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JavaScript is an optional part of the epub 3.0 specification:

EPUB Content Documents may contain scripting using the facilities
defined for this in the respective underlying specifications ([HTML5]
and [SVG]).

What this means is that even a fully-compliant epub 3.0 device doesn't need to implement JavaScript support. The ones that do will generally be the "more bells and whistles" devices; the iPad, for example, supports JavaScript. The IDPF's epub Chrome extension Readium does as well.

Note that according to the epub 3.0 specification, the following criteria for reading systems that support JavaScript must be met:

› It must support container-constrained scripting and may support
spine-level scripting.

› It may render Scripted Content Documents as an interactive, scripted
User Agent according to [HTML5].

› It must not allow a container-constrained script to modify the DOM
of the parent Content Document or other contents in the EPUB
Publication, and must not allow it to manipulate the size of its
containing rectangle. (Note: Even if a script is not
container-constrained, the Reading System may impose restrictions on
modifications (see also the dom-manipulation feature).)

› It may place additional limitations on the capabilities provided to
scripts during execution (e.g., limiting networking).

› It must implement the JavaScript navigator extension object
epubReadingSystem defined in Appendix A, JavaScript epubReadingSystem
Object . It also must support the dom-manipulation and layout-change
features defined in Features in container-constrained scripting
contexts.

› It must regard the scripted [Publications301] property of the
Package Document manifest item element as the authoritative definition
of whether an EPUB Content Document includes scripting.

EDIT: Popup text and images are definitely possible using JavaScript in iBooks. For an example, check out Beneath The Ink.


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