No Specimen Left Behind: industrial scale digitisation of natural history collections


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Blagoderov V. and Smith V.S. 2011. No Specimen Left Behind: industrial scale digitisation of natural history collections. Life and Literature, Biodiversity Heritage Library conference, Chicago, Illinois, USA, 14 – 15 November, 2011.

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No Specimen Left Behind: industrial scale digitisation of natural history collections

  1. 1. No Specimen Left Behind Industrial scale digitisation of natural history collections Vladimir Blagoderov & Vincent Smith  •  Natural History Museum London The Problems With Digitisation The Current Situation The Potential “ the rate of progress by the UK taxonomic In collections management institutions in digitising and making collections information available is • Accurate specimen counts for the entire collection disappointingly low. Unless a more strategic • Collections audit and security view is taken... there is a significant risk of • Saving curator & visitor time damage to the international reputation of major institutions ” • Improving curation 2009 UK House of Lords Science and Technology Committee • Updating identifications online Report on Taxonomy and Systematics • Encouraging typification (discovery of unrecognized types) • Populating specimen databases • At present rates it would take approximately 900 years to get the data off the Natural History In research Museum’s 70 million specimens, and 500 years to • Acquiring images for use with automated take the pictures. identification software • New technologies have the potential to speed this • Supporting manual taxonomic identifications to completion within twenty years. • Morphometric analysis of specimens • These advances mean that selecting specimens • Support the monitoring of environmental change for digitisation now takes longer than the act of digitising them. • Supporting biodiversity conservation research • Metadata capture is the rate-limiting step, • Studies on colour pattern variations but using a staged approach even this can be overcome. In public engagement • This offers the potential to build comprehensive • Visual & engaging equipment on public display digital museum, with new ways to use and • Innovative crowd sourcing possibilities organise the collection. with the public • Meets museum strategic commitments on collection accessibility The daunting task of digitising natural history collections PHOTO: L . Livermore Our Solution SatScan Key Facts SatScan • Objects >10mm usefully digitised at standard resolution • i.e. 85 k of the 135 k collection draws in NHM Entomology collection • The process would take 8 years for 1 person and 1 machine • Higher resolution options available at lower throughput rates • 1, 2 & 4 k dpi options, corresponding depth of field 3cm - 5mm and file sizes of 300MB - 4.8GB • Software setup wizard enables use by The effort of individually handling Working with SmartDrive, we have The machine is combination A telecentic camera with the untrained volunteers the NHM’s 70 million specimens developed a machine ( SatScan ) of hardware and software that attached lens is moved in two would be enormous, but most that can produce a ultra-high provides automated capture of dimensions along precision rails • Metadata Creator Tool for rapid specimens are grouped in such a resolution digital image of a draw lower resolution images, which positioned above the imaged metadata collection way that makes them much easier in 5 minutes. From this image we are then assembled ( stitched ) object. This method maximises • Images cropped back to individual specimens to handle. Eg. the entomology can examine the specimens in into a larger panoramic image, depth of field of the captured department has 28 million detail. generating an extremely high images and minimises distortion • Physical identifiers ( barcodes ) permanently link the specimens in just 135,000 drawers. resolution final image. and parallax artifacts. specimen, image & metadata together The Workflow Next Steps • The SatScan system is primarily used by collections management but on an ad hoc basis • We need to develop a more comprehensive program of digitisation for an exemplar collection • Target groups include the synoptic British collections ( insects & plants ), Lepidoptera and lichens • We are working on a web interface to crowd source image cropping and metadata collection • The NHM Digital Asset Management System andAcknowledgements our Collections Management System are beingSmartDrive NHM Poster Design integrated into this processD. Murphy I . Kitching M . Nikunlassi T. Simonsen L . Livermore • We plan to assign DataCite DOIs to each specimen, its metadata record and its digital imageRead more: http : // hdl . handle . net /10101/npre . 2010. 4486.1 http : // www. smartdrive .co. uk / http: // vbrant . eu /