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This pilot project utilised a volunteer workforce of 45 people, in teams of 3 - 7 people per day, to scan ~100,000 microscope slides over 10 months using the SatScan TM (Smartdrive Ltd.) and industrial approaches as described by Blagoderov et al. 2019), similar to that run at Naturalis, Leiden ( Heerlien et al. In 2015, the Museum’s DCP ran a pilot project for mass digitisation of microscope slides using a multi-slide imaging template and downstream image segmentation ( Summerfield et al. Furthermore, slide holders may partially obscure label data, while labels on the reverse side of the slide cannot currently be captured. While many of these automated scanners are able to capture a low resolution overview image of the slide, these images tend to be poorly lit, which could impact automated label extraction through optical character recognition. (Fig.1 1).Įxamples of natural history microscope slides that are damaged or non-standard in size and mountant thickness.įor natural history slide collections, the data on the labels is as important as the slide mounted material / specimen(s). 2019) - issues that can be frequent in natural history collections (Fig. While there have been several pilot projects that have used specially modified histology slide scanners adapted for natural history specimens, they cannot accommodate damaged slides or slides with non-standard thickness or length ( Musson et al. While automated slide digitisation systems, designed for higher resolution imaging, have existed for over a decade, these have been confined to medical slides with no other large-scale digitisation projects of natural history slides known to us ( Rojo et al. botany, entomology, mineralogy, palaeontology and zoology), with each group having its own distinct slide preparation technique and standards. These slides are distributed across diverse curatorial groups (e.g. We estimate that the NHM holds 2.4 million microscope slides in its collection. One of the aims of the DCP is to develop new digitisation workflows to speed up the efficiency of mass digitisation.
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In 2014, the Natural History Museum, London (NHM) embarked on an ambitious Digital Collections Programme (DCP) to digitise its collections, estimated to comprise 80 million specimens. The greatest barrier to this digital transformation is the relatively low proportion of specimens, especially entomological specimens, that have digital data ( Sikes et al. It is now possible to construct datasets with millions of records, with global coverage, drawing on a mix of historical and contemporary observations of species to address questions such as why the natural world is changing, how humans are influencing this change and what we might do to minimise this loss ( Purvis et al. These digital copies not only provide an unprecedented level of access to data that has hitherto been restricted to those with privileged physical access to the specimens, but the scope, scale and speed with which new digital records can be acquired, are transforming our understanding of the natural world. 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.ĭigital surrogates of natural history specimens, comprising a combination of specimen data and images, are creating new audiences and new research opportunities for natural history collections ( Drew et al.
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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. By using a series of barcodes encoding information associated with each slide (i.e. Here we describe a novel process of semi-automated mass digitisation using both temporary and permanent barcode labels applied before and during slide imaging. This paper presents the workflow developed to digitise the entire Phthiraptera (parasitic lice) microscope slide collection (70,663 slides). 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. The Natural History Museum, London (NHM) has embarked on an ambitious programme to digitise its collections.