Whole-drawer imaging for digital management and curation of a large entomological collection

Beth Mantle; John LaSalle; Nicole Fisher

doi:10.3897/zookeys.209.3169

Amanda Domingues de Araújo, Renato Guimarães Delfino, Roberta Lima Caldeira, Cristiane Lafetá Furtado Mendonça, Omar dos Santos Carvalho (2023)
Implementation of the QR Code system in the Medical Malacology Collection of the René Rachou Institute, Oswaldo Cruz Foundation. Zoologia (Curitiba) 40: .

DOI: 10.1590/s1984-4689.v40.e23009

Michael Balke, Stefan Schmidt, Axel Hausmann, Emmanuel FA Toussaint, Johannes Bergsten, Matthew Buffington, Christoph L Häuser, Alexander Kroupa, Gregor Hagedorn, Alexander Riedel, Andrew Polaszek, Rosichon Ubaidillah, Lars Krogmann, Andreas Zwick, Martin Fikáček, Jiří Hájek, Mariano C Michat, Christopher Dietrich, John La Salle, Beth Mantle, Peter KL Ng, Donald Hobern (2013)
Biodiversity into your hands - A call for a virtual global natural history ‘metacollection’. Frontiers in Zoology 10: 55.

DOI: 10.1186/1742-9994-10-55

Laura Johnson, Beth Mantle, Janet Gardner, Patricia Backwell (2013)
Morphometric measurements of dragonfly wings: the accuracy of pinned, scanned and detached measurement methods. ZooKeys 276: 77.

DOI: 10.3897/zookeys.276.4207

Marco Pombi, Wamdaogo M Guelbeogo, Maria Calzetta, N’Fale Sagnon, Vincenzo Petrarca, Vincenzo La Gioia, Alessandra della Torre (2015)
Evaluation of a protocol for remote identification of mosquito vector species reveals BG-Sentinel trap as an efficient tool for Anopheles gambiae outdoor collection in Burkina Faso. Malaria Journal 14: .

DOI: 10.1186/s12936-015-0674-7

YUCHEN ANG, JAYANTHI PUNIAMOORTHY, ADRIAN C. PONT, MIROSLAV BARTAK, WOLF U. BLANCKENHORN, WILLIAM G. EBERHARD, NALINI PUNIAMOORTHY, VERA C. SILVA, LORENZO MUNARI, RUDOLF MEIER (2013)
A plea for digital reference collections and other science‐based digitization initiatives in taxonomy: Sepsidnet as exemplar. Systematic Entomology 38: 637.

DOI: 10.1111/syen.12015

Ana Dal Molin, James B. Woolley (2020)
Notes on types of Australian Chartocerus Motschulsky (Hymenoptera: Signiphoridae). Journal of Natural History 54: 681.

DOI: 10.1080/00222933.2020.1785573

Fabian Plum, David Labonte (2021)
scAnt—an open-source platform for the creation of 3D models of arthropods (and other small objects). PeerJ 9: e11155.

DOI: 10.7717/peerj.11155

Yichen He, Christopher R. Cooney, Steve Maddock, Gavin H. Thomas, Samuel V. Scarpino (2023)
Using pose estimation to identify regions and points on natural history specimens. PLOS Computational Biology 19: e1010933.

DOI: 10.1371/journal.pcbi.1010933

Chuong V. Nguyen, David R. Lovell, Matt Adcock, John La Salle, Carlos López-Vaamonde (2014)
Capturing Natural-Colour 3D Models of Insects for Species Discovery and Diagnostics. PLoS ONE 9: e94346.

DOI: 10.1371/journal.pone.0094346

Jan Mertens, Martijn Van Roie, Jonas Merckx, Wouter Dekoninck (2017)
The use of low cost compact cameras with focus stacking functionality in entomological digitization projects. ZooKeys 712: 141.

DOI: 10.3897/zookeys.712.20505

Dirk Steinke, Jaclyn T. A. McKeown, Allison Zyba, Joschka McLeod, Corey Feng, Paul D. N. Hebert (2024)
Low-cost, high-volume imaging for entomological digitization. ZooKeys 1206: 315.

