Five task clusters that enable efficient and effective digitization of biological collections

Gil Nelson; Deborah Paul; Greg Riccardi; Austin Mast

doi:10.3897/zookeys.209.3135

Piotr Niedzielski, Joanna Markiewicz (2023)
DIGITALIZATION OF HERBARIUM COLLECTIONS AS A TOOL FOR THE COMMERCIALIZATION OF SCIENTIFIC KNOWLEDGE. Procedia Computer Science 225: 2194.

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A. P. Seregin, V. N. Pashkina, I. N. Pospelov (2023)
GEODATA OF THE MOSCOW UNIVERSITY HERBARIUM: DATA STRUCTURE AND GEOREFERENCING METHODICS. Ботанический журнал 108: 491.

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Simone Papalini, Valerio Di Vittori, Alice Pieri, Marina Allegrezza, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Elisa Bellucci, Tania Gioia, Luis Guasch Pereira, Karolina Susek, Maud Tenaillon, Kerstin Neumann, Roberto Papa (2023)
Challenges and Opportunities behind the Use of Herbaria in Paleogenomics Studies. Plants 12: 3452.

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A. Townsend Peterson, Alex Asase, Dora Canhos, Sidnei de Souza, John Wieczorek (2018)
Data Leakage and Loss in Biodiversity Informatics. Biodiversity Data Journal 6: .

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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: .

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Emily M. Braker (2022)
Phototank setup and focus stack imaging method for reptile and amphibian specimens (Amphibia, Reptilia). ZooKeys 1134: 185.

DOI: 10.3897/zookeys.1134.96103

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: .

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Alex Asase, Moses N. Sainge, Raoufou A. Radji, Omokafe A. Ugbogu, A. Townsend Peterson (2020)
A new model for efficient, need‐driven progress in generating primary biodiversity information resources. Applications in Plant Sciences 8: .

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Vladimir Blagoderov, Malcolm Penn, Mike Sadka, Adrian Hine, Stephen Brooks, Darrell Siebert, Chris Sleep, Steve Cafferty, Elisa Cane, Geoff Martin, Flavia Toloni, Peter Wing, John Chainey, Liz Duffell, Rob Huxley, Sophie Ledger, Caitlin McLaughlin, Gerardo Mazzetta, Jasmin Perera, Robyn Crowther, Lyndsey Douglas, Joanna Durant, Elisabetta Scialabba, Martin Honey, Blanca Huertas, Theresa Howard, Victoria Carter, Sara Albuquerque, Gordon Paterson, Ian Kitching (2017)
iCollections methodology: workflow, results and lessons learned. Biodiversity Data Journal 5: .

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Michael C. Zalot (2023)
The vanishing arcade redemption token: intermediate digitization and commercialization of local gaming exonumia. Atlantic Journal of Communication 31: 438.

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Arnald Marcer, Agustí Escobar, Arthur Chapman, John Wieczorek (2023)
GeoPick: Georeferencing Made Easy. Biodiversity Information Science and Standards 7: .

DOI: 10.3897/biss.7.111036

Mathias Dillen, Quentin Groom, Simon Chagnoux, Anton Güntsch, Alex Hardisty, Elspeth Haston, Laurence Livermore, Veljo Runnel, Leif Schulman, Luc Willemse, Zhengzhe Wu, Sarah Phillips (2019)
A benchmark dataset of herbarium specimen images with label data. Biodiversity Data Journal 7: .

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Caitlin N. Terry, Aura M. Alonso‐Rodríguez, Scott E. Miller, Catherine M. Hulshof (2023)
Lepidoptera research in Puerto Rico: Reconnecting with historical legacies to guide future priorities. Biotropica 55: 1215.

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Theresa Dellinger, Victoria Wong, Paul Marek (2016)
Makelabels: a Bash script for generating data matrix codes for collection management. Biodiversity Data Journal 4: e9583.

