Journal articles on the topic 'Digitised specimens'
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1
Phillips, Carina. "Digitised Diseases." Bulletin of the Royal College of Surgeons of England 95, no. 5 (May 1, 2013): 164–65. http://dx.doi.org/10.1308/003588413x13643054409342.
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Over the past year RCS museum staff have been working on a project called Digitised Diseases. This Joint Information Systems Committee (JISC)-funded project is a collaboration with the university of Bradford and Museum of London Archaeology (MOLA). Digitised Diseases aims to bridge the gap between modern clinical medicine, historic medical collections and archaeological assemblages in the study of osteological pathology. The project will produce an archive of 3D case studies of exemplar specimens that can be studied virtually.
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Takano, Atsuko, Yasuhiko Horiuchi, Yu Fujimoto, Kouta Aoki, Hiromune Mitsuhashi, and Akira Takahashi. "Simple but long-lasting: A specimen imaging method applicable for small- and medium-sized herbaria." PhytoKeys 118 (February 18, 2019): 1–14. http://dx.doi.org/10.3897/phytokeys.118.29434.
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Major international herbaria, natural history museums and universities have recently begun to digitise their collections to facilitate studies and improve access to collections. In Japan, more than 10 million herbarium specimens are housed in various universities/museums; however, only 1% of these have been digitised. In this paper, we describe a new method for imaging herbarium specimens that is applicable to local/small herbaria. It is safe, fast, simple and inexpensive, but also satisfies usage guidelines for minimum image quality and can produce digital files suitable for long-term storage and future post production. During an eight-month trial at the Museum of Nature and Human Activities, Hyogo, with three part-time workers using a custom-made copy stand and a mirrorless interchangeable lens camera with a large LED light bank system, we were able to image 73,180 herbarium specimens (571 per day on average), obtaining two RAW and two JPEG files for each specimen.
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Astono, Indriani P., James S. Welsh, Christopher W. Rowe, and Phillip Jobling. "Objective quantification of nerves in immunohistochemistry specimens of thyroid cancer utilising deep learning." PLOS Computational Biology 18, no. 2 (February 28, 2022): e1009912. http://dx.doi.org/10.1371/journal.pcbi.1009912.
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Accurate quantification of nerves in cancer specimens is important to understand cancer behaviour. Typically, nerves are manually detected and counted in digitised images of thin tissue sections from excised tumours using immunohistochemistry. However the images are of a large size with nerves having substantial variation in morphology that renders accurate and objective quantification difficult using existing manual and automated counting techniques. Manual counting is precise, but time-consuming, susceptible to inconsistency and has a high rate of false negatives. Existing automated techniques using digitised tissue sections and colour filters are sensitive, however, have a high rate of false positives. In this paper we develop a new automated nerve detection approach, based on a deep learning model with an augmented classification structure. This approach involves pre-processing to extract the image patches for the deep learning model, followed by pixel-level nerve detection utilising the proposed deep learning model. Outcomes assessed were a) sensitivity of the model in detecting manually identified nerves (expert annotations), and b) the precision of additional model-detected nerves. The proposed deep learning model based approach results in a sensitivity of 89% and a precision of 75%. The code and pre-trained model are publicly available at https://github.com/IA92/Automated_Nerves_Quantification.
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Favret, Colin, Étienne Normandin, and Louise Cloutier. "The Ouellet-Robert Entomological Collection: new electronic resources and perspectives." Canadian Entomologist 151, no. 04 (June 20, 2019): 423–31. http://dx.doi.org/10.4039/tce.2019.34.
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AbstractThe Ouellet-Robert Entomological Collection (Université de Montréal, Montréal, Québec, Canada) is one of the largest and most important university collections in Canada. Although officially dedicated in 1984, much of the material in the collection dates to the 1930s and 1940s work of the Clerics of Saint Viator, Joseph Ouellet and Adrien Robert. In order to establish curatorial priorities, a collection profile was conducted grading eight criteria on a scale of 1–4, the most important being the conservation status of the specimens. A taxonomic inventory of the collection was also conducted, including the number of pinned specimens and alcohol vials, as well as a brief geographic description: whether or not at least one specimen of each species was collected in Québec or in North America. Finally, the specimen metadata for Odonata, Ephemeroptera, and Trichoptera were digitised. The inventory and specimen data can be downloaded at Canadensys.net. The collection houses approximately 1.5 million specimens, of which one-third are pinned, representing 20 000 species. Half of those species are recorded from Québec. The inventory and profile will be updated and the specimen database grown as portions of the collection are re-curated by personnel and volunteers, including the student-run organisation, “Club QMOR”.
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Aleksandrowicz, Oleg, Zbigniew Sobisz, Mariola Truchan, and Konrad Wiśniewski. "Przyrodnicze kolekcje naukowe Akademii Pomorskiej w Słupsku." Kosmos 70, no. 2 (September 12, 2021): 167–72. http://dx.doi.org/10.36921/kos.2021_2790.
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Pomeranian University in Słupsk hosts two significant natural history collections, i.e. the Herbarium Slupensis (SLTC) botanical collection and the zoological collection, which contains mainly the arthropods. In the Herbarium both the historical and contemporary material is stored, including fungi, lichens, bryophytes and vascular plants that were collected mainly in the Polish Pomerania. The zoological collection contains predominantly the specimens of beetles and spiders, originating from Belarus and Poland (from Pomerania, but also from Masuria and Lower Silesia). In the two collections there are representatives of very valuable species. Both the Herbarium and the zoological collection are presently being digitised, supplemented with new specimens and developed. They present a significant contribution to knowledge on diversity of fauna and flora in the region and in Poland.
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Rokrok, B., K. Edalati, E. Yahaghi, N. Mohammadzadeh, N. Rastkhah, and A. Movafeghi. "Three-dimensional mapping of non-complex specimens by image processing and optical density evaluation of digitised radiographs." Insight - Non-Destructive Testing and Condition Monitoring 51, no. 6 (June 2009): 315–20. http://dx.doi.org/10.1784/insi.2009.51.6.315.
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Khidas, Kamal, and Stéphanie Tessier. "Building Next-Generation Collections: Natural History Specimens, Just One Click Away!" Biodiversity Information Science and Standards 2 (July 4, 2018): e26145. http://dx.doi.org/10.3897/biss.2.26145.
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Digitisation has made significant advances in many natural history collections since the 1980s. The Vertebrate Zoology Collections team of the Canadian Museum of Nature (CMNVZC; ca. 1,250,000 catalogued specimens) has the ambition to go fully digital with our physical objects and associated data. Organising CMNVZC data electronically (primary digitisation) through computerisation for collection management purposes was initiated in 1972 and systematically implemented since the 1980s. This databasing process involved several stages, each with its own objectives and challenges. It resulted in ca. 100% of the CMNVZC being now digitised and core specimen data being retrievable from the Web (e.g., GBIF, and VertNet). Digitising requires regular updates to reflect the changing needs of the collections-based research community, and to capitalise on new opportunities that arise with the advances in technology. In this digital age, improving collections accessibility and usability through realistic and sustainable digitisation, while avoiding the downside of information overload, remains the most pressing challenge. Increasing CMNVZC accessibility necessitates further consolidation and information standardisation of various types (e.g. collecting data) to be retrieved from several sources (e.g., field notes, original data sheets, and maps). Optimising collections usability can be achieved by adding value to existing records (secondary digitisation) by means of additional information as mentioned above, georeferencing, as well as 2D and 3D imaging. Virtual sharing of 3D specimen images allows for remote examination of specimens usually inaccessible through loans, such as type and rare specimens, and the possibility for morphometric analyses. Digital imaging of the vertebrate collection, however, represents a major challenge given the complexity and variation of shapes and sizes among specimens. Limitations of current 3D surface imaging technology, none of which have been specifically designed for natural history specimens, hamper CMNVZC imaging workflows. Digital tools are key to the success of increasing usability of natural history collections and play an important role in preserving information. Digitisation activities should endeavour to improve online access of physical objects and their full array of data with optimized usability.
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Kanavati, Fahdi, Naoki Hirose, Takahiro Ishii, Ayaka Fukuda, Shin Ichihara, and Masayuki Tsuneki. "A Deep Learning Model for Cervical Cancer Screening on Liquid-Based Cytology Specimens in Whole Slide Images." Cancers 14, no. 5 (February 24, 2022): 1159. http://dx.doi.org/10.3390/cancers14051159.
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Liquid-based cytology (LBC) for cervical cancer screening is now more common than the conventional smears, which when digitised from glass slides into whole-slide images (WSIs), opens up the possibility of artificial intelligence (AI)-based automated image analysis. Since conventional screening processes by cytoscreeners and cytopathologists using microscopes is limited in terms of human resources, it is important to develop new computational techniques that can automatically and rapidly diagnose a large amount of specimens without delay, which would be of great benefit for clinical laboratories and hospitals. The goal of this study was to investigate the use of a deep learning model for the classification of WSIs of LBC specimens into neoplastic and non-neoplastic. To do so, we used a dataset of 1605 cervical WSIs. We evaluated the model on three test sets with a combined total of 1468 WSIs, achieving ROC AUCs for WSI diagnosis in the range of 0.89–0.96, demonstrating the promising potential use of such models for aiding screening processes.
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Zeko, Antonija, Vedran Šegota, Tihana Vilović, Nikola Koletić, and Antun Alegro. "Aquatic plants of Croatia: Data derived from the ZA herbarium collection." Natura Croatica 29, no. 2 (March 31, 2021): 205–16. http://dx.doi.org/10.20302/nc.2020.29.27.
