Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach

Elspeth Haston; Robert Cubey; Martin Pullan; Hannah Atkins; David Harris

doi:10.3897/zookeys.209.3121

Jun Wen, Stefanie M. Ickert‐Bond, Marc S. Appelhans, Laurence J. Dorr, Vicki A. Funk (2015)
Collections‐based systematics: Opportunities and outlook for 2050. Journal of Systematics and Evolution 53: 477.

DOI: 10.1111/jse.12181

Willi Egloff, Donat Agosti, Puneet Kishor, David Patterson, Jeremy Miller (2017)
Copyright and the Use of Images as Biodiversity Data. Research Ideas and Outcomes 3: .

DOI: 10.3897/rio.3.e12502

Barbara M. Thiers, Melissa C. Tulig, Kimberly A. Watson (2016)
Digitization of The New York Botanical Garden Herbarium. Brittonia 68: 324.

DOI: 10.1007/s12228-016-9423-7

Atsuko Takano, Theodor C. H. Cole, Hajime Konagai (2024)
A novel automated label data extraction and data base generation system from herbarium specimen images using OCR and NER. Scientific Reports 14: .

DOI: 10.1038/s41598-023-50179-0

Joaquim Santos, Paulo Rupino da Cunha, Fátima Sales (2020)
A strategy to digitise natural history collections with limited resources. Biodiversity Data Journal 8: .

DOI: 10.3897/BDJ.8.e55959

Amanda S. Gallinat, Luca Russo, Eli K. Melaas, Charles G. Willis, Richard B. Primack (2018)
Herbarium specimens show patterns of fruiting phenology in native and invasive plant species across New England. American Journal of Botany 105: 31.

DOI: 10.1002/ajb2.1005

Karen M. Thompson, Robert Turnbull, Emily Fitzgerald, Joanne L. Birch (2023)
Identification of herbarium specimen sheet components from high‐resolution images using deep learning. Ecology and Evolution 13: .

DOI: 10.1002/ece3.10395

Meghan A. Balk, John Bradley, M. Maruf, Bahadir Altintaş, Yasin Bakiş, Henry L. Bart, David Breen, Christopher R. Florian, Jane Greenberg, Anuj Karpatne, Kevin Karnani, Paula Mabee, Joel Pepper, Dom Jebbia, Thibault Tabarin, Xiaojun Wang, Hilmar Lapp (2024)
A FAIR and modular image‐based workflow for knowledge discovery in the emerging field of imageomics. Methods in Ecology and Evolution 15: 1129.

DOI: 10.1111/2041-210X.14327

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

Atsuko Takano, Yasuhiko Horiuchi, Yu Fujimoto, Kouta Aoki, Hiromune Mitsuhashi, Akira Takahashi (2019)
Simple but long-lasting: A specimen imaging method applicable for small- and medium-sized herbaria. PhytoKeys 118: 1.

DOI: 10.3897/phytokeys.118.29434

Luiz M. R. Gadelha, Pedro C. de Siracusa, Eduardo Couto Dalcin, Luís Alexandre Estevão da Silva, Douglas A. Augusto, Eduardo Krempser, Helen Michelle Affe, Raquel Lopes Costa, Maria Luiza Mondelli, Pedro Milet Meirelles, Fabiano Thompson, Marcia Chame, Artur Ziviani, Marinez Ferreira de Siqueira (2021)
A survey of biodiversity informatics: Concepts, practices, and challenges. WIREs Data Mining and Knowledge Discovery 11: .

DOI: 10.1002/widm.1394

Karen Thompson, Joanne Birch (2023)
Mapping the Digitisation Workflow in a University Herbarium. Research Ideas and Outcomes 9: .

DOI: 10.3897/rio.9.e106883

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

DOI: 10.3897/zookeys.209.3699

Patricia L. M. Lang, Franziska M. Willems, J. F. Scheepens, Hernán A. Burbano, Oliver Bossdorf (2019)
Using herbaria to study global environmental change. New Phytologist 221: 110.

