Review
Forestry
Jose Luis Silva, Rui Bordalo, Jose Pissarra, Paloma de Palacios
Summary: Wood identification is an important tool in various fields. Computer vision-based technology provides a fast and accurate method for wood identification, but its application in fields like cultural heritage is still limited.
Article
Plant Sciences
Prabu Ravindran, Frank C. Owens, Adam C. Wade, Patricia Vega, Rolando Montenegro, Rubin Shmulsky, Alex C. Wiedenhoeft
Summary: Illegal logging poses a major threat to forests in Peru and globally. To address this issue, a convolutional neural network was trained using transfer learning for wood identification, achieving high accuracy and readiness for real-world field screening scenarios. This technology helps monitor, incentivize, and monetize legal and sustainable wood value chains.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemical Research Methods
Sung-Wook Hwang, Junji Sugiyama
Summary: The advancements in computer vision and machine learning have revolutionized scientific disciplines and created a new research field in wood science known as computer vision-based wood identification. Research has reviewed mainstream studies using machine learning procedures to familiarize wood scientists with this area and help them choose appropriate techniques in wood science.
Review
Agronomy
Ya-Hong Wang, Wen-Hao Su
Summary: Computer vision combined with deep convolutional neural networks is a reliable method for characterizing and quantifying high-throughput phenotyping of different grain crops. Developing corresponding imaging systems can increase stakeholders' confidence in grain crop cultivation, bringing technical and economic benefits.
Article
Robotics
Adrian Salazar Gomez, Erchan Aptoula, Simon Parsons, Petra Bosilj
Summary: This study compared three methods for counting fruit or grains in images, showing that as object density increases, counting by regression becomes more accurate than counting by detection. The error in count predicted by detection-based methods can be up to 5 times higher than regression-based methods when there are more than a hundred objects per image.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2021)
Article
Biochemical Research Methods
Shuo Zhou, Xiujuan Chai, Zixuan Yang, Hongwu Wang, Chenxue Yang, Tan Sun
Summary: This study introduces Maize-IAS, an integrated application that supports one-click analysis of maize phenotype using advanced deep learning methods. The software provides a user-friendly interface for rapid calculation of important phenotypic characteristics, demonstrating the efficiency and potential capability of AI technology in agriculture and plant science.
Article
Food Science & Technology
Ke Sun, Yu-Jie Zhang, Si-Yuan Tong, Meng-Di Tang, Chang-Bao Wang
Summary: This study aims to develop a high-speed and nondestructive method for detecting mildewed rice grains. By establishing YOLO-v5 models and analyzing the relationship between the proportion of mildewed regions and the total number of colonies, the proposed method achieves accurate detection of different fungal contaminations in rice grains on the verification set.
Article
Biochemical Research Methods
Marina Creydt, Lea Ludwig, Michael Kohl, Jorg Fromm, Markus Fischer
Summary: The analysis of wood geographical origin using different extraction methods can effectively distinguish the geographic source of wood, helping to prevent illegal logging and timber trade. Multivariate data analysis can extract differences related to geographic origin, and the identification of marker substances reveals metabolic pathways affected by geographical influences.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Biochemical Research Methods
Marina Creydt, Silke Lautner, Joerg Fromm, Markus Fischer
Summary: A non-targeted metabolomics-based approach using liquid chromatography high-resolution mass spectrometry was used to differentiate spruce wood from different geographic source areas. Despite the small distance (250 km) between the two sample sites in Germany, a distinction between the sample groups was achieved based on non-polar data sets using supervised multivariate methods. Major metabolites contributing to differentiation were identified through MS/MS experiments.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Ecology
Moritz D. Luerig
Summary: Digital images are widely used by biologists to capture and analyze organismal phenotypes. phenopype is a high-throughput phenotyping pipeline for Python that aims to extract high-dimensional phenotypic data from digital images efficiently. It provides functions for image preprocessing, segmentation, data extraction, visualization, and data export, facilitating scientific image analysis for biologists with little coding experience. This software helps in increasing the speed and reproducibility of data collection, making it a valuable tool for researchers in ecological, evolutionary, and developmental biology.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Forestry
Prabu Ravindran, Frank C. Owens, Adam C. Wade, Rubin Shmulsky, Alex C. Wiedenhoeft
Summary: Wood identification is vitally important for ensuring the legality of North American hardwood value chains. This study demonstrates the effectiveness of computer vision wood identification (CVWID) systems in accurately identifying North American ring porous hardwoods. Deep-learning models achieved high accuracy in both training and testing datasets, highlighting the potential of CVWID systems for field operations.
