Designing an herbarium digitisation workflow with built-in image quality management

Digitisation of natural history collections has evolved from creating databases for the recording of specimens’ catalogue and label data to include digital images of specimens. This has been driven by several important factors, such as a need to increase global accessibility to specimens and to preserve the original specimens by limiting their manual handling. The size of the collections pointed to the need of high throughput digitisation workflows. However, digital imaging of large numbers of fragile specimens is an expensive and time-consuming process that should be performed only once. To achieve this, the digital images produced need to be useful for the largest set of applications possible and have a potentially unlimited shelf life. The constraints on digitisation speed need to be balanced against the applicability and longevity of the images, which, in turn, depend directly on the quality of those images. As a result, the quality criteria that specimen images need to fulfil influence the design, implementation and execution of digitisation workflows. Different standards and guidelines for producing quality research images from specimens have been proposed; however, their actual adaptation to suit the needs of different types of specimens requires further analysis. This paper presents the digitisation workflow implemented by Meise Botanic Garden (MBG). This workflow is relevant because of its modular design, its strong focus on image quality assessment, its flexibility that allows combining in-house and outsourced digitisation, processing, preservation and publishing facilities and its capacity to evolve for integrating alternative components from different sources. The design and operation of the digitisation workflow is provided to showcase how it was derived, with particular attention to the built-in audit trail within the workflow, which ensures the scalable production of high-quality specimen images and how this audit trail ensures that new modules do not affect either the speed of imaging or the quality of the images produced

Managing a Mass Digitization Project at Meise Botanic Garden: From Start to Finish

Mass digitization is a large undertaking for a collection. It is disruptive of routine and can challenge long-held practises. Having been through the procedure and survived, we feel we have a lot of experience to share with other institutions who are considering taking on this challenge. The changes that digitization has made to our institution are positive and the digitization a success, but that is not to say that we would not have done some things differently, were we to repeat the exercise. In 2015 Meise Botanic Garden received a grant from the Flemish Government to upgrade its digitization infrastructure and mass digitize 1.2 million specimens from its African and Belgian Herbaria. The new infrastructure improved our workflow significantly, enabling us to digitize specimens five to ten times faster while also improving their quality. The mass digitization part of the project was split into two parts, imaging and transcription. The contract was awarded and out-sourced to Picturae, who started imaging in May 2016 using a conveyor belt installation. Prior to starting, a significant amount of preparation was required at the herbarium. Within one year, 1.2 million specimens were imaged. The images were captured as TIFF files and stored in triplicate at The Flemish Institute for Archiving (VIAA), while smaller derived JPEG 2000 and JPEG files were generated for day-to-day use. The second part of the project was label transcription. A third of the specimens were transcribed in-house for capturing minimal data (barcode, filing name, collector, collector number & country of origin). This was partly done to reduce costs, but also allowed us to compare in-house to out-sourced transcription. Some 500,000 specimens were transcribed, either completely or partially, by Alembo (subcontracted by Picturae).The remaining 200.000 specimens from our Belgian Herbarium are being transcribed using crowdsourcing. The latter is being realized through the citizen science platform DoeDat (www.doedat.be) that was launched in November 2017. Many lessons have been learnt with respect to implementing mass digitization, both practically and sociologically. Many of the problems encountered during the project could have been avoided by changing the workflow. The addition of extra control points during the process could have reduced problems encountered later in the data capture process. Solving these problems at a later stage was time consuming. Trying to “save money” can result in a disruptive workflow, which may lead to a number of costly errors. Mass digitization has fundamentally changed the workflow in our collections and the way in which our herbarium is managed. All images for the African and Belgian collections may be now found on our new virtual herbarium www.botanicalcollections.be

How Mass Digitization is changing Herbarium Collection Management at the Botanic Garden Meise (BR) – Teaching old dogs new tricks!