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As many as 963 herbarium sheets featuring 76 aquatic plant taxa from the ZA collection were digitised and published online through the Virtual Herbarium. Aquatic plants have been collected over a period of 176 years, with three peaks (second decade of the 20th century, in the 1940s and 1950s, and in the current decade). Most of the specimens were collected in Croatia and a smaller number in neighbouring and geographically close countries. The importance of the collection is expressed through the specimens of many rare and threatened species, because it represents the only evidence of their presence in Croatia (the regionally extinct Caldessia parnassifolia, as well as Luronium natans, Callitriche platycarpa, C. truncata, C. hermaphroditica, Potamogeton alpinus, P. compressus, P. polygonifolius, Nuphar × spenneriana and Sparganium minimum). The collection in ZA is a valuable source of data about the historical and recent distribution of aquatic plants that constitute a foundation for the estimation of distribution changes, threat assessment and conservation policies.
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Dwivedi, A. K. "Morphometric variations between seasonal migrants of anadromous shad Tenualosa ilisha (Hamilton, 1822) from Hooghly Estuary, India." Marine and Freshwater Research 70, no. 10 (2019): 1427. http://dx.doi.org/10.1071/mf19004.
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The morphometric variations between two seasonal migrants (winter and monsoon) of anadromous shad Tenualosa ilisha from Hooghly Estuary were evaluated and compared using geometric morphometrics (GM). Altogether, 128 fish samples of T. ilisha, comprising 64 samples each from winter and the monsoon season, were collected for two successive years (2017 and 2018) and 14 landmarks were digitised uniformly on each individual. Relative warps (RW), principal component analysis (PCA), canonical variate analysis (CVA) and discriminant function analysis (DFA) were used to determine shape variations between seasonal runs. The deformation grid of RW showed that monsoon specimens have a deeper body profile, whereas winter specimens have a slender body profile. The PCA showed low variance (40.45% for first two principal components) and high overlap among all the groups. The CVA-extracted Mahalanobis and Procrustes distances (3.473 and 0.032 respectively) between the two groups (winter and monsoon) were highly significant (P<0.0001). The DFA also separated two groups with high cross-validated classification rates (85.94 and 95.31% of winter and monsoon specimens respectively were correctly classified). Hence, the results of RW, CVA and DFA clearly indicate the existence of two morphologically distinct units of T. ilisha in Hooghly Estuary.
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Groom, Quentin, Ann Bogaerts, Sofie De Smedt, and Sarah Phillips. "Crowdsourcing, is it a good option for your collection digitization?" Biodiversity Information Science and Standards 2 (May 21, 2018): e25410. http://dx.doi.org/10.3897/biss.2.25410.
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Globally there are a number of citizen science portals to support digitisation of biodiversity collections. Digitisation not only involves imaging of the specimen itself, but also includes the digital transcription of label and ledger data, georeferencing and linking to other digital resources. Making use of the skills and enthusiasm of volunteers is potentially a good way to reduce the great backlog of specimens to be digitised. These citizen science portals engage the public and are liberating data that would otherwise remain on paper. There is also considerable scope for expansion into other countries and languages. Therefore, should we continue to expand? Volunteers give their time for free, but the creation and maintenance of the platform is not without costs. Given a finite budget, what can you get for your money? How does the quality compare with other methods? Is crowdsourcing of label transcription faster, better and cheaper than other forms of transcription system? We will summarize the use of volunteer transcription from our own experience and the reports of other projects. We will make our evaluation based on the costs, speed and quality of the systems and reach conclusions on why you should or should not use this method.
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Damthongdee, Anissara, Kithisak Aongyong, and Tanawat Chaowasku. "Orophea sichaikhanii (Annonaceae), a new species from southern Thailand, with a key to the species of Orophea in Thailand and notes on some species." Plant Ecology and Evolution 154, no. 2 (June 24, 2021): 307–15. http://dx.doi.org/10.5091/plecevo.2021.1780.
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Background and aims – Recent botanical expeditions in Ranong Province, southern Thailand yielded unidentifiable collections of Orophea subgenus Sphaerocarpon (Annonaceae). To elucidate the taxonomic status of these collections, detailed morphological examinations and comparisons with morphologically similar species are made.Material and methods – This study followed standard practices of herbarium taxonomy. Specimens of Orophea spp. in BKF, CMUB, L, and QBG herbaria were studied. Digitised type specimens deposited in BM, E, G, K, and L herbaria were accessed. A stereo microscope was used for morphological observations and measurements. Key results – A new species Orophea sichaikhanii is described and illustrated. The Peninsular Malaysian O. hastata and O. kingiana are the species most similar to the new species. Orophea sichaikhanii is different from O. hastata in several traits: indumentum on ovaries and young twigs; length of pedicels, inner petals, and inner petal claw; and inner petal colour and tip. The new species differs from O. kingiana by having dissimilar colour and tip of inner petals; lower number of stamens and carpels per flower; and glabrous ovaries. Additionally, a key to the species of Orophea in Thailand and notes on certain species are provided.
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Dyson, P. W., A. E. C. Spargo, P. A. Tulloch, and A. W. S. Johnson. "Calculated dynamical scattering in a fibrous protein structure." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 2 (August 1992): 1176–77. http://dx.doi.org/10.1017/s0424820100130511.
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Despite many technical, experimental and in principle difficulties, particularly in regard to radiation damage and stability of the structure at the atomic level, considerable progress has been made in the application of the combined electron microscopy/electron diffraction (EM/ED) technique to the solution of protein structures. The technique now represents a possible alternative to x-ray diffraction for those cases where the protein is difficult or impossible to grow as macrocrystals, provided that the molecule can be incorporated in microcrystals or two-dimensional ordered arrays. Encouraged by this we have recently recorded images and diffraction intensities from microcrystals of an alpha-helical coiledcoil protein extracted from the ootheca of the praying mantis. The ED data shows reflections out to beyond 2Å, though not uniformly in all directions. Fourier transforms of the corresponding digitised images show resolution out to nearly 3Å and this data is being used to phase the ED data. All data was recorded from frozen-hydrated specimens at 400kV in a super-fluid helium specimen stage of a JEM 4000EX electron microscope using spot-scan and low-dose imaging techniques. Further work aimed at collecting a 3-d data set to a resolution of 3Å using tilted crystals is continuing.
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Fleury, Kane, Emma Burns, Barbara Anderson, Robert Hoare, and Ralf Ohlemuller. "Books and Drawers full of Moths." Biodiversity Information Science and Standards 2 (June 15, 2018): e26710. http://dx.doi.org/10.3897/biss.2.26710.
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The Otago Museum houses one of New Zealand’s largest Lepidoptera collections that consists of more than 31,000 macro moth specimens collected across New Zealand over the last 30 years. Alongside this collection, supplementary information is found in detailed field notebooks that cover, for most sites, the total abundance of the different species present in these samples. We have been able to use the notebooks to work out the sampling intensity and sites to map both the collections and the abundances to some degree. It is impractical to collect everything. As a result, the common species are left out of collections and the rare and unusual sightings fill the collections. When planning to resample collecting sites to investigate changes in ecosystems, just relying on collections for species presence and absence would skew the results. It should also be noted that field notebooks are not a panacea for biological information as the information in them ages, so too can the reliability and accuracy of the notes within. Here we discuss how the field notebook data compares with the information accompanying the specimens housed within the museum collection. This is a recently digitised collection and allows an insight into the collectors sampling, vouchering and data practices and how these can affect modern interpretation and variation in repeat sampling.
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Ngo, Vuong M., Thuy-Van T. Duong, Tat-Bao-Thien Nguyen, Phuong T. Nguyen, and Owen Conlan. "An Efficient Classification Algorithm for Traditional Textile Patterns from Different Cultures Based on Structures." Journal on Computing and Cultural Heritage 14, no. 4 (December 31, 2021): 1–22. http://dx.doi.org/10.1145/3465381.
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Textiles have an important role in many cultures and have been digitised. They are three-dimensional objects and have complex structures, especially archaeological fabric specimens and artifact textiles created manually by traditional craftsmen. In this article, we propose a novel algorithm for textile classification based on their structures. First, a hypergraph is used to represent the textile structure. Second, multisets of k -neighbourhoods are extracted from the hypergraph and converted to one feature vector for representation of each textile. Then, the k -neighbourhood vectors are classified using seven most popular supervised learning methods. Finally, we evaluate experimentally the different variants of our approach on a data set of 1,600 textile samples with the 4-fold cross-validation technique. The experimental results indicate that comparing the variants, the best classification accuracies are 0.999 with LR, 0.994 with LDA, 0.996 with KNN, 0.994 with CART, 0.998 with NB, 0.974 with SVM, and 0.999 with NNM.
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Gyurika, István Gábor, and Tibor Szalay. "Examination of the Average Chipping Rate on the Edges of Milled Granite Surfaces." Measurement Science Review 15, no. 1 (February 1, 2015): 1–8. http://dx.doi.org/10.1515/msr-2015-0001.
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Abstract The research described in this article was carried out for the purpose of developing a quantitative marker for defining the average edge chipping rate of milled granite surfaces and for testing and proving whether this quantitative marker can effectively be applied. Another aim of the research was to test the applicability of the developed measurement method and the precision of the body representing the volume loss caused by chipping. The surface edges of the milled specimens were digitised using a laser scanner and chipped volumes were defined on the basis of a body generated with the help of a point cloud, and then the errors of the volumes produced by the evaluation-purpose software were examined using a digital microscope. The investigations proved that the proposed measurement method is accurate and that the replacement body defined through measurements appropriately approximates the volume of chippings in the case of milled granite surfaces.
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Soltis, Pamela. "Data Attribution from Download to Publication." Biodiversity Information Science and Standards 2 (May 18, 2018): e26060. http://dx.doi.org/10.3897/biss.2.26060.
