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Plants
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Imaging Tools for the Plant Sciences
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Imaging Tools for the Plant Sciences

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Cell Biology".

Deadline for manuscript submissions: closed (15 March 2022) | Viewed by 27814

Special Issue Editor

Dr. Raymond Wightman

E-Mail Website
Guest Editor
Microscopy Core Facility, Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
Interests: plant imaging; cryoSEM; fluorescence/confocal microscopy; cell walls; plant growth; alpine plants

Special Issue Information

Dear Colleagues,

Many branches of the plant sciences require us to see our favourite organism, organ, tissue, cells and subcellular compartments in different ways. This inevitably requires development of novel imaging approaches or refinements of existing techniques, with improved ways of interpreting the data. Porting existing techniques directly from the animal and biomedical fields is not always a solution, given the extra challenges we face for our samples, such as autofluorescence, a desire for gravity and diffractive thick cell walls. We are increasingly utilising a wider range of techniques, sometimes in tandem on the same sample (correlative microscopy), giving rise to ever more complex and large datasets and sometimes requiring heavy computational approaches.

This special issue will focus on new approaches to imaging, covering a wide range of macro-, micro- and nano-related techniques applied specifically to the study of plants. Examples include (but are not limited to) fluorescence microscopy (widefield, confocal, lifetime, super-res, light sheet), light, chemical (IR/Raman/EDX mapping and chemical probes), electron (cryo, fixed, block face imaging), X-ray, mechanobiology (AFM, Brillouin, mechanical probes), sample preparation (including microfluidics) and various methods of dealing with the data (3D visualisation, segmentation, big data, correlative data).

For research articles or short communications, submissions should either be a description of a new technique with a proof-of-concept plant-related application or significant development of an existing technique that demonstrates a greater understanding of plant biology. Expertise in any area of imaging and microscopy can vary widely and a detailed methodology should not just cater to experts but be supplied in a way that can be followed and applied by an advanced beginner or proficient user, using supplementary material for further in-depth descriptions and diagrams. Full raw datasets and software tools need to be made available through a suitable repository and cited within the article.

Dr. Raymond Wightman
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Light microscopy
  • Fluorescence
  • Confocal
  • Super resolution and nanoimaging
  • Electron microscopy
  • Mechanobiology
  • Prototype devices for imaging
  • Sample preparation
  • Image analysis
  • Reagents

Published Papers (8 papers)

