Digitising Royal Botanic Gardens, Kew Microscope Slide Collection

February 29, 2016 ZEISS Microscopy

Lab-based Collections team describes how they digitise the largest botanical slide collection worldwide with ZEISS Axio Scan.Z1

 

ZEISS Axio Scan.Z1
ZEISS Axio Scan.Z1

The Royal Botanic Gardens, Kew was founded in 1759 and declared a UNESCO World Heritage Site in 2003. Royal Botanic Gardens, Kew is one of London’s top visitor attractions and Wakehurst, the second garden in West Sussex, is home to Royal Botanic Gardens, Kew Millennium Seed Bank. Over the past 250 years Royal Botanic Gardens, Kew has made innumerable contributions to increasing the understanding of plants and fungi with many benefits for mankind.

In this article, members of the Royal Botanic Gardens, Kew Lab-based Collections team describe the first steps in the process of digitising the large and diverse microscope slide collection, which includes thin sections of leaves, stems, roots, wood, flowers and pollen. The microscope slide collection is the largest of its kind worldwide, and the automated digital slide scanner ZEISS Axio Scan.Z1 was picked as the ideal instrument for the task.

 

Slide digitisation – what, why and how?

A slide from the collection that has been excluded from scanning due to existing damage (Photo: A.Musson/Kew Gardens).

One of the major elements of Royal Botanic Gardens, Kew’s Science Strategy 2015-2020 is the digitisation of the diverse collections. Royal Botanic Gardens, 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 Royal Botanic Gardens, 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.

The Lab-based Collections team is 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 are scanned with the recently purchased ZEISS Axio Scan.Z1 digital slide scanner. Developed to produce high quality virtual slides, Axio Scan.Z1 scans up to 100 microscope slides at a time, enabling more efficient digitisation with ZEN slidescan imaging software.

For the pilot Royal Botanic Gardens, Kew’s team is 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 Royal Botanic Gardens, Kew enables the Department for Environment, Food & Rural Affairs (Defra, UKI) 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 Royal Botanic Gardens, Kew. Whilst many wood slides have been photographed and are on the ’Inside Wood’ online database it is not the intention of the team to duplicate this, but to make Royal Botanic Gardens, 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.

A preview scan of a slide showing the three sections of a typical wood slide (Photo: A.Musson/Kew Gardens).
A preview scan of a slide showing the three sections of a typical wood slide (Photo: A.Musson/Kew Gardens).

So far, the team has 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.

 

Producing an image with extended depth of field from a Z-stack of image slices (A.Musson/Kew Gardens).

The team 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. The figure explains the procedure for an image with extended depth of field from a Z-stack of image slices (A.Musson/Royal Botanic Gardens, Kew).

 

Scans produced with 10x objective and extended depth of field showing transverse sections: (L>R) Swietenia humilis (standard hardwood), Dalbergia retusa (non-standard hardwood), and Taxus cuspidata (softwood) (Photo: A.Musson/Royal Botanic Gardens, Kew).
Scans produced with 10x objective and extended depth of field showing transverse sections: (L>R) Swietenia humilis (standard hardwood), Dalbergia retusa (non-standard hardwood), and Taxus cuspidata (softwood) (Photo: A.Musson/Royal Botanic Gardens, Kew).

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.

Checked and cleaned slides being loaded into a tray for scanning (Photo: A.Musson/Royal Botanic Gardens, Kew).
Checked and cleaned slides being loaded into a tray for scanning (Photo: A.Musson/Royal Botanic Gardens, Kew).

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 ZEISS Axio Scan.Z1 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.

Barcodes will be attached to slides before scanning (Photo: A.Musson/Royal Botanic Gardens, Kew).
Barcodes will be attached to slides before scanning (Photo: A.Musson/Royal Botanic Gardens, Kew).

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 to archive the 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 Royal Botanic Gardens, Kew’s aim to digitise 80% of its scientific collections by 2020. ZEISS is proud to contribute to the effort with Axio Scan.Z1 and our team of dedicated specialists.

 

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About Royal Botanic Gardens, Kew 

The Royal Botanic Gardens, Kew was founded in 1759 and declared a UNESCO World Heritage Site in 2003. Royal Botanic Gardens, Kew is one of London’s top visitor attractions and Wakehurst, the second garden in West Sussex, is home to Royal Botanic Gardens, Kew’s Millennium Seed Bank. Over the past 250 years Royal Botanic Gardens, Kew has made innumerable contributions to increasing the understanding of plants and fungi with many benefits for mankind. Royal Botanic Gardens, Kew’s science and conservation work helps to discover and describe the world’s plant and fungal diversity, safeguards the world’s plant life for our future and promotes the sustainable use of plants.

 

The article first appeared in the blog of Kew Science, courtesy of Alicia Musson, Lucy Reed, Magdalena Bojarska & Tim Fulcher. ZEISS wishes to express our gratitude to the members of Kew’s Lab-based Collections team for contributing to this article, and for conserving one of the most amazing slide collections in the world for the future. YOU make it visible.

The post Digitising Royal Botanic Gardens, Kew Microscope Slide Collection appeared first on Microscopy News Blog.

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