No specimen left behindA system for mass digitizationat the Natural History Museum

Vince Smith, Vladimir Blagoderov, Ian Kitching & Thomas Simonsen

Vince Smith

No software left behindThe Open Source requirement at iEvoBio

Rate of digitisation at the NHM

1400 YEARS to digitize the NHM’s 70 million specimens!

SatScan v.1 (by SmartDrive)

2010 system trials

$$$

• 5 minutes scan time• 5 minutes stitch time (batched)• Telecentric lens

Digitizing specimens

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

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 OpenSource

The current workflow

Not OpenSource

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?