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No specimen left behind A system for mass digitization at the Natural History Museum

No specimen left behind A system for mass digitization at the Natural History Museum. Vince Smith, Vladimir Blagoderov, Ian Kitching & Thomas Simonsen. No software left behind The Open Source requirement at iEvoBio. Vince Smith. 1400 YEARS to digitize the NHM’s 70 million specimens!.

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No specimen left behind A system for mass digitization at the Natural History Museum

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

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

  3. 1400 YEARS to digitize the NHM’s 70 million specimens! Rate of digitisation at the NHM

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

  5. Digitizing specimens

  6. http://precedings.nature.com/documents/4486/version/1 • Objects >10mm usefully digitized • 85k of 135k ent. draws usefully digitized • < 8 yrs, 1 person, 1 machine • Including draw level metadata Report & recommendations

  7. SatScan v.2 (by SmartDrive) • 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

  8. Resolution examples

  9. Not Open Source The current workflow

  10. Not Open Source The planned workflow

  11. Recent non open-source software

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

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

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