Digitization workflows for flat sheets and packets of plants, algae, and fungi

Nelson, Gil; Sweeney, Patrick W.; Wallace, Lisa E.; Rabeler, Richard K.; Allard, Dorothy J.; Brown, Herrick; Carter, J. Richard; Denslow, Michael W.; Ellwood, Elizabeth R.; Germain-Aubrey, Charlotte C.; Gilbert, Ed; Gillespie, Emily L.; Goertzen, Leslie R.; Legler, Ben; Marchant, Dominique; Marsico, Travis D.; Morris, Ashley B.; Murrell, Zack E.; Nazaire, Mare; Neefus, Chris; Oberreiter, Shanna; Paul, Deborah; Ruhfel, Brad R.; Sasek, Thomas W.; Shaw, Joey; Soltis, Pamela S.; Watson, Kimberly A.; Weeks, Andrea; Mast, Austin

doi:10.3732/apps.1500065

Cited by 47 publications

(40 citation statements)

References 25 publications

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“…https://www.idigbio.org/, www.gbif.org, http://vh.gbif.de/vh/or http://avh.chah.org.au/), but the digitization task is enormouswith over 350 million specimens to processand expensive. To optimize and speed up the process, various larger and smaller institutions have developed affordable digitization workflows (Haston et al, 2012;Nelson et al, 2015;Thiers et al, 2016;Harris & Marsico, 2017). Depending on data needs, digitization could be done in a prioritized way.…”

Section: Box 3 Digitization Challengementioning

confidence: 99%

Using herbaria to study global environmental change

et al. 2018

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During the last centuries, humans have transformed global ecosystems. With their temporal dimension, herbaria provide the otherwise scarce long-term data crucial for tracking ecological and evolutionary changes over this period of intense global change. The sheer size of herbaria, together with their increasing digitization and the possibility of sequencing DNA from the preserved plant material, makes them invaluable resources for understanding ecological and evolutionary species' responses to global environmental change. Following the chronology of global change, we highlight how herbaria can inform about long-term effects on plants of at least four of the main drivers of global change: pollution, habitat change, climate change and invasive species. We summarize how herbarium specimens so far have been used in global change research, discuss future opportunities and challenges posed by the nature of these data, and advocate for an intensified use of these 'windows into the past' for global change research and beyond.

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Section: Box 3 Digitization Challengementioning

confidence: 99%

Using herbaria to study global environmental change

et al. 2018

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“…The digitizing process consists of predigitization curation, imaging specimens, databasing label and identifying information, and georeferencing locality information (Barkworth and Murrell, 2012; Nelson et al, 2015). Each of these steps can take a considerable amount of time to accomplish, so it is important to note that digitization often happens in stages.…”

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Digitizing specimens in a small herbarium: A viable workflow for collections working with limited resources

Harris

Marsico

2017

Appl Plant Sci

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Premise of the study:Small herbaria represent a significant portion of herbaria in the United States, but many are not digitizing their collections.Methods:At the Arkansas State University Herbarium (STAR), we have created a viable workflow to help small herbaria begin the digitization process, including suggestions for publishing data on the Internet. We calculated hourly rates of each phase of the digitization process. We also mapped accessions at the county level to determine geographic strengths in the collection.Results:All 17,678 accessioned flowering plant specimens at STAR are imaged, databased in Specify, and available electronically on the herbarium’s website. Students imaged the specimens at a mean rate of 145/h. We found differences in databasing rates between the graduate student leading the project (47/h) and undergraduate assistants (25/h). The majority of specimens at STAR were collected within the counties neighboring the institution.Discussion:With this workflow, we estimate that one person can digitize a 20,000-specimen collection in less than 2.5 yr by working only 10 h/wk. Because STAR is a small herbarium with limited resources, the application of the workflow described should assist curators of similar-sized collections as they contemplate and undertake the digitization process.

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“…Recommendations for tools, as well as step‐by‐step guidelines on how to use them for image capture and manual batch image post‐processing tasks, are available on iDigBio's website (Nelson et al., ; Tulig et al., ). Among the equipment recommended for imaging is a standardized color reference chart (CRC), which may be used later for color normalization during post‐processing (Nelson et al., ). Currently, post‐processing tasks using CRCs require manual intervention by trained technicians, proprietary software, as well as time for the import and export processes, requiring considerable amounts of time for technician training and their processing of images.…”

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Enabling automated herbarium sheet image post‐processing using neural network models for color reference chart detection

et al. 2020

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Premise Large‐scale efforts to digitize herbaria have resulted in more than 18 million publicly available Plantae images on sites such as iDigBio. The automation of image post‐processing will lead to time savings in the digitization of biological specimens, as well as improvements in data quality. Here, new and modified neural network methodologies were developed to automatically detect color reference charts (CRC), enabling the future automation of various post‐processing tasks. Methods and Results We used 1000 herbarium specimen images from 52 herbaria to test our novel neural network model, ColorNet, which was developed to identify CRCs smaller than 4 cm2, resulting in a 30% increase in accuracy over the performance of other state‐of‐the‐art models such as Faster R‐CNN. For larger CRCs, we propose modifications to Faster R‐CNN to increase inference speed. Conclusions Our proposed neural networks detect a range of CRCs, which may enable the automation of post‐processing tasks found in herbarium digitization workflows, such as image orientation or white balance correction.

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Digitization workflows for flat sheets and packets of plants, algae, and fungi

Cited by 47 publications

References 25 publications

Using herbaria to study global environmental change

Using herbaria to study global environmental change

Digitizing specimens in a small herbarium: A viable workflow for collections working with limited resources

Enabling automated herbarium sheet image post‐processing using neural network models for color reference chart detection

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