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Single microscope slide digitisation (RBGK)

High resolution specimen images with extended depth of focus (manual slide scanning).
           
Axio Imager.M2 (for slides that could not be scanned with the Axio Scan.Z1 – scanned individually).
Not transportable
Specialized training
Description
Depends on magnification of objective used and size of specimen
Different sizes of microscope slides.

Contributors: Picture:
Copyright: xxx Licence: CC BY NC ND
Click on the image to see the full resolution image

Contributors: Picture:
Copyright: xxx Licence: CC BY NC ND
Click on the images to see the full resolution image

- A library of CITES-listed timbers has been developed to support sustainable timber use, working with CITES scientific authority.

https://www.kew.org/science/collections-and-resources/collections/microscope-slide-collection

https://www.kew.org/science/training-and-education/continuing-professional-development/wood-identification

 

- C4 photosynthesis in Cyperaceae – involving a statistical analysis of leaf measurements for research into characterisation and evolution.  

 

- Machine learning projects – image segmentation for species identification and improving the digitisation pipeline.

 

- Images have further been used for publications (e.g. the Kew Science Collections Strategy 2018-2028), events (e.g. the Circle of Benefactors dinner at Kew 2017 and 2018; the Kew Science Festival 2018 and 2019), interpretation (e.g. displayed in the restored Temperate House at Kew), and product for retail (e.g. scarves sold in the Kew shop) to advertise the scientific work carried out at Kew.

https://www.kew.org/science/our-science/publications-and-reports/science-reports/kew-collections-strategy

https://issuu.com/kewfoundation/docs/10688_roy_2017_final

https://www.kew.org/science/engage/get-involved/science-festival

Pipeline

Preparation: Cleaning slide and loading onto the scanner. Updating spreadsheets with information about the scanning of the slide.

Image capture: Creating a preview image, adjusting profile settings for each slide, generating high resolution scans.

Image processing/analysis: Processing of scan files: extended depth of focus, stitching tiles together, compressing files, and exporting/converting to Tif. Once processing is finished – checking the quality of image files for focus and dirt, and updating spreadsheets with scanning information. 

Adjusting image files in Photoshop: After scanning and processing, image files are cropped, cleaned, and the exposure adjusted in Photoshop. A scale bar is also added to each image. 

Image upload: All images are imported into RBGK Digital Asset Management system: Digifolia (https://dams.kew.org/). This system is comprised of two components: 

1) Aetopia – where derivatives of images are held (https://www.aetopia.com/).

2) Arkivum – off-site tape storage for original, full-sized images. These images can be accessed and downloaded by the user (https://arkivum.com). A new storage system (to replace Arkivum) will soon be used with Digifolia.

Derivatives of images are produced from the images stored in Arkivum in an automated workflow and displayed in the corresponding pages of the Plants of the World Online website (http://www.plantsoftheworldonline.org/).

Metadata for the slides held in the EarthCape database (https://earthcape.com/) will be automatically imported into Digifolia.

Images from each slide are linked together in Digifolia, and assets are sent for approval.

ZEISS ZEN, Adobe Photoshop.

Digitisation on demand of microscope slides would follow the following format:

Data:

Microscope slide digitisation request → microscope slides → digitisation → specimen data → EarthCape → Digifolia

Images:

Microscope slide digitisation request → microscope slides → digitisation → specimen image(s) → Digifolia → Plants of the World Online → URLs added to EarthCape

High resolution Tif images are currently uploaded to Arkivum (through Digifolia) for long-term tape storage. A new storage system (to replace Arkivum) will soon be used with Digifolia.

All images and data are available to view on Digifolia.  This is not presently accessible to the public, but we are in the process of developing an external portal. Most images are also available to view on the website Plants of the World Online. 

All data will be available to view on the EarthCape database, and URLs in this system will link to images in Digifolia.

High resolution images available for download from Digifolia, IIIF (International Image Interoperability Framework) compatibility is coming soon.

Cost(s)
-Preparation and image capture: Cleaning slide and loading onto scanner. Creating a preview and adjusting profile settings for each slide. Time – 5 min to 15 min per slide. -Adjusting image files in Photoshop: After scanning and processing, image files are cropped, cleaned, and the exposure adjusted in Photoshop. Time – 15 min to 1 hr per slide (depending on size of image and adjustments needed). -Uploading images and data to Digital Asset Management System: Preparing and importing metadata, linking images from each slide together, approving assets. Time – 15 min to 20 min per slide.
-Image capture: Scanning. Time varies greatly depending on lens used, size of specimen, and number of z-slices – can range from 5 min to 6 hr. -Image processing: Extended depth of focus – can be 15 min to 3 hr per slide or longer depending on size of file. Stitching tiles together – can be 30 sec to 2 min per slide or longer depending on size of file. Compressing files – can be 50 sec to 2 min per slide or longer depending on size of file. Exporting/converting to Tiff – 2 min to 3 min per slide. -Adjusting image files in Photoshop: Adding a scale bar to each image – action in Photoshop used. Time – 10 sec per slide (only a couple of seconds per image). -Uploading images and data to Digital Asset Management System: Uploading images. Time – 15 min to 1 hr per slide (typically 4 images per slide).
For detailed cost information please inquire.
Contents
Image PNG image Zeiss Axio.png