DOI: 10.3897/zookeys.1206.123670

Alexander N. Schmidt-Lebuhn, Nunzio Knerr (2023)
Efficient Generation of Training Libraries for Image Classification Models from Photos of Herbarium Specimens. International Journal of Plant Sciences 184: 387.

DOI: 10.1086/724950

Gil Nelson, Patrick Sweeney, Lisa E. Wallace, Richard K. Rabeler, Dorothy Allard, Herrick Brown, J. Richard Carter, Michael W. Denslow, Elizabeth R. Ellwood, Charlotte C. Germain‐Aubrey, Ed Gilbert, Emily Gillespie, Leslie R. Goertzen, Ben Legler, D. Blaine Marchant, Travis D. Marsico, Ashley B. Morris, Zack Murrell, Mare Nazaire, Chris Neefus, Shanna Oberreiter, Deborah Paul, Brad R. Ruhfel, Thomas Sasek, Joey Shaw, Pamela S. Soltis, Kimberly Watson, Andrea Weeks, Austin R. Mast (2015)
Digitization workflows for flat sheets and packets of plants, algae, and fungi. Applications in Plant Sciences 3: .

DOI: 10.3732/apps.1500065

John La Salle, Kristen J. Williams, Craig Moritz (2016)
Biodiversity analysis in the digital era. Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150337.

DOI: 10.1098/rstb.2015.0337

Alexander Knyshov, Samantha Hoang, Christiane Weirauch, Elizabeth Jockusch (2021)
Pretrained Convolutional Neural Networks Perform Well in a Challenging Test Case: Identification of Plant Bugs (Hemiptera: Miridae) Using a Small Number of Training Images. Insect Systematics and Diversity 5: .

DOI: 10.1093/isd/ixab004

Alex Hardisty, Hannu Saarenmaa, Ana Casino, Mathias Dillen, Karsten Gödderz, Quentin Groom, Helen Hardy, Dimitris Koureas, Abraham Nieva de la Hidalga, Deborah Paul, Veljo Runnel, Xavier Vermeersch, Myriam van Walsum, Luc Willemse (2020)
Conceptual design blueprint for the DiSSCo digitization infrastructure - DELIVERABLE D8.1. Research Ideas and Outcomes 6: .

DOI: 10.3897/rio.6.e54280

Vincent Smith, Vladimir Blagoderov (2012)
Bringing collections out of the dark. ZooKeys 209: 1.

DOI: 10.3897/zookeys.209.3699

Andrew Edward Z. Short, Torsten Dikow, Corrie S. Moreau (2018)
Entomological Collections in the Age of Big Data. Annual Review of Entomology 63: 513.

DOI: 10.1146/annurev-ento-031616-035536

Riitta Tegelberg, Tero Mononen, Hannu Saarenmaa (2014)
High‐performance digitization of natural history collections: Automated imaging lines for herbarium and insect specimens. TAXON 63: 1307.

DOI: 10.12705/636.13

Jan Mertens, Martijn Van Roie, Jonas Merckx, Wouter Dekoninck (2017)
The use of low cost compact cameras with focus stacking functionality in entomological digitization projects. ZooKeys 712: 141.

DOI: 10.3897/zookeys.5555.20505

Leonardo M. Borges, Victor Candido Reis, Rafael Izbicki, Natalie Cooper (2020)
Schrödinger's phenotypes: Herbarium specimens show two‐dimensional images are both good and (not so) bad sources of morphological data. Methods in Ecology and Evolution 11: 1296.

DOI: 10.1111/2041-210X.13450

Oleksandr Holovachov, Andriy Zatushevsky, Ihor Shydlovsky (2014)
Whole-Drawer Imaging of Entomological Collections: Benefits, Limitations and Alternative Applications. Journal of Conservation and Museum Studies 12: .

DOI: 10.5334/jcms.1021218

Peter Decker, Axel Christian, Willi E.R. Xylander (2018)
VIRMISCO – The Virtual Microscope Slide Collection. ZooKeys 741: 271.

DOI: 10.3897/zookeys.741.22284

Maarten Heerlien, Joost Van Leusen, Stephanie Schnörr, Suzanne De Jong-Kole, Niels Raes, Kirsten Van Hulsen (2015)
The Natural History Production Line. Journal on Computing and Cultural Heritage 8: 1.

