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    Amira-Avizo — Thermo Scientific Amira-Avizo and Pergeos Software are the leading high-performance 3D visualization and analysis solutions for scientific and industrial data. Wherever 3D imaging data sets need to be processed, Amira-Avizo and Pergeos Software offer abundant state-of-the-art image data processing, exploration and analysis features within an intuitive workflow and easy-to-use graphical interface.
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    imod — IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, Suraj Khochare, and John Heumann at the University of Colorado.
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    tomopy — Tomographic reconstruction creates three-dimensional views of an object by combining two-dimensional images taken from multiple directions, for example in how a CAT (computer-aided tomography) scanner allows 3D views of the heart or brain.