What is the best way to put the viewer in its own container so it only takes up part of the page?
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If you are using iipmooviewer 2.0 beta or github version, this should work fine. Just create a container div of the size and position you want. Make sure this works without the viewer first. Then when it's correctly layed out connect the viewer to this div.
If it still doesn't work, post a link so that we can take a look.