DOI: 10.3897/BDJ.4.e9583

Aleksey V. Vaganov, Alexander I. Shmakov, Sergey V. Smirnov, Nadezda A. Usik, Alena A. Shibanova, Aleksey A. Kechaykin, Petr A. Kosachev, Tatyana M. Kopytina, Elizaveta A. Zholnerova, Kristina E. Medvedeva, Vladimir F. Zaikov, Tatyana A. Sinitsyna, Alexander P. Shalimov, Evgenij V. Antonyuk, Polina D. Gudkova, Denis A. Dmitriev, Alexander A. Batkin, Dmitry E. Kasatkin, Denis L. Belkin (2021)
Virtual Herbarium ALTB: collection of vascular plants of the Altai Mountain Country. Biodiversity Data Journal 9: .

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

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Song‐Quan Ong, Nurzatil Sharleeza Mat Jalaluddin, Kien Thai Yong, Su Ping Ong, Kooi Fong Lim, Suhaila Azhar (2023)
Digitization of natural history collections: A guideline and nationwide capacity building workshop in Malaysia. Ecology and Evolution 13: .

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Diana L. Soteropoulos, Travis D. Marsico (2022)
Community Science Success for Herbarium Transcription in Arkansas: Building a Network of Students and Volunteers for Notes from Nature. Castanea 87: .

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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.

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

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Bogdan Jackowiak, Jerzy Błoszyk, Zbigniew Celka, Szymon Konwerski, Piotr Szkudlarz, Justyna Wiland-Szymańska (2022)
The natural history collections of Adam Mickiewicz University in Poznań (Poland): an outline of their history and content. Biodiversity Research and Conservation 65: 1.

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

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Serdar Aslan, Rasim Murat Aydınkal, Necmi Aksoy, Neval Güneş Özkan (2024)
Modern Sayısal Herbaryumlar İçin Öne Çıkan Bir Model: Düzce Üniversitesi Orman Fakültesi (DUOF) Sanal Herbaryumu. Düzce Üniversitesi Orman Fakültesi Ormancılık Dergisi 20: 78.

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Azalea Guerra‐García, Tania Gioia, Eric von Wettberg, Giuseppina Logozzo, Roberto Papa, Elena Bitocchi, Kirstin E Bett (2021)
Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well‐Represented Collections. Current Protocols 1: .

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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: .

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Erin M. Dillon, Emma M. Dunne, Tom M. Womack, Miranta Kouvari, Ekaterina Larina, Jordan Ray Claytor, Angelina Ivkić, Mark Juhn, Pablo S. Milla Carmona, Selina Viktor Robson, Anwesha Saha, Jaime A. Villafaña, Michelle E. Zill (2023)
Challenges and directions in analytical paleobiology. Paleobiology 49: 377.

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Vladimir Blagoderov, Malcolm Penn, Mike Sadka, Adrian Hine, Stephen Brooks, Darrell Siebert, Chris Sleep, Steve Cafferty, Elisa Cane, Geoff Martin, Flavia Toloni, Peter Wing, John Chainey, Liz Duffell, Rob Huxley, Sophie Ledger, Caitlin McLaughlin, Gerardo Mazzetta, Jasmin Perera, Robyn Crowther, Lyndsey Douglas, Joanna Durant, Martin Honey, Blanca Huertas, Theresa Howard, Victoria Carter, Sara Albuquerque, Gordon Paterson, Ian Kitching (2017)
iCollections methodology: workflow, results and lessons learned. Biodiversity Data Journal 5: .

DOI: 10.3897/BDJ.5.e19893

Gil Nelson, Shari Ellis (2019)
The history and impact of digitization and digital data mobilization on biodiversity research. Philosophical Transactions of the Royal Society B: Biological Sciences 374: 20170391.

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Elizabeth K. Shea, Petra Sierwald, Rüdiger Bieler, Gary Rosenberg (2018)
Priorities and Opportunities for Digitizing Mollusk Collections. American Malacological Bulletin 36: 171.