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Research

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15 pages, 4011 KiB  
Article
Introducing Three-Dimensional Scanning for Phenotyping of Olive Fruits Based on an Extensive Germplasm Survey
by Ioanna Manolikaki, Chrysi Sergentani, Safiye Tul and Georgios Koubouris
Plants 2022, 11(11), 1501; https://doi.org/10.3390/plants11111501 - 2 Jun 2022
Cited by 3 | Viewed by 1968
Abstract
Morphological characterization of olive (Olea europaea L.) varieties to detect desirable traits has been based on the training of expert panels and implementation of laborious multiyear measurements with limitations in accuracy and throughput of measurements. The present study compares two- and three-dimensional [...] Read more.
Morphological characterization of olive (Olea europaea L.) varieties to detect desirable traits has been based on the training of expert panels and implementation of laborious multiyear measurements with limitations in accuracy and throughput of measurements. The present study compares two- and three-dimensional imaging systems for phenotyping a large dataset of 50 olive varieties maintained in the National Germplasm Depository of Greece, employing this technology for the first time in olive fruit and endocarps. The olive varieties employed for the present study exhibited high phenotypic variation, particularly for the endocarp shadow area, which ranged from 0.17–3.34 cm2 as evaluated via 2D and 0.32–2.59 cm2 as determined by 3D scanning. We found significant positive correlations (p < 0.001) between the two methods for eight quantitative morphological traits using the Pearson correlation coefficient. The highest correlation between the two methods was detected for the endocarp length (r = 1) and width (r = 1) followed by the fruit length (r = 0.9865), mucro length (r = 0.9631), fruit shadow area (r = 0.9573), fruit width (r = 0.9480), nipple length (r = 0.9441), and endocarp area (r = 0.9184). The present study unraveled novel morphological indicators of olive fruits and endocarps such as volume, total area, up- and down-skin area, and center of gravity using 3D scanning. The highest volume and area regarding both endocarp and fruit were observed for ‘Gaidourelia’. This methodology could be integrated into existing olive breeding programs, especially when the speed of scanning increases. Another potential future application could be assessing olive fruit quality on the trees or in the processing facilities. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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15 pages, 3353 KiB  
Article
Development of Microscopic Techniques for the Visualization of Plant–Root-Knot Nematode Interaction
by Helena Vernet, Aïda Magdalena Fullana, Francisco Javier Sorribas and Emilio J. Gualda
Plants 2022, 11(9), 1165; https://doi.org/10.3390/plants11091165 - 26 Apr 2022
Cited by 3 | Viewed by 2410
Abstract
Plant-parasitic nematodes are a significant cause of yield losses and food security issues. Specifically, nematodes of the genus Meloidogyne can cause significant production losses in horticultural crops around the world. Understanding the mechanisms of the ever-changing physiology of plant roots by imaging the [...] Read more.
Plant-parasitic nematodes are a significant cause of yield losses and food security issues. Specifically, nematodes of the genus Meloidogyne can cause significant production losses in horticultural crops around the world. Understanding the mechanisms of the ever-changing physiology of plant roots by imaging the galls induced by nematodes could provide a great insight into their control. However, infected roots are unsuitable for light microscopy investigation due to the opacity of plant tissues. Thus, samples must be cleared to visualize the interior of whole plants in order to make them transparent using clearing agents. This work aims to identify which clearing protocol and microscopy system is the most appropriate to obtain 3D images of tomato cv. Durinta and eggplant cv. Cristal samples infected with Meloidogyne incognita to visualize and study the root–nematode interaction. To that extent, two clearing solutions (BABB and ECi), combined with three different dehydration solvents (ethanol, methanol and 1-propanol), are tested. In addition, the advantages and disadvantages of alternative imaging techniques to confocal microscopy are analyzed by employing an experimental custom-made setup that combines two microscopic techniques, light sheet fluorescence microscopy and optical projection tomography, on a single instrument. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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12 pages, 4089 KiB  
Article
Radiographic Imaging as a Quality Index Proxy for Brachiaria brizantha Seeds
by Leonardo Vieira Campos, Arthur Almeida Rodrigues, Juliana de Fátima Sales, Douglas Almeida Rodrigues, Sebastião Carvalho Vasconcelos Filho, Cássia Lino Rodrigues, Dheynne Alves Vieira, Stella Tomaz de Castro and Aurélio Rubio Neto
Plants 2022, 11(8), 1014; https://doi.org/10.3390/plants11081014 - 8 Apr 2022
Cited by 1 | Viewed by 1534
Abstract
Efficient methodologies for automated seed quality evaluations are important for the seed industry. Advanced seed technology research requires the use of adequate methods to ensure good seed performance under adverse environmental conditions; thus, providing producers with detailed, quick, and accurate information on structural [...] Read more.
