From specimens to drawers

Stefan Schmidt, Jörg SpelaZoologische Staatssammlung München – Bavarian State Collection of Zoology

Mass digitisation efforts at theBavarian State Collection of Zoologyin Munich, Germany

staatlichenaturwissenschaftlichesammlungen bayerns

SNSB - Bavarian Natural History Collections

The Bavarian State Collection of Zoology

Insects

Coleoptera 3.5 million

Diptera 400 000

Insecta varia 200 000

Hemiptera 500 000

Hymenoptera 3 million

Lepidoptera 10 million

Collections

Specimen level digitisation: Hymenoptera

Hymenoptera

Standard drawers 12,500

Specimens (incl. accessions) 3 million

Type specimens 6,250

Specimens digitised(DNA Barcoding)

26,330 (0.04%)

Type specimens digitised (GBIF)

1,284 (21%)(625 Symphyta, 659 Ichneumonidae)

Specimen level digitisation: Hymenoptera

Hymenoptera

Standard drawers 12,500

Specimens (incl. accessions) 3 million

Type specimens 6,250

Specimens digitised(DNA Barcoding)

26,330 (0.04%)

Type specimens digitised (GBIF)

1,284 (21%)(625 Symphyta, 659 Ichneumonidae)

Specimen level digitisation: Types

At mininum:• 2-3 images of specimen• Label• Metadata: original combination

Specimen level digitisation: DNA-Barcoding

• 1 image of specimen• Metadata:

• Voucher info: specimen ID, collection code, institution storing

• Taxonomy: phylum, class, order family, genus, species, identifier

• Specimen details: sex, reproduction, life stage

• Collection data: collector, collection date, country, state/province, exact site, latitude, longitude, elevation

Whole drawer digitisation: first attempts

Whole drawer digitisation using Gigapan

Gigapan panoramic head with compact camera

Whole drawer scanning using the GigaPan system

Advantages• Relatively low costs ($ 1,000–1,500)• No parallax error

Disadvantages• Strong barrel distortion• Focussing problems with autofocus• Slow (10–15 minutes per drawer)

Whole drawer digitisation with DScanAdvantages

• Fast (3–4 minutes per drawer)• No barrel distortion• No change of object distance• Resolution adjustable by object distance

Disadvantages• No portability• More expensive ($ 40,000 for the whole setup)• Risk of parallax error

GigaPan + Camera Drawer scanner

Whole drawer scanning: parallax error

DScan: Camera + Lens Combinations

Camera Sensor(MPix)

Lens(macro)

Distance (cm)

Images per drawer

Megapixel

DSLR 12 90 mm 60 56 310

DSLR 12 90 mm 52 99 500

DSRL 24 90 mm 60 56 520

DSLR 24 60 mm 60 30 400

DSLR 24 105 mm 60 99 670

DScan: Time Requirements

Process Times (minutes

Scanning 3–4

Stitching 4–5

Creation of multi resolution image 1.5

56 images per drawer

• http://media.zsm-entomology.de/dd/hym/HD-2012-0007/HD-2012-0007.html

• http://media.zsm-entomology.de/dd/lep/ZSM-LD-0000010-1402.html

DScan: Examples

• http://media.zsm-entomology.de/dd/hym/HD-2012-0007/HD-2012-0007.html

• http://media.zsm-entomology.de/dd/lep/ZSM-LD-0000010-1402.html

Digitisation time requirements

Object type / unit Metadata Time (minutes)

Whole insect drawer (50–300 specimens) ID, species 30

Specimen + label (3–4 images) ID, species 30

Microscope slide ID, species 10

Slide preparation with extended DOF ID, species 30

DNA barcoding voucher ID, label data 10

WDD: current activities and challenges

• DScan upgrade

• replacing stepper with servo motors

• simplified graphical UI

• presets for different scan programs

• Improving image workflow

• Focus stacking to improve DOF

• Management of drawer data and images (Diversity Workbench)

• Replacing proprietary with open source software

• Ditigisation of special collections (local, historic collections)

• Virtual collections (ZSM, MfN)