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      High-Throughput Digitisation of Natural History Specimens

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      Biodiversity Information Science and Standards

      Pensoft Publishers

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          Abstract

          The Natural History Museum, London (NHM) has embarked on an ambitious Digital Collections Programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. Pilot projects have been carried out for a variety of collection types, from which high-throughput imaging workflows have been developed and refined. These workflows have focused on pinned insect specimens (Blagoderov et al. 2012, Paterson et al. 2016, Blagoderov et al. 2017, Price et al. 2018), microscope slides (whole slide and specimen imaging; Allan et al. 2018, Allan et al. 2019) and herbarium sheets. The rate and time taken to digitise specimens is influenced by a number of factors that include, among others, the level of preparation and post-processing required, imaging approach, the type of specimens as well as the complexity and condition of the collection. As part of this presentation we will include information on the rate, cost and time to digitise various NHM collections, illustrating how our processes have improved digitisation efficiency and allowed us to maintain quality. The programme has run a variety of digitisation projects, gathering data about rates of digitisation (preparation, imaging, transcription etc.) and developing improvements. Collection types such as microscope slides and herbarium sheets lend themselves to higher imaging rates, while other collections such as pinned insects, which require greater amounts of specimen handling to remove labels, tend to have lower imaging rates (Fig. 1). In order to increase efficiency, we have developed approaches that minimise specimen handling. For example, workflows for pinned insects such as the Angled Label Image Capture and Extraction (ALICE) do not require the removal of specimen labels from the pin as the system can capture angled images of the labels, thus increasing the imaging rate three-fold (Fig. 1).  Another approach taken is to semi-automate mass digitisation using a combination of  temporary and permanent Data Matrix barcode labels (Allan et al. 2019). By using multiple barcodes at the imaging stage to encode information associated with each specimen (i.e. unique identifier, location in the collection, taxonomic name, type status etc.; Fig. 2), we can run a series of automated processes, including file renaming, image processing and bulk import into the Museum’s collection management system. Through adaptation of our workflows with this new approach we have increased the efficiency of digitisation processes, illustrating how simple activities, like automated file renaming, reduces image post-processing time, minimises human error and can be applied across multiple collection types.

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          Most cited references 6

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          No specimen left behind: industrial scale digitization of natural history collections

          Abstract Traditional approaches for digitizing natural history collections, which include both imaging and metadata capture, are both labour- and time-intensive. Mass-digitization can only be completed if the resource-intensive steps, such as specimen selection and databasing of associated information, are minimized. Digitization of larger collections should employ an “industrial” approach, using the principles of automation and crowd sourcing, with minimal initial metadata collection including a mandatory persistent identifier. A new workflow for the mass-digitization of natural history museum collections based on these principles, and using SatScan® tray scanning system, is described.
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            A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides

            Abstract The Natural History Museum, London (NHM) has embarked on an ambitious programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. This paper presents the workflow developed to digitise the entire Phthiraptera (parasitic lice) microscope slide collection (70,663 slides). Here we describe a novel process of semi-automated mass digitisation using both temporary and permanent barcode labels applied before and during slide imaging. By using a series of barcodes encoding information associated with each slide (i.e. unique identifier, location in the collection and taxonomic name), we can run a series of automated processes, including file renaming, image processing and bulk import into the NHM’s collection management system. We provide data on the comparative efficiency of these processes, illustrating how simple activities, like automated file renaming, reduces image post-processing time, minimises human error and can be applied across multiple collection types.
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              iCollections – Digitising the British and Irish Butterflies in the Natural History Museum, London

              Abstract Background The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections . The first phase of this programme has been to undertake a series of pilot projects that will develop the necessary workflows and infrastructure development 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. This paper explains the way the data were obtained and the background to the collections which made up the project. New information Specimen-level data associated with British and Irish butterfly specimens have not been available before and the iCollections project has released this valuable resource through the NHM data portal.
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                Author and article information

                Journal
                Biodiversity Information Science and Standards
                BISS
                Pensoft Publishers
                2535-0897
                June 25 2019
                June 25 2019
                : 3
                Article
                10.3897/biss.3.37337
                f61bf171-5720-4bfa-b9e0-c1e67e2ef0ae
                © 2019

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