Self contained demo of a converted Aperio SVS file running in OpenSeadragon
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CMU-1-Small-Region_files
js/openseadragon
original_svs_file
CMU-1-Small-Region.dzi
LICENCE.txt
OpenSlideLicence.txt
README.md
index.html

README.md

OpenSeadragon-Web-Microscopy-Example

This repository contains a self contained demo of a converted Aperio SVS file running in OpenSeadragon that you can just extract to your web server and view in a browser.

If you want to create your own DZI files from Aperio SVS files then you can do the following:

Install VIPS

The first step is to install VIPS. VIPS is a command line image processing utility that is able to use OpenSlide and will handle the image conversion for us. To install it fire up a terminal and execute the following command:

brew install https://raw.github.com/jcupitt/homebrew-science/3fda4568544a67743b2a880ad1c5f844b4ff3515/vips.rb --with-openslide

This will take quite a while as it builds and installs VIPS and all its dependencies. If you have any problems, the full VIPS build/install instructions are available on their Wiki.

The next step is to use VIPS to convert the SVS image in to a format that OpenSeadragon can understand.

Converting SVS to DZI

To convert your SVS file to a DZI file execute the following command:

vips dzsave /path/to/your/image.svs /path/to/output/directory

For example running the following:

vips dzsave ~/mucocoele.svs ~/webMucocoele

Will create a file called mucocoele.dzi and a folder called mucocoele_files. Both of these are required.

NB if your source svs image is large this conversion can take a long time!

NB.2 if you receive a "VipsForeignLoad" error then you probably didn't include the "--with-openslide" parameter when installing VIPS. You'll need to brew uninstall it and rebuild including the parameter.

Change index.html

To get your new files in to the web page you'll need to put them in a public folder and then change the "tileSources" parameter to point to the relative path of your new file.

A more comprehensive guide is available in this blog post