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Digitized natural history data are enabling a broad range of innovative studies of biodiversity. Large-scale data aggregators such as Global Biodiversity Information facility (GBIF) and Integrated Digitized Biocollections (iDigBio) provide easy, global access to millions of specimen records contributed by thousands of collections. A developing community of eager users of specimen data – whether locality, image, trait, etc. – is perhaps unaware of the effort and resources required to curate specimens, digitize information, capture images, mobilize records, serve the data, and maintain the infrastructure (human and cyber) to support all of these activities. Tracking of specimen information throughout the research process is needed to provide appropriate attribution to the institutions and staff that have supplied and served the records. Such tracking may also allow for annotation and comment on particular records or collections by the global community. Detailed data tracking is also required for open, reproducible science. Despite growing recognition of the value and need for thorough data tracking, both technical and sociological challenges continue to impede progress. In this talk, I will present a brief vision of how application of a DOI to each iteration of a data set in a typical research project could provide attribution to the provider, opportunity for comment and annotation of records, and the foundation for reproducible science based on natural history specimen records. Sociological change – such as journal requirements for data deposition of all iterations of a data set – can be accomplished using community meetings and workshops, along with editorial efforts, as were applied to DNA sequence data two decades ago.
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Groom, Quentin, Sofie De Smedt, Nuno Veríssimo Pereira, Ann Bogaerts, and Henry Engledow. "DoeDat, the Crowdsourcing Platform of Meise Botanic Garden." Biodiversity Information Science and Standards 2 (June 15, 2018): e26803. http://dx.doi.org/10.3897/biss.2.26803.
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Herbarium specimens hold a wealth of data about plants; where they come from, where they were collected and by whom. Once digitized, these data can be searched, mapped and compared. However, the information on specimens is often handwritten and even the best software systems cannot read it. This is where we get real value from citizen involvement. Digitizing these data is only possible with the aid of human intelligence. DoeDat is a multilingual open-source platform for transcription, based upon the DigiVol program of the Australian Museum and Atlas of Living Australia. DoeDat is a product of our digitization project Digital Access to Cultural Heritage Collections (DOE!), funded by the Flemish Government. DoeDat is about creating data and also, ‘Doe Dat’ means ‘do that’ in Dutch. DoeDat will help us digitize our collections, and will also give the public the chance to take an active part in the process. We aim to build a community of enthusiastic online volunteers who will help us liberate botanical data from specimen labels and documents. We launched the platform on Science Day and within two months, more than one hundred volunteers had transcribed more than 4,000 specimens. Join in at www.DoeDat.be
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Niu, Haicheng, Lei Wang, Jianhua Li, and Jiakun Ji. "Experimental Study on Mechanical Properties of Steel-Polyvinyl Alcohol Fibre-Reinforced Recycled Concrete." Applied Sciences 11, no. 22 (November 9, 2021): 10550. http://dx.doi.org/10.3390/app112210550.
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Research on the utilization of recycled concrete in civil engineering applications is gaining popularity world-wide due to the increased efforts to promote preservation of the environment and sustainable development. Recycled concrete is, however, presently still limited to nonstructural applications. This is due to the poor mechanical properties of recycled concrete, which make it difficult to cope with complex mechanical environments. Therefore, an experimental work is presented to investigate the mechanical behaviour of recycled concrete, focusing on the cube, flexural, and uniaxial compressive mechanical properties of steel-polyvinyl alcohol fibre-doped specimens. The test results showed that the compressive strength and the flexural strength of the recycled concrete increased by 6.0% and 55.2%, respectively, when steel fibre was single-incorporated. The cubic compressive strength of the recycled concrete decreased by 14.1% when polyvinyl alcohol fibre was single-incorporated, but there was a 47.9% increase in the flexural strength of recycled concrete. Based on these tests, the elastic modulus, the Poisson’s ratio, and the uniaxial compression toughness were digitised to derive mathematical expressions that provided a theoretical understanding of the mechanical properties of steel-polyvinyl alcohol fibre-reinforced recycled concrete. Moreover, combining the characteristics of the uniaxial compressive stress–strain curve of fibre-reinforced recycled concrete, an equation for the uniaxial compressive stress–strain curve of recycled concrete associated with the fibre characteristic value was established, which agreed well with the test results.
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Pearson, Katelin D., Gil Nelson, Myla F. J. Aronson, Pierre Bonnet, Laura Brenskelle, Charles C. Davis, Ellen G. Denny, et al. "Machine Learning Using Digitized Herbarium Specimens to Advance Phenological Research." BioScience 70, no. 7 (May 13, 2020): 610–20. http://dx.doi.org/10.1093/biosci/biaa044.
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Abstract Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens—preserved plant material curated in natural history collections—but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.
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Hedrick, Brandon P., J. Mason Heberling, Emily K. Meineke, Kathryn G. Turner, Christopher J. Grassa, Daniel S. Park, Jonathan Kennedy, et al. "Digitization and the Future of Natural History Collections." BioScience 70, no. 3 (February 7, 2020): 243–51. http://dx.doi.org/10.1093/biosci/biz163.
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Abstract Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.
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Rinaldo, Constance, Linda Ford, and Joseph deVeer. "Museum, Library and Archives Partnership: Leveraging Digitized Data from Historical Sources." Biodiversity Information Science and Standards 2 (June 13, 2018): e25920. http://dx.doi.org/10.3897/biss.2.25920.
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The Museum of Comparative Zoology at Harvard University (MCZ), founded in 1859, has approximately 20 million extant and fossil invertebrate and vertebrate specimens. These historical collections continue to be a focus of research and teaching for the MCZ, Harvard and outside researchers. The Ernst Mayr Library/Archives (EMLA) of the MCZ is a founding member of the Biodiversity Heritage Library (BHL), an international consortium with a mission to make biodiversity literature openly available for use. Meeting the needs of the MCZ is a priority for EML Museum/library and achives collaboration One collaborative Museum/Library project was the digitization of approximately 81,000 MCZ specimen ledger pages/cards associated with various collections. These historical items, once digitized and deposited in the Harvard Digital Repository Service (DRS), were linked to the relevant specimen records in MCZbase, the museum-wide database. Over 1.2 million specimen records are now linked with digitized sources which benefit all users by adding to the provenance of the specimen data and allowing direct referral to the primary collection source. The EMLA holds an extensive collection of field notes, letters and manuscripts of researchers associated with the MCZ. Collector records are a gold mine of unpublished observations, notes, sketches, specimen lists and narratives. They are primary source data at its most personal, and may be the only documentation of a scientist’s thought processes and observations, particularly for unpublished materials. William Brewster was a prominent late 19th, early 20th century naturalist associated with the MCZ Ornithology Department until his death in 1919. Brewster provided authoritative and novel additions to the knowledge of birds, and his detailed, long-term observations are the key to his published contributions. Brewster’s unpublished scientific legacy is being digitized and deposited in the Harvard DRS and BHL by the EMLA. Transcribed notebook pages will be attached to images in BHL thus improving data discovery. Brewster deposited over 45,000 specimens in the MCZ Ornithology Collection. Combining specimens and unpublished notes is an opportunity to link hidden data and enhance research capabilities. Next steps for this collaborative project include finely grained cross-linking of specific pages, correspondence and photographs to and from the MCZ’s specimen database and BHL. We show how MCZ has leveraged data in digital repositories to enhance and directly relate to MCZbase, with citations to notes, transcriptions and published literature. These collaborations enhance discoverability of hidden data while promoting cross-discipline research to interrelated historical sources.
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Marais, Petro, Maggie Menyatso, Robin Lyle, and Simangele Chiloane. "The National Collection of Arachnida, South Africa: Making the Collection more Accessible." Biodiversity Information Science and Standards 2 (April 23, 2018): e26111. http://dx.doi.org/10.3897/biss.2.26111.
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The National Collection of Arachnida (NCA) was established in 1976 at the Agricultural Research Council – Plant Health & Protection (ARC-PHP) in Pretoria, South Africa. This collection forms part of South Africa’s National Assets, which the ARC manages and maintains on behalf of the Department of Agriculture, Forestry and Fisheries (DAFF) and the Department of Science and Technology (DST). The specimen holdings of the NCA contain a wealth of associated taxonomic, biological and geographical information. Currently the collection is managed by a dedicated collection manager responsible for the day-to-day running of the collection assisted by one research assistant. It is utilized for various research activities and knowledge generation in the fields of agriculture and natural resource management. The specimens are preserved using 75% alcohol and held in a double vial method in order to maximize protection of the specimens against evaporation and breakage. Hand-written catalogue books are still used to record and allocate a unique NCA – AcAT number for each specimen. This number links to all primary data recorded for the specimen. Furthermore, the data associated with the specimens are digitized according to Darwin-Core guidelines in an Structured Query Language (SQL) relational database. The database was developed by the ARC-Information Technology services. The entire NCA presently houses approximately 77,780 catalogue entries representing more than 233,300 specimens from six Arachnida orders. The NCA is made up mainly of reference specimens, but also has a type specimen collection of newly described species. The type collection currently contains 1,018 type specimens representing 321 species in 136 genera and 42 families. Of these, 207 specimens are holotypes. The type collection is housed separately from the reference collection and was recently moved to a newly acquired fireproof cabinet. Further planned activities include taking photos of all type specimens using a Zeiss V.16 Zoom microscope so that all type holdings are fully digitized. This will allow the implementation of an electronic loans system. Updating of the types list in the collection will facilitate availability for the wider community. The NCA provides support for key services such as the identification of arachnid predators that have an impact on agricultural production and bio-security as well as a specimen identification and advisory service to government, farmers, industry, researchers, students and the public. These services are essential for research projects on biosystematics and relevant related fields such as conservation, decision-making, agriculture and natural resource management.
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Zhang, J., K. H. Olsen, and K. A. Schoessow. "Quantitative measurement of surface roughness of TEM specimens." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 1 (August 1992): 406–7. http://dx.doi.org/10.1017/s0424820100122435.
