is already obvious that we will have to find other ways to collaborate with maintained travel restrictions, and to communicate with increased online processes for workshops and conferences.
IPPN would
  • like to continue to support IPPN members even under restricted travel and collaboration situations and request input on how IPPN could be helpful.
  • develop further online communication between IPPN members in working groups, workshops and conferences
  • support conferences and training, e.g., by covering them to online delivery.

However, what is clear as well, is that

in the future, after the COVID-19 pandemic, plant phenotyping will be as important or probably even more important than before, since plant phenotyping is an essential element to assure crop productivity in breeding and management. The virus will stay with us and the pandemic will not be a short-term issue. Therefore, major challenges like food security, climate change, sustainable agriculture and biodiversity loss will be overlaid by a virus pandemic and associated societal demands for financial resources. In some countries, food security issues will become even more pronounced during the pandemic and some countries are already discussing the importance of more regional production of food for resilience of delivery when global or regional supply chains are not functional anymore. We have seen pandemics that affect humans and animal husbandry; we are probably even less prepared for the spread of a major disease affecting crop production. At the same time, funding opportunities may shift away from plant science due to the emphasis on biomedical research. Therefore,
IPPN would be interested to
  • learn how perspectives on plant phenotyping in your country, your research organisation and your business are affected by the COVID-19 crisis.
  • do you see or expect changes/shifts in funding?
  • do you see novel topics arising or shifts in importance/ priority which would require proactive developments in the plant phenotyping community?
  • do you see options where IPPN could support developments to stabilize or increase the support and visibility needed for the future of plant phenotyping, when other issues like the pandemic overwrite many previously identified challenges? We make this request while recognizing that it may become more important to tackle acute and underlying challenges?

Plant phenotyping and we as a community are and will be strongly affected by the immediate impact of this pandemic and the changes that will be happening as a consequence. Please contact us and give feedback on your views about this topic and how IPPN could/ should respond to the needs of its members, the community, the sector and the wider societal challenges that are linked to this situation.
 


Yours,

Uli Schurr
(IPPN PRimary Chair)





 

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NEWS


 

IPPS2021 will take place in Wageningen (Netherlands)!


The IPPN Board has announced that Wageningen University & Research (WUR) has been elected to host & co-organise the 7th International Plant Phenotyping Symposium in October 2021.
On that occasion, the brand new and unique Wageningen NPEC facilities will be officially opened. These facilities are part of the Netherlands Plant Eco-Phenotyping Centre (NPEC), a joint plant phenotyping centre between Wageningen University & Research and Utrecht University.
Wageningen's application did win by simple majority of the IPPN members against the two other possible venues Aarhus (Aarhus University) and Avignon (INRAe).

 

What we read 


 

Global Wheat Head Challenge 


For several years, agricultural research has been using sensors to observe plants at key moments in their development. However, some important plant traits are still measured manually.

There is the need for a robust and accurate computer model that is capable of counting wheat ears from digital images. This model will benefit phenotyping research and help producers around the world assess ear density, health and maturity more effectively. Some work has already been done in deep learning, though it has resulted in too little data to have a generic model.  

The Global Wheat Head Challenge, an international data science competition, was created to address this need. The objective is to have a software model capable of locating ears on a wide variety of data, without bias. Data Scientists, hackers, scientists and the curious re invited to join forces with the initiators to solve this challenge & to gain the opportunity to receive up to 8,000 USD price money!

New Chinese Webinar Platform "Agri-X Forum" features Plant Phenotyping Seminars online


Also in other parts of the world scientists and practitioners in the space of plant phenotyping are required to stay at home and/or can’t perform their usual work routines, du to SARS-CoV-2. China, as the first country that was affected by rigorous lock-down measures found a way to keep phenotypers in & out of China connected. Since the beginning of March, the Chinese plant phenotyping community hence organized an online platform on „Digital Agriculture“ via the Vzan broadcast platform & WeChat, where (up-to-now) over 5000 scientists, breeders and students subscribed to. The webinar was initiated by Phenotrait & three other companies (NovoSeed, BioBin & MolBreeding) & currently reports >1000 viewers who log-in to the individual seminars making it one of the biggest scientific webinars in China within two months.

One of the organizers (and also member oft he IPPN Executive Board) David Han about the Webinar: „We wish to make sure that the plant phenotyping community can continue to communicate their latest work during these difficult times and establish a platform on which scientists & practitioners may connect regardless of where they are located“.

Despite the vast amount of content being in Chinese language, also international speakers present their work within this webinar series. Next of which will be the IPPN Primary Chair Prof. Ulrich Schurr (Forschungszentrum Juelich; IBG-2) on May 29th, 14:00 (Berlin time) / 20:00 (Beijing time) / 7:00am (CDT).

