Publications
2025
2024
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Martje Fentener van Vlissingen, Jaap Heringa, Ruben Kok, Dimitris Koureas, Reinout Raijmakers and co-authors Rick van de Zedde, Mark Aarts, Valerian Meline, ao. (2024). Sustaining Dutch strength in European Life and Medical Science (LMS) research infrastructures: A collective perspective on the long-term sustainability of national participation in European LMS research infrastructures. DOI: https://doi.org/10.5281/zenodo.14506536. (Research report)
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Fotis Palaiochorinos (2024). Genetic Analysis of Drought Responses of Quinoa in a Combined Mapping Population Using Advanced Phenotyping. (MSc thesis)
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S.A. Bengoa Luoni, F. Garassino, and M.G.M. Aarts (2024). A High-Throughput Approach for Photosynthesis Studies in a Brassicaceae Panel. Plant Functional Genomics. Methods in Molecular Biology, vol 2787. Humana, New York, NY. DOI: https://doi.org/10.1007/978-1-0716-3778-4_2. (Other)
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Motzer C., A. El-Moghazy, A. Allende, M.I. Gil, Y. Weesepoel, L. van Overbeek, C. Liu, R. Van De Zedde, Y. Bouzembrak, N. Nitin, R. Ivanek, M. Wiedmann (2024). Food safety related data analytics, digital, and Artificial Intelligence needs and opportunities in Controlled Environment Agriculture. Food Protection Trends. (Publication)
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Fatemeh Maghuly (2024). Plant Functional Genomics. Methods in Molecular Biology. DOI: https://doi.org/10.1007/978-1-0716-3778-4. (Book)
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Myrthe Praat, Zhang Jiang, Joe Earle, Sjef Smeekens, and Martijn van Zanten (2024). Using a thermal gradient table to study plant temperature signalling and response across a temperature spectrum. Plant Methods. DOI: https://doi.org/10.1186/s13007-024-01230-2. (Publication)
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Christian Bachem (2024). Hybrid Potatoes – A Climate-Smart Solution for Potato Farmers. Wikifarmer. (Other)
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Laavanya Rayaprolu, Keshav Jayasankar, Mark G. M. Aarts, and Jeremy Harbinson (2024). Response of photosynthetic efficiency to short-term fluctuating light and cold in tomato. Bio Rxiv. DOI: https://doi.org/10.1101/2024.07.02.601750. (Other)
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Xinxin Wang, Gerrit Polder, Marlous Focker, and Cheng Liu (2024). Sága, a Deep Learning Spectral Analysis Tool for Fungal Detection in Grains—A Case Study to Detect Fusarium in Winter Wheat. Toxins. DOI: https://doi.org/10.3390/toxins16080354. (Publication)
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Federico Jurado-Ruiz, Thu-Phuong Nguyen, Joseph Peller, María José Aranzana, Gerrit Polder, and Mark G. M. Aarts (2024). LeTra: a leaf tracking workflow based on convolutional neural networks and intersection over union. Plant Methods. DOI: https://doi.org/10.1186/s13007-024-01138-x. (Publication)
2023
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Anamarija Agnič, Veronika Bračič, Tinkara Butara, Ana Hočevar, Jan Hočevar, Jan Jerovšek, Iva Klofutar, Irena Kralj Cigić, Zala Perko, Klara Razboršek, Ervin Rems, Francesco Rucci, Manca Šincek, and Tina Urh (2023). Erlenmayerica. Faculty of chemistry and chemical technology. (Other)
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L. Fiorentino, T.C.A.E. Wouters, Wouter van As, J. Wiedmer, P.J. Wolters, Y.C. Torres Ascurra, A. Andriani, D.M. Brink, J.W. Verstegen, P.M.J. van Rossum, L.H.G. Schmitz, H.J. van de Zedde, R.G.F. Visser, V.G.A.A. Vleeshouwers (2023). High-throughput phenotyping for resistance to Verticillium dahliae in wild Solanum species. (Poster)
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Christo Schiphorst, Cas Koeman, Ludovico Caracciolo, Koen Staring, Tom P. J. M. Theeuwen, Steven M. Driever, Jeremy Harbinson and Emilie Wientjes (2023). The effects of different daily irradiance profiles on Arabidopsis growth, with special attention to the role of PsbS. Frontiers in Plant Science. DOI: https://doi.org/10.3389/fpls.2023.1070218. (Publication)
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Francesco C.L. Garassino (2023). Blazing a trail towards higher photosynthetic efficiency: A multi-dimensional study of Hirschfeldia incana. DOI: https://doi.org/10.18174/639737. (PhD thesis)