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The thickness and the local thickness variation of thin film specimens are critical parameters for many types of AEM analysis. The local thickness variation of the thin film specimen can be estimated from the surface roughness of the specimen. TEM specimens of most materials, especially multi-phase materials, have rough surfaces as observed by secondary electron imaging. However, there is little quantitative assessment of the surface roughness because of the difficulty of specimen thickness measurement. In this study, surface roughness of TEM specimens prepared using chemical etching, electropolishing, and ion beam thinning was measured using a direct phase detecting optical interferometer. This interferometer gives a quantitative three dimensional map of the surface topography with a depth resolution of ∼0.7 nm by converting digitized light intensity at each point of a 1024×1024 array into the optical path difference using the three-measurement algorithm. The horizontal resolution of the interferometer (∼340 nm) is limited by optical diffraction and is poor by the TEM standard. The quantitative information obtained by the interferometer is complimentary to the secondary electron imaging in STEM or PEG SEM for characterizing TEM specimen surfaces.
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Cobb, Neil S., Lawrence F. Gall, Jennifer M. Zaspel, Nicolas J. Dowdy, Lindsie M. McCabe, and Akito Y. Kawahara. "Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research." PeerJ 7 (November 25, 2019): e8086. http://dx.doi.org/10.7717/peerj.8086.
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Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.
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Walker, Lindsay, Erica Krimmel, Jann Vendetti, and Austin Hendy. "Leveraging Collective Experience to Digitize the Fossil Insects of Los Angeles." Biodiversity Information Science and Standards 2 (June 13, 2018): e26385. http://dx.doi.org/10.3897/biss.2.26385.
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The Invertebrate Paleontology Collection at the Natural History Museum of Los Angeles County (NHMLA) has received support from the United States National Science Foundation (NSF DBI 1702342) to digitize the museum’s unique and historic collection of 28,000+ fossil insects. The primary goal of this project, “Fossil Insects of L.A.”, is to increase access to these collections for both research and education. Key collections to be become discoverable through iDigBio and iDigPaleo include the Georg Statz Collection (Oligocene, Rott Formation, Germany) and three faunas from Southern California: Barstow (Miocene), Rancho La Brea (Pleistocene), and McKittrick (Pleistocene). Fossil Insects of L.A. constitutes the final contribution to the Fossil Insect Collaborative Thematic Collections Network (TCN), a consortium of institutions that have been digitizing the largest fossil insect collections in the United States. As a project beginning at the tail-end of the TCN’s active funding, Fossil Insects of L.A. is actively leveraging existing TCN knowledge and resources to streamline workflows and efficiently achieve project goals. In addition to basing imaging and preservation protocols on those designed by TCN partners, Fossil Insects of L.A. is using a layered approach to provide high-quality taxonomic information without sacrificing the pace of specimen digitization. Previously unidentified specimens are initially identified only to Order, allowing them to quickly continue through the digitization process; specimens can then be re-examined by experienced project participants and external experts, who are able to reference the specimen images generated during digitization. A critical and novel aspect of this component of the project’s workflow is the concurrent digitization of the literature associated with the Statz Collection. These data will be used as a test case for the "Enhancing Paleontological and Neontological Data Discovery API" (ePANDDA) project (NSF ICER 1821039), which seeks to associate related datasets found in iDigBio, iDigPaleo, and the Paleobiology Database. Fossil Insects of L.A. will digitize and make 10,960 specimens publically available online, of which over 6,200 will include images. An additional 15,684 specimen records from the Rancho La Brea Tar Pits will also be included in the data mobilization. In doing so, Fossil Insects of L.A. intends to dramatically enhance the research potential of these formerly hidden collections, as well as synthesize and demonstrate digitization best practices generated through the TCN.
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Palmer, Lisa. "Dancing Tables: Digitizing 11,000 Film-based Slides in Ten Days." Biodiversity Information Science and Standards 2 (July 5, 2018): e28093. http://dx.doi.org/10.3897/biss.2.28093.
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How long does it take to digitize 11,000 film-based slides? Converting film to a raster graphic may take a relatively short period of time, but what is needed to prepare for the process, and then once images are digitized, what work is required to push data out for public access? And how much does the entire conversion process cost? A case study of a rapid-capture digitization project at the Smithsonian Institution will be reviewed. In early 2016, the Smithsonian Institution National Museum of Natural History (NMNH) Division of Fishes acquired 10,559 film-based slides from world-renown ichthyologist John (Jack) Randall. The first-generation slides contain images of color patterns of hundreds of fish species with locality information for each specimen written on the cardboard slide mount. When Jack began his photography in the 1960’s, his images were at the forefront of color photography for fishes. He also collected specimens in remote island archipelagos in the Pacific and Indian Oceans, thus many localities were, and continue to be, rare. The species represented on the slide are important to the scientific community, and the collection event data written on the slide mount makes the image and its metadata an invaluable package of information. Upon receipt of Jack’s significant donation, the Division of Fishes received multiple requests from ichthyologists for digital access to the slides. The Division of Fishes immediately implemented a plan to digitally capture data. With many rapid-capture projects at the Smithsonian, the objects and specimens are digitized, and then at some later point, any associated data is transcribed. The Division approached this project differently in that the Randall collection was relatively small, and Smithsonian staff, primarily interns, were available to transcribe data before image conversion. Post-production work included hiring two contractors to import images and associated metadata into NMNH’s collections management system. This presentation will review our processes before, during, and after data conversion. Workflows include transcribing handwritten data, staging and digitizing film, and importing data into the EMu client as well as using redundancies to ensure quality of data.
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Steven, Alasdair C., Robert Stall, Peter M. Steinert, and Benes L. Trus. "Computational Straightening of Images of Curved Macromolecular Helices by Cubic Spline Interpolation Facilitates Structural Analysis By Fourier Methods." Proceedings, annual meeting, Electron Microscopy Society of America 43 (August 1985): 738–39. http://dx.doi.org/10.1017/s0424820100120345.
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Powerful methods based on Fourier analysis have been devised for deducing the helical symmetries of macromolecular filaments and reconstructing their 3-dimensional density maps from electron images of negatively stained specimens. However, their applicability is restricted by the requirement that the particles be precisely straight. Only a limited number of specimens are sufficiently rigid to meet this constraint. Filamentous particles that exhibit varying degrees of flexibility constitute a much wider class of specimens, but their curvature impairs the coherence of their diffraction patterns. A solution to this problem is afforded by computational a posteriori straightening, effected by interpolating the digitized images on to a curvilinear coordinate system defined by the curve described by the particle axis. Here, we describe an algorithm for this purpose based on natural cubic spline interpolation, and illustrate its operation with model data and as applied to a flexuous biological specimen.
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Valente, Roberta De Melo, and José Raimundo Rocha Guimarães. "Dryophthorinae (Coleoptera: Curculionidae) in the Collection of the Museu Paraense Emílio Goeldi: inventory and type specimens." Boletim do Museu Paraense Emílio Goeldi - Ciências Naturais 16, no. 1 (May 4, 2021): 33–50. http://dx.doi.org/10.46357/bcnaturais.v16i1.306.
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This paper reports the results of the curation of specimens of Dryophthorinae (Coleoptera: Curculionidae) housed in the Entomological Collection of the Museu Paraense Emílio Goeldi (MPEG), Belém, state of Pará, Brazil. The Collection holds a total of 1,071 specimens, with 90% of them previously unidentified. We reviewed all specimens and identified them to species level, resulting in 16 genera and 32 species of Dryophthorinae. These include the type specimens of three species: Cyrtomasius marluciae Vanin, 1998; Foveolus maculatus O’Brien, 2003; and Paramasius cristulatus Vanin, 1998. The genus Rhodobaenus Le Conte, 1876 was recorded for the first time to Brazilian Amazon. All specimen data were digitized and are now publicly available. Currently, 50% of the richness of the Dryophthorinae recorded from Brazilian Amazon is present in the Collection. The occurrence and the species richness of the Dryophthorinae examined are shown on a map. All labels contents and remarks to type material are presented. High resolution photographs of the primary types are also provided. The material examined represents a temporal and spatial record of Amazonian Dryophthorinae.
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Bramble, Katherine, Michael E. Burns, and Philip J. Currie. "Enhancing bonebed mapping with GIS technology using the Danek Bonebed (Upper Cretaceous Horseshoe Canyon Formation, Edmonton, Alberta, Canada) as a case study." Canadian Journal of Earth Sciences 51, no. 11 (November 2014): 987–91. http://dx.doi.org/10.1139/cjes-2014-0056.
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The Danek Bonebed is a monodominant Edmontosaurus bonebed preserving predominantly disarticulated material from the Upper Campanian Horseshoe Canyon Formation within the city limits of Edmonton, Alberta, Canada. To date, at least six dinosaur taxa have been identified at the site: Albertosaurus sarcophagus, Chasmosaurinae indet., Dromaeosauridae indet., Edmontosaurus regalis, Ornithomimidae indet., and Troodontidae indet. This bonebed has been used as a case study for creating a digital, searchable bonebed map using a geographic information system (GIS) platform. The original quarry maps produced on site are refined when digitized with new anatomical information gathered during preparation of collected specimens. Each specimen is labeled with the known specimen identification, quarry coordinates, and catalogue number. Creating a digital map of the bonebed allows easier interpretation of data and the ability to share maps to compare specific elements within the bonebed.
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Munshi, Dipanjan. "Scope of using Biological Metadata for Digitized Natural History Specimens in India." Library Herald 56, no. 1 (2018): 164. http://dx.doi.org/10.5958/0976-2469.2018.00015.5.
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KIM, Yoon-Su, and Sang-Hun OH. "Morphometric analysis of the Daphne kiusiana complex (Thymelaeaceae) using digitized herbarium specimens." Korean Journal of Plant Taxonomy 52, no. 3 (September 30, 2022): 144–55. http://dx.doi.org/10.11110/kjpt.2022.52.3.144.
