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Category: Volume Rendering

Volume Rendering a 3D data set is similar to taking an Xray. Objects with high density are opaque, object with low density are transparent. With volume rendering, you have control of the opacity, usually dependent on the values in the data set.

For sample images and techniques see http://www.msi.umn.edu/user_support/scivis/techniques/volvis.html.

Amira

Description

Amira is an interactive visualization package with support for scripting and batch use. It includes tools for working with:

3D and 2D image data processing and segmentation
Chemistry visualization (AmiraMol extension)
Volume rendering
Surface reconstruction and simplification
Tetrahedral grid generation
Animation
General visualization and data exploration

To use Amira, type:

module load AMIRA

Amira is stared by typing:

amira

More Information

Amira tutorial - Introductory tutorial for Amira.
Amira Tools - A collection of scripts for creating animation and various other functions as well as examples of data, nets and miscellaneous scripts.
User's Guide - On line user guide from the vendor.
Version 3.0 Release Notes - Detailed list of modifications and new features.

Version: 3.1
Labs: Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Scientific Development and Visualization Lab
System(s): All SGI workstations in VWL, BSCL and SDVL, All Sun workstations in SDVL and VWL, bs1 in BSCL
Categories: Visualization, Animation, Data Analysis, Image Display, Image Processing, Isosurfaces, Vector Fields, Volume Rendering

Bob/Animabob

Bob (Brick-of-Bytes) has been installed on the SGI workstations. Bob is a tool for browsing three dimensional data sets. The program was designed to render portions of potentially large time-dependent volumes quickly. Bob can also create a series of images that can be later compiled into a movie. To learn how to use Bob access on-line documentation using man bob.

Animabob is the latest release of bob and adds animation capabilities.

Revision: Bob 1.2 (SDVL), Animabob 1.00b4 (SDVL and BSCL)

Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Visualization, Volume Rendering

IBM Data Visualization Explorer

IBM Data Visualization Explorer (dx) is a general purpose, easy to use, visualization tool. You control dx by linking a modules together with the mouse. It can read in both structured and unstructured data in many different formats, as well as TIFF images. Once the data is read in, the individual modules handle both structured and unstructured data.

With 2D data, dx can produce shaded contours, contour lines, graphs, ....
With 3D data sets, dx can volume render, display arbitrary slices of the data and isosurfaces. The transparence of the slices and the isosurfaces can be set according to data values, along with their colors.
Vector fields and stream traces can be drawn with 2D or 3D data. Text and color bars are easily added.
DX can be programmed to read in a sequence of files, or write a sequence of files. If the output files are images, these can be put togther into an animation.
Chemistry extensions are installed that allow dx to read and manipulate molelcules stored in the PDB format.

Documentation is available in the Institute's reference library and through online help from within dx. The man page (man dx) describes the environment variables and command line options.

Version: 4.3.2
Labs: Scientific Development and Visualization Lab, IBM SP, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): SDVL & BSCL:all SGI workstations, UM-IBM: all sp2 nodes
License: SDVL: 2 concurrent user, BSCL: 1 concurrent user, UM-IBM: 1 concurrent user
Categories: Visualization, Volume Rendering, Isosurfaces, Contours, Graphs, Vector Fields

For sample images produced with dx at the Supercomputing Institute, a very brief introduction, and some tips and hints, see http://www.msi.umn.edu/software/dx/tutorial/index.html.

Karma

Karma is a library of applications designed for interactive visualization of radio-telescope data. It also contains a general-purpose programmer's toolkit for utilizing these applications. Some of the features available through Karma modules include on-the-fly rescaling of images; superimposing images; slicing through three-dimensional datasets; volume rendering with a variety of optical thicknesses and gas temperatures; and animations. There are also modules for very specialized tasks, e.g. identifying expanding shells (supernova remnants). Karma modules can read a wide variety of different file types, including Miriad- and FITS-format files. This makes Karma an ideal counterpart to the radio-telescope data analysis tool Miriad.

For more information, see http://www.atnf.csiro.au/karma/.

Version: 1.6.31
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations
Categories: Visualization, Volume Rendering, Image Processing

Volocity

Description

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

Fast and highly interactive volume exploration in 3D and 4D.
Export and publication of 3D images and data in standard file formats.
Volume rendering
Object classification, measurement and tracking in all dimensions.
Measurements from multiple channels for channel comparison and colocalization.
High quality restoration of confocal and wide field microscope images.
Animation template creation for prototypes

How to run Volocity

Launch Volocity from the Start menu:
A registration dialog shows up on starting for the first time. Click 'Server address' and enter the license server information. Next, enter your Volocity login information. If you do not have a username and password, contact help@msi.umn.edu to get your Volocity login details.

Volocity access reservation

In order to avoid license conflicts, there is a reservation facility available online at http://www.msi.umn.edu/cgi-bin/res/index.html This holds good for accessing the license on any system.

More Information

User's Guide - On line user guide from the vendor.
Version Release Notes - Detailed list of modifications and new features.

Version: 3.0.1
Labs: Basic Sciences Computing Lab, Scientific Development and Visualization Lab, Computational Genetics Laboratory
System(s): Mac workstations in SDVL, PCs bpc1, bpc2 in BSCL, SDVLAPP1, PCs in CGL (One concurrent license)
Categories: Visualization, Animation, Data Analysis, Image Display, Image Processing, Volume Rendering

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