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Vaa3D

Vaa3D [1, 2, 3] is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions ... It is also Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily...

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ITK-SNAP

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pythonxy

Python(x,y) is a free scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment.

Many python libraries related to numerical calculation are packaged, so you do not need to search and install them individually.

Included libraries are listed here.

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3D Slicer

Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X.

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BioImageXD

BioImageXD is a free open source software package for analyzing, processing and visualizing multi-dimensional microscopy images. It's a collaborative project, designed and developed by microscopists, cell biologists and software engineers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG in Dresden, Germany and collaborators worldwide. BioImageXD was published in the July 2012 issue of Nature Methods.

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MATLAB/ Qu

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CreaTools

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pythonxy

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