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  • Amira is a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities.

  • Anaconda is a free Python distribtion from Continuum Analytics.  It is optimized to run cross-platform.  It comes built in with various scientific

  • Analyze is a comprehensive biomedical imaging software suite for visualization and analysis. It is distributed by AnalyzeDirect, and was developed at Mayo Clinic.

  • Avizo software is a powerful, multifaceted tool for visualizing, manipulating, and understanding scientific and industrial data.

  • Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data.

  • Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

  • CLC Genomics Workbench (CLCGWB) is a cross-platform desktop application and graphical user interface for visualizing and analyzing next-generation sequencing data.

  • Ensight is a client/server scientific visualization package providing a complete tool for all types of engineering analysis, postprocessing, visualization and communication.

  • Python is a high level programming language that aims to combine remarkable power with very clear syntax.

  • Fast is an interactive computational fluid dynamics Post-Processing software package from NASA for SGI workstations. Due to its many features, it is used by researchers at the Supercomputing Institute for many different fields.

  • Gnuplot is a command-driven interactive function plotting program. If files are given, gnuplot loads each file with the load command, in the order specified. gnuplot exits after the last file is processed.

  • Grace is a tool for 2-D plots. It is derived from Xmgr.

  • The Huygens System is an image processing software package specifically designed to facilitate the restoration of microscopic images. It provides many arithmetic operations on image types ranging from simple 2D images of unsigned bytes to multi-parameter, 3D time series of complex values.

  • IDL

    IDL (Interactive Data Language) is a widely used general purpose visualization package. With IDL, you can create graphs and visualize 2 and 3 - D data using contours, iso-surfaces and slices. IDL has image processing capabilities such as smoothing, sharpening and thresholding.

  • Imaris suite provides a complete set of features for working with three-dimensional multi-channel images. It allows users to conveniently load, process and visualize images in any widely accepted image format to gain new insight from microscopic data.
  • Mathematica is a widely used software package for numerical and symbolic mathematical computations.
  • Mimics is useful for visualization and segmentation of CT / MR images and 3D rendering of objects. It also provides an interface to create FEM meshes.
    MSI currently has the following modules
    • Mimics basic - Allows segmentation, registration and measurement on 3D object
  • Octave (a.k.a GNU Octave) is a open source computational software built to be compatible with Matlab.

  • Origin is an easy-to-use data analysis and graphing software used by over 100,000 scientists and engineers worldwide.

  • ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large.

  • PyMOL is a Python-enhanced molecular graphics program. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. It also has a number of third party plugins available.

  • SAS

    SAS is a scalable, integrated software environment and a flexible and extensible programming language designed for data access, data manipulation, and data analysis. It offers data management and predictive analytic capabilities, data mining process, drug discovery solutions, and much more.

  • Slicer, or 3D Slicer, is a free, open source software package for visualization and image analysis. It includes tools for segmentation, rendering, registration of MRI, CT, US, nuclear medicine, and microscopy images.

  • Tecplot is a powerful interactive plotting program for visualizing and analyzing engineering and scientific data. It integrates XY plotting with two and three-dimensional surface data-visualization capabilities into a single easy-to-use program.

  • Volocity is an interactive volume visualization system for time-resolved biomedical image data.. It includes tools for:

  • VolView is an intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data on a standard PC. Users can easily generate informative images and navigate the data for further analysis.

  • Xaim is a X11 Motif graphical user interface to several programs based on some aspects of the Theory of Atoms in Molecules developed by Prof. R.F.W. Bader and coworkers.