no specimen left behind a system for mass digitization at the natural history museum vince smith,...
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No specimen left behindA system for mass digitizationat the Natural History Museum
Vince Smith, Vladimir Blagoderov, Ian Kitching & Thomas Simonsen
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Vince Smith
No software left behindThe Open Source requirement at iEvoBio
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Rate of digitisation at the NHM
1400 YEARS to digitize the NHM’s 70 million specimens!
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SatScan v.1 (by SmartDrive)
2010 system trials
$$$
• 5 minutes scan time• 5 minutes stitch time (batched)• Telecentric lens
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Digitizing specimens
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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
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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)
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Resolution examples
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Not OpenSource
The current workflow
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Not OpenSource
The planned workflow
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Recent non open-source software
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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
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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?