From specimens to drawers Stefan Schmidt, Jörg Spela Zoologische Staatssammlung München – Bavarian State Collection of Zoology Mass digitisation efforts.

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Presentation transcript:

From specimens to drawers Stefan Schmidt, Jörg Spela Zoologische Staatssammlung München – Bavarian State Collection of Zoology Mass digitisation efforts at the Bavarian State Collection of Zoology in Munich, Germany SNSB - Bavarian Natural History Collections

The Bavarian State Collection of Zoology Insects Coleoptera3.5 million Diptera Insecta varia Hemiptera Hymenoptera3 million Lepidoptera10 million Collections

Specimen level digitisation: Hymenoptera Hymenoptera Standard drawers12,500 Specimens (incl. accessions)3 million Type specimens6,250 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 drawers12,500 Specimens (incl. accessions)3 million Type specimens6,250 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 DScan Advantages 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 CameraSensor (MPix) Lens (macro) Distance (cm) Images per drawer Megapixel DSLR1290 mm DSLR1290 mm DSRL2490 mm DSLR2460 mm DSLR24105 mm

DScan: Time Requirements ProcessTimes (minutes Scanning3–43–4 Stitching4–54–5 Creation of multi resolution image images per drawer

DScan: Examples

Digitisation time requirements Object type / unitMetadataTime (minutes) Whole insect drawer (50–300 specimens)ID, species30 Specimen + label (3–4 images)ID, species30 Microscope slideID, species10 Slide preparation with extended DOFID, species30 DNA barcoding voucherID, label data10

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)