Imaris (Ultimate Collection)
Imaris provides functionality for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets. It combines speed, precision, ease-of-use, and a complete set of features for working with multi-channel images of any size, from a few megabytes to multiple gigabytes in size. The modules available in the Ultimate Collection provide volume rendering, isosurface reconstruction, cell tracking and analysis, visualizing and measuring filament structures, colocalization analysis for multiple components, measurements of many types, and an interface to various programming languages and scripting software. This is the featured software on the SVIS (Scientific Visualization and Imaging System) computer provided by the UA imaging and microscopy community.
Amira (Multi-Component Analysis, Skeleton Pack, and DicomReader options)
Amira is a software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities. The Multi-Component Analysis module provides processing, manipulation, registration, segmentation, and analysis of image stacks. The Skeletonization module supports reconstruction and analysis of vascular, dendritic, and fracture networks for the researcher who studies and analyzes neurons or micro-vascular networks.
MATLAB is a high-level language and interactive environment for numerical computation, visualization, and programming. MATLAB can be used to analyze data, develop algorithms, and create models and applications. MATLAB is a flexible platform commonly used in a wide range of applications including signal processing and communications, image and video processing, control systems, test and measurement, computational finance, and computational biology.
VisIt is an open-source tool designed for interactive visualization, animation and analysis. It is a distributed, parallel visualization and graphical analysis tool which contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on 2D and 3D structured, adaptive and unstructured meshes. Because of its customizeable plugin design, VisIt is capabable of visualizing data from over 120 different scientific data formats.
ParaView is an open-source, multi-platform data analysis and visualization application which uses the Visualization Toolkit (VTK) as the data processing and rendering engine. It was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of exascale size as well as on laptops for smaller data. Data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.
Visualization Toolkit (VTK)
The Visualization ToolKit is an open-source, freely-available software system for 3-D computer graphics, image processing and visualization. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture and volumetric methods; and advanced modeling techniques like implicit modelling, polygon reduction, mesh smoothing, cutting, contouring and Delaunay triangulation. There are also dozens of integrated imaging algorithms, so a programmer can mix 2-D imaging with 3-D graphics algorithms and data. VTK includes a textbook published by Prentice-Hall ("The Visualization Toolkit, An Object-Oriented Approach To 3-D Graphics, 2nd edition"), a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python.