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Gerrit van Steenbergen, Jean-Marie Michielsen, Ard Nieuwenhuizen, Mostafa Snoussi, and Hein Stallinga (2023). Effectiviteit van driftreducerende spuittechnieken in onkruidbestrijding. Wageningen Plant Research. DOI: https://doi.org/10.18174/588941. (Research report)
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Daoud Urdu, Daan Goense, Johan Booij, Conny Graumans, Corné Kempenaar (2023). Analysis of metadata standards for the exchange of image datasets and algorithms in the agricultural domain. Wageningen Plant Research. DOI: https://doi.org/10.18174/632203. (Publication)
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Bolai Xin, Ji Sun, Harm Bartholomeus, and Gert Kootstra (2023). 3D data-augmentation methods for semantic segmentation of tomato plant parts. Frontiers in Plant Science. DOI: https://doi.org/10.3389/fpls.2023.1045545. (Publication)
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Nicole Szeluga, Patricia Baldrich, Ryan DelPercio, Blake C. Meyers, and Margaret H. Frank (2023). Introduction of barnase/barstar in soybean produces a rescuable male sterility system for hybrid breeding. Plant Biotechnology Journal. DOI: https://doi.org/10.1111/pbi.14155. (Publication)
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Maryam Bagheri, Andries Temme, Rick van de Zedde, Diego Rubiales, Carla S. Santos, and Marta W. Vasconcelos (2023). High-throughput phenotyping of pea physiological traits for drought stress tolerance. (Poster)
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Tim van Daalen, Kararina Streit, Daniela Korts, and Jochem Evers (2023). Realtime input of sensor-based phenotypic traits for functional-structural plant modelling of tomato. (Book of Abstracts)
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Katarina Smolenova (2023). Development of a digital twin for tomato crops. (Book of Abstracts)
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Tim van Daalen, Katarina Streit, Daniela Bustos Korts, and Jochem Evers (2023). Towards automated Functional-Structural Plant Model parameterisation. (Book of Abstracts)
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Katarina Streit, Nastassia Vilfan, Pieter de Visser, and Jochem B. Evers (2023). From functional-structural tomato model to tomato digital twin. (Book of Abstracts)
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Narawitch Lertngim (2023). Improving Non-invasive Biomass Estimation by Combining Different Types of Image-Based Phenotypic Traits: A Study in Pea under Drought Stress. (MSc Research Practice)
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Stephen N. Njane, Shogo Tsuda, Bart M. van Marrewijk, Gerrit Polder, Kenji Katayama, and Hiroyuki Tsuji (2023). Effect of varying UAV height on the precise estimation of potato crop growth. Frontiers in Plant Science. DOI: https://doi.org/10.3389/fpls.2023.1233349. (Publication)
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Hendrik Poorter, Grégoire M. Hummel, Kerstin A. Nagel, Fabio Fiorani, Philipp von Gillhaussen, Olivia Virnich, Ulrich Schurr, Johannes A. Postma, Rick van de Zedde, and Anika Wiese-Klinkenberg (2023). Pitfalls and potential of high-throughput plant phenotyping platforms. Frontiers in Plant Science. DOI: https://doi.org/10.3389/fpls.2023.1233794. (Publication)
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Marta Nidola (2023). Assessing Water Stress in Maize Using UAV Thermal Infrared Sensing. (MSc thesis)
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Naftali Slob, William Hurst, Rick van de Zedde, and Bedir Tekinerdogan (2023). Virtual reality-based digital twins for greenhouses: A focus on human interaction. Computers and Electronics in Agriculture. DOI: https://doi.org/10.1016/j.compag.2023.107815. (Publication)
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Delfi Dorussen (2023). Exploring plasmotypic variation in Arabidopsis thaliana. (MSc thesis)
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Tom P.J.M. Theeuwen (2023). Exploring the unexplored: Unravelling the cyto-nuclear interactions in Arabidopsis thaliana to improve photosynthesis. (PhD thesis)
2022
