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Batch Slide digitisation 2D+ (RBGK)

High resolution specimen images with extended depth of focus (automated slide scanning).
           
Axio Scan.Z1 (batches of up to 100 slides scanned at one time) A composite image of a mounted specimen can be made at different magnifications (microscope lenses 5x, 10x, 20x, 40x, 100x) and using Z-stacking.
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 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 slides and loading into the scanner. Updating spreadsheets with information about the scanning of the slides.

Image capture: Creating preview images, tissue detection (selecting the areas to be scanned for each slide), producing 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: Cleaning slides and loading into the scanner. Updating spreadsheets with information about the scanning of the slides. Time – 5 min to 10 min per slide, additional 2 min to 3 min per slide for re-scans. -Image capture: Tissue detection – selecting the areas to be scanned for each slide. Minimal human time is required for setting up preview scans and scanning. Time – 50 sec to 2 min per slide, additional 50 sec to 2 min per slide for re-scans. -Image processing/analysis: Minimal human time is required for setting up the processing of scan files: extended depth of focus, stitching, compressing, and exporting/converting to Tiff. Once processing is finished – checking the quality of image files for focus and dirt, and updating spreadsheets with scanning information. Time – 5 min to 10 min per slide, additional 5 min to 10 min per slide for re-scans. -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: Preview scans – 18 sec to 30 sec per slide. Scanning – 15 min to 30 min per slide (can be more, depends on settings). -Image processing/analysis: Extended depth of focus – varies greatly, but can be 15 min to 3 hr per slide. Stitching tiles together – 30 sec to 2 min per slide. Compressing files – 50 sec to 2 min per slide. Exporting/converting to Tif – 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 Axio Z1.png