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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

C. L. Wood, K. L. Leslie, D. Claar, N. Mastick, W. Preisser, M. P.M. Vanhove, R. Welicky (2023)
How to use natural history collections to resurrect information on historical parasite abundances. Journal of Helminthology 97: .

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Kari M. Harris, Travis D. Marsico (2017)
Digitizing specimens in a small herbarium: A viable workflow for collections working with limited resources. Applications in Plant Sciences 5: .

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

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Colin Favret, Joseph Moisan-De Serres, Maxim Larrivée, Jean-Philippe Lessard (2020)
The Odonata of Quebec: Specimen data from seven collections. Biodiversity Data Journal 8: .

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Bogdan Jackowiak, Marcin Lawenda, Maciej M. Nowak, Paweł Wolniewicz, Jerzy Błoszyk, Michał Urbaniak, Piotr Szkudlarz, Damian Jędrasiak, Justyna Wiland-Szymańska, Rafał Bajaczyk, Norbert Meyer (2022)
Open Access to the Digital Biodiversity Database: A Comprehensive Functional Model of the Natural History Collections. Diversity 14: 596.

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Caleb Powell, Alaina Krakowiak, Rachel Fuller, Erica Rylander, Emily Gillespie, Shawn Krosnick, Brad Ruhfel, Ashley B. Morris, Joey Shaw (2021)
Estimating herbarium specimen digitization rates: Accounting for human experience. Applications in Plant Sciences 9: .

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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.

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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.

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E Louise Allan, Laurence Livermore, Benjamin Price, Olha Shchedrina, Vincent Smith (2019)
A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides. Biodiversity Data Journal 7: .

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Madelynn von Baeyer, John M. Marston (2021)
Best practices for digitizing a wood slide collection: The Bailey-Wetmore Wood Collection of the Harvard University Herbaria. Quaternary International 593-594: 50.

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Alex Hardisty, Laurence Livermore, Stephanie Walton, Matt Woodburn, Helen Hardy (2020)
Costbook of the digitisation infrastructure of DiSSCo. Research Ideas and Outcomes 6: .

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Alexey P. Seregin (2016)
Making the Russian Flora Visible: Fast Digitisation of the Moscow University Herbarium (MW) in 2015. TAXON 65: 205.

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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.

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Linda Seggi, Raffaella Trabucco, Stefano Martellos (2024)
Valorization of Historical Natural History Collections Through Digitization: The Algarium Vatova–Schiffner. Plants 13: 2901.

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Elizabeth R. Ellwood, Betty A. Dunckel, Paul Flemons, Robert Guralnick, Gil Nelson, Greg Newman, Sarah Newman, Deborah Paul, Greg Riccardi, Nelson Rios, Katja C. Seltmann, Austin R. Mast (2015)
Accelerating the Digitization of Biodiversity Research Specimens through Online Public Participation. BioScience 65: 383.

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Elizabeth R Ellwood, Paul Kimberly, Robert Guralnick, Paul Flemons, Kevin Love, Shari Ellis, Julie M Allen, Jason H Best, Richard Carter, Simon Chagnoux, Robert Costello, Michael W Denslow, Betty A Dunckel, Meghan M Ferriter, Edward E Gilbert, Christine Goforth, Quentin Groom, Erica R Krimmel, Raphael LaFrance, Joann Lacey Martinec, Andrew N Miller, Jamie Minnaert-Grote, Thomas Nash, Peter Oboyski, Deborah L Paul, Katelin D Pearson, N Dean Pentcheff, Mari A Roberts, Carrie E Seltzer, Pamela S Soltis, Rhiannon Stephens, Patrick W Sweeney, Matt von Konrat, Adam Wall, Regina Wetzer, Charles Zimmerman, Austin R Mast (2018)
Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar. BioScience 68: 112.