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Giada Ceola (2022). Assessing the relationship between bee/flower diversity and vegetation structural heterogeneity through UAV photogrammetry. University of Bologna. (MSc thesis)
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Sven Warris, Rick van de Zedde (2022). High-throughput phenotyping and machine learning applications. (Conference paper)
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Rutger Vreezen (2022). The effect of including leaf optical and photosynthetic vertical profiles on the functionality of the Digital Tomato Crop. (MSc thesis)
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Jara J. Besó (2022). Unveiling the effect of Burren locus duplication in non-photochemical quenching & cyclic electron flow. (MSc thesis)
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Federico F. Espinosa (2022). Revealing plasmotype variability affecting photosystem II efficiency and growth parameters in Arabidopsis thaliana. (MSc thesis)
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Konrad Łosiński (2022). Identification of genes responsible for Ely’s photosynthesis phenotype. (MSc thesis)
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Tom P.J.M. Theeuwen, Louise L. Logie, Jeremy Harbinson, and Mark G.M. Aarts (2022). Genetics as a key to improving crop photosynthesis. Journal of Experimental Botany. DOI: https://doi.org/10.1093/jxb/erac076. (Publication)
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Bart M. van Marrewijk, Gerrit Polder, and Gert Kootstra (2022). Investigation of the added value of CycleGAN on the plant pathology dataset. IFAC-PapersOnLine. DOI: https://doi.org/10.1016/j.ifacol.2022.11.120. (Publication)
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Tom P.J.M. Theeuwen, Louise L. Logie, Sanne Put, Hedayat Bagheri, Konrad Łosiński, Justine Drouault, Pádraic J. Flood, Corrie Hanhart, Frank F.M. Becker, Raúl Wijfjes, David Hall, David M. Kramer, Jeremy Harbinson, and Mark G.M. Aarts (2022). Plethora of QTLs found in Arabidopsis thaliana reveals complexity of genetic variation for photosynthesis in dynamic light conditions. bioRxiv. DOI: https://doi.org/10.1101/2022.11.13.516256. (Publication)
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Tom P.J.M. Theeuwen, Aaron W. Lawson, Dillian Tijink, Federico Fornaguera, Frank F.M. Becker, Ludovico Caracciolo, Nicholas Fisher, David M. Kramer, Erik Wijnker, Jeremy Harbinson, and Mark G.M. Aarts (2022). The NDH complex reveals a trade-off that constrains maximising photosynthesis in Arabidopsis thaliana. bioRxiv. DOI: https://doi.org/10.1101/2022.11.13.516254. (Publication)
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Rick van de Zedde, and Lili Yao (2022). Book chapter: Field robots for plant phenotyping. Advances in plant phenotyping for more sustainable crop production. Editor: Dr Achim Walter. (Book)
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Robert D. Hall, John C. D’Auria, Antonio C. Silva Ferreira, Yves Gibon, Dariusz Kruszka, Puneet Mishra, and Rick van de Zedde (2022). High-throughput plant phenotyping: a role for metabolomics?. Trends in Plant Science. DOI: https://doi.org/10.1016/j.tplants.2022.02.001. (Publication)
2021
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S. H. van Delden, M. SharathKumar, M. Butturini, L. J. A. Graamans, E. Heuvelink, M. Kacira, E. Kaiser, R. S. Klamer, L. Klerkx, G. Kootstra, A. Loeber, R. E. Schouten, C. Stanghellini, W. van Ieperen, J. C. Verdonk, S. Vialet-Chabrand, E. J. Woltering, R. van de Zedde, Y. Zhang, and L. F. M. Marcelis (2021). Current status and future challenges in implementing and upscaling vertical farming systems. Nature food. DOI: https://doi.org/10.1038/s43016-021-00402-w. (Review article)
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Viviana J. Roman (2021). Salt Tolerance Strategies of the Ancient Andean Crop Quinoa. Wageningen University and Research . DOI: https://doi.org/10.18174/535249. (PhD thesis)
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Selwin Hageraats, Jos Ruizendaal, and Gerrit Polder (2021). Spectrale beeldverwerking van planten. Nederlands Tijdschrift voor Natuurkunde. (Publication)
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Sanne Put (2021). Unravelling nuclear natural variation under fluctuating light conditions reveals the complexity of photosynthesis. (MSc thesis)