The webinar can be accessed via this link: https://wx.vzan.com//live/channelpage-161816

Phenotyping as exhibit - at the Guggenheim museum in New York


The architect Rem Koolhaas has opened the exposition Countryside The Future on the top floor of the Guggenheim museum in New York. In this exposition one of PhenoVation’s product is displayed to show the public what is possible in plant imaging. The Phenomate system measures over 1000 plants automatically and autonomously on Fv/Fm (efficiency of photosynthesis) color and multi-spectral imaging.

 

IPPN SERVICE


 

New "Phenomics Webinars" Series


The recent spread of SARS-CoV-2 limits opportunities to actively interact, discuss latest results, technological developments as many conferences, workshops and events have been cancelled. To compensate for these shortcomings the plant phenotyping initiatives IPPN, EPPN2020, EMPHASIS provide an exchange platform for the community by organizing a Plant Phenomics Webinar Series that will address all relevant topics in this field.

Abstract submission is open now!

We are seeking contributions from all plant phenotyping related work fields across all career stages, Including research highlights & use-cases from research & application, from the public- & private sector related to plant phenotyping or which use plant phenotyping as an aspect of their work.
We especially encourage those fields which have yet been under-represented in plant phenotyping aiming to advance the scope of applications for which this methodology can be used.

The Phenomics Webinars will present single talks (and/or sessions with multiple speakers) in a bi-weekly manner for a yet undefined time span, starting Friday May 15th with the first webinar by one of the highly cited researchers 2019, Dr. Hendrik Poorter on "Phenomics, Meta-Phenomics, and the many ways plants acclimate to growth light intensity".

For more upcoming webinar-announcements of this series (and also others), please keep an eye on our social media accounts!

EMPHASIS Photo Competition


The EU Phenotyping Infrastructure Project "EMPHASIS" & IPPN are looking for the best photograph portraying plant phenotyping.
The winning photographer will receive a high-end camera worth 2500 Euro,
which is made possible through our sponsors Lemnatec Gmbh (main sponsor) & DPPN.

Submissions may include (but are not restricted to) research images, photographs of researchers, plants, phenotyping facilities, equipment and also creative and artistic interpretations of the topic. 
All short-listed photographs will be published by EMPHASIS and its partners and exhibited at various occasions. 

Submission is now open

The deadline for submission is 31 August 2020.


Upcoming (E-)vents 


 

Free Online Course: Image Analysis Methods for Biologists 
(University of Nottingham)


The use of automatic image analysis in the biological sciences has increased significantly in recent years, especially with automated image capture and the rise of phenotyping.
The University of Nottinham offers free 4-week online courses starting on various dates throughout the year.

This course is designed for postgraduate and postdoctoral researchers in biological sciences and is meant to improve your understanding of image analysis methods, and improve your practical skills and ability to apply the techniques to your images.

More information here

NPPN Virtual Field Day 17th June 2020


Because of travel restrictions and group size limits due to COVID-19, the NPPN annual field day will be held via virtual conference on ZOOM!   

The conference will be divided into a morning and afternoon session, 9:00 to 11:00 and 13:00 to 15:00, respectively.  The first session will focus on the advances of Robotics and Virtual Reality technologies in the field of agriculture, with presentations from researchers at the Norwegian University of Life Sciences (NMBU) and Making View AS.  The second session will highlight Applications & Field Observations, with presentations from Graminor and NMBU's Vollebekk Research Farm. 

More information & preliminary program

CVPR Virtual Conference on Computer Vision


CVPR is the US' premier annual computer vision event comprising the main conference and several co-located workshops and short courses. With its high quality and low cost, it provides an exceptional value for students, academics and industry researchers.

Because of the current SARS-CoV-2 pandemic, CVPR will take place as a virtual conference. More information on modalities, here

ECCV 2020 Workshop on Computer Vision Problems in Plant Phenotyping (CVPPP 2020) 


After the successful CVPPP workshops from recent years at ECCV, BMVC, ICCV, and CVPR, CVPPP this year is held in conjunction with ECCV 2020. The goal of this sixth workshop is to continue to showcase the challenges raised by and extend the state of the art in computer vision for plant phenotyping.
The workshop is made possible through callaborative efforts & funding from IPPN, DPPN, Phenorob, Forschungszentrum Juelich, The University of Edinburgh & The University of Nottingham.

We welcome both full papers and extended abstracts. For further information about the workshop and challenges please see our link on the IPPN Website.

