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Nieradzik L, Sieburg-Rockel J, Helmling S, Keuper J, Weibel T, Olbrich A, Stephani H. Automating Wood Species Detection and Classification in Microscopic Images of Fibrous Materials with Deep Learning. Microsc Microanal 2024:ozae038. [PMID: 38709570 DOI: 10.1093/mam/ozae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 05/08/2024]
Abstract
We have developed a methodology for the systematic generation of a large image dataset of macerated wood references, which we used to generate image data for nine hardwood genera. This is the basis for a substantial approach to automate, for the first time, the identification of hardwood species in microscopic images of fibrous materials by deep learning. Our methodology includes a flexible pipeline for easy annotation of vessel elements. We compare the performance of different neural network architectures and hyperparameters. Our proposed method performs similarly well to human experts. In the future, this will improve controls on global wood fiber product flows to protect forests.
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Affiliation(s)
- Lars Nieradzik
- Image Processing Department, Fraunhofer ITWM, Fraunhofer Platz 1, Kaiserslautern 67663, Rhineland-Palatinate, Germany
| | | | - Stephanie Helmling
- Thünen Institute of Wood Research, Leuschnerstraße 91, Hamburg 21031, Germany
| | - Janis Keuper
- Institute for Machine Learning and Analysis (IMLA), Offenburg University, Badstr. 24, Offenburg 77652, Baden-Wuerttemberg, Germany
| | - Thomas Weibel
- Image Processing Department, Fraunhofer ITWM, Fraunhofer Platz 1, Kaiserslautern 67663, Rhineland-Palatinate, Germany
| | - Andrea Olbrich
- Thünen Institute of Wood Research, Leuschnerstraße 91, Hamburg 21031, Germany
| | - Henrike Stephani
- Image Processing Department, Fraunhofer ITWM, Fraunhofer Platz 1, Kaiserslautern 67663, Rhineland-Palatinate, Germany
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Abbas N, Zafar M, Ahmad M, Althobaiti AT, Ramadan MF, Makhkamov T, Gafforov Y, Khaydarov K, Kabir M, Sultana S, Majeed S, Batool T. Tendril Anatomy: A Tool for Correct Identification among Cucurbitaceous Taxa. Plants (Basel) 2022; 11:3273. [PMID: 36501313 PMCID: PMC9735582 DOI: 10.3390/plants11233273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
This research examined the histological micro-structure of tendril vasculature in cucurbitaceous taxa. In this research, the tendril anatomy of 17 taxa of Cucurbitaceae categorized into seven genera, including Cucumis (five species), Cucurbita and Luffa (three species each), Citrullus and Momordica (two species each) while Lagenaria and Praecitrullus (one species each), collected from different areas of the Thal desert were examined via microscopic imaging to explore its taxonomic significance. Tendril transverse sections were cut with a Shandon Microtome to prepare slides. The distinctive characteristics of taxonomic value (qualitative and quantitative) include tendril and vascular bundle shape, variation in the number of vascular bundles, tendril diameter length, layers of sclerenchyma, and shape of collenchyma and epidermal cells. Tendril shapes observed are irregular, slightly oval-shaped, slightly C shaped, angular (4-angled, 6-angled, or polygonal), and star shaped. Quantitative measurements were taken to analyze the data statistically using SPSS software. Cucurbita pepo had a maximum tendril diameter length of 656.1 µm and a minimum in Momordica balsamina of 123.05 µm. The highest number of vascular bundles (12) were noticed in Luffa acutangula var.amara. Angular type was prominent in collenchyma, and irregular shape was dominant in sclerenchyma cells. A maximum of seven to nine sclerenchyma layers were present in Lagenaria siceraria and a minimum of two or three layers in Cucumis melo subsp. agrestis, Cucumis melo var. flexuosus, and Cucumis melo var.cantalupensis. Epidermis cells also show great variations with a rectangular shape being dominant. Statistical UPGMA dendrogram clustering of tendril vasculature traits shows that histological sections studied with microscopic techniques can be used to identify species and will play a vital role in future taxonomic and phylogenic linkages.
