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See also: Working with footnotes and endnotes in the Jutoh manual
In Jutoh 2, you can specify that footnotes should pop up for Epub files viewed in Apple Books (iBooks).
In your configuration:
Change Epub version to 3.
Change Namespaces to the second (longer) of the two available choices (required for Epub 3), or leave as "(auto)".
Check Popup footnotes.
If you have trouble finding these options, you can search in the field at the bottom of the configuration panel.
Note that popup footnotes don't work in Apple Books if the footnotes are in a separate section - that is, if you specified Generate endnotes in the Footnotes tab in Project Properties. In this case, not only does the footnote not pop up, the link doesn't work at all. So if you need your footnotes to be in a separate section, clear Popup footnotes. The link to the endnote will then work, and Apple Books also shows a link back to the original page so you can continue reading where you left off.
You might like to create a new configuration for Apple Books Epubs so you don't have to change the settings when you want to generate a non-Apple Books file. If so, change the filename so the two Epub files don't overwrite each other.
Contents | Start | End | Previous: KB0108: Why are some GIF or JPEG images not displayed in my Epub using Adobe Digital Editions? | Next: KB0110: Why is Jutoh slow to load a document created by Google Docs?