Python is a high level programming language that aims to combine remarkable power with very clear syntax. Anaconda is a free cross-platform Python distribution from Continuum Analytics. It comes built in with various scientific Python packages such as NumPy, SciPy, Pandas, Matplotlib, Numba, etc.
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.
FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.
ImageJ is a public domain utility for image processing and analysis. It is based on Java and can be extended to create several plugins and develop applications from its toolkit.
Matlab is a high level technical computing language and interactive environment for data visualization, data analysis, numerical computation, and algorithm development.
Analyze is a comprehensive biomedical imaging software suite for visualization and analysis. It is distributed by AnalyzeDirect, and was developed at Mayo Clinic. Analyze supports various features like Volume Rendering, Virtual Endoscopy, Segmentation, Image Fusion, Surface Rendering, ROI measurement and many other imaging functions on practically any medical imaging dataset including MR, CT and PET.
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.