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Affiliation(s)
- Naveed Abbas
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Zafar
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Mushtaq Ahmad
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Pakistan Academy of Sciences Islamabad, Islamabad 46000, Pakistan
| | - Ashwaq T. Althobaiti
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mohamed Fawzy Ramadan
- Department of Clinical Nutrition, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21961, Saudi Arabia
| | - Trobjon Makhkamov
- Department of Forestry and Landscape Design, Tashkent State Agrarian University, 2 A., Universitet Str., Kibray District, Tashkent 100700, Uzbekistan
| | - Yusufjon Gafforov
- Mycology Laboratory, Institute of Botany, Academy of Sciences of Republic of Uzbekistan, 32 Durmon Yuli, Tashkent 100125, Uzbekistan
- AKFA University, 264 Milliy Bog Street, Tashkent 111221, Uzbekistan
| | - Khislat Khaydarov
- Faculty of Biology, Samarkand State University, Universitetsty Bulvvar Street-15, Samarkand 140104, Uzbekistan
| | - Muhammad Kabir
- Department of Biological Sciences, Ex University of Sargodha Sub Campus Bhakkr, Thal University Bhakkar, Bhakkar 30000, Pakistan
| | - Shazia Sultana
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Salman Majeed
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Department of Botany, University of Mianwali, Mianwali 42200, Pakistan
| | - Tajalla Batool
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Jorge NDC, Freitas MDSC, Caffaro RM, Vale FHA, Lemos-Filho JP, Isaias RMDS. Vascular traits of stem galls: Cell increment versus morphogenetic constraints in wood anatomy. Plant Biol (Stuttg) 2022; 24:450-457. [PMID: 35098632 DOI: 10.1111/plb.13392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Eremanthus erythropappus hosts globoid stem galls induced by Neolasioptera sp. (Diptera: Cecidomyiidae) close to the stem apex, which do not compromise the shoot apical meristem (SAM). We hypothesize that maintenance of the SAM, as well as the increasing number of leaves per branch and of galled stem lengths and diameters, are a consequence of alterations in vascular cells and, consequently, in the priority for water flow from non-galled stems to the stem galls. Our study focuses on the globoid stem galls to evaluate if gall induction and development promote changes in structure and function of secondary xylem cells. Anatomical, cytological, histometric and physiological methods were used to analyse non-galled stem branches (NGS), mature globoid stem galls and stem portions below and above the galls. These analyses revealed that vessel elements are larger in stem galls and in stem portions above the galls. Under Neolasioptera sp. induction activity, the vascular cambium of E. erythropappus produces less numerous but larger vessel elements and overproduces parenchyma cells. Contrary to the vascular constriction hypothesis proposed for bacterial galls, the vascular traits of the Neolasioptera sp. stem galls on E. erythropappus result in priority for water flow to galls and the non-galled portions above the galls, allowing the maintenance of galled stem growth and development.
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Affiliation(s)
- N D C Jorge
- Laboratório de Anatomia Vegetal, Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M D S C Freitas
- Laboratório de Anatomia Vegetal, Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - R M Caffaro
- Laboratório de Anatomia Vegetal, Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - F H A Vale
- Laboratório de Anatomia Vegetal, Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - J P Lemos-Filho
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - R M D S Isaias
- Laboratório de Anatomia Vegetal, Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Maceda A, Soto-Hernández M, Peña-Valdivia CB, Trejo C, Terrazas T. Differences in the Structural Chemical Composition of the Primary Xylem of Cactaceae: A Topochemical Perspective. Front Plant Sci 2019; 10:1497. [PMID: 31850014 PMCID: PMC6892835 DOI: 10.3389/fpls.2019.01497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/29/2019] [Indexed: 05/25/2023]
Abstract
The xylem of Cactaceae is a complex system with different types of cells whose main function is to conduct and store water, mostly during the development of primary xylem, which has vessel elements and wide-band tracheids. The anatomy of primary xylem of Cactaceae has been widely studied, but little is known about its chemical composition. The aim of this study was to determine the structural chemical composition of the primary xylem of Cactaceae and to compare it with the anatomy in the group. Seeds from eight cacti species were used, representing the Pereskioideae, Opuntioideae, and Cactoideae subfamilies. Seeds were germinated and grown for 8 months. Subsequently, only the stem of the seedling was selected, dried, milled, and processed following the TAPPI T-222 om-02 norm; lignin was quantified using the Klason method and cellulose with the Kurshner-Höffer method. Using Fourier transform infrared spectroscopy, the percentage of syringyl and guaiacyl in lignin was calculated. Seedlings of each species were fixed, sectioned, and stained for their anatomical description and fluorescence microscopy analysis for the topochemistry of the primary xylem. The results showed that there were significant differences between species (p < 0.05), except in the hemicelluloses. Through a principal component analysis, it was found that the amount of extractive-free stem and hot water-soluble extractives were the variables that separated the species, followed by cellulose and hemicelluloses since the seedlings developed mainly parenchyma cells and the conductive tissue showed vessel elements and wide-band tracheids, both with annular and helical thickenings in secondary walls. The type of lignin with the highest percentage was guaiacyl-type, which is accumulated mainly in the vessels, providing rigidity. Whereas in the wide-band tracheids from metaxylem, syringyl lignin accumulated in the secondary walls S2 and S3, which permits an efficient flow of water and gives the plant the ability to endure difficult conditions during seedling development. Only one species can be considered to have paedomorphosis since the conductive elements had a similar chemistry in primary and secondary xylem.