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Patrick W. Sweeney, Binil Starly, Paul J. Morris, Yiming Xu, Aimee Jones, Sridhar Radhakrishnan, Christopher J. Grassa, Charles C. Davis (2018)
Large–scale digitization of herbarium specimens: Development and usage of an automated, high–throughput conveyor system. TAXON 67: 165.

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Chelsea L. Wood, Maarten P. M. Vanhove (2023)
Is the world wormier than it used to be? We'll never know without natural history collections. Journal of Animal Ecology 92: 250.

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Charles C. Davis, Jonathan A. Kennedy, Christopher J. Grassa (2021)
Back to the future: A refined single‐user photostation for massively scaling herbarium digitization. TAXON 70: 635.

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Dakila A. Ledesma, Caleb A. Powell, Joey Shaw, Hong Qin (2020)
Enabling automated herbarium sheet image post‐processing using neural network models for color reference chart detection. Applications in Plant Sciences 8: .

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R. DeWalt, Matthew Yoder, Elise Snyder, Dmitry Dmitriev, Geoffrey Ower (2018)
Wet collections accession: a workflow based on a large stonefly (Insecta, Plecoptera) donation. Biodiversity Data Journal 6: .

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Dori L. Contreras (2018)
A workflow and protocol describing the field to digitization process for new project‐based fossil leaf collections. Applications in Plant Sciences 6: .

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Gaia Cortinovis, Markus Oppermann, Kerstin Neumann, Andreas Graner, Tania Gioia, Marco Marsella, Saleh Alseekh, Alisdair R. Fernie, Roberto Papa, Elisa Bellucci, Elena Bitocchi (2021)
Towards the Development, Maintenance, and Standardized Phenotypic Characterization of Single‐Seed‐Descent Genetic Resources for Common Bean. Current Protocols 1: .

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Victoria Slonosky, Renée Sieber, Gordon Burr, Lori Podolsky, Robert Smith, Madeleine Bartlett, Eun Park, Jeremy Cullen, Frédéric Fabry (2019)
From books to bytes: A new data rescue tool. Geoscience Data Journal 6: 58.

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Icaro Alzuru, Andrea Matsunaga, Mauricio Tsugawa, Jose A.B. Fortes (2017)
SELFIE: Self-Aware Information Extraction from Digitized Biocollections. 2017 IEEE 13th International Conference on e-Science (e-Science) : 69.

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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.

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Alexander Tianara, Bhisma Gusti Anugra, Wisnu Wardhana (2023)
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Luciane Marinoni, Elisandra de Almeida Chiquito, Chirlei Glienke, Clara Baringo Fonseca, Keila Elizabeth Macfadem Juarez, Daniel Silva Basílio, Diego Knop Henriques, Desirrê Alexia Lourenço Petters Vandresen, Gisele dos Santos Morais, Isaac Jorge, Alexandre Dias Pimenta, Anamaria Dal Molin, Aline da Silva Soares Souto, Cleverson Rannieri Meira dos Santos, Cristiana Silveira Serejo, Cristina Maria de Souza-Motta, Derlene Attili-Angelis, Fernanda P. Werneck, Fernando Rogério Carvalho, Guilherme Siniciato Terra Garbino, João Renato Stehmann, Leandro Lacerda Giacomin, Maria Aparecida de Jesus, Manuela da Silva, Marcelo Veronesi Fukuda, Ricardo de Souza Rosa, Rodrigo Costa-Araújo, Márcia Motta Maués, Silvana Carvalho Thiengo, Tania Regina dos Santos Silva, Tânia Sueli de Andrade, Taciana Barbosa Cavalcanti, Valquiria Ferreira Dutra, Vania Aparecida Vicente, André Luís de Gasper (2024)
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Olga Pisarenko, Igor Artemov, Sergey Kazanovsky, Ekaterina Prelovskaya (2019)
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