Efficient methodologies for automated seed quality evaluations are important for the seed industry. Advanced seed technology research requires the use of adequate methods to ensure good seed performance under adverse environmental conditions; thus, providing producers with detailed, quick, and accurate information on structural seed integrity and ensuring vigorous production. To address this problem, this study aimed to determine Brachiaria brizantha (Marandu cv., Piatã cv. and Xaraés cv.) seed quality through radiographic imaging analyses associated with vigor tests and anatomical characterizations. Brachiaria seed cultivars displaying different physical and physiological attributes were selected and subjected to the 1000-seed weight test, water content determinations, X-ray analyses, germination tests, and anatomical characterizations. The X-ray analyses made it possible to establish a relationship between the X-ray images and other determined variables. Furthermore, the X-ray images can indicate evidence of internal and external damage that could later compromise germination. The Marandu and Piatã cultivars presented the highest germination percentages, germination speed indices, normal seedling development, and cellular structure preservation compared to the Xaraés cultivar. To summarize, X-ray analyses are efficient methods used for the selection of higher physical quality cultivars and can aid in the decision-making processes of companies and seed producers worldwide. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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21 pages, 5980 KiB  
Article
Spatial Distribution of Polyphenolic Compounds in Corn Grains (Zea mays L. var. Pioneer) Studied by Laser Confocal Microscopy and High-Resolution Mass Spectrometry
by Mayya Razgonova, Yulia Zinchenko, Konstantin Pikula, Lyudmila Tekutyeva, Oksana Son, Alexander Zakharenko, Tatiana Kalenik and Kirill Golokhvast
Plants 2022, 11(5), 630; https://doi.org/10.3390/plants11050630 - 25 Feb 2022
Cited by 5 | Viewed by 3359
Abstract
Desirable changes in the biochemical composition of food plants is a key outcome of breeding strategies. The subsequent localization of nutritional phytochemicals in plant tissues gives important information regarding the extent of their synthesis across a tissue. We performed a detailed metabolomic analysis [...] Read more.
Desirable changes in the biochemical composition of food plants is a key outcome of breeding strategies. The subsequent localization of nutritional phytochemicals in plant tissues gives important information regarding the extent of their synthesis across a tissue. We performed a detailed metabolomic analysis of phytochemical substances of grains from Zea mays L. (var. Pioneer) by tandem mass spectrometry and localization by confocal microscopy. We found that anthocyanins are located mainly in the aleurone layer of the grain. High-performance liquid chromatography in combination with ion trap tandem mass spectrometry revealed the presence of 56 compounds, including 30 polyphenols. This method allows for effective and rapid analysis of anthocyanins by plotting their distribution in seeds and grains of different plants. This approach will permit a more efficient screening of phenotypic varieties during food plant breeding. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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9 pages, 3917 KiB  
Communication
Flip-Flap: A Simple Dual-View Imaging Method for 3D Reconstruction of Thick Plant Samples
by Leo Serra, Sovanna Tan, Sarah Robinson and Jane A. Langdale
Plants 2022, 11(4), 506; https://doi.org/10.3390/plants11040506 - 13 Feb 2022
Cited by 1 | Viewed by 4480
Abstract
Plant development is a complex process that relies on molecular and cellular events being co-ordinated in space and time. Microscopy is one of the most powerful tools available to investigate this spatiotemporal complexity. One step towards a better understanding of complexity in plants [...] Read more.
Plant development is a complex process that relies on molecular and cellular events being co-ordinated in space and time. Microscopy is one of the most powerful tools available to investigate this spatiotemporal complexity. One step towards a better understanding of complexity in plants would be the acquisition of 3D images of entire organs. However, 3D imaging of intact plant samples is not always simple and often requires expensive and/or non-trivial approaches. In particular, the inner tissues of thick samples are challenging to image. Here, we present the Flip-Flap method, a simple imaging protocol to produce 3D images of cleared plant samples at the organ scale. This method allows full 3D reconstruction of plant organs suitable for 3D segmentation and further related analysis and can be easily handled by relatively inexperienced microscopists. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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13 pages, 4314 KiB  
Article
Optimizing the Experimental Method for Stomata-Profiling Automation of Soybean Leaves Based on Deep Learning
by Syada Nizer Sultana, Halim Park, Sung Hoon Choi, Hyun Jo, Jong Tae Song, Jeong-Dong Lee and Yang Jae Kang
Plants 2021, 10(12), 2714; https://doi.org/10.3390/plants10122714 - 10 Dec 2021
Cited by 3 | Viewed by 3628
Abstract
Stomatal observation and automatic stomatal detection are useful analyses of stomata for taxonomic, biological, physiological, and eco-physiological studies. We present a new clearing method for improved microscopic imaging of stomata in soybean followed by automated stomatal detection by deep learning. We tested eight [...] Read more.
Stomatal observation and automatic stomatal detection are useful analyses of stomata for taxonomic, biological, physiological, and eco-physiological studies. We present a new clearing method for improved microscopic imaging of stomata in soybean followed by automated stomatal detection by deep learning. We tested eight clearing agent formulations based upon different ethanol and sodium hypochlorite (NaOCl) concentrations in order to improve the transparency in leaves. An optimal formulation—a 1:1 (v/v) mixture of 95% ethanol and NaOCl (6–14%)—produced better quality images of soybean stomata. Additionally, we evaluated fixatives and dehydrating agents and selected absolute ethanol for both fixation and dehydration. This is a good substitute for formaldehyde, which is more toxic to handle. Using imaging data from this clearing method, we developed an automatic stomatal detector using deep learning and improved a deep-learning algorithm that automatically analyzes stomata through an object detection model using YOLO. The YOLO deep-learning model successfully recognized stomata with high mAP (~0.99). A web-based interface is provided to apply the model of stomatal detection for any soybean data that makes use of the new clearing protocol. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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Review