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Dillian Tijink (2021). Zooming in on plasmotypic variation of Arabidopsis thaliana. (MSc thesis)
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Viviana J. Roman , Rick van de Zedde, Joseph Peller, Richard G. F. Visser, C. Gerard van der Linden, and Eibertus N. van Loo (2021). High-Resolution Analysis of Growth and Transpiration of Quinoa Under Saline Conditions. Frontiers in Plant Science. DOI: https://doi.org/10.3389/fpls.2021.634311. (Publication)
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Lili Yao, George Kowalchuk, and Rick van de Zedde (2021). Recent developments and potential of robotics in plant eco-phenotyping. Emerging Topics in Life Sciences. DOI: https://doi.org/10.1042/ETLS20200275. (Publication)
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Jeremy Harbinson, Mark G.M. Aarts, Herbert van Amerongen, Ralph Bock, Elizabete Carmo-Silva, Roberta Croce, Giovanni Finazzi, Dolf Weijers, and Rene M. Klein Lankhorst (2021). Photosynthesis 2.0. Wageningen University and Research. (Publication)
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Jeremy Harbinson, Martin A.J. Parry, Jess Davies, Norbert Rolland, Francesco Loreto, Ralf Wilhelm, Karin Metzlaff, and René Klein Lankhorst (2021). Designing the Crops for the Future; The CropBooster Program. Biology. DOI: https://doi.org/10.3390/biology10070690. (Publication)
2020
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Maryam Bagheri, Narawitch Lertngim, Steven M. Driever, Rick van de Zedde, Diego Rubiales, Carla S. Santos, and Marta W. Vasconcelos (2020). Optimizing Pea Biomass Estimation: Unveiling Insights from Multimodal Image-Based Phenotyping under Drought Conditions. CBQF and Wageningen UR. (Poster)
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Puneet Mishra, Santosh Lohumi, Haris Ahmad Khan, and Alison Nordon (2020). Close-range hyperspectral imaging of whole plants for digital phenotyping: Recent applications and illumination correction approaches. Computers and Electronics in Agriculture. DOI: https://doi.org/10.1016/j.compag.2020.105780. (Publication)
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Aaron Lawson (2020). Revealing cyto-nuclear interactions through phenotypic variation: a study on cybrids of outdoor grown Arabidopsis thaliana. (MSc thesis)
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Pádraic J. Flood, Tom P.J.M. Theeuwen, Korbinian Schneeberger, Paul Keizer, Willem Kruijer, Edouard Severing, and Erik Wijnker (2020). Reciprocal cybrids reveal how organellar genomes affect plant phenotypes. Nature Plants. DOI: https://doi.org/10.1038/s41477-019-0575-9. (Publication)
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Mark Aarts (2020). Faster plant growth through more efficient photosynthesis. Weblog Wageningen University & Research. (Publication)
2019
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Justine Drouault (2019). Exploring the genetics and physiology underlying the non-photochemical quenching phenotype of the Ely nucleus. (MSc thesis)
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Louise Logie (2019). Preliminary exploration of the NPQ phenotype of the Ely nucleotype. (MSc thesis)
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Ayodeji O. Deolu-Ajayi, A. Jessica Meyer, Michel A. Haring, Magdalena M. Julkowska, and Christa Testerink (2019). Genetic Loci Associated with Early Salt Stress Responses of Roots. iScience. DOI: https://doi.org/10.1016/j.isci.2019.10.043. (Publication)
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Ke Yu, Corné M.J. Pieterse, Peter A.H.M. Bakker, and Roeland L. Berendsen (2019). Beneficial microbes going underground of root immunity. Plant, Cell & Environment. DOI: https://doi.org/10.1111/pce.13632. (Publication)
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Weinan Shi, Rick van de Zedde, Huanyu Jiang, and Gert Kootstra (2019). Plant-part segmentation using deep learning and multi-view vision. Biosystems Engineering. DOI: https://doi.org/10.1016/j.biosystemseng.2019.08.014. (Publication)
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Eva Rosenqvist, Dominik K. Großkinsky, Carl-Otto Ottosen and Rick van de Zedde (2019). The Phenotyping Dilemma—The Challenges of a Diversified Phenotyping Community. Frontiers in Plant Science. DOI: https://doi.org/10.3389/fpls.2019.00163. (Publication)