Major international herbaria, natural history museums and universities have recently begun to digitise their collections to facilitate studies and improve access to collections. In Japan, more than 10 million herbarium specimens are housed in various universities/museums; however, only 1% of these have been digitised. In this paper, we describe a new method for imaging herbarium specimens that is applicable to local/small herbaria. It is safe, fast, simple and inexpensive, but also satisfies usage guidelines for minimum image quality and can produce digital files suitable for long-term storage and future post production. During an eight-month trial at the Museum of Nature and Human Activities, Hyogo, with three part-time workers using a custom-made copy stand and a mirrorless interchangeable lens camera with a large LED light bank system, we were able to image 73,180 herbarium specimens (571 per day on average), obtaining two RAW and two JPEG files for each specimen.

Digitisation, Herbarium specimen, Imaging

The digitisation of museum collections has recently become a major topic of discussion (e.g. Thiers et al. 2016, Le Bras et al. 2017, Barber et al. 2018, Sweeney et al. 2018). The Naturalis Biodiversity Center is in the process of digitising 37 million objects (https://science.naturalis.nl/en/collection/digitization/digitization/). The Finnish Museum of Natural History (Tabelberg et al. 2012) is running mass digitisation programmes for their entire collections. Furthermore, major herbaria around the world – such as Harvard University (A, GH, NEBC), the Royal Botanic Garden, Edinburgh (E), the Royal Botanic Gardens, Kew (K), the French Muséum national d’histoire naturelle vascular plant herbarium (P, Le Bras et al. 2017) and the Meise Botanic Garden (BR, De Smedt et al. 2018) – have also conducted digitisation. China (the Chinese Virtual herbarium [http://www.cvh.ac.cn/]) and the United States (Integrated Digitized Biocollections [iDigBio]; https://www.idigbio.org/) promote specimen digitisation as national projects. A list of the major digital herbaria in the world was compiled and is shown in Table 1.

Compared to the aforementioned countries, Japan is rather behind (Ogawa 2008, Moriguchi et al. 2012, Akihiro et al. 2018). About 10 million herbarium specimens are housed in universities and museums in Japan (The Unions of the Japanese Societies for Systematic Biology 2015) and half of these are deposited at the three largest herbaria: The University of Tokyo (TI) with ca. 1.8 million specimens, the National Museum of Science and Nature (TNS) with ca. 1.7 million specimens and the Kyoto UniversityMuseum (KYO) with ca. 1.2 million, while the rest are dispersed in smaller, local herbaria. At present, 20% (ca. 2 million) of the specimen data in Japan have been deposited in the Global Biodiversity Information Facility (G-BIF) (https://www.gbif.org/) via J-BIF, the Japan node of G-BIF (http://www.gbif.jp/v2/). This facility provides text without images. Some herbaria in Japan – such as TI (http://umdb.um.u-tokyo.ac.jp/DShokubu/herbarium/en_ver2/index.php), TNS (http://www.type.kahaku.go.jp/TypeDB/) and the Metropolitan University of Tokyo (MAK) (http://ameba.i.hosei.ac.jp/BIDP/MakinoCD/makino/html_e/index0.html) – have published databases of their herbarium collections with specimen images. However, these are limited to specimen type collections or specimens from certain areas (e.g. Nepal and oceanic Islands). The largest herbarium database in Japan with specimen images is the Shimane University virtual herbarium (http://tayousei.life.shimane-u.ac.jp/harbarium/) (Akihiro et al. 2018). Currently, ca. 100,000 specimen images from the Tottori Prefecture Museum (TRPM), the Shimane Nature Museum of Mt. Sanbe Sahimel, the Rikuzentakata City Museum and the Herbarium of Faculty of Symbiotic Systems Science at Fukushima University (FKSE) are available online.

