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

      Blagoderov, V; Kitching, I; Livermore, L; Simonsen, TJ; Smith, V (2012-07-20)
    • A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides

      Allan, Louise; Livermore, L; Price, BW; Shchedrina, O; Smith, V (Pensoft Publishers, 2019-03-01)
      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.
    • Sex biases in bird and mammal natural history collections.

      Cooper, N; Bond, AL; Davis, JL; Portela Miguez, R; Tomsett, L; Helgen, Kristofer (Royal Society, 2019-10-23)
      Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.
    • SYNTHESYS+ Virtual Access - Report on the Ideas Call (October to November 2019)

      Hardy, Helen; Knapp, S; Allan, Louise; Berger, F; Dixey, K; Döme, B; Gagnier, P-Y; Frank, J; Haston, E; Holstein, J; et al. (Pensoft Publishers, 2020-01-24)
      The SYNTHESYS consortium has been operational since 2004, and has facilitated physical access by individual researchers to European natural history collections through its Transnational Access programme (TA). For the first time, SYNTHESYS+ will be offering virtual access to collections through digitisation, with two calls for the programme, the first in 2020 and the second in 2021. The Virtual Access (VA) programme is not a direct digital parallel of Transnational Access - proposals for collections digitisation will be prioritised and carried out based on community demand, and data must be made openly available immediately. A key feature of Virtual Access is that, unlike TA, it does not select the researchers to whom access is provided. Because Virtual Access in this way is new to the community and to the collections-holding institutions, the SYNTHESYS+ consortium invited ideas through an Ideas Call, that opened on 7th October 2019 and closed on 22nd November 2019, in order to assess interest and to trial procedures. This report is intended to provide feedback to those who participated in the Ideas Call and to help all applicants to the first SYNTHESYS+Virtual Access Call that will be launched on 20<jats:sup>th</jats:sup> of February 2020.
    • The unknown planktonic foraminiferal pioneer Henry A. Buckley and his collection at The Natural History Museum, London

      Rillo, MC; Whittaker, J; Ezard, THG; Purvis, A; Henderson, AS; Stukins, S; Giles Miller, C (2016-12-22)