The Dorot Foundation is in the process of digitizing the collection of the DSS at the Shrine of the Book museum in Jerusalem. At present only three scrolls are available (the Aleppo Codex, Isaiah Scroll, and Temple Scroll), but the Foundation has done an impressive job. Clicking the link to the Isaiah and Temple Scrolls produces a scan in which shows the scrolls as one would read them in a synagogue, i.e. they are partially open. At the bottom of the window is a button, which by moving to the left or right, moves the scroll either frontwards or backwards. Similarly, the Aleppo Codex appears as a book, and clicking a button advances or retreats through it leaf by leaf. There's also an option for zooming, but it is fairly limited.
http://www.imj.org.il/shrine_center/
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