DOI: 10.1111/nph.15401

Abraham Nieva de la Hidalga, Paul Rosin, Xianfang Sun, Ann Bogaerts, Niko De Meeter, Sofie De Smedt, Maarten Strack van Schijndel, Paul Van Wambeke, Quentin Groom (2020)
Designing an Herbarium Digitisation Workflow with Built-In Image Quality Management. Biodiversity Data Journal 8: .

DOI: 10.3897/BDJ.8.e47051

Krisztina Lohonya, Laurence Livermore, Jacek Wajer, Robyn Crowther, Elizabeth Devenish (2022)
Digitisation of the Natural History Museum’s collection of Dalbergia, Pterocarpus and the subtribe Phaseolinae (Fabaceae, Faboideae). Biodiversity Data Journal 10: .

DOI: 10.3897/BDJ.10.e94939

Kai Li, Jane Greenberg, Jillian Dunic (2020)
Data objects and documenting scientific processes: An analysis of data events in biodiversity data papers. Journal of the Association for Information Science and Technology 71: 172.

DOI: 10.1002/asi.24226

E. N. F. Souza, J. A. Hawkins (2017)
Comparison of Herbarium Label Data and Published Medicinal Use: Herbaria as an Underutilized Source of Ethnobotanical Information. Economic Botany 71: 1.

DOI: 10.1007/s12231-017-9367-1

Thomas Borsch, Albert-Dieter Stevens, Eva Häffner, Anton Güntsch, Walter G. Berendsohn, Marc Appelhans, Christina Barilaro, Bánk Beszteri, Frank Blattner, Oliver Bossdorf, Helmut Dalitz, Stefan Dressler, Rhinaixa Duque-Thüs, Hans-Joachim Esser, Andreas Franzke, Dethardt Goetze, Michaela Grein, Uta Grünert, Frank Hellwig, Jörn Hentschel, Elvira Hörandl, Thomas Janßen, Norbert Jürgens, Gudrun Kadereit, Timm Karisch, Marcus Koch, Frank Müller, Jochen Müller, Dietrich Ober, Stefan Porembski, Peter Poschlod, Christian Printzen, Martin Röser, Peter Sack, Philipp Schlüter, Marco Schmidt, Martin Schnittler, Markus Scholler, Matthias Schultz, Elke Seeber, Josef Simmel, Michael Stiller, Mike Thiv, Holger Thüs, Natalia Tkach, Dagmar Triebel, Ursula Warnke, Tanja Weibulat, Karsten Wesche, Andrey Yurkov, Georg Zizka (2020)
A complete digitization of German herbaria is possible, sensible and should be started now. Research Ideas and Outcomes 6: .

DOI: 10.3897/rio.6.e50675

Alexey Seregin, Nina Stepanova (2020)
MHA Herbarium: Eastern European collections of vascular plants. Biodiversity Data Journal 8: .

DOI: 10.3897/BDJ.8.e57512

Stephan Helfer (2014)
The type collections of rust fungi (Uredinales) in Berlin. Willdenowia 44: 345.

DOI: 10.3372/wi.44.44304

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

Agnes Kirchhoff, Ulrich Bügel, Eduard Santamaria, Fabian Reimeier, Dominik Röpert, Alexander Tebbje, Anton Güntsch, Fernando Chaves, Karl-Heinz Steinke, Walter Berendsohn (2018)
Toward a service-based workflow for automated information extraction from herbarium specimens. Database 2018: .

DOI: 10.1093/database/bay103

Pascal Dugenie, Nuno Freire, Daan Broeder (2017)
Building new knowledge from distributed scientific corpus: HERBADROP & EUROPEANA: Two concrete case studies for exploring big archival data. 2017 IEEE International Conference on Big Data (Big Data) : 2231.

DOI: 10.1109/BigData.2017.8258174