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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
MDSTk is a collection of 2D/3D image processing tools aimed at medical images. It contains routines for volume data processing (3D filtering, segmentation, etc.) as well as fast low-level vector graphics library for surface and tetrahedral meshing.
MDSTk has been forked by 3Dim Laboratory s.r.o. to provide better support and further push its development forward.
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.