CASE STUDY
05
Digitising eight million plant and fungal specimens
at the Royal Botanic Gardens, Kew
at the Royal Botanic Gardens, Kew
The Royal Botanic Gardens, Kew is home to one of the world’s largest collections of plant and fungal samples, with over eight million specimens from around the world residing there.
Though in-person access to Kew’s Herbarium and Fungarium is made freely available to researchers, it’s accepted that the global scientific community would derive untold benefits from these resources being even more accessible. That is why the team at RBG Kew has taken on the colossal task of digitising their entire collection using FUJIFILM GFX100S and FUJINON GF63mmF2.8 R WR.
“We are currently embarking on our most ambitious project to date – to complete the digitisation of over eight million plant and fungi specimens,” explains Marie-Hélène Weech, lead digitisation operations manager at RBG Kew.
“These specimens underpin research into our greatest global challenges. Making all our images and specimens freely available online will allow people to access them from all over the world, accelerating research.”
Image 2024 © Fujifilm
An issue of scale
Digitising eight million items has presented difficulties of an entirely new magnitude, explains Marie-Hélène. “It has been a massive logistical operation,” she notes.
Since the outset of the digitisation project, RBG Kew has had to recruit, train and supervise a sizeable team – including digitisation officers, quality assurance officers, operations, support and curation staff, team leaders and data managers.
“We did not close the Herbarium or Fungarium to researchers and visitors,” Marie-Hélène continues. “However, this led to challenges in finding space for over 40 imaging workstations – around the building.”
Image 2024 © Fujifilm
FUJIFILM GFX100S
Requiring an imaging solution that offers extreme accuracy alongside ease of use within a scalable workflow, the team at RBG Kew gravitated towards the FUJIFILM GFX System.
“Our standard-size specimen sheets are being photographed with GFX100S cameras and the GF63mmF2.8 R WR lens,” explains imaging support officer Jonny Davies. “The cameras have been mounted to lightboxes: partially encased imaging stations typically lit with Kaiser RB 555 AS LED lighting units.
“We produce images for scientific research; therefore, high accuracy and resolution were two immovable factors,” he points out. “The GFX100S contains a 100-megapixel large format sensor. The physical size of this sensor maximises the detail in the image, meaning when researchers use these photos, the resolution enables them to really interrogate the texture and intricate structure of the plant parts.
“Another factor was logistics,” Jonny adds. “The imaging takes place in-situ across the Herbarium and Fungarium rather than in a controlled studio environment. The challenges, whether they be limitation of space or impact on the work of other colleagues at Kew, are partly mitigated by the small form factor of the GFX100S.”
Click the mark on the left to see an enlarged image of that part.
The imaging process
“Because we’re imaging around the Herbarium, exposure settings differ from station to station,” describes Jonny. “Our apertures typically fall between F11 to F13, keeping depth-of-field sufficient to accommodate the range of specimen heights.
“We then balance the shutter speed and ISO against this aperture. There is some footfall around the stations, so we need to be wary of camera shake when setting the shutter speed. We keep ISO as low as possible in the circumstances.
“To maintain consistency, our images are analysed against FADGI (Federal Agencies Digital Guidelines Initiative) imaging standards, using GoldenThread NXT Software. The use of these guidelines primarily allows us to maintain consistency across a large number of stations.
“We aim for a three-star minimum standard – with parameter performance levels based on those used for unbound documents or paintings and two-dimensional art.
Image 2024 © Fujifilm
The volume of specimens which can be photographed in quick succession has been vastly increased – and the overall process simplified – by connecting each GFX100S to a dedicated computer and using software for operation.
“Our cameras are tethered to Mac Minis and connected to Capture One,” notes Jonny. He explains that digitisation officers can then employ Capture One’s Live View focus assist tools to ensure optimal focus and use keyboard commands to release the shutter without touching the camera body.
The file can then quickly be named using a handheld barcode scanner, before being exported, converted to TIFF and digitised using Max Communications’ bespoke metadata software. “The GFX100S is such a user-friendly, unintimidating piece of equipment,” adds Jonny. “This has been helpful given our digitisers do not necessarily have a photography background.”
All-important technical support from a digitisation perspective is provided by project partner, Max Communications, who also built the bespoke stations. The firm’s proprietary cloud-based management software allows transcribing and metadata recording to be achieved in the least time-intensive way possible.
What next?
With an archive this big, it was inevitable that some hidden treasures would be uncovered. The occasional rediscovery of specimens handled by famous Victorian-era scientists, including Charles Darwin, has punctuated the process – and these pieces of biological history present opportunities for study in many fields.
“We hope our data portal and information made available on GBIF (the Global Biodiversity Information Facility) will be a better resource for botanists, taxonomists, plant scientists and others in biological fields,” enthuses Marie-Hélène.
With over two million specimens already available digitally on GBIF and almost 1.5 million on the Kew Data Portal as of July 2024, important research is already being carried out using the digitised archive – including a conservation project aiming to protect endangered species in the British Virgin Islands. The benefits to broader climate change research are potentially vast.
“We are quite excited about seeing how people will make use of the collection in other ways, of which we have not yet thought,” concludes Marie-Hélène. “Ultimately, the aim is that the digital collections will be a key element in providing new knowledge and solutions, leading to a real impact on tackling global challenges.”
