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Digital Imaging of Biological Type Specimens a Manual of Best Practice

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Digital Imaging of Biological Type Specimens a Manual of Best Practice Digital Imaging of Biological Type Specimens A Manual of Best Practice Results from a study of the European Network for Biodiversity Information Editors: Christoph L. Häuser, Axel Steiner, Joachim Holstein & Malcolm J. Scoble Stuttgart 2005 Editors: Christoph L. Häuser, Axel Steiner, Joachim Holstein (Stuttgart) & Malcolm J. Scoble (London) Staatliches Museum für Naturkunde, Stuttgart Rosenstein 1, D-70191 Stuttgart, Germany The Natural History Museum, London Cromwell Road, London SW7 5BD, UK This publication should be cited as: HÄUSER, C.L., STEINER, A., HOLSTEIN, J. & SCOBLE, M. J. (eds.) (2005): Digital Imaging of Biological Type Specimens. A Manual of Best Practice. Results from a study of the European Network for Biodiversity Information. Stuttgart. viii + 309 pp. Contributions in this publication should be cited as: CRICK, M. (2005): Image File Management. In: HÄUSER et al. (eds.): Digital Imaging of Biological Type Specimens. A Manual of Best Practice. Results from a study of the European Network for Biodiversity Information: 41-55. Stuttgart. The European Network for Biodiversity Information (ENBI) is solely responsible for the contents of this ENBI Digital Imaging Manual, it does not represent the opinion of the European Commission and the European Commission is not responsible for any use that might be made of data from this ENBI Digital Imaging Manual. ENBI is a thematic network supported by the European Commission under the 5th Framework Programme. Contract number: EVK2-CT-2002-20020. http://www.enbi.info Any commercial products and protected brand names mentioned or recommended in this volume reflect solely the personal views of the respective authors. Individual chapters of this publication may be reproduced in any form without prior permission, provided that the source is acknowledged by citation of the author(s) and editors as indicated above. This publication can be obtained as a book or as a CD from: Staatliches Museum für Naturkunde, Rosenstein 1, D-70191 Stuttgart, Germany, or: ENBI Bureau, Zoological Museum Amsterdam, Faculty of Science/University of Amsterdam, PO Box 94766, NL-1090 GT Amsterdam, The Netherlands. Printed by Oehler Offset, Fellbach © 2005 by Staatliches Museum für Naturkunde, Stuttgart, ISBN: 3-00-017240-8 Cover graphics: JOACHIM HOLSTEIN, using photographs from this book. Digital Imaging of Biological Type Specimens iii Preface by WOUTER LOS This book addresses a number of important issues about the digital imaging of biological objects. These topics were explored in two workshops organised by the European Network for Biodiversity Infor- mation (ENBI), and the Global Biodiversity Information Facility (GBIF). With the digital imaging of a growing number of biological objects, it has become of great importance to agree on common approaches and standards. Such standardization is particularly important for natural history specimens so as to compare specimens often with only subtle differences in morphology. Emerging technolo- gies are leading to exciting new opportunities in scientific studies and the field of biodiversity is notable among them. I wish to thank all authors and the editors for bringing together and highlighting many new developments in this book. On behalf of the ENBI membership I also want to acknowledge the support from the European Commission for the ENBI network which made it possible to publish this book. Wouter Los Co-ordinator of the European Network for Biodiversity Information (University of Amsterdam) iv Digital Imaging of Biological Type Specimens Contents Preface WOUTER LOS ........................................................................... iii List of Contributors ....................................................................... vi Introduction CHRISTOPH L. HÄUSER & MALCOLM J. SCOBLE .......................... 1 The Place of the Manual in the European Network of Biodiversity Information MALCOLM J. SCOBLE ................................................................. 7 General Subjects E-Types – A New Resource for Taxonomic Research LARRY SPEERS ....................................................................... 13 Image Metadata Standards and Practices ROBERT A. MORRIS ................................................................ 19 Colour Management ROBERT A. MORRIS ................................................................ 35 Image File Management MARION CRICK ....................................................................... 41 Online Acquisition of Scientific Archive Documents – A Survey and Manual ANDY C. DOWNTON ................................................................ 