You can configure the Java Viewer Magnifier to:
strDocWrite+='<param name="
externalMagnifier" value="true">';
The default mode is "false". In the default mode, the Magnifier window appears within the display area when a user clicks the Magnifier button.
strDocWrite+='<param name="
magnifierPersistent" value="true">';
When this parameter is set to "true", the Magnifier window reappears in its last form (same size, position, and magnitude) when the user opens a new document. The default mode is "false," which hides the Magnifier window when the user opens a new document, requiring the user to manually display it each time. If users repeatedly magnify the same image area in a set of documents, set this parameter to "true" to keep the Magnifier window open while paging through images.