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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
Scribe Software is a software system for the nondestructive scanning and digitization of books with the Internet Archive's Scribe machine. The Java UI and PHP image processing pipeline produce books for www.archive.org and other digital libraries.
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later. HOME @ http://rsb.info.nih.gov/ij/