CANADIAN JOURNAL OF FOREST RESEARCH
(2022)
Article
Computer Science, Information Systems
Ting Zhang, Muhammad Waqas, Zhaoying Liu, Shanshan Tu, Zahid Halim, Sadaqat Ur Rehman, Yujian Li, Zhu Han
Summary: A fusing framework of shortcut convolutional neural networks (S-CNN) is proposed to integrate features from different layers, outperforming standard CNNs in terms of accuracy and stability. Comprehensive experiments show that S-CNN performs better than standard CNNs on various visual tasks and is competitive with ResNet.
INFORMATION SCIENCES
(2021)
Article
Plant Sciences
Prabu Ravindran, Frank C. Owens, Adam C. Wade, Rubin Shmulsky, Alex C. Wiedenhoeft
Summary: The availability and access to wood identification expertise or technology is crucial for promoting sustainable practices and conservation efforts in the forest products value chain. This study trained 22 image-based deep learning models for the identification of North American diffuse porous hardwoods, and evaluated their performance on an open-source field-deployable platform.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Hubert Fonteijn, Manya Afonso, Dick Lensink, Marcel Mooij, Nanne Faber, Arjan Vroegop, Gerrit Polder, Ron Wehrens
Summary: High-throughput phenotyping is becoming increasingly important in agriculture, used by breeders and growers for estimating genetic value and predicting yield. Image analysis plays a crucial role in most phenotyping applications, with recent advances in robotics, image registration, and image segmentation improving the feasibility of fully integrated automatic phenotyping systems. However, challenges remain in developing complete phenotyping systems for routine use in production environments.
Article
Computer Science, Artificial Intelligence
Rudiger Schmitz, Frederic Madesta, Maximilian Nielsen, Jenny Krause, Stefan Steurer, Rene Werner, Thomas Rosch
Summary: The study introduces multi-encoder fully-convolutional neural networks to integrate information from different spatial scales, enhancing the accuracy and efficiency of histopathologic diagnosis.
MEDICAL IMAGE ANALYSIS
(2021)
Article
Plant Sciences
Ajaree Thonglim, Sylvain Delzon, Maximilian Larter, Omid Karami, Arezoo Rahimi, Remko Offringa, Joost J. B. Keurentjes, Salma Balazadeh, Erik Smets, Frederic Lens
Summary: This study investigated embolism resistance in inflorescence stems of four Arabidopsis thaliana accessions and evaluated vulnerability to xylem embolism using detailed anatomical observations and the centrifuge technique. The results showed that intervessel pit membrane thickness is the key functional trait underlying the variation in embolism resistance amongst the accessions studied.
Article
Forestry
Georg von Arx, Marco Carrer, Alan Crivellaro, Veronica De Micco, Patrick Fonti, Frederic Lens, Angela Luisa Prendin, Sabine Rosner, Ute Sass-Klaassen
Summary: Quantitative wood anatomy (QWA) is a dynamic research approach with growing interest, but the lack of common protocols and knowledge gaps have hindered its full potential. The establishment of Q-NET as an interdisciplinary platform for exchange and research around QWA is crucial in fostering international cooperation and collaboration in this field.
