Mass digitisation of a herbarium collection: ten lessons learned from Meise Botanic Garden

The lessons were published in the open-access journal PhytoKeys.

Herbarium specimens on a conveyor belt at Meise Botanic Garden
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Herbaria – collections of preserved plant specimens – are crucial in botanical research and biodiversity conservation. Digitising these collections is an important step towards making data available to all, preserving specimens by reducing the need for handling, and creating new research opportunities.

Herbarium specimens on a conveyor belt at Meise Botanic Garden.
Mass digitisation of herbarium specimens on a conveyor belt at Meise Botanic Garden, allowing the imaging of 3,000–5,000 specimens per day.

Meise Botanic Garden recently completed a six-year project to digitise approximately three million specimens of their herbarium collection. While it was a big change for their organisation, it was one they deemed necessary to bring their collection into the digital age. 

The digitisation project contributes to the Distributed System of Scientific Collections (DiSSCo) research infrastructure aiming to unify access to biodiversity and geodiversity specimens under common standards, giving users access to specimens and their data from European institutions. DiSSCo has also created a website with digitisation guides and the DiSSCo Knowledge Base

Several people sitting at tables working on herbarium specimens.
Joint restoration session of the herbarium team at Meise Botanic Garden.

Based on their experience, the team published ten valuable lessons they learned during the process to assist  other institutions embarking on similar digitisation projects. These lessons are available in the open-access journal PhytoKeys.

1. Knowing yourself is the beginning of all wisdom ― Aristotle

Before starting digitisation, it is important to understand the full scope of your collection. This involves detailed inventory checks and assessments of the state of the specimens. Knowing the exact number and condition of the specimens will help in accurate budgeting and planning. A detailed inventory of a representative tenth of your collection can be extrapolated to the entire collection.

2. Prioritise (if lack of money forces you to do so)

If resources are limited, prioritising which parts of the collection to digitise first is key. Consider factors such as the scientific importance of the specimens, their physical state, and stakeholder needs. It is important to note that digitising the entire collection can be more efficient than selecting subcollections, as partial digitisation can complicate management.

3. Learn from other people’s successes – and mistakes

Do not reinvent the wheel. Engage with other institutions that have undertaken similar projects to learn from their successes and mistakes. Follow existing guidelines and adapt them to fit your specific needs. If you think you have a better way of doing things, talk it over with someone with experience. 

4. Decide whether to do it yourself or have it done for you

Deciding whether to conduct the digitisation in-house or to outsource it depends on available resources. Consider the skills and availability of your staff and the costs associated with outsourcing. Some tasks, such as imaging or data transcription, might be more efficiently handled by external specialists.

5. Make a plan

A well-thought-out plan is crucial. Define workflows, procedures, and quality control mechanisms. And be specific about your requirements when outsourcing parts of the project to avoid any misunderstandings.

6. Go shopping

Ensure that all necessary supplies, such as barcodes, storage containers, and IT infrastructure, are in place before starting the digitisation process. Bulk purchasing is often cost-effective, and having everything ready will prevent delays.

7. Make your collection look its best for the photographer

Prepare the specimens for imaging by incorporating pre-digitisation curation steps like repairing damaged specimens and adding barcodes. 

8. Expect problems, particularly ones that you don’t expect

Problems will arise, from equipment malfunctions to human errors. Establish quality control processes to catch issues early. Automate checks where possible and ensure prompt human review for aspects like image focus and lighting.

9. Make your data visible – make a big deal of it

Making digitised data publicly accessible is vital. Use online portals and ensure the data adheres to FAIR principles (Findable, Accessible, Interoperable, Reusable). Publicity will increase the use and impact of your collection.

10. Save your data for the future

Make sure the digitised data is backed up in a secure, offsite archive. Long-term storage solutions should be considered to preserve the data for future use. And factor this ongoing cost into the budget.

To read extended advice from Meise Botanic Garden, as well as four case studies, check out the full research paper below:

Original source

De Smedt S, Bogaerts A, De Meeter N, Dillen M, Engledow H, Van Wambeke P, Leliaert F, Groom Q (2024) Ten lessons learned from the mass digitisation of a herbarium collection. PhytoKeys 244: 23-37. 


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