European Conference on Computer Vision (ECCV 2020): 23 – 28 August 2020


The 2020 European Conference on Computer Vision (ECCV 2020) is the top European conference in the image analysis area.
This conference follows the tradition set by previous instances of the conference, with the most recent in Amsterdam (2016) and Munich (2018).

ECCV 2020 will be a four day single-track conference, with additional activities: over 1000 posters, workshops, tutorials, and an industrial exhibition. The conference will present high quality previously unpublished research on many aspects of computer vision.

Regarding the recent Coronavirus spread, ECCV 2020 will continue to take advice from respective healthcare and government authorities. So far, ECCV will be held as planned in Glasgow from 23 – 28 August 2020.

Save the date for the 6th Annual NPPN Workshop 2020


The 6th Annual NPPN Workshop will be held on November 26 -27, 2020 in Båstad, Sweden.  Details of the event and registration information will be sent out later. But save the date in your calendar!

Winter School on Image Analysis for Plant Phenotyping (2021)


Wageningen University & Research (WUR) is offering again in 2021 a training course for a complete overview of image analysis techniques for automatic plant phenotyping? The Winter School will provide a mixture of underlying theory and practical hands-on training. There will be the opportunity to work on real plant image analysis problems to  directly apply and combine the theory in practice.
The programme is primarily intended for researchers working on automatic phenotyping and technical experts in breeding companies who use, or plan to use, image analysis.

More information here

 

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 

Plant Physiology Focus Issue on "Digital Agriculture":  Deadline December 1st, 2020; Publication date: June 2021 


The Focus Issue on crop improvement in the age of Digital Agriculture will cover a broad range of topics relevant to improvement of plant-based agricultural systems. Articles covering the following topics will be considered: genetic diversity, genomes/transcriptomes, microbiomes, and linking such information to phenotype (in the field and controlled environments) to breed new varieties/crops that are high yielding, nutritious, and sustainable; requiring less water, fertilizers, and pesticides, yet able to grow on marginal lands with reduced greenhouse gas emissions and energy inputs. The Digital Agriculture Focus Issue seeks submissions of Research Articles, Research Reports, and Letters in the areas mentioned.

Authors submitting to this Focus Issue should indicate their interest in the cover letter when submitting papers online. Please select “Digital Agriculture” from the Focus Issue list in the online submission system.

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

 

PUBLICATIONS



 

Research Spotlight: Yang et. al: Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives


Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years.

Anderson SL, Murray SC, Chen Y, Malambo M, Chang A, Popescu S, Cope D, Jung J. (2019) Unoccupied aerial system enabled functional modeling of maize (Zea mays L.) height reveals dynamic expression of loci associated to temporal growth. Dryad Digital Repository. doi: https://doi.org/10.1101/848531 

Beleggia et al (2020) Comparative analysis based on transcriptomics and metabolomics data reveal differences 1between emmer and durum wheat in response to nitrogen starvation. BioRxiv, https://doi.org/10.1101/2020.02.03.931717

Bendel N, Kicherer A, Backhaus A, et al. (2020) Evaluating the Suitability of Hyper- and Multispectral Imaging to Detect Foliar Symptoms of the Grapevine Trunk Disease Esca in Vineyards. Research Square; 2020. DOI: 10.21203/rs.3.rs-25654/v1.

Boudiar et al (2020) Effects of Low Water Availability on Root Placement and Shoot Development in Landraces and Modern Barley Cultivars. Agronomy 2020, 10, 134. https://www.mdpi.com/2073-4395/10/1/134

Herrmann, P.S.P.; Sydoruk, V.; Marques Porto, F.N. (2020) Microwave Transmittance Technique Using Microstrip Patch Antennas, as a Non-Invasive Tool to Determine Soil Moisture in Rhizoboxes. Sensors20(4), 1166. https://doi.org/10.3390/s20041166

Lak, Z.A.; Sandén, H.; Mayer, M.; Godbold, D.L.; Rewald, B. (2020) Plasticity of Root Traits under Competition for a Nutrient-Rich Patch Depends on Tree Species and Possesses a Large Congruency between Intra- and Interspecific Situations. Forests, 11, 528, https://doi.org/10.3390/f11050528.

Li, H., Feng, H., Guo, C., Yang, S., Huang, W., Xiong, X., Liu, J., Chen, G., Liu, Q., Xiong, L., Liu, K. and Yang, W. (2020), High‐throughput phenotyping accelerates the dissection of the dynamic genetic architecture of plant growth and yield improvement in rapeseed. Plant Biotechnol J. Accepted Author Manuscript. doi:10.1111/pbi.13396

Anastasios Mazis, Sruti Das Choudhury, Patrick B. Morgan, Vincent Stoerger, Jeremy Hiller, Yufeng Ge, Tala Awada (2020) Application of high-throughput plant phenotyping for assessing biophysical traits and drought response in two oak species under controlled environment,Forest Ecology and Management, Volume 465, 118101, ISSN 0378-1127, https://doi.org/10.1016/j.foreco.2020.118101.