Article
Ecology
Francesco Maria Sabatini, Jonathan Lenoir, Tarek Hattab, Elise Aimee Arnst, Milan Chytry, Juergen Dengler, Patrice De Ruffray, Stephan M. Hennekens, Ute Jandt, Florian Jansen, Borja Jimenez-Alfaro, Jens Kattge, Aurora Levesley, Valerio D. Pillar, Oliver Purschke, Brody Sandel, Fahmida Sultana, Tsipe Aavik, Svetlana Acic, Alicia T. R. Acosta, Emiliano Agrillo, Miguel Alvarez, Iva Apostolova, Mohammed A. S. Arfin Khan, Luzmila Arroyo, Fabio Attorre, Isabelle Aubin, Arindam Banerjee, Marijn Bauters, Yves Bergeron, Erwin Bergmeier, Idoia Biurrun, Anne D. Bjorkman, Gianmaria Bonari, Viktoria Bondareva, Jorg Brunet, Andraz Carni, Laura Casella, Luis Cayuela, Tomas Cerny, Victor Chepinoga, Janos Csiky, Renata Custerevska, Els De Bie, Andre Luis de Gasper, Michele De Sanctis, Panayotis Dimopoulos, Jiri Dolezal, Tetiana Dziuba, Mohamed Abd El-Rouf Mousa El-Sheikh, Brian Enquist, Joerg Ewald, Farideh Fazayeli, Richard Field, Manfred Finckh, Sophie Gachet, Antonio Galan-de-Mera, Emmanuel Garbolino, Hamid Gholizadeh, Melisa Giorgis, Valentin Golub, Inger Greve Alsos, John-Arvid Grytnes, Gregory Richard Guerin, Alvaro G. Gutierrez, Sylvia Haider, Mohamed Z. Hatim, Bruno Herault, Guillermo Hinojos Mendoza, Norbert Hoelzel, Juergen Homeier, Wannes Hubau, Adrian Indreica, John A. M. Janssen, Birgit Jedrzejek, Anke Jentsch, Norbert Juergens, Zygmunt Kacki, Jutta Kapfer, Dirk Nikolaus Karger, Ali Kavgaci, Elizabeth Kearsley, Michael Kessler, Larisa Khanina, Timothy Killeen, Andrey Korolyuk, Holger Kreft, Hjalmar S. Kuehl, Anna Kuzemko, Flavia Landucci, Attila Lengyel, Frederic Lens, Debora Vanessa Lingner, Hongyan Liu, Tatiana Lysenko, Miguel D. Mahecha, Corrado Marceno, Vasiliy Martynenko, Jesper Erenskjold Moeslund, Abel Monteagudo Mendoza, Ladislav Mucina, Jonas V. Muller, Jerome Munzinger, Alireza Naqinezhad, Jalil Noroozi, Arkadiusz Nowak, Viktor Onyshchenko, Gerhard E. Overbeck, Meelis Partel, Anibal Pauchard, Robert K. Peet, Josep Penuelas, Aaron Perez-Haase, Tomas Peterka, Petr Petrik, Gwendolyn Peyre, Oliver L. Phillips, Vadim Prokhorov, Valerijus Rasomavicius, Rasmus Revermann, Gonzalo Rivas-Torres, John S. Rodwell, Eszter Ruprecht, Solvita Rusina, Cyrus Samimi, Marco Schmidt, Franziska Schrodt, Hanhuai Shan, Pavel Shirokikh, Jozef Sibik, Urban Silc, Petr Sklenar, Zeljko Skvorc, Ben Sparrow, Marta Gaia Sperandii, Zvjezdana Stancic, Jens-Christian Svenning, Zhiyao Tang, Cindy Q. Tang, Ioannis Tsiripidis, Kim Andre Vanselow, Rodolfo Vasquez Martinez, Kiril Vassilev, Eduardo Velez-Martin, Roberto Venanzoni, Alexander Christian Vibrans, Cyrille Violle, Risto Virtanen, Henrik von Wehrden, Viktoria Wagner, Donald A. Walker, Donald M. Waller, Hua-Feng Wang, Karsten Wesche, Timothy J. S. Whitfeld, Wolfgang Willner, Susan K. Wiser, Thomas Wohlgemuth, Sergey Yamalov, Martin Zobel, Helge Bruelheide
Summary: Assessing global biodiversity status and trends in plant communities is essential for understanding the impact of global change on ecosystems. The sPlotOpen dataset, compiled through resampling vegetation plots and obtaining permissions from data holders, provides valuable information for exploring global plant community diversity, remote sensing applications, and biodiversity monitoring.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2021)
Article
Plant Sciences
Kasper P. Hendriks, Terezie Mandakova, Nikolai M. Hay, Elfy Ly, Alex Hooft van Huysduynen, Rubin Tamrakar, Shawn K. Thomas, Oscar Toro-Nunez, J. Chris Pires, Lachezar A. Nikolov, Marcus A. Koch, Michael D. Windham, Martin A. Lysak, Felix Forest, Klaus Mummenhoff, William J. Baker, Frederic Lens, C. Donovan Bailey
Summary: By combining universal probes and lineage-specific probes in a single hybridization reaction, researchers were able to easily extend sampling of genomic regions and provide expanded data sets for answering research questions with wider applications in the research community.