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Affiliation(s)
- Agustín Maceda
- Programa de Botánica, Colegio de Postgraduados en Ciencias Agrícolas, Texcoco, Mexico
| | - Marcos Soto-Hernández
- Programa de Botánica, Colegio de Postgraduados en Ciencias Agrícolas, Texcoco, Mexico
| | | | - Carlos Trejo
- Programa de Botánica, Colegio de Postgraduados en Ciencias Agrícolas, Texcoco, Mexico
| | - Teresa Terrazas
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Trueba S, Delzon S, Isnard S, Lens F. Similar hydraulic efficiency and safety across vesselless angiosperms and vessel-bearing species with scalariform perforation plates. J Exp Bot 2019; 70:3227-3240. [PMID: 30921455 DOI: 10.1093/jxb/erz133] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The evolution of xylem vessels from tracheids is put forward as a key innovation that boosted hydraulic conductivity and photosynthetic capacities in angiosperms. Yet, the role of xylem anatomy and interconduit pits in hydraulic performance across vesselless and vessel-bearing angiosperms is incompletely known, and there is a lack of functional comparisons of ultrastructural pits between species with different conduit types. We assessed xylem hydraulic conductivity and vulnerability to drought-induced embolism in 12 rain forest species from New Caledonia, including five vesselless species, and seven vessel-bearing species with scalariform perforation plates. We measured xylem conduit traits, along with ultrastructural features of the interconduit pits, to assess the relationships between conduit traits and hydraulic efficiency and safety. In spite of major differences in conduit diameter, conduit density, and the presence/absence of perforation plates, the species studied showed similar hydraulic conductivity and vulnerability to drought-induced embolism, indicating functional similarity between both types of conduits. Interconduit pit membrane thickness (Tm) was the only measured anatomical feature that showed a relationship to significant vulnerability to embolism. Our results suggest that the incidence of drought in rain forest ecosystems can have similar effects on species bearing water-conducting cells with different morphologies.
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Affiliation(s)
- Santiago Trueba
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 621 Charles E. Young Dr. South, Los Angeles, CA, USA
- AMAP, IRD, CIRAD, CNRS, INRA, Université de Montpellier, Nouméa, New Caledonia
| | | | - Sandrine Isnard
- AMAP, IRD, CIRAD, CNRS, INRA, Université de Montpellier, Nouméa, New Caledonia
| | - Frederic Lens
- Naturalis Biodiversity Center, Leiden University, Leiden, The Netherlands
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Sandhya S, Ventaka RK, Vinod K. Pharmacognostical Standardization of Tephrosia purpurea Pers Root. Anc Sci Life 2010; 30:1-6. [PMID: 22557415 PMCID: PMC3336270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Wild Indigo or Purple Tephrosia or fish poison occurs throughout the Indian subcontinent. It is widely used in the treatment of inflammation, diabetes, rheumatism, asthma, diarrhoea and many other ailments. But so far the pharmacognostic standardization has not been reported for its proper identification. Hence the present study is a pharmacognosy work carried out for the root part. This may help in the identification of the plant species. A thin transverse section, powder microscopy, measurement of the dimensions of cell structures, fluorescence analysis and physico chemical parameters were conducted for the root. From the TS, the secondary xylem fibres and vessels were found to be the tissues of diagnostic importance. The xylem vessels were of two types: narrow and long; broad and short. The important characters in the powdered microscopy were vessel elements, fibres and xylem parenchyma cells. The different fluorescent light shades were obtained under short and long UV light for both powder as well as the extracts of the root. The proximate analysis values were also obtained in a satisfactory way. Combining all these data a suitable root profile for plant can be constructed which may help in the identification of quality of the plant part.
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Affiliation(s)
- S. Sandhya
- Department of Pharmacognosy, Nalanda College of Pharmacy, Hyderabad Main Road, Cherlapally Nalgonda, Andhra Pradesh, India, Corresponding author
| | - Ramana K. Ventaka
- Department of Pharmacognosy, ASN Pharmacy College, Burripalem, Tenali, Andhra Pradesh, India
| | - K.R Vinod
- Department of Pharmacognosy, Nalanda College of Pharmacy, Hyderabad Main Road, Cherlapally Nalgonda, Andhra Pradesh, India
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