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XMIPP is an imageprocessing 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
spmjob is a free batch processingtoolbox for SPM 2 (Statistical Parametric Mapping). It supports preprocessing, parameter estimation, contrasts and second level analysis. spmjob has both flexible scripting support and a user friendly GUI.
OpenVL is a framework for handling, processing & visualizing volumetric data (CT, MRI etc). It provides: powerful data access & layout API, plugins for volume processing tasks (imageprocessing, segmentation etc), and support for multiple file-formats.