APPLICATIONS IN PLANT SCIENCES
(2021)
Article
Ecology
Julia S. Joswig, Christian Wirth, Meredith C. Schuman, Jens Kattge, Bjorn Reu, Ian J. Wright, Sebastian D. Sippel, Nadja Rueger, Ronny Richter, Michael E. Schaepman, Peter M. van Bodegom, J. H. C. Cornelissen, Sandra Diaz, Wesley N. Hattingh, Koen Kramer, Frederic Lens, Ulo Niinemets, Peter B. Reich, Markus Reichstein, Christine Roemermann, Franziska Schrodt, Madhur Anand, Michael Bahn, Chaeho Byun, Giandiego Campetella, Bruno E. L. Cerabolini, Joseph M. Craine, Andres Gonzalez-Melo, Alvaro G. Gutierrez, Tianhua He, Pedro Higuchi, Herve Jactel, Nathan J. B. Kraft, Vanessa Minden, Vladimir Onipchenko, Josep Penuelas, Valerio D. Pillar, Enio Sosinski, Nadejda A. Soudzilovskaia, Evan Weiher, Miguel D. Mahecha
Summary: The study reveals that variation in plant size is mainly influenced by latitudinal gradients in water or energy limitation, while variation in leaf economics traits is primarily influenced by climate, soil fertility, and their interactions. These findings help improve predictions and understanding of biodiversity patterns and the impacts of climate change on biogeochemical cycles.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Horticulture
Dewi Pramanik, Marlies Spaans, Twan Kranenburg, Diego Bogarin, Reinout Heijungs, Frederic Lens, Erik Smets, Barbara Gravendeel
Summary: Phalaenopsis is an important ornamental pot plant for the global horticultural market. This study investigated the lignification patterns and orientation of Phalaenopsis inflorescence stems and found significant differences among different species and hybrids. The study also revealed a positive correlation between inflorescence orientation and the degree of lignification.
SCIENTIA HORTICULTURAE
(2022)
Article
Biochemical Research Methods
Rutger A. Vos, Catharina A. M. Van der Veen-van Wijk, M. Eric Schranz, Klaas Vrieling, Peter G. L. Klinkhamer, Frederic Lens
Summary: The study developed a Gene Ontology-mediated approach to investigate key genes within QTLs, applied to flowering time in giant woody Jersey kale, identifying genes regulating flowering time through enrichment of the circadian rhythm pathway. Results show that the ontology-mediated approach aids in gene exploration and discovery.
Article
Plant Sciences
Vicky Beckers, Alessandro Rapini, Erik Smets, Frederic Lens
Summary: This study provides a wood anatomical overview of the Apocynaceae subfamilies Secamonoideae and Asclepiadoideae, and also presents a list of derived woody species. The findings reveal that these subfamilies have undergone multiple transitions in growth form and degree of woodiness, with drought possibly being the main driver of these transitions.
Review
Plant Sciences
Frederic Lens, Sean M. Gleason, Giovanni Bortolami, Craig Brodersen, Sylvain Delzon, Steven Jansen
Summary: Studying hydraulic failure in plants is crucial for understanding reduced productivity and mortality. There is a need to reevaluate the relationship between vessel diameter and vulnerability caused by drought-induced embolism. Nanoscale biophysical processes play a key role in determining the formation and spread of embolism.
