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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
BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
This toolkit allows complete control of a microscopy setup from Labview, Matlab, Scilab, Python, .Net, VB, IgorPro, Mathematica and more. Included is a standalone program for image acquisition and scripting control of a scientific microscope.
Computer Controlled Optical Microscopy is a package to enable camera equipped microscopes to generate multi-modal time-lapse image sequences
of 3D volumes. This is achieved by periodically changing optical settings, xyz positions and acquiring images.
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This is a collection of different little tools written in MATLAB, JAVA, Python. They all have to to do with Imaging & Microscopy for life science research and related topics or problems. Some of them are meant to be used with ImageJ and MicroManager.