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Daphne kiusiana is an evergreen shrub with dense head-like umbels of white flowers distributed in southern Korea, Japan, China, and Taiwan. Plants in China and Taiwan are recognized as var. atrocaulis by having a dark purple stem, elliptic leaves, and persistent bracts. Recently, plants on Jejudo Island were segregated as a separate species, D. jejudoensis, given their elliptic leaves with an acuminate apex, a long hypanthium and sepals, and a glabrous hypanthium. Morphological variations of three closely related taxa, the D. kiusiana complex, were investigated across the distributional range to clarify the taxonomic delimitation of members of the complex. Twelve characters of the leaf and flower were measured from digitized herbarium specimens using the image analysis program ImageJ and were included in a morphometric analysis, the results of which indicate that the level of variation in the characters is very high. The results of a principal component analysis weakly separated D. jejudoensis from D. kiusiana according to their floral characteristics, such as a longer, glabrous hypanthium, and larger sepals. However, some individuals of D. kiusiana, particularly those from Bigeumdo Island, were included in D. jejudoensis. Recognition of D. kiusiana var. atrocaulis based on the leaf shape was not supported in the analysis, and D. jejudoensis may be recognized as a variety of D. kiusiana. Our morphometric analysis shows that digitized images of herbarium specimens could be useful and an additional method by which to investigate more diverse specimens.
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Barber, Anne, C. Skema, Michelle Mancini, and Timothy Block. "Assessing Herbarium Specimen Image Quality with FineFocus." Biodiversity Information Science and Standards 2 (June 15, 2018): e26181. http://dx.doi.org/10.3897/biss.2.26181.
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The Mid-Atlantic Megalopolis Thematic Collections Network, a digitization project funded by the U.S. National Science Foundation, seeks to digitize ca. 800,000 herbarium specimens through imaging, transcription, and georeferencing. The use of autofocus alone in herbarium specimen imaging with a digital single-lens reflex camera does not yield consistently sharp images, even with relatively two-dimensional specimens and a proper selection of focus point. The FineFocus technique provides a way of assessing contrast, as a proxy for focus quality, through analysis of a standard text target using two freeware programs run through a batch script. By calculating a numeric value, this protocol provides an objective way to obtain a high level of focus quality for a specific imaging rig with given conditions before proceeding with imaging. Adjusting focus with FineFocus yields noticeably sharper images, allowing users to see fine details otherwise obscured by poor focus, such as secondary venation. This technique can be easily implemented in herbarium digitization workflows to improve the quality of specimen images.
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Thalluri, Jyothi, and Joy Penman. "Virtual Pathology Learning Resource: A Promising Strategy in Teaching Pathology to Allied Health Science Students." Issues in Informing Science and Information Technology 15 (2018): 015–33. http://dx.doi.org/10.28945/4026.
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Aim/Purpose: The objective of this study was to concept test a new instructional aid called Virtual Pathology Learning Resource (VPLR), which was used as a vehicle to communicate information and enhance teaching and learning of basic sciences (Anatomy, Physiology, and Pathology) to allied health science students at a South Australian university. Background: Pathology was traditionally taught using potted specimens to review disease manifestations independently. However, this approach was found inadequate and ineffective. VPLR is a new teaching platform comprising of digitised human normal and human pathology specimens (histology, histopathology), patient case studies, short answer and critical thinking questions, and self-assessment quizzes. Using authentic learning theory as an educational pedagogy, this learning resource was developed to enhance the teaching and learning of Pathology. Methodology: Cross-sectional study design was used. A survey, given at the end of the course, gathered qualitative and quantitative data concerning the perceptions and experiences of the students about VPLR and its components. The online tool SurveyMonkey was utilised so that students could respond anonymously to a web link that displayed the questionnaire. The perceived impact on students was assessed using an 18-item questionnaire seeking agreement or disagreement with statements about VPLR, multiple choice and open-ended questions querying the best things about VPLR, benefits to be derived, and areas for improvement. Descriptive and frequency analyses were performed. Contribution: The VPLR approach involved rich learning situations, contextualised content, and facilitated greater understanding of disease concepts and problems. Findings: In a sample of 103 Medical Radiation students, 42% of students (N=43) responded to the post-intervention survey. The majority of students reported highly positive effects for each component of the VPLR. The overall results indicated that this tool was a promising strategy in teaching Pathology as it assisted students’ gaining knowledge of the science, facilitated connections between sciences, and allowed students to make better links with professional practice and skills. Recommendations for Practitioners: As students found VPLR to be beneficial, it is recommended that the same approach is applied for the teaching of Pathology to other health science students, such as Nursing. Other universities might consider adopting the innovation for their courses. Recommendation for Researchers: Applying VPLR to teaching other allied health science students will be undertaken next. The innovation will be appropriate for other health science students with particular emphasis on case-based or problem-based learning and combined with clinical experiences. Impact on Society: In reshaping the way of teaching a science course, students are benefited with greater depth of understanding of content and increase motivation to study. These are important to keep students engaged and ready for practice. VPLR may impact on education and technology trends so that exploration and possibilities of initiatives are ongoing to help students become successful learners. Other impacts are the new forms of learning discovered, the renewed focus on group work and collaboration, and maximising the use of technology in innovation. Future Research: Future directions of this research would be to conduct a follow-up of this cohort of students to determine whether the impacts of the innovation were durable, meaning the change in perceptions and behaviour is sustained over time.
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Adrain, T. S., A. F. Budd, and J. M. Adrain. "Digitizing collections: experiences from the University of Iowa Paleontology Repository Digitization Project." Geological Curator 9, no. 5 (May 2011): 291–99. http://dx.doi.org/10.55468/gc84.
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The University of Iowa Paleontology Repository is the fifth largest university fossil collection in the U.S., holding over 1 million specimens from all geologic ages, worldwide. A digitization project, funded by the National Science Foundation (DBI- 0544235; $284,724), has made previously inaccessible collections available to researchers, including the Amoco Conodont Collection, the Paleozoic Coral Collection, the Neogene Coral Collection, the Trilobite Collection, the Amoco South Florida Collection, and the Micromammal Collection. Specimen data are captured using a Specify Biodiversity Collections Database and shared with the Paleontology Portal (www.paleoportal.org). Inventories of new, as yet uncatalogued, collections are available on the Paleontology Repository website (http://geoscience.clas.uiowa. edu/paleo/index.html), including the Crossman Crinoid Collection and the Pope Collection. Ancillary materials have been digitized and made available, including 1,316 Amoco conodont locality folders and 7,000 field photographs (funded in part by a University of Iowa Innovations in Instructional Computing award). Along with specimen samples, cores, and maps, these photographs form the basis for the Tropical America Virtual Field School, an on-line teaching resource drawing on collections made during 30 years of fieldwork in South Florida and the Caribbean. A database of specimen images is being developed, particularly useful for fragile specimens that cannot be loaned. Information for researchers is complemented with information for the public, using different methods of data access and presentation. The Fossils in My Back Yard website provides a user-friendly option for looking at the same specimen data without overwhelming the non-scientist.
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Ariño, Arturo. "Putting your Finger upon the Simplest Data." Biodiversity Information Science and Standards 2 (June 15, 2018): e26300. http://dx.doi.org/10.3897/biss.2.26300.
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Over the past decades, digitization endeavors across many institutions holding natural history collections (NHCs) have multiplied with three broad aims: first, to facilitate collection management by moving existing analog catalogues into digital form; second, to efficiently document and inventory specimens in collections, including imaging them as taxonomical surrogates; and third, to enable discovery of, and access to, the resulting collection data. NHCs contain a unique wealth of potential knowledge in the form of primary biodiversity data records (PBR): at its most basic level, the “what, where and when” of occurrences of the specimens in the collections. But as T.S. Eliot famously said, “knowledge is invariably a matter of degree”. For such data to be transformed into digitally accessible knowledge (DAK) that is conducive to an understanding about how the natural world works, release of digitized data (the “this we know”) is necessary. At least two billion specimens are estimated to exist in NHCs already, but only a small fraction can be considered properly DAK: most have either not been digitized yet, or not released through a discovery facility. Digitizing is relatively costly as it often entails manually processing each specimen unit (e.g. a herbarium sheet, a pinned insect, or a vial full of invertebrates). How long could it take us to transform all NHCs into DAK? Can we keep up with the natural growth in collections? The Global Biodiversity Information Facility (GBIF) has become the de facto main index of PBR, both originated in NHCs or as field observations. Digitized NHC that are standards-compliant and can be connected to, or harvested by, GBIF, effectively become DAK. I have examined GBIF growth data looking for a pattern of DAK generation. I found that the rate of NHC-based PBR accrual is remarkably constant: the total DAK shows a strongly linear growth, as opposed to the exponential growth exhibited by cumulative observation data. Projecting the trend to the estimated holdings shoots the completion many decades ahead. In addition, digitized data appear to be taxonomically biased. Digitization efforts must therefore step up qualitatively in order to enable processing the backlog, let alone newly-acquired accessions, within one generation. Among several possible solutions, emerging, industrial-scale mass-digitization techniques may help harnessing this otherwise daunting task—but there’s also a risk that DAK becomes even more uneven across taxon groups because of the narrow application specificity of such techniques, thus potentially biasing our knowledge of nature.
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Martin, Elissa, Susan Butts, Leanne Elder, Lawrence Gall, Christina Lutz, Christopher Norris, and Jessica Utrup. "Cretaceous World TCN: Digitizing the Western Interior Seaway at the Yale Peabody Museum." Biodiversity Information Science and Standards 2 (June 15, 2018): e26115. http://dx.doi.org/10.3897/biss.2.26115.