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27 pages, 5793 KiB  
Review
Mass Spectrometry Imaging for Spatial Chemical Profiling of Vegetative Parts of Plants
by Akhila Ajith, Phillip J. Milnes, Giles N. Johnson and Nicholas P. Lockyer
Plants 2022, 11(9), 1234; https://doi.org/10.3390/plants11091234 - 2 May 2022
Cited by 4 | Viewed by 3725
Abstract
The detection of chemical species and understanding their respective localisations in tissues have important implications in plant science. The conventional methods for imaging spatial localisation of chemical species are often restricted by the number of species that can be identified and is mostly [...] Read more.
The detection of chemical species and understanding their respective localisations in tissues have important implications in plant science. The conventional methods for imaging spatial localisation of chemical species are often restricted by the number of species that can be identified and is mostly done in a targeted manner. Mass spectrometry imaging combines the ability of traditional mass spectrometry to detect numerous chemical species in a sample with their spatial localisation information by analysing the specimen in a 2D manner. This article details the popular mass spectrometry imaging methodologies which are widely pursued along with their respective sample preparation and the data analysis methods that are commonly used. We also review the advancements through the years in the usage of the technique for the spatial profiling of endogenous metabolites, detection of xenobiotic agrochemicals and disease detection in plants. As an actively pursued area of research, we also address the hurdles in the analysis of plant tissues, the future scopes and an integrated approach to analyse samples combining different mass spectrometry imaging methods to obtain the most information from a sample of interest. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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15 pages, 1877 KiB  
Review
An Overview of Cryo-Scanning Electron Microscopy Techniques for Plant Imaging
by Raymond Wightman
Plants 2022, 11(9), 1113; https://doi.org/10.3390/plants11091113 - 20 Apr 2022
Cited by 10 | Viewed by 4940
Abstract
Many research questions require the study of plant morphology, in particular cells and tissues, as close to their native context as possible and without physical deformations from some preparatory chemical reagents or sample drying. Cryo-scanning electron microscopy (cryoSEM) involves rapid freezing and maintenance [...] Read more.
Many research questions require the study of plant morphology, in particular cells and tissues, as close to their native context as possible and without physical deformations from some preparatory chemical reagents or sample drying. Cryo-scanning electron microscopy (cryoSEM) involves rapid freezing and maintenance of the sample at an ultra-low temperature for detailed surface imaging by a scanning electron beam. The data are useful for exploring tissue/cell morphogenesis, plus an additional cryofracture/cryoplaning/milling step gives information on air and water spaces as well as subcellular ultrastructure. This review gives an overview from sample preparation through to imaging and a detailed account of how this has been applied across diverse areas of plant research. Future directions and improvements to the technique are discussed. Full article
(This article belongs to the Special Issue Imaging Tools for the Plant Sciences)
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