Narisetti, N., Henke, M., Seiler, C. et al. (2019) Semi-automated Root Image Analysis (saRIA). Sci Rep 9, 19674. https://doi.org/10.1038/s41598-019-55876-3

Ribes, Mathieu; Russias, Gaspard; Tregoat, Denis; Fournier, Antoine (2020) Towards Low-Cost Hyperspectral Single-Pixel Imaging for Plant Phenotyping. Sensors 20, no. 4: 1132. https://doi.org/10.3390/s20041132

Santos, T.T.; de Souza, L.L.; dos Santos, A.A.; Avila, A. (2020) Grape detection, segmentation, and tracking using deep neural networks and three-dimensional association. Computers and Electronics in Agriculture, 170. https://doi.org/10.1016/j.compag.2020.105247

Sheng Wu, Weiliang Wen, Yongjian Wang, et al. (2020) MVS-Pheno: A Portable and Low-Cost Phenotyping Platform for Maize Shoots Using Multiview Stereo 3D Reconstruction,” Plant Phenomics, vol. 2020, Article ID 1848437, 17 pages, 2020. https://doi.org/10.34133/2020/1848437

Xiao, S.; Chai, H.; Shao, K.; Shen, M.; Wang, Q.; Wang, R.; Sui, Y.; Ma, Y. (2020) Image-Based Dynamic Quantification of Aboveground Structure of Sugar Beet in Field. Remote Sens., 12, 269, https://doi.org/10.3390/rs12020269

Xinxin Chen, Qishuo Ding, Ruiyin He, Huixin Li, (2019) A protocol of field-based phenotyping procedure for no-till wheat root system architecture based on data-driven model-assist,
Artificial Intelligence in Agriculture, Volume 3, ISSN 2589-7217,https://doi.org/10.1016/j.aiia.2019.10.002.

Xu, Ling-Xiang & Jiawei, Chen & Ding, Yanfeng & Zhu, Yan & Guohui, Ding & Zhou, Ji. (2020). Indoor phenotyping platforms and associated trait measurement: progress and prospects. Information Processing in Agriculture. 2. 23-42. 10.12133/j.smartag.2020.2.1.202003-SA002

Yao, M., Guan, M., Zhang, Z. et al. (2020) GWAS and co-expression network combination uncovers multigenes with close linkage effects on the oleic acid content accumulation in Brassica napus. BMC Genomics 21, 320 (2020). https://doi.org/10.1186/s12864-020-6711-0

Yu Jiang and Changying Li (2020) Convolutional Neural Networks for Image-Based High-Throughput Plant Phenotyping: A Review, Plant Phenomics, vol. 2020, Article ID 4152816, 22 pages. https://doi.org/10.34133/2020/4152816

Laura Zabawa, Anna Kicherer, Lasse Klingbeil, Reinhard Töpfer, Heiner Kuhlmann, Ribana Roscher (2020) Counting of grapevine berries in images via semantic segmentation using convolutional neural networks, ISPRS Journal of Photogrammetry and Remote Sensing, Volume 164, Pages 73-83, ISSN 0924-2716, https://doi.org/10.1016/j.isprsjprs.2020.04.002.

Zhang, X. & Whalley, P. & Ashton, R. & Evans, J. & Hawkesford, Malcolm & Griffiths, S. & Huang, Z. & Zhou, Hu & Mooney, Sacha & Whalley, W.. (2020). A comparison between water uptake and root length density in winter wheat: effects of root density and rhizosphere properties. Plant and Soil. 10. 1007/s11104-020-04530-3
 
 

PLANT

PHENOTYPING

JOBS


 

Open Positions

Disease Phenotyping Scientist, Bayer, CA, USA

Plant Researcher in plant phenotyping, InFarm, Germany

Head of Phenomics, Bayer, St. Louis, USA

Research scientist in the field of Bioinformatics and Data Management, IBG-2, Germany

Grant-Funded Researcher (B) - School of Agriculture, Food and Wine, TPA Adelaide, AUS

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

Two Postdoc positions in modelling plant-environment and soil-plant interactions, SLU, Sweden

Post-doc Scholar in Plant Sensors, North Carolina State University, NC, USA

Post-doc Position at The Department of Plant Microbe Interactions at the MPIPZ in Cologne, Germany

Post-doc Position in Phenomics of Plant Disease, ETH Zurich, Switzerland

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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