DOI: 10.1145/2644822

Bernhard Ströbel, Sebastian Schmelzle, Nico Blüthgen, Michael Heethoff (2018)
An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging. ZooKeys 759: 1.

DOI: 10.3897/zookeys.759.24584

Joan E. Ball-Damerow, Laura Brenskelle, Narayani Barve, Pamela S. Soltis, Petra Sierwald, Rüdiger Bieler, Raphael LaFrance, Arturo H. Ariño, Robert P. Guralnick, Daniel de Paiva Silva (2019)
Research applications of primary biodiversity databases in the digital age. PLOS ONE 14: e0215794.

DOI: 10.1371/journal.pone.0215794

Natalia Rosas-Ramos, Paloma Mas-Peinado, Diego Gil-Tapetado, Ernesto Recuero, José L. Ruiz, Mario García-París (2020)
Catalogue, distribution, taxonomic notes, and conservation of the Western Palearctic endemic hunchback beetles (Tenebrionidae, Misolampus). ZooKeys 963: 81.

DOI: 10.3897/zookeys.963.53500

Thanh-Nghi Doan, Chuong V. Nguyen (2024)
A low-cost digital 3D insect scanner. Information Processing in Agriculture 11: 337.

DOI: 10.1016/j.inpa.2023.03.003

John W.H. Trueman, David K. Yeates (2015)
Can whole-drawer images measure up? A reply to Johnson et al. (2013)?. ZooKeys 500: 141.

DOI: 10.3897/zookeys.500.9139

Michael Greeff, Max Caspers, Vincent Kalkman, Luc Willemse, Barry Sunderland, Olaf Bánki, Laurens Hogeweg (2022)
Sharing taxonomic expertise between natural history collections using image recognition. Research Ideas and Outcomes 8: .

DOI: 10.3897/rio.8.e79187

Mansi Mungee, Ramana Athreya (2020)
Rapid photogrammetry of morphological traits of free‐ranging moths. Ecological Entomology 45: 911.

DOI: 10.1111/een.12907

F. V. Konstantinov, A. A. Namyatova (2019)
Taxonomic Revisions and Specimen Databases in the Internet Age: Dealing with a Species Rich Insect Taxon. Entomological Review 99: 340.

DOI: 10.1134/S0013873819030072

Vladimir Blagoderov, Ian Kitching, Laurence Livermore, Thomas Simonsen, Vincent Smith (2012)
No specimen left behind: industrial scale digitization of natural history collections. ZooKeys 209: 133.

DOI: 10.3897/zookeys.209.3178

Oskar L. P. Hansen, Jens‐Christian Svenning, Kent Olsen, Steen Dupont, Beulah H. Garner, Alexandros Iosifidis, Benjamin W. Price, Toke T. Høye (2020)
Species‐level image classification with convolutional neural network enables insect identification from habitus images. Ecology and Evolution 10: 737.

DOI: 10.1002/ece3.5921

Kika T. Tuff, Caroline K. Glidden, Brett A. Melbourne, Jacqui A. Meyers, Henry A. Nix, Stephen D. Sarre, Kendi F. Davies (2019)
Shrinking skinks: lizard body size declines in a long-term forest fragmentation experiment. Landscape Ecology 34: 1395.

DOI: 10.1007/s10980-019-00853-4

Alexander Popkov, Fedor Konstantinov, Vladimir Neimorovets, Alexey Solodovnikov (2022)
Machine learning for expert‐level image‐based identification of very similar species in the hyperdiverse plant bug family Miridae (Hemiptera: Heteroptera). Systematic Entomology 47: 487.

DOI: 10.1111/syen.12543

Lawrence N. Hudson, Vladimir Blagoderov, Alice Heaton, Pieter Holtzhausen, Laurence Livermore, Benjamin W. Price, Stéfan van der Walt, Vincent S. Smith, Nico Cellinese (2015)
Inselect: Automating the Digitization of Natural History Collections. PLOS ONE 10: e0143402.

