The Expanding Role of Natural History Collections

Hilton, Eric J.; Watkins‐Colwell, Gregory J.; Huber, Sarah K.

doi:10.1643/t2020018

Cited by 30 publications

(17 citation statements)

References 58 publications

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“…They are primary evidence of the distribution and life history of an organism, and also historically irreplaceable historical data. Therefore, increasing the distribution and availability of specimen information through digital imaging of natural history collections and the publication of specimen image archives on the web will facilitate future biodiversity research [2][3][4] .…”

Section: Introductionmentioning

confidence: 99%

Advancements in data extraction from natural history collections: automatic label extraction from specimen images using OCR and NER

Takano,

Cole,

Konagai

2023

Preprint

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Digital extraction of label data from natural history specimens along with more efficient procedures of data entry will become essential for documentation and global information availability in the near future. Herbarium collections have made great advances in this direction lately. In this study, using optical character recognition (OCR) and named entity recognition (NER) techniques, we have been able to almost automatically extract label data from herbarium specimen images. This system can be developed and run on a PC with standard specifications, and can also be applied to extracting label data from diverse kinds of natural history specimens, such as those in entomological collections. This system can facilitate the digitization and publication of natural history museum specimens around the world.

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Section: Introductionmentioning

confidence: 99%

Advancements in data extraction from natural history collections: automatic label extraction from specimen images using OCR and NER

Takano,

Cole,

Konagai

2023

Preprint

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“…These collections are also critical for education and promotion of inquiry‐based training and active learning (Lacey et al, 2017; Powers et al, 2014). These well‐established and common applications of natural history collections have, in recent decades, been complemented by a variety of new approaches facilitated by technological advances, including next generation sequencing and isotope analysis, as well as by extensive efforts in specimen digitization and online data sharing (Hedrick et al, 2020; Hilton et al, 2021; Meineke et al, 2018; Nelson & Ellis, 2019). As a result of these developments, studies in a variety of realms such as functional ecology, ecological modelling, phenology, morphometrics and education have been greatly stimulated by the increasing availability of big data captured from specimens (Heberling, 2022; Hedrick et al, 2020; Monfils et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Parasitic flowering plant collections embody the extended specimen

et al. 2022

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The widespread digitization of natural history collections, combined with novel tools and approaches is revolutionizing biodiversity science. The ‘extended specimen’ concept advocates a more holistic approach in which a specimen is framed as a diverse stream of interconnected data. Herbarium specimens that by their very nature capture multispecies relationships, such as certain parasites, fungi and lichens, hold great potential to provide a broader and more integrative view of the ecology and evolution of symbiotic interactions. This particularly applies to parasite–host associations, which owing to their interconnectedness are especially vulnerable to global environmental change. Here, we present an overview of how parasitic flowering plants is represented in herbarium collections. We then discuss the variety of data that can be gathered from parasitic plant specimens, and how they can be used to understand global change impacts at multiple scales. Finally, we review best practices for sampling parasitic plants in the field, and subsequently preparing and digitizing these specimens. Plant parasitism has evolved 12 times within angiosperms, and similar to other plant taxa, herbarium collections represent the foundation for analysing key aspects of their ecology and evolution. Yet these collections hold far greater potential. Data and metadata obtained from parasitic plant specimens can inform analyses of co‐distribution patterns, changes in eco‐physiology and species plasticity spanning temporal and spatial scales, chemical ecology of tripartite interactions (e.g. host–parasite–herbivore), and molecular data critical for species conservation. Moreover, owing to the historic nature and sheer size of global herbarium collections, these data provide the spatiotemporal breadth essential for investigating organismal response to global change. Parasitic plant specimens are primed to serve as ideal examples of extended specimen concept and help motivate the next generation of creative and impactful collection‐based science. Continued digitization efforts and improved curatorial practices will contribute to opening these specimens to a broader audience, allowing integrative research spanning multiple domains and offering novel opportunities for education.

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“…Since then, the external and internal anatomy of an ever increasing number of both fresh and preserved fish species have been digitized in these ways and more coelacanth specimens have undergone careful CT and MRI examinations [16][17][18]. As Hilton and others have observed, the adoption of imaging technologies, originally developed for medical use, by ichthyologists to reveal internal anatomy of fishes in some way parallels the clearing and staining revolution of the 1960s and 1970s [15,19]. However, CT and MRI are fundamentally different from single projection-based imaging approaches such as photography of cleared specimens or simple X-ray images, in that these technologies, if used carefully, provide the potential to generate quantitative measurements on tissue components [20].…”

Section: Introductionmentioning

confidence: 99%

Buoyancy and hydrostatic balance in a West Indian Ocean coelacanth Latimeria chalumnae

et al. 2022

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Background Buoyancy and balance are important parameters for slow-moving, low-metabolic, aquatic organisms. The extant coelacanths have among the lowest metabolic rates of any living vertebrate and can afford little energy to keep station. Previous observations on living coelacanths support the hypothesis that the coelacanth is neutrally buoyant and in close-to-perfect hydrostatic balance. However, precise measurements of buoyancy and balance at different depths have never been made. Results Here we show, using non-invasive imaging, that buoyancy of the coelacanth closely matches its depth distribution. We found that the lipid-filled fatty organ is well suited to support neutral buoyancy, and due to a close-to-perfect hydrostatic balance, simple maneuvers of fins can cause a considerable shift in torque around the pitch axis allowing the coelacanth to assume different body orientations with little physical effort. Conclusions Our results demonstrate a close match between tissue composition, depth range and behavior, and our collection-based approach could be used to predict depth range of less well-studied coelacanth life stages as well as of deep sea fishes in general.

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The Expanding Role of Natural History Collections

Abstract: BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses.

Cited by 30 publications

References 58 publications

Advancements in data extraction from natural history collections: automatic label extraction from specimen images using OCR and NER

Advancements in data extraction from natural history collections: automatic label extraction from specimen images using OCR and NER

Parasitic flowering plant collections embody the extended specimen

Buoyancy and hydrostatic balance in a West Indian Ocean coelacanth Latimeria chalumnae

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