No specimen (software) left behind

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 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

Report & recommendations 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

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

The current workflow Not Open Source

The planned workflow Not Open Source

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 ”
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?

No specimen (software) left behind

by Vincent Smith

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