Article
Multidisciplinary Sciences
Alexander Zizka, Renske E. Onstein, Roberto Rozzi, Patrick Weigelt, Holger Kreft, Manuel J. Steinbauer, Helge Bruelheide, Frederic Lens
Summary: Insular woodiness (IW), the transition from herbaceousness to woodiness, is a distinctive feature of island floras. Previous studies have proposed several drivers of IW, including competition for sunlight, drought, increased lifespan, and reduced herbivory. This study identified 1,097 insular woody species on 375 islands and inferred at least 175 evolutionary transitions on 31 archipelagos. Structural equation models revealed the correlation between insular woody species richness and favorable climate, drought, and island isolation. The results highlight the importance of archipelagos as natural laboratories for studying convergent evolution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Ajaree Thonglim, Giovanni Bortolami, Sylvain Delzon, Maximilian Larter, Remko Offringa, Joost J. B. Keurentjes, Erik Smets, Salma Balazadeh, Frederic Lens
Summary: The synergy between drought-responsive traits across different organs is crucial in influencing drought resilience at the whole-plant level. This study investigated the response to drought in Arabidopsis thaliana genotypes by analyzing the stems and leaves. The findings reveal that anatomical, ecophysiological, and molecular adaptations across organs are intertwined and determine the drought response strategies.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Ecology
Thore Engel, Helge Bruelheide, Daniela Hoss, Francesco M. Sabatini, Jan Altman, Mohammed A. S. Arfin-Khan, Erwin Bergmeier, Tomas Cerny, Milan Chytry, Matteo Dainese, Juergen Dengler, Jiri Dolezal, Richard Field, Felicia M. Fischer, Dries Huygens, Ute Jandt, Florian Jansen, Anke Jentsch, Dirk N. Karger, Jens Kattge, Jonathan Lenoir, Frederic Lens, Jaqueline Loos, Ulo Niinemets, Gerhard E. Overbeck, Wim A. Ozinga, Josep Penuelas, Gwendolyn Peyre, Oliver Phillips, Peter B. Reich, Christine Roemermann, Brody Sandel, Marco Schmidt, Franziska Schrodt, Eduardo Velez-Martin, Cyrille Violle, Valerio Pillar
Summary: This study evaluates the effects of dominance and niche partitioning on biodiversity-ecosystem functioning (BEF) relationships in grassland systems worldwide. The results indicate that dominance effects, related to the traits of the dominant species, have a significant impact on BEF relationships, while functional diversity (FD) does not affect primary productivity (NDVI).
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Plant Sciences
Dmitry A. German, Kasper P. Hendriks, Marcus A. Koch, Frederic Lens, Martin A. Lysak, C. Donovan Bailey, Klaus Mummenhoff, Ihsan A. Al-Shehbaz
Summary: Based on recent phylogenetic studies, a new classification system for Brassicaceae is proposed, with improvements at the subfamilial and supertribal levels. The family is now divided into two subfamilies, Aethionemoideae and Brassicoideae. The Brassicoideae is further divided into five supertribes, including Arabodae, Camelinodae, Heliophilodae, and Hesperodae. Additionally, several newly recognized tribes are described, and clarifications are provided for 17 other tribes.
Article
Plant Sciences
Nikolai M. Hay, Michael D. Windham, Terezie Mandakova, Martin A. Lysak, Kasper P. Hendriks, Klaus Mummenhoff, Frederic Lens, Kathleen M. Pryer, C. Donovan Bailey
Summary: This study successfully resolved the phylogeny of the Boechera tribe using sequence data from target enrichment approaches. The results provide a foundation for a new taxonomy and further research on Boechera as a model system.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Kasper P. Hendriks, Christiane Kiefer, Ihsan A. Al-Shehbaz, C. Donovan Bailey, Alex Hooft van Huysduynen, Lachezar A. Nikolov, Lars Nauheimer, Alexandre R. Zuntini, Dmitry A. German, Andreas Franzke, Marcus A. Koch, Martin A. Lysak, Oscar Toro-Nunez, Baris Ozudogru, Vanessa R. Invernon, Nora Walden, Olivier Maurin, Nikolai M. Hay, Philip Shushkov, Terezie Mandakova, M. Eric Schranz, Mats Thulin, Michael D. Windham, Ivana Resetnik, Stanislav Spaniel, Elfy Ly, J. Chris Pires, Alex Harkess, Barbara Neuffer, Robert Vogt, Christian Brauchler, Heimo Rainer, Steven B. Janssens, Michaela Schmull, Alan Forrest, Alessia Guggisberg, Sue Zmarzty, Brendan J. Lepschi, Neville Scarlett, Fred W. Stauffer, Ines Schonberger, Peter Heenan, William J. Baker, Felix Forest, Klaus Mummenhoff, Frederic Lens
Summary: This study presents the most complete genus-level family phylogenies of the Brassicaceae family to date, based on nuclear and plastome data. The study reveals cytonuclear discordance and evaluates the impact of hybridization on nuclear phylogeny reconstruction. The results support a recently published new family classification and provide an essential tool for biodiversity and plant biology research.