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Yale Peabody Museum (YPM) is a partner in the Western Interior Seaway Thematic Collections Network (TCN), along with the University of Kansas (lead) and seven other institutions (National Science Foundation Award # DBI-1601884). This project seeks to digitize the fossil organisms of the Western Interior Seaway, a shallow sea that covered inland North America from 100 to 65 million years ago. The resultant data will be a resource for K-16 education and will enable scientists to answer fundamental questions about the changing environment of a marine ecosystem during a key time in the history of life. The data generated will be ideal for use with an assortment of modern quantitative tools like paleoecological niche modeling (PaleoENM) and will help improve paleoclimate and paleoceanographic models. Less than two years into this three-year project, the YPM has digitized nearly 70,000 Cretaceous fossils from the seaway. Specimens are georeferenced and most have multiple images. To achieve project goals, we have overcome obstacles of digitizing multi-specimen concretions and foraminifera microslides by developing high-throughput digitization workflows that incorporate the open-source Inselect program and scripts to streamline image naming, image formatting, and uploading to our Axiell EMu collection management system. To facilitate use of the data in K-16 environments, an easy to use collections interface has been built using the iDigPaleo platform (idigpaleo.org). Cretaceous World (cretaceousworld.org) pulls data from iDigBio for all Cretaceous World TCN providers. Students can browse specimens using filters, rather than entering specific search terms. Navigation is simplified using common names harvested from the Encyclopedia of Life. Specimens are displayed as images accompanied by collection and locality data and plotted on a map. Registration provides access to tools supporting annotation, measurement, specimen record commenting, and social media sharing. Images can be curated as galleries and used for education. This includes sharing of galleries between students and teachers and PDF or PowerPoint exports. Fifty-eight 3D models of vertebrates and invertebrates have been placed on morphosource.org and will be made available via a 3D embedded viewer on cretaceousworld.org for use in K-16 education. Undergraduate students from Dartmouth, Oberlin, Southern Connecticut State University, and Yale, have participated in the project and served as mentors for high school interns. These interns, recruited from the Peabody EVOLUTIONS afterschool program, gained first-hand experience in collections-based research, digitization, and imaging techniques, while learning about the science of paleontology and the process of curating museum collections, and researching and reconstructing food webs in this fascinating ancient ecosystem.
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Christensen, JC, HL Driscoll, and AF Tencer. "1994 William J. Stickel Gold Award. Contact characteristics of the ankle joint. Part 2. The effects of talar dome cartilage defects." Journal of the American Podiatric Medical Association 84, no. 11 (November 1, 1994): 537–47. http://dx.doi.org/10.7547/87507315-84-11-537.
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Variations in ankle joint contact characteristics caused by articular defects of the talar dome were investigated in 14 fresh-frozen cadaver specimens using pressure-sensitive film. Intact ankle and foot specimens were mounted in a materials tester on a loading frame which allowed positioning in neutral, and 20 degrees of dorsiflexion and plantarflexion. Joint contact prints were recorded while an 800 N load was axially applied through the leg. Specimens were randomly placed into two lesion groups: either anterolateral or posteromedial. During testing, each specimen had four concentrically placed lesions on the talar dome, graduated in size. Following removal, the film transducers were digitized along with pressure calibration prints. The images were analyzed quantitatively to determine contact areas, mean contact pressures, ratio of to contact plafond areas, and high pressure centroid position as a function of lesion size and location. The results demonstrated significant changes in contact characteristics for larger lesions (> or = 7.5 x 15 mm) (P < 0.05). These findings suggest that determining the size of a lesion may assist in predicting the long-term outcome of ankles with cartilage defects.
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Blagoderov, Vladimir, Malcolm Penn, Mike Sadka, Adrian Hine, Stephen Brooks, Darrell Siebert, Chris Sleep, et al. "iCollections methodology: workflow, results and lessons learned." Biodiversity Data Journal 5 (September 25, 2017). http://dx.doi.org/10.3897/bdj.5.e19893.
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The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.
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Blagoderov, Vladimir, Malcolm Penn, Mike Sadka, Adrian Hine, Stephen Brooks, Darrell Siebert, Chris Sleep, et al. "iCollections methodology: workflow, results and lessons learned." Biodiversity Data Journal 5 (September 28, 2017). http://dx.doi.org/10.3897/bdj.5.e21277.
Full textAbstract:
The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.
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King, Sally, Bhaskar Adhikari, Pratikshya Chalise, Sajita Dhakal, and Til Kumari Thapa. "Developing a High-speed Imaging Set-up for Small Herbaria: a case study from a national herbarium of Nepal (KATH)." Biodiversity Information Science and Standards 3 (June 13, 2019). http://dx.doi.org/10.3897/biss.3.37095.
Full textAbstract:
The Himalayan region is recognised as one of the ‘hottest’ global Biodiversity hotspots, with a third of all species within its range occurring in Nepal. The documentation of the Flora of Nepal is therefore of great importance both nationally and internationally (National Herbarium & Plant Laboratories (KATH) 2019). The Royal Botanic Garden Edinburgh (RBGE) leads the Flora of Nepal project in collaboration with the Department of Plant Resources (DPR, part of the Ministry of Forests and Environment), Nepal Academy of Science and Technology (NAST), Central Department of Botany, Tribhuvan University (CDB-TU) and the Society of Himalayan Botany, Tokyo (SHB) (Royal Botanic Gardens Edinburgh 2014). The National Herbarium and Plant Laboratories (KATH), Kathmandu, Nepal – part of DPR – contains approximately 165,000 herbarium specimens, representing 50% of vascular plant species and 25% of lower plant species known to exist in Nepal. The digitisation of herbarium specimens held at KATH will facilitate access to specimen data, expedite the flora writing process, and make it possible to update species distributions to inform conservation priorities. The existing rate of digitisation was slow with 70-75 specimens being fully digitised a day by three digitisers. Specimen collection labels were fully databased in a Microsoft Access database and imaged at 600 PPI using a single Herbscan. At the current rate of digitisation it will take 7 – 8 years to completely digitise the KATH herbarium. As part of the Darwin Initiative project: Science-based interventions reversing negative impacts of invasive plants in Nepal (http://www.darwininitiative.org.uk/project/23031), a new camera imaging set-up and workflow was devised at RBGE, with installation and staff training provided on-site at KATH herbarium (Fig. 1). This has almost tripled the rate of digitisation to 180-200 specimens per day. The decision making processes that took place regarding hardware and software are discussed including: speed versus quality, some on-site considerations, the installation process and the proposals put forward to further improve the rate of digitisation.
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Kommineni, Vamsi Krishna, Susanne Tautenhahn, Pramod Baddam, Jitendra Gaikwad, Barbara Wieczorek, Abdelaziz Triki, and Jens Kattge. "Comprehensive leaf size traits dataset for seven plant species from digitised herbarium specimen images covering more than two centuries." Biodiversity Data Journal 9 (July 13, 2021). http://dx.doi.org/10.3897/bdj.9.e69806.
Full textAbstract:
Morphological leaf traits are frequently used to quantify, understand and predict plant and vegetation functional diversity and ecology, including environmental and climate change responses. Although morphological leaf traits are easy to measure, their coverage for characterising variation within species and across temporal scales is limited. At the same time, there are about 3100 herbaria worldwide, containing approximately 390 million plant specimens dating from the 16th to 21st century, which can potentially be used to extract morphological leaf traits. Globally, plant specimens are rapidly being digitised and images are made openly available via various biodiversity data platforms, such as iDigBio and GBIF. Based on a pilot study to identify the availability and appropriateness of herbarium specimen images for comprehensive trait data extraction, we developed a spatio-temporal dataset on intraspecific trait variability containing 128,036 morphological leaf trait measurements for seven selected species. After scrutinising the metadata of digitised herbarium specimen images available from iDigBio and GBIF (21.9 million and 31.6 million images for Tracheophyta; accessed date December 2020), we identified approximately 10 million images potentially appropriate for our study. From the 10 million images, we selected seven species (Salix bebbiana Sarg., Alnus incana (L.) Moench, Viola canina L., Salix glauca L., Chenopodium album L., Impatiens capensis Meerb. and Solanum dulcamara L.) , which have a simple leaf shape, are well represented in space and time and have high availability of specimens per species. We downloaded 17,383 images. Out of these, we discarded 5779 images due to quality issues. We used the remaining 11,604 images to measure the area, length, width and perimeter on 32,009 individual leaf blades using the semi-automated tool TraitEx. The resulting dataset contains 128,036 trait records. We demonstrate its comparability to trait data measured in natural environments following standard protocols by comparing trait values from the TRY database. We conclude that the herbarium specimens provide valuable information on leaf sizes. The dataset created in our study, by extracting leaf traits from the digitised herbarium specimen images of seven selected species, is a promising opportunity to improve ecological knowledge about the adaptation of size-related leaf traits to environmental changes in space and time.
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Woodburn, Matt, Deborah L. Paul, William Ulate, and Niels Raes. "Exposing the Dark Data of Undigitized Collections: A TDWG global standard for collection descriptions." Biodiversity Information Science and Standards 3 (June 19, 2019). http://dx.doi.org/10.3897/biss.3.37201.