DOI: 10.1371/journal.pone.0143402

Beulah H. Garner, Thomas J. Creedy, Elizabeth L. Allan, Robyn Crowther, Elizabeth Devenish, Phaedra Kokkini, Laurence Livermore, Krisztina Lohonya, Nicola Lowndes, Peter Wing, Alfried P. Vogler (2024)
The taxonomic composition and chronology of a museum collection of Coleoptera revealed through large-scale digitisation. Frontiers in Ecology and Evolution 12: .

DOI: 10.3389/fevo.2024.1305931

Keanu Buschbacher, Dirk Ahrens, Marianne Espeland, Volker Steinhage (2020)
Image-based species identification of wild bees using convolutional neural networks. Ecological Informatics 55: 101017.

DOI: 10.1016/j.ecoinf.2019.101017

Maria Consuelo Sendino (2013)
Use of QR Code Labels in Museum Collection Management. Collections: A Journal for Museum and Archives Professionals 9: 239.

DOI: 10.1177/155019061300900302

Chuong Nguyen, Matt Adcock, Stuart Anderson, David Lovell, Nicole Fisher, John La Salle (2017)
Towards High-Throughput 3D Insect Capture for Species Discovery and Diagnostics. 2017 IEEE 13th International Conference on e-Science (e-Science) : 559.

DOI: 10.1109/eScience.2017.90

Riitta Tegelberg, Jere Kahanpaa, Janne Karppinen, Tero Mononen, Zhenzhe Wu, Hannu Saarenmaa (2017)
Mass Digitization of Individual Pinned Insects Using Conveyor-Driven Imaging. 2017 IEEE 13th International Conference on e-Science (e-Science) : 523.

DOI: 10.1109/eScience.2017.85

Nitin Agarwal, Nicola Ferrier, Mark Hereld (2018)
Towards Automated Transcription of Label Text from Pinned Insect Collections. 2018 IEEE Winter Conference on Applications of Computer Vision (WACV) : 189.

DOI: 10.1109/WACV.2018.00027

Changming Sun, Paul Flemons, Yongsheng Gao, Dadong Wang, Nicole Fisher, John La Salle (2016)
Automated Image Analysis on Insect Soups. 2016 International Conference on Digital Image Computing: Techniques and Applications (DICTA) : 1.

DOI: 10.1109/DICTA.2016.7797010

Chuong Nguyen, David Lovell, Rolf Oberprieler, Debbie Jennings, Matt Adcock, Eleanor Gates-Stuart, John La Salle (2013)
Virtual 3D Models of Insects for Accelerated Quarantine Control. 2013 IEEE International Conference on Computer Vision Workshops : 161.

DOI: 10.1109/ICCVW.2013.27

Maarten Heerlien, Joost van Leusen, Stephanie Schnorr, Kirsten van Hulsen (2013)
The natural history production line: An industrial approach to the digitization of scientific collections. 2013 Digital Heritage International Congress (DigitalHeritage) : 289.

DOI: 10.1109/DigitalHeritage.2013.6744766

Lorenz Wührl, Kirsten Rotmann, Rudolf Meier, Emily Hartop, Nathalie Klug, Christian Pylatiuk (2023)
DiversityScanner-360°: An Automated System for Digitizing Invertebrate Bulk Samples. 2023 3rd International Conference on Robotics, Automation and Artificial Intelligence (RAAI) : 226.

DOI: 10.1109/RAAI59955.2023.10601274

Stuart Anderson, Matt Adcock, Beth Mantle, John La Salle, Chuong Nguyen, David Lovell (2015)
Towards web-based semantic enrichment of 3D insects. Proceedings of the 20th International Conference on 3D Web Technology : 163.

DOI: 10.1145/2775292.2778305

Sundaram Muthu, Taj Wedutenko, Jinguang Tong, Chuong Nguyen, Lars Petersson (2023)
Towards End-to-End Automatic Insect Handling and Insect Scanning. 2023 International Conference on Digital Image Computing: Techniques and Applications (DICTA) : 168.

DOI: 10.1109/DICTA60407.2023.00031

Olivia Dry, Sundaram Muthu, Jinguang Tong, Chuong Nguyen, Lars Petersson (2023)
IQScan: Automatic Insect Loading and 3D Scanning. 2023 International Conference on Digital Image Computing: Techniques and Applications (DICTA) : 205.

DOI: 10.1109/DICTA60407.2023.00036