No specimen left behind A system for mass digitization at the Natural History Museum Vince Smith, Vladimir Blagoderov, Ian Kitching & Thomas Simonsen.

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Presentation transcript:

No specimen left behind A system for mass digitization at the Natural History Museum Vince Smith, Vladimir Blagoderov, Ian Kitching & Thomas Simonsen

Vince Smith No software left behind The Open Source requirement at iEvoBio

Rate of digitisation at the NHM 1400 YEARS to digitize the NHMs 70 million specimens!

SatScan v.1 (by SmartDrive) 2010 system trials $$$ 5 minutes scan time 5 minutes stitch time (batched) Telecentric lens

Digitizing specimens

Objects >10mm usefully digitized 85k of 135k ent. draws usefully digitized < 8 yrs, 1 person, 1 machine Including draw level metadata Report & recommendations

Key SatScan v.2 improvements Higher resolution, 1,2 &4k dpi (3cm-5mm dpth; 300Mb- 4.8Gb) Z-axis (for image stacking) Software setup wizard Improved public offer Metadata creator tool Specimen cropping SatScan v.2 (by SmartDrive)

Resolution examples

Not Open Source The current workflow

Not Open Source The planned workflow

Recent non open-source software

Open source issues raised Is open-source a philosophy, or a pragmatic methodology? But open-source does not guarantee the end-product, source-material, blueprints, and documentation available at no cost to the public Arguably, open-source provides our informatics provenance Open-source does not guarantee the longevity of software Open-source is not (on its own) a business model

Questions for Birds of a feather 1.Is there a case for non-open source software (and hardware) at iEvoBio? 2.If there is, how might we do this be done while incentivizing open source? (twin tracks, shorter talks?) 3.How to we create sustainable future for biodiversity informatics software?