The Botanic Garden Meise (BR) has been involved in a mass digitization project over the past 2.5 years. At present, over 1.2 million herbarium specimens have been imaged. A third of these images already have minimal data, while the remainder data are presently being captured and should be finished in the coming months. Many lessons have been learned along the way with respect to the pitfalls of implementing mass digitization, both technically and sociologically. Mass digitization has also fundamentally changed the management workflow of our collections. This includes the creation of new protocols to ensure that new and returning material be photographed before being incorporated into already digitized collections, thus ensuring that data are not lost. A new portal has been created following an independent analysis of user requirements. This will result in increased visibility of our collections, making them more discoverable. The new portal provides additional functionality, including unique stable Uniform Resource Identifiers (URI) for each specimen and a machine readable version of the data. These identifiers follow the recommendations of the Consortium of European Taxonomic Facilities (http://cetaf.org/cetaf-stable-identifiers). The identifiers are a valuable tool and resource for researchers, but it is incumbent upon them to use this resource responsibly for the citation of specimens. Many research staff have not been actively involved in the mass digitization exercise and need to be educated on its impact and importance. As more and more images and data are linked to publications, they become easier to evaluate and verify. These digital data may also be repurposed in other studies, thus advancing science and herbarium management. As an increased number of institutions place their collections online, the greater this resource becomes for both collection management as well as research, particularly as links between collections become apparent. These links may include improved georeferencing, establishing collector itineraries, and new determinations for duplicate specimens

How Mass Digitization is changing Herbarium Collection Management at the Botanic Garden Meise (BR) – Teaching old dogs new tricks!

The Botanic Garden Meise (BR) has been involved in a mass digitization project over the past 2.5 years. At present, over 1.2 million herbarium specimens have been imaged. A third of these images already have minimal data, while the remainder data are presently being captured and should be finished in the coming months. Many lessons have been learned along the way with respect to the pitfalls of implementing mass digitization, both technically and sociologically. Mass digitization has also fundamentally changed the management workflow of our collections. This includes the creation of new protocols to ensure that new and returning material be photographed before being incorporated into already digitized collections, thus ensuring that data are not lost. A new portal has been created following an independent analysis of user requirements. This will result in increased visibility of our collections, making them more discoverable. The new portal provides additional functionality, including unique stable Uniform Resource Identifiers (URI) for each specimen and a machine readable version of the data. These identifiers follow the recommendations of the Consortium of European Taxonomic Facilities (http://cetaf.org/cetaf-stable-identifiers). The identifiers are a valuable tool and resource for researchers, but it is incumbent upon them to use this resource responsibly for the citation of specimens. Many research staff have not been actively involved in the mass digitization exercise and need to be educated on its impact and importance. As more and more images and data are linked to publications, they become easier to evaluate and verify. These digital data may also be repurposed in other studies, thus advancing science and herbarium management. As an increased number of institutions place their collections online, the greater this resource becomes for both collection management as well as research, particularly as links between collections become apparent. These links may include improved georeferencing, establishing collector itineraries, and new determinations for duplicate specimens

Ten lessons learned from the mass digitisation of a herbarium collection

Worldwide, herbaria maintain collections of reference specimens representing global plant diversity. These collections are a valuable resource for fundamental botanical research and applied scientific research across various disciplines, and play a significant role in addressing major societal challenges such as biodiversity conservation. The digitisation of herbarium specimens and their online dissemination is one of the most important recent developments in the curation of these collections. Digitisation significantly enhances access to the collections for the research community and facilitates large-scale analysis of biodiversity data. Digitisation also provides a means for preserving the physical specimens, as it reduces the need for handling and transportation. Rapid technological developments have greatly accelerated the rate of databasing and digital imaging of collections. Meise Botanic Garden recently completed a six-year project to mass digitise its herbarium collections of about 3 million specimens mounted on sheets and through this process we have learned valuable lessons. We have captured our experience in 10 recommendations for other collection-holding institutions to take inspiration from as they start planning their own digitisation efforts. We also present case studies where we delve deeper into certain topics as examples

Mass Digitization of the Herbarium collection BR at the Botanic Garden Meise

A overview of the Mass Digitization of the Herbarium collection BR at the Botanic Garden Meise