Full textAbstract:
Aggregating content of museum and scientific collections worldwide offers us the opportunity to realize a virtual museum of our planet and the life upon it through space and time. By mapping specimen-level data records to standards and publishing this information, an increasing number of collections contribute to a digitally accessible wealth of knowledge. Visualizing these digital records by parameters such as collection type and geographic origin, helps collections and institutions to better understand their digital holdings and compare them to other such collections, as well as enabling researchers to find specimens and specimen data quickly (Singer et al. 2018). At the higher level of collections, related people and their activities, and especially the great majority of material that is yet to be digitised, we know much less. Many collections hold material not yet digitally discoverable in any form. For those that do publish collection-level data, it is commonly text-based data without the Global Unique Identifiers (GUIDs) or the controlled vocabularies that would support quantitative collection metrics and aid discovery of related expertise and publications. To best understand and plan for our world’s bio- and geodiversity represented in collections, we need standardised, quantitative collections-level metadata. Various groups planet-wide are actively developing tools to capture this much-needed metadata, including information about the backlog, and more detailed information about institutions and their activities (e.g. staffing, space, species-level inventories, geographic and taxonomic expertise, and related publications) (Smith et al. 2018). The Biodiversity Information Standards organization (TDWG) Collection Descriptions (CD) Data Standard Task Group aims to provide a data standard for describing natural scientific collections, which enables the ability to provide: automated metrics, using standardised collection descriptions and/or data derived from specimen datasets (e.g., counts of specimens) and a global registry of physical collections (either digitised or non-digitised). automated metrics, using standardised collection descriptions and/or data derived from specimen datasets (e.g., counts of specimens) and a global registry of physical collections (either digitised or non-digitised). The group will also produce a data model to underpin the new standard, and provide guidance and reference implementations for the practical use of the standard in institutional and collaborative data infrastructures. Our task group includes members from a myriad of groups with a stake in mobilizing such data at local, regional, domain-specific and global levels. With such a standard adopted, it will be possible to effectively share data across different community resources. So far, we have carried out landscape analyses of existing collection description frameworks, and amassed a portfolio of use cases from the group as well as from a range of other sources, including the Collection Descriptions Dashboard working group of ICEDIG ("Innovation and consolidation for large scale digitisation of natural heritage"), iDigBio (Integrated Digitized Biocollections), Smithsonian, Index Herbariorum, the Field Museum, GBIF (Global Biodiversity Information Facility), GRBio (Global Registry of Biodiversity Repositories) and fishfindR.net. These were used to develop a draft data model, and between them inform the first iteration of CD draft data standard. A variety of challenges present themselves in developing this standard. Some relate to the standard development process itself, such as identifying (often learning) effective tools and methods for collaborative working and communication across globally distributed volunteers. Others concern the scope and gaining consensus from stakeholders, across a wide range of disciplines, while maintaining achievable goals. Further challenges arise from the requirement to develop a data model and standard that support such a variety of use cases and priorities, while retaining interoperability and manageability of the data. We will present some of these challenges and methods for addressing them, and summarise the progress and draft outputs of the group so far. We will also discuss the vision of how the new standard may be adopted and its potential impact on collections discoverability across the natural science collections community.
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Nieva de la Hidalga, Abraham, Nicolas Cazenave, Donat Agosti, Zhengzhe Wu, Mathias Dillen, and Lars Nielsen. "Use of European Open Science Cloud and National e-Infrastructures for the Long-Term Storage of Digitised Assets from Natural History Collections." Biodiversity Information Science and Standards 3 (June 18, 2019). http://dx.doi.org/10.3897/biss.3.37164.
Full textAbstract:
Digitisation of Natural History Collections (NHC) has evolved from transcription of specimen catalogues in databases to web portals providing access to data, digital images, and 3D models of specimens. These portals increase global accessibility to specimens and help preserve the physical specimens by reducing their handling. The size of the NHC requires developing high-throughput digitisation workflows, as well as research into novel acquisition systems, image standardisation, curation, preservation, and publishing. Nowadays, herbarium sheet digitisation workflows (and fast digitisation stations) can digitise up to 6,000 specimens per day. Operating those digitisation stations in parallel, can increase the digitisation capacity. The high-resolution images obtained from these specimens, and their volume require substantial bandwidth, and disk space and tapes for storage of original digitised materials, as well as availability of computational processing resources for generating derivatives, information extraction, and publishing. While large institutions have dedicated digitisation teams that manage the whole workflow from acquisition to publishing, other institutions cannot dedicate resources to support all digitisation activities, in particular long-term storage. National and European e-infrastructures can provide an alternative solution by supporting different parts of the digitisation workflows. In the context of the Innovation and consolidation for large scale digitisation of natural heritage (ICEDIG Project 2018), three different e-infrastructures providing long-term storage have been analysed through three pilot studies: EUDAT-CINES, Zenodo, and National Infrastructures. The EUDAT-CINES pilot centred on transferring large digitised herbarium collections from the National Museum of Natural History France (MNHN) to the storage infrastructure provided by the Centre Informatique National de l’Enseignement Supérieur (CINES 2014), a European trusted digital repository. The upload, processing, and access services are supported by a combination of services provided by the European Collaborative Data Infrastructure (EUDAT CDI 2019) and CINES . The Zenodo pilot included the upload of herbarium collections from Meise Botanic Garden (APM) and other European herbaria into the Zenodo repository (Zenodo 2019). The upload, processing and access services are supported by Zenodo services, accessed by APM. The National Infrastructures pilot facilitated the upload of digital assets derived from specimens of herbarium and entomology collections held at the Finnish Museum of Natural History (LUOMUS) into the Finnish Biodiversity Information Facility (FinBIF 2019). This pilot concentrates on simplifying the integration of digitisation facilities to Finnish national e-infrastructures, using services developed by LUOMUS to access FinBIF resources. The data models employed in the pilots allow defining data schemas according to the types of collection and specimen images stored. For EUDAT-CINES, data were composed of the specimen data and its business metadata (those the institution making the deposit, in this case MNHN, considers relevant for the data objects being stored), enhanced by archiving metadata, added during the archiving process (institution, licensing, identifiers, project, archiving date, etc). EUDAT uses ePIC identifiers (ePIC 2019) to identify each deposit. The Zenodo pilot was designed to allow defining specimen data and metadata supporting indexing and access to resources. Zenodo uses DataCite Digital Object Identifiers (DOI) and the underlying data types as the main identifiers for the resources, augmented with fields based on standard TDWG vocabularies. FinBIF compiles Finnish biodiversity information to one single service for open access sharing. In FinBIF, HTTP URI based identifiers are used for all data, which link the specimen data with other information, such as images. The pilot infrastructure design reports describe features, capacities, functions and costs for each model, in three specific contexts are relevant for the implementation of the Distributed Systems of Scientific Collections (DiSSCo 2019) research infrastructure, informing the options for long-term storage and archiving digitised specimen data. The explored options allow preservation of assets and support easy access. In a wider context, the results provide a template for service evaluation in the European Open Science Cloud (EOSC 2019) which can guide similar efforts.
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Lohonya, Krisztina, Laurence Livermore, Jacek Wajer, Robyn Crowther, and Elizabeth Devenish. "Digitisation of the Natural History Museum’s collection of Dalbergia, Pterocarpus and the subtribe Phaseolinae (Fabaceae, Faboideae)." Biodiversity Data Journal 10 (November 14, 2022). http://dx.doi.org/10.3897/bdj.10.e94939.
Full textAbstract:
In 2018, the Natural History Museum (NHMUK, herbarium code: BM) undertook a pilot digitisation project together with the Royal Botanic Gardens Kew (project Lead) and the Royal Botanic Garden Edinburgh to collectively digitise non-type herbarium material of the subtribe Phaseolinae and the genera Dalbergia L.f. and Pterocarpus Jacq. (rosewoods and padauk), all from the economically important family of legumes (Leguminosae or Fabaceae). These taxonomic groups were chosen to provide specimen data for two potential use cases: 1) to support the development of dry beans as a sustainable and resilient crop; 2) to aid conservation and sustainable use of rosewoods and padauk. Collectively, these use case studies support the aims of the UK’s Department for Environment Food & Rural Affairs (DEFRA)-allocated, Official Development Assistance (ODA) funding. We present the images and metadata for 11,222 NHMUK specimens. The metadata includes label transcription and georeferencing, along with summary data on geographic, taxonomic, collector and temporal coverage. We also provide timings and the methodology for our transcription and georeferencing protocols. Approximately 35% of specimens digitised were collected in ODA-listed countries, in tropical Africa, but also in South East Asia and South America.
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Seregin, Alexey, and Nina Stepanova. "MHA Herbarium: Eastern European collections of vascular plants." Biodiversity Data Journal 8 (October 23, 2020). http://dx.doi.org/10.3897/bdj.8.e57512.
Full textAbstract:
World herbaria with 387.5M specimens (Thiers 2019) are being rapidly digitised. At least 79.9M plant specimens (20.6%) are already databased throughout the globe in the standard form of GBIF-mediated data. The contribution of smaller herbaria has been steadily growing over the last few years due to cost reduction, usage of platforms and solutions developed by the leaders. A web-resource the Moscow Digital Herbarium (Seregin 2020b) was launched by the Lomonosov Moscow State University in October, 2016 for publication of specimens imaged and databased in the Moscow University Herbarium (MW). As of 31 December 2018, the web-portal included 968,031 images of 971,732 specimens digitised in MW. This dataset is available in GBIF (Seregin 2020). The global trend is largely the same in Russia, where a dozen herbaria started to scan their holdings after imaging of the nation’s second largest herbarium (Kislov et al. 2017, Kovtonyuk et al. 2019, Seregin 2020a). In 2019, we started to use Moscow Digital Herbarium as a web-repository for digitised herbarium specimens from some Russian collections, starting with the Herbarium of Tsitsin Main Botanical Gaden, Russian Academy of Sciences (MHA). Due to this, a single-university system became a multi-institutional consortium in April 2019 (Seregin 2020a). The dataset of the Moscow collections and partly of the Eastern European collections of the MHA Herbarium is now available in GBIF (Seregin and Stepanova 2020). MHA Herbarium imaged 64,008 specimens from Moscow Region and partly from other regions of Eastern Europe at 600 dpi and provided key metadata. These data are now fully available in the Moscow Digital Herbarium and GBIF. Complete georeferencing of the specimens from the City of Moscow was a key task in 2020. As of May 2020, 50,324 specimens, including 49,732 specimens from Russia, have been georeferenced (78.6%) and 39,448 specimens have fully-captured label transcriptions (61.6%). Based on these data, we give a detailed overview of the collections including spatial, temporal and taxonomic description of the dataset.
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Raes, Niels, Emily van Egmond, Ana Casino, Matt Woodburn, and Deborah L. Paul. "Towards a Global Collection Description Standard." Biodiversity Information Science and Standards 3 (July 4, 2019). http://dx.doi.org/10.3897/biss.3.37894.
