CASK Virtual Microscopy Viewer

CASK Virtual Microscopy Viewer is an open source* web-based virtual microscopy viewer, developed by the CASK (Clinical Anatomical Skills) e-learning group at the Department of Anatomy & Embryology of Leiden University Medical Center, the Netherlands.

It aims to enable easy virtual microscopy, without software installation, by running natively in the browser: "Click and view". It can be used over the Web, or locally on a computer or from an USB-drive, and both on desktop and tablets.

Users (teachers, students) can place labels online (or local). Direct links can be obtained to a specific slide at a pre-set position and zoom-level and with specific labels.

Slides can be grouped (for instance for a practical) and accessed via a menu-system. Only references are used, allowing to allocate the same slide or pre-set view to an infinite number of groupings.

Details:

• Works on Windows/ Internet Explorer 7-10, Firefox, Chrome, Safari; Mac/ Safari, and on tablets, such as iPad and Android tablets. HTML5 based, does not use plugins such as Java or Flash.
• Zoom in or out on any (eccentric) location of interest. To do so, place the mouse cursor on the desired spot and zoom, the image will zoom centered on this location. Most virtual microscopy viewers zoom center-based, causing everything around to move outward, making it hard to zoom in or out centered on a spot of interest.
• Labels are superimposed dynamically on a slide: the same slide can be offered with different sets of labels. You could for instance offer a slide both with informative labels and with question labels.
• Direct links to a specific slide at a specific position, zoom-level, and with specific labels can be created and used on the fly or stored and accessed via shortcut-URLs. These links can be used in manuals or presentations.
• Logo's and credit texts can be adapted.
• Setting up the viewer (adding slides, creating menus and slide-sets, storing direct links) is done in plain text files.
• Elaborate manuals are available (see below).
• Free for non-commercial use as long as proper credit is given, and any derivative works are released to the public under the same conditions (see exact requirements below).

* It was originally based on the open source Brainmaps viewer, but our latest viewer code is entirely created from the open-source Leaflet JavaScript library

See it life

See the viewer in use at https://www.caskanatomy.info/microscopy

Download viewer

Manuals

• Manual 1. Create / convert virtual slides for the CASK Virtual Microscopy viewer (for ultra large slide data see manual 2)
• Manual 2. Slide conversion software tips and tutorial for ultra large datasets
• Manual 3. Setting up CASK Virtual Microscopy viewer and adding slides
• Manual 4. End user manual CASK Virtual Microscopy viewer

Screenshots

History

• July 20152.9.021
  • Older CASK Virtual Microscopy Viewer now on GitHub
• Oct 20142.9.001
  • Project Leiden University Fund, Gratama Foundation, started, to extend CASK Virtual Microscopy Viewer to allow very large slides and in-browser drawing on slides:
    https://www.luf.nl/subsidies/wetenschappelijke-projecten/toekenningen/2014:
    
    Carolina R. Jost, PhD and Frank G.A. Faas, PhD: Virtual electron microscopy for teaching, sharing and annotating large electron microscopy data sets
• April 20132.1.747
  • Tweaks on iPad to circumvent performance limitations that caused slides to grey out at larger enlargements or after a few swipes
  • Made CASK viewer version 2 available for download
  • Elaborate manuals
  • Mobile usability improvements
• March 20132.1
  • Online labelling
  • Creating direct URL links to specific slides with specific position, zoom-level and labels
  • Touch functionality for tablet and mobile
  • Conversion to HTML5
  • Storage of direct URL links, addressable via shortcuts named 'Views'
  • Option to place credits on slides
  • Correction on iPad and iPhone of auto-enlarging viewport that caused slides to drift
• Febr. 20132.0
  • Menu's referencing slides by body region and/or by teaching course
  • Start of regular usage of CASK viewer in microscopy practicals at LUMC
  • First series of LUMC slides added
• 2011Made CASK viewer version 1 available for download on www.caskanatomy.info
• 20101.0 First release of CASK Microscopy viewer based on the Brainmaps API, with several modifications:
  • Listing of slides with thumb images
  • Zooming centered on mouse position instead of center-based, allowing to focus on any point whilst zooming
  • Basic viewing on iPad and mobile
  • Bugfixes: thumbnail working on Internet Explorer, prevention of image going off-screen
  • Holding mouse button pressed zooms out
  • Option to switch zoom-direction on mouse-scroll