From specimens to drawers Stefan Schmidt, Jörg Spela Zoologische Staatssammlung München –...
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Transcript of From specimens to drawers Stefan Schmidt, Jörg Spela Zoologische Staatssammlung München –...
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)