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Digitisation of large sets of microscope slides 2D (RBGK)

Whole slide images that show label data.
         
*Digital camera Leaf Aptus-II 12 back [80MP] mounted onto a Cambo sliding back and bellows *Rodenstock 90mm lens *Schneider electronic shutter control *Flash/Studio light
Basic training
Description
3 MB per final image of each microscope slide.
Different sizes of microscope slides.

- 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: Selecting slides from Collection, cleaning, barcoding, databasing (currently an internal Access database, but soon to be: EarthCape: https://earthcape.com/ where the data will be exposed to the public in a new data portal) and updating spreadsheets with relevant information. 

Image capture: Slides arranged in batches on a template, which sits on a lightbox under the camera. High resolution image of each batch of slides captured with colour chart scale and labels to identify type of slides, date, and batch number.

Image analysis: Quality of images checked and some adjustments made in Photoshop. Images of batches of slides are segmented to produce individual images for each slide and annotated using Inselect software.

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/).

Data from EarthCape will be automatically imported into Digifolia.

Inselect.

CaptureOne, Lightroom, 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: Selecting slides from Collection, cleaning, barcoding, databasing and updating spreadsheets with relevant information. Time ranges from 10 min to 1 hr per slide. Image capture: Slides arranged in batches on a template, which sits on a lightbox under the camera. High resolution image of each batch of slides captured with colour chart scale and labels to identify type of slides, date, and batch number. Time – 1 min to 2 min per slide. Image analysis: Quality of images checked and some adjustments made in Photoshop. Images of batches of slides are segmented to produce individual images for each slide and annotated using Inselect software. Time – up to 5 min per slide.
Image Capture: Instantaneous using CaptureOne to shoot images. Image analysis: Work carried out in Photoshop and some of the processing in Inselect is reliant on human time, the rest of the processing in Inselect is automated – less than a minute per slide.
For detailed cost information please inquire.
Contents
Image PNG image leafaptus.png