Full textAbstract:
With digitisation of natural history collections over the past decades, their traditional roles — for taxonomic studies and public education — have been greatly expanded into the fields of biodiversity assessments, climate change impact studies, trait analyses, sequencing, 3D object analyses etc. (Nelson and Ellis 2019; Watanabe 2019). Initial estimates of the global natural history collection range between 1.2 and 2.1 billion specimens (Ariño 2010), of which 169 million (8-14% - as of April 2019) are available at some level of digitisation through the Global Biodiversity Information Facility (GBIF). With iDigBio (Integrated Digitized Biocollections) established in the United States and with the European DiSSCo (Distributed Systems of Scientific Collections) accepted on the ESFRI roadmap, it has become a priority to digitize natural history collections at an industrialized scale. Both iDigBio and DiSSCo aim at mobilising, unifying and delivering bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. In order to prioritise digitisation based on scientific demand, and efficiency using industrial digitisation pipelines, it is required to arrive at a uniform and unambiguously accepted collection description standard that would allow comparing, grouping and analysing natural history collections at diverse levels. Several initiatives attempt to unambiguously describe natural history collections using taxonomic and storage classification schemes. These initiatives include One World Collection, Global Registry of Scientific Collections (GRSciColl), TDWG (Taxonomic Databases Working Group) Natural Collection Descriptions (NCD) and CETAF (Consortium of European Taxonomy Facilities) passports, among others. In a collaborative effort of DiSSCo, ICEDIG (Innovation and consolidation for large scale digitisation of natural heritage), iDigBio, TDWG and the Task Group Collection Digitisation Dashboards, the various schemes were compared in a cross-walk analysis to propose a preliminary natural collection description standard that is supported by the wider community. In the process, two main user groups of collection descriptions standards were identified; scientists and collection managers. The classification produced intends to meet requirements from them both, resulting in three classification schemes that exist in parallel to each other (van Egmond et al. 2019). For scientific purposes a ‘Taxonomic’ and ‘Stratigraphic’ classification were defined, and for management purposes a ‘Storage’ classification. The latter is derived from specimen preservation types (e.g. dried, liquid preserved) defining storage requirements and the physical location of specimens in collection holding facilities. The three parallel collection classifications can be cross-sectioned with a ‘Geographic’ classification to assign sub-collections to major terrestrial and marine regions, which allow scientists to identify particular taxonomic or stratigraphic (sub-)collections from major geographical or marine regions of interest. Finally, to measure the level of digitisation of institutional collections and progress of digitisation through time, the number of digitised specimens for each geographically cross-sectioned (sub-)collection can be derived from institutional collection management systems (CMS). As digitisation has different levels of completeness a ‘Digitisation’ scheme has been adopted to quantify the level of digitisation of a collection from Saarenmaa et al. 2019, ranging from ‘not digitised’ to extensively digitised, recorded in a progressive scale of MIDS (Minimal Information for Digital Specimen). The applicability of this preliminary classification will be discussed and visualized in a Collection Digitisation Dashboards (CDD) to demonstrate how the implementation of a collection description standard allows the identification of existing gaps in taxonomic and geographic coverage and levels of digitisation of natural history collections. This set of common classification schemes and dashboard design (van Egmond et al. 2019) will be contributed to the TDWG Collection Description interest group to ultimately arrive at the common goal of a 'World Collection Catalogue'.
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Hardisty, Alex, Keping Ma, Gil Nelson, and Jose Fortes. "‘openDS’ – A New Standard for Digital Specimens and Other Natural Science Digital Object Types." Biodiversity Information Science and Standards 3 (June 18, 2019). http://dx.doi.org/10.3897/biss.3.37033.
Full textAbstract:
With projected lifespans of many decades, infrastructure initiatives such as Europe’s Distributed System of Scientific Collections (DiSSCo), USA’s Integrated Digitized Biocollections (iDigBio), National Specimen Information Infrastructure (NSII) of China and Australia’s digitisation of national research collections (NRCA Digital) aim at transforming today’s slow, inefficient and limited practices of working with natural science collections. The need to borrow specimens (plants, animals, fossils or rocks) or physically visit collections, and absence of linkages to other relevant information represent significant impediments to answering today’s scientific and societal questions. A logical extension of the Internet, Digital Object Architecture (Kahn and Wilensky 2006) offers a way of grouping, managing and processing fragments of information relating to a natural science specimen. A ‘digital specimen’ acts as a surrogate in cyberspace for a specific physical specimen, identifying its actual location and authoritatively saying something about its collection event (who, when, where) and taxonomy, as well as providing links to high-resolution images. A digital specimen exposes supplementary information about related literature, traits, tissue samples and DNA sequences, chemical analyses, environmental information, etc. stored elsewhere than in the natural science collection itself. By presenting digital specimens as a new layer between data infrastructure of natural science collections and user applications for processing and interacting with information about specimens and collections, it’s possible to seamlessly organise global access spanning multiple collection-holding institutions and sources. Virtual collections of digital specimens with unique identifiers offer possibilities for wider, more flexible, and ‘FAIR’ (Findable, Accessible, Interoperable, Reusable) access for varied research and policy uses: recognising curatorial work, annotating with latest taxonomic treatments, understanding variations, working with DNA sequences or chemical analyses, supporting regulatory processes for health, food, security, sustainability and environmental change, inventions/products critical to the bio-economy, and educational uses. Adopting a digital specimen approach is expected to lead to faster insights for lower cost on many fronts. We propose that realising this vision requires a new TDWG standard. OpenDS is a specification of digital specimen and other object types essential to mass digitisation of natural science collections and their digital use. For five principal digital object types corresponding to major categories of collections and specimens’ information, OpenDS defines structure and content, and behaviours that can act upon them: Digital specimen: Representing a digitised physical specimen, contains information about a single specimen with links to related supplementary information; Storage container: Representing groups of specimens stored within a single container, such as insect tray, drawer or sample jar; Collection: Information about characteristics of a collection; Organisation: Information about the legal-entity owning the specimen and collection to which it belongs; and, Interpretation: Assertion(s) made on or about the specimen such as determination of species and comments. Digital specimen: Representing a digitised physical specimen, contains information about a single specimen with links to related supplementary information; Storage container: Representing groups of specimens stored within a single container, such as insect tray, drawer or sample jar; Collection: Information about characteristics of a collection; Organisation: Information about the legal-entity owning the specimen and collection to which it belongs; and, Interpretation: Assertion(s) made on or about the specimen such as determination of species and comments. Secondary classes gather presentation/preservation characteristics (e.g., herbarium sheets, pinned insects, specimens in glass jars, etc.), the general classification of a specimen (i.e., plant, animal, fossil, rock, etc.) and history of actions on the object (provenance). Equivalencing concepts in ABCD 3.0 and EFG extension for geo-sciences, OpenDS is also an ontology extending OBO Foundry’s Biological Collection Ontology (BCO) (Walls et al. 2014) from bco:MaterialSample, which has preferred label dwc:specimen from Darwin Core, thus linking it also with that standard. OpenDS object content can be serialized to specific formats/representations (e.g. JSON) for different exchange and processing purposes.
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De Smedt, Sofie, Ann Bogaerts, Henry Engledow, and Quentin Groom. "Different Approaches between First and Second Mass Digitisation Project for the Herbarium (BR) at Meise Botanic Garden." Biodiversity Information Science and Standards 3 (June 19, 2019). http://dx.doi.org/10.3897/biss.3.37259.
Full textAbstract:
The Herbarium of Meise Botanic Garden is in the top 15 herbaria worldwide. The collection comprises some four million specimens, which are important for scientific research. Digitisation of specimens includes imaging, transcription of label information, linking data and making the results publicly accessible online. In addition to facilitating researchers’ access to specimens, digitisation also brings new possibilities for analysis and discovery of new data, such as the vast amount of information on handwritten labels. In the DOE! project (Digitale Ontsluiting Erfgoedcollecties), funded by the Flemish Government, 1.2 million herbarium sheets from the African and Belgian collections were digitised. We have received additional funding to digitise a further 1.4 million specimens for the remaining vascular plants and macro-algae collections, by October 2021. These include the historic collections of Von Martius and Van Heurck. Carl Friedrich Philipp von Martius (1794–1868) was a pioneering explorer whose expeditions led to the discovery of many species. He amassed over 300,000 specimens, some of which were used to compile the first Flora of Brazil. Henri Van Heurck (1838–1909) also gathered herbarium specimens from all over the world, including a specimen originally from the collection of Linnaeus. Despite this being our second mass digitisation project, there are significant differences in our approach. This is partly due to lessons learned from the first project and partly to the nature of the collections themselves. The differences in the tendering process, specimen preparation, workflow and data capture will be explained. Making these specimens openly available online through www.botanicalcollections.be is valuable to scientific research as well as valorising of our collections. Currently, the site attracts 7000 users a year, which adds up to 15,000 sessions a year and the average session is more than 8 minutes. This means that people are actively using our website and these numbers can be expected to grow as we add more specimens and functionality.
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Younis, Sohaib, Marco Schmidt, Claus Weiland, Stefan Dressler, Bernhard Seeger, and Thomas Hickler. "Detection and annotation of plant organs from digitised herbarium scans using deep learning." Biodiversity Data Journal 8 (December 10, 2020). http://dx.doi.org/10.3897/bdj.8.e57090.
Full textAbstract:
As herbarium specimens are increasingly becoming digitised and accessible in online repositories, advanced computer vision techniques are being used to extract information from them. The presence of certain plant organs on herbarium sheets is useful information in various scientific contexts and automatic recognition of these organs will help mobilise such information. In our study, we use deep learning to detect plant organs on digitised herbarium specimens with Faster R-CNN. For our experiment, we manually annotated hundreds of herbarium scans with thousands of bounding boxes for six types of plant organs and used them for training and evaluating the plant organ detection model. The model worked particularly well on leaves and stems, while flowers were also present in large numbers in the sheets, but were not equally well recognised.