56 Taxonomic-Grade Images ARTURO H. ARIÑO & DAVID GALICIA ......................................... 87 A Photographer’s Viewpoint HAROLD TAYLOR .................................................................. 126 Current Approaches for Different Groups of Organisms Digital Imaging of Prokaryotes for Taxonomic Purposes DAGMAR FRITZE ................................................................... 153 Digital Imaging at the Herbarium Berolinense WALTER BERENDSOHN, B. EINSIEDEL, U. MERKEL, H. NOWAK- KRAWIETZ, D. RÖPERT & I. WILL ........................................... 172 Imaging Soil Mesofauna: The Land in Between ARTURO H. ARIÑO, ENRIQUE BAQUERO & RAFAEL JORDANA ... 188 Digital Imaging of Biological Type Specimens v Digital Imaging of Beetles (Coleoptera) and Other Three- Dimensional Insects ALEXANDER RIEDEL .............................................................. 222 Digital Imaging of Butterflies and Other Lepidoptera: More or Less 'Flat' Objects? CHRISTOPH L. HÄUSER, AXEL STEINER & JOACHIM HOLSTEIN . 251 Imaging Type Specimens of Fishes at the Natural History Museum, London PHIL HURST & DARRELL SIEBERT ........................................... 265 3D Imaging for a Virtual Museum: Bird Type Specimens of the Zoological Museum Amsterdam HUUB VELDHUIZEN VAN ZANTEN, EDWIN VAN SPRONSEN & RUUD ALTENBURG ................................................................. 276 Case Studies – Equipment and Standards Used for Selected Taxa and Projects Plants PIET STOFFELEN, ALAIN VANDER VELDE, PATRICIA MERGEN & FRÉDÉRIC WAUTELET ........................................................................................ 291 Earwigs (Dermaptera) FABIAN HAAS .................................................................................... 293 Fruit Flies (Diptera: Tephritidae) I. M. WHITE & MARC DE MEYER ........................................................ 295 Parasitic Hymenoptera MATTHEW L. BUFFINGTON & ROGER A. BURKS .................................... 297 Butterflies 1 (Lepidoptera: Papilionoidea, Hesperioidea) CHRISTOPH L. HÄUSER, AXEL STEINER & JOACHIM HOLSTEIN ............... 303 Butterflies 2 (Lepidoptera: Papilionoidea, Hesperioidea) UGO DALL'ASTA ................................................................................ 305 Geometrid Moths (Lepidoptera: Geometridae) AXEL HAUSMANN & SVEN ERLACHER .................................................. 307 Cichlids (Pisces: Cichlidae) JOS SNOEKS .................................................................................... 309 vi Digital Imaging of Biological Type Specimens List of Contributors RUUD ALTENBURG ETI BioInformatics, University of Amsterdam, Mauritskade 61, NL-1092 AD Amsterdam, The Netherlands. E-mail:: [email protected] ARTURO H. ARIÑO Department of Zoology and Ecology, University of Navarra, E-31080 Pamplona, Spain. E-mail: [email protected] ENRIQUE BAQUERO Department of Zoology and Ecology, University of Navarra, E-31080 Pamplona, Spain. E-mail: [email protected] WALTER G. BERENDSOHN Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14191 Berlin, Germany. E-mail: w.berendsohn@ bgbm.org MATTHEW L. BUFFINGTON Florida State University/CDFA, 3294 Meadowview Rd, Sacaramento, CA 95832- 1448 USA. E-mail: [email protected] ROGER A. BURKS Department of Entomology, UC Riverside, Riverside, CA 92521 USA. E-mail: [email protected] MARION CRICK ePic Project, Royal Botanic Gardens, Kew, Kew Green, Richmond, TW9 3AE, United Kingdom. E-mail: [email protected] UGO DALL'ASTA Department of African Zoology / Entomology, Musée Royal de l'Afrique Centrale, Leuvensesteenweg 13, B-3080 Tervuren, Belgium. E-mail: ugo.dallasta@ africamuseum.be MARC DE MEYER Department of African Zoology / Entomology, Musée Royal de l'Afrique Centrale, Leuvensesteenweg 13, B-3080 Tervuren, Belgium. E-mail: marc.de.meyer@ africamuseum.be ANDY C. DOWNTON Department of Electronic Systems Engineering, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom. Email: [email protected] BARBARA EINSIEDEL Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14191 Berlin, Germany. SVEN ERLACHER Zoologische Staatssammlung München, Münchhausenstr. 21, D-81247 München, Germany. E-mail: [email protected] DAGMAR FRITZE DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D-38124 Braunschweig, Germany. E-mail: [email protected] Digital Imaging of Biological Type Specimens vii DAVID GALICIA Department of Zoology and Ecology, University of Navarra, E-31080 Pamplona, Spain. E-mail: [email protected] FABIAN HAAS Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, D-70191 Stuttgart, Germany. E-mail: [email protected] CHRISTOPH L. HÄUSER Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, D-70191 Stuttgart, Germany. E-mail: [email protected]
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