Digitising Kew's microscope slide collection
Members of Kew's Lab-based Collections team describe the first steps in the process of digitising Kew's large and diverse microscope slide collection, which includes thin sections of leaves, stems, roots, wood, flowers and pollen.
Slide digitisation – what, why and how?
One of the major elements of Kew’s Science Strategy 2015-2020 is the digitisation of Kew’s diverse collections. Kew’s microscope slide collection is the largest of its kind worldwide, incorporating over 130,000 slides and representing a unique resource for trait analysis and plant authentication. The collection has been compiled over many decades, primarily from Kew's extensive living collections, herbarium collections and wood collection, but also from wild-sourced material and international exchanges. The fragile glass slides are stored in fire-resistant cabinets in the Jodrell Laboratory. They include thin sections of leaves, stems, roots, wood and flowers, and preparations of pollen grains and root tips displaying cell divisions.
In the Lab-based Collections team, we are currently carrying out a two-month pilot study, which aims to assess how best to digitise the microscope slide collection as a whole, to make it more accessible to external researchers and to pinpoint gaps in the collection for future work. Microscope slides will be scanned with a recently purchased Zeiss Axio Scan. Developed to produce high quality virtual slides, the Axio Scan can scan 100 microscope slides at a time, enabling more efficient digitisation. The Axio Scan is operated by Carl Zeiss ZEN imaging software.
For the pilot we are using wood anatomy slides, of which there are approximately 45,000 specimens in the database at Kew. CITES-listed species are of particular interest, and these are well represented in the collection due to their research value and Kew’s role in identifying wood samples used in commercial trade, an area where Kew enables Defra to meet its international obligations. Timber-yielding species are useful for providing natural capital and are often from Tropical Important Plant Areas (TIPAs). There are eight timber-yielding tree species on CITES Appendix I and 85 on Appendix II, with new listings created every year. Kew holds one of the world’s most important reference collections of wood samples and microscope slides of the relevant taxa.
The slides and any images made for publication are generally unavailable outside of Kew. Whilst many wood slides have been photographed and are on the’ Inside Wood’ online database it is not our intention to duplicate this, but to make Kew’s microscope slide collection more accessible to the general user.
Imaging the slides
Typical wood slides comprise three sections, transverse (TS), tangential longitudinal (TLS) and radial longitudinal (RLS). Each section will be scanned individually, providing three images highlighting different anatomical features. These will be linked to images of the entire slide and label, both scanned at a lower resolution.
So far, we have been experimenting with wood slides of differing type, density and staining. These include hardwoods such as Swietenia, Quercus, Dalbergia and Diospyros and softwoods such as Pinus, Abies and Taxus. Certain woods, particularly the denser woods such as Diospyros, have proved more problematic to image, while others such as the softwoods, which are fairly uniform in their anatomy, are relatively straightforward.
We developed 12 initial scanning profiles for woods, created for standard hardwoods, non-standard hardwoods (particularly dark or dense hardwoods) and softwoods; these varied according to the type of objective used for scanning and whether focus stacking (Z-stacking) was used. Z-stacking involves scanning the slides at different focal planes, creating several image ‘slices’, with each slice having different areas of focus according to the focal plane it has been imaged at. The sharpest points of focus for each slice are then combined to produce an image with an extended depth of field (EDF). Due to the clarity of the images produced in this way, this process will be used for all future scans.
Developing a digitisation workflow
In developing a standardised workflow for digitisation of the microscope slide collection, it is necessary to consider different elements of the process. Care during the physical handling of slides is important to prevent damage occurring, and there are a number of steps to be taken before scanning. These include checks to exclude slides with existing damage or those of non-standard thickness or length, and cleaning slides to ensure optimum condition for scanning.
In addition to image capture we also need to capture the label data – either from the physical slide, before or after scanning, or at a later date using the label image. Since the Axio Scan is able to read barcodes and link these codes to the image files, attaching barcodes to the slides prior to scanning allows images, data, and the physical slide collection to be properly linked.
Quality control will be carried out throughout the process, with scans being manually checked to make sure they are correctly focused and exposed.
Data storage and management
Slide images, exported in tiff format, and associated metadata will be incorporated into the slide database. With the images and data linked through barcodes, all supplementary data associated with the slide, for example collector details and sample origin, can be easily tracked through the scanned images.
Kew uses the Digital Asset Management (DAM) system Aetopia, which provides the capability to upload images and associated metadata to a central system. Linking metadata to the images enables them to be sorted, filtered and retrieved. It is of course vital that we archive our images and metadata securely to ensure their accessibility for the future, so all data will be transferred to Arkivum, a long-term tape-based storage and archive system. This pilot study is an important first step in the digitisation of the slide collection and contributes towards Kew's aim to digitise 80% of its scientific collections by 2020.
Gasson, P. (2011). How precise can wood identification be? Wood anatomy's role in support of the legal timber trade, especially CITES. IAWA Journal 32(2): 137-154. Available online
Gasson, P., Baas, P. & Wheeler, E. (2011). Wood anatomy of CITES-listed tree species. IAWA Journal 32(2): 155-197. Available online