Nelson et al. (2015) described three widely used imaging station alternatives for herbarium digitisation: (1) A copy stand with fluorescent lighting, (2) a light box with internal lighting and (3) an inverted flatbed scanner. In the present study, we explored another method and developed a custom-made digitisation system for herbarium specimens using a mirrorless interchangeable-lens camera (MILC) and a large bank light system, even though inverted flatbed scanners are most commonly used in Japan (e.g. Suh et al.2006, Ogawa 2008, Moriguchi et al. 2012, Akihiro et al. 2018). There were two reasons for using a digital camera: firstly, it is easier to take multiple images of one specimen in various forms using a camera. For security in the long-term storage of specimen images, it is better to have files of multiple kinds. The long term preservation of digital images is discussed in terms of file formats (Digital Preservation Handbook, 2^nd edition 2018). Well-known formats are PNG, TIFF, JPEG and JPEG 2000, whose specifications are freely available to users. Although JPEG is the common file format amongst these, it involves using non-invertible compression of the image. Due to this, TIFF is preferred in digital archiving projects, but there are currently no reasonably priced digital cameras able to save TIFF directly. Therefore, we acquired lossless RAW images, which can be converted to TIFF images in parallel with JPEG images. In contrast, flatbed scanners can obtain only one image file per scan and one scan takes up to several minutes to obtain sufficient image quality. Therefore, if we want to obtain multiple images in multiple formats per specimen using a scanner, the time taken will increase accordingly. Secondly, the thickness of specimens does not affect digital camera images. Bulky specimens (e.g. conifer cones and aroid bulbs) are difficult to scan but pose no problem for cameras.

The system we have developed is simple and inexpensive, requires minimal space, could be managed by part-time workers and makes it possible to easily obtain multiple standardised digital files of several kinds. Using a digital camera has often been avoided because it is thought to be extremely difficult to provide sufficient lighting for quality specimen imaging (Suh et al. 2006). We overcame this problem by adopting a light-bank system using LED light. This system is suitable for small and medium-sized herbaria where staff, space and budget are limited, as well as for larger herbaria with larger numbers of staff members and stations. It may also be applied when digitising other kinds of collections, including entomological, mineralogical and fossil collections.

Specimen images, obtained using our method, are of a quality suitable for OCR output (Fig. 4). All procedures, from pre-digitisation curation to storage and archiving of images, were performed by two part-time workers between 9 am and 5 pm each day. The speed of imaging depended on how many specimens needed conservation or clean-up before and/or after imaging. Most herbaceous specimens, especially Poaceae, Cyperaceae and Saxifragaceae, contained substantial amounts of sand or dry mud amongst their roots and took time to clean-up before imaging. Therefore, we sometimes obtained only 1,200 images (300 specimens) per day. In contrast, for woody or large herbaceous specimens without roots (and associated soil), imaging ran smoothly and we could obtain up to 4,000 images (1,000 specimens) per day. From the start of guidance and training on 10 Nov 2017 to 4 July 2018, a total of 73,180 specimens were imaged and stored as RAW and JPEG files.

Figure 4. 

An image of herbarium specimens taken using imaging method described in this study (Cedrus deodara (Roxb.)D.Don, HYOID: C2-018127).

Our imaging system minimises both initial costs and space requirements using a custom-made copy stand alongside an MILC and other ordinary devices. The imaging system described here costs ca. 314,000 JPY in total (US $2,778), including 170,000 JPY for the MILC camera, lens, adaptor and monitor, 90,000 for the bank light system (incl. LED lights, ramp folders, diffusion film etc.) and 54,000 for the camera stand. The development of new technologies has afforded us the use of LED or OLED lighting at a low cost. Using a large LED bank light system, we were able to obtain images that were rich in contrast and gradation without high resolution. In addition, the working space was minimised by putting a copy stand and before and after imaging of specimens in line on the same desk, making the workflow compact and smooth. This system is easy to operate, making it simple to train workers. It provides the ability to obtain multiple 48-bit RAW and JPEG files for each specimen. Obtaining multiple files and multiple kinds of digital files is important for long-term storage.

We developed a new digital imaging system for herbaria that takes up little space, minimises costs, is simple to use and quickly creates data that can be archived long-term and we provide here a step-by-step guide to create the system. We hope our imaging system will facilitate the digitisation of small- and medium- sized herbaria where investment possibilities are limited.

We would like to give sincere thanks to Prof. Dr. Kunio Iwatsuki, Director Emeritus, Museum of Nature and Human Activities, Hyogo (HYO) & Professor Emeritus, The University of Tokyo, for his donation to HYO and warm encouragement for this project. Thanks are also given to two reviewers and Dr. Sandra Knapp, the handling editor of this paper for their critical suggestions and constructive comments. Enago (www.enago.jp) provided the English language review for this paper. Moriya Sangyo Co. Ltd. donated some consumables. Part of the study was also supported by JSPS (no. 26440227 to A.T.).