Category: Visualization

The complete listing of visualization software. This includes categories such as 2D Graphs, 3D graphs, Contours, Isosurfaces, Volume Rendering, and many many more.

Adobe Photoshop

Adobe Photoshop allows you to create color images and edit all or part of an existing images. With Photoshop you can add text, change the color balance, replace colors, change the brightness, blur or sharpen, and adjust an image or part of an image in hundreds of different ways. Photoshop can also resize or change the resolution of an image. It is the most powerful image manipulation tool at the Institute. Documentation is available on line (within the program) and via the web from Adobe.

Photoshop supports many image formats. These include PHOTOSHOP, BMP, PICT, EPS, PCS, GIF, JPEG, PIXAR, RAW, PNG, SCITEX, TARGA, and TIFF. For best results on images produced on an SGI workstation, convert them to TIFF and then scp them to the Macintosh for use in Photoshop. Likewise, in Photoshop, save images in the TIFF format, before sending them to an SGI workstation.

PhotoShop can also be used on m1 to scan images or documents using the Epson Scanner plugin (under Import on the File menu).

Version: 7.0
Labs: Scientific Development and Visualization Lab
System(s): The Macintosh m1 & m2
Categories:Image Display, Image Processing, Visualization

Amira

Description

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

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

Blender

Description

Blender is a complete and integrated suite for 3D modeling, animation, rendering and post-production.

Home Page

http://www.neogeo.nl

Tutorial

Found on http://www.neogeo.nl/stuff/index.html

Documentation

A postscript formatted manual is found in /usr/local/blender/blender_manual_1.03.ps

Setting Up Your Environment

You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated fils. To do this, enter the following command:

module add blender

If you access this package on a regular basis, you can add this line to your ~/.cshrc file so that your environment will be initialized for Blender every time you log in.

eg:

  ...
  # initialize and load modules

  if( -e /usr/local/share/modules/init/tcsh ) then
     unsetenv PATH MANPATH
     source /usr/local/share/modules/init/tcsh
     module load base
     module add blender 
  endif
  ...

Running Blender

Once you have setup your environment, use the following command to run Blender

blender

Version: v1.54
Labs: Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Animation, Visualization

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

Chime

From the Chime home page:

To facilitate the exchange of chemical information globally, MDL provides the Chemscape Chime Web browser plug-in free of charge. Chemscape Chime allows scientists to view chemical graphics directly on an HTML page.

Chime supports most of the popular structure display formats that scientists use including MDL Information Systems' Molfile and Rxnfile and many of the popular 3D display formats such as the Brookhaven Protein Databank (PDB) format (3D rendering and RasMol scripting code courtesy of Roger Sayle.)

NOTE: This plug-in is for 8-bit color graphics displays. For 24-bit systems you must use the Netscape command line option "-visual pseudocolor". Most SDVL and BSCL workstations have 24-bit graphics.

Version: 0.9e
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): all SGI workstations
License: Freeware
Categories: Visualization, Molecular Modeling

Contours

A public domain program from NCSA, Contours, is used to generate contour plots from data generated by other programs.

Version: 1.0b
Labs: Scientific Development and Visualization Lab
System(s): all Macintosh workstations
Location: Applications:Data Analysis and Display:Contours
Categories: Visualization, Contours

Dicer

Dicer is an easy to use visualization tools for 3D data sets. Dicer works best with Matrix data and accepts several types of data formats, including binary, ascii and hdf. Dicer can display isosurfaces and slices of the 3D data.

Version: 2.0
Labs: Scientific Development and Visualization Lab
System(s): the Macintosh m2
Categories: Visualization, Isosurfaces

Ensight

A Scientific Visualization Package.

To run ensight from a workstation, with the server on the SP On a workstation type:

module load ensight
ensight7.client -cm

Then on the IBM SP type:

module load ensight
ensight7.server -c workstation_hostname

Version 7.4 is the default. Version 7.3 may be accessed by:

module load ensight/ensight73
on the SP and workstation.

Ensight clients are installed on the SDVL's and BSCL's workstations.

Version:7.3 and 7.4
Labs: IBM SP, Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): IBM SP, all workstations
License: 1 Concurrent users
Categories:Visualization

Fast

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 from many different fields. Features of FAST include: Drawing shaded meshes, isosurfaces, streamlines, vector fields, particle traces and contours. It can output Postscript. Annotation and legends are easy to add. FAST specializes in curvilinear grids and reads in PLOT3D data files. Copies of the FAST User Guide are available in the Institute's reference library. FAST has a good deal of on-line help while in the program itself. There is a brief man page (man fast).

Version: 1.1a
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Fluid Dynamics, Visualization, Isosurfaces, Contours, Vector Fields

For more information, see http://www.msi.umn.edu/software/fast/tutorial/index.html.

Gnuplot

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. It plots any number of functions, built up of C operators, C library functions, and some things C doesn't have, such as **, sgn(), etc. It also provides support for plotting data files, to compare actual data to theoretical curves, user-defined X and Y ranges (optional auto-ranging), smart axes scaling, and smart tick marks.

For more information, see the gnuplot man page (man gnuplot), or the on-line help from within the emacs editor. A pdf manual is available ghostview/usr/local/doc/gnuplot.pdf .

Version: 3.7
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Visualization, Isosurfaces, Contours, Graphs

Grace

Grace is a tool for 2-D plots. It is derived from Xmgr. To use, first load the grace module (module add grace), then type xmgrace.

Documentation is available from within grace.

Version: 5.1.0(gamma)
Labs: Scientific Development and Visualization Lab
System(s): all Unix workstations
Categories: Visualization, Graphs

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.

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.

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.

To run IDL, first load the idl module (module add idl), then type idl for a command line interface or idlde for IDL's development environment, which is a X interface to IDL.

Manuals are in the Institute's library and in pdf files in /usr/local/rsi/idl_5.4/idl/docs.

For more information, see http://www.msi.umn.edu/software/idl/tutorial/index.html.

Version:6.0
Labs: Scientific Development and Visualization Lab, IBM SP
System(s): all UNIX workstations
License: 1 concurrent user.
Categories: Visualization, Isosurfaces, Contours, Graphs, Image Processing

Icol

Icol, or Interpolated Color Map Editor, has been installed on the SGI workstations. Icol is an interactive tool for sketching and modifying 256-level color maps that can be interpolated between key points. Color maps are often used to create images from arrays of scalar data, such as temperature, density or stress. Icol can assign colors to key values and interpolate in several color spaces. Icol can also edit maps of different lengths. Icol has many different formats for saving and retrieving color maps, so it may be readily used with most applications.

Version: 1.1
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations
Categories: Visualization

Igor

Igor is an integrated graphing and data analysis environment. It generates waves, graphs, tables, and page layouts.

Version: 1.26
Labs: Scientific Development and Visualization Lab
System(s): all Macintosh workstations
Location:Applications:Data Analysis and Display:Igor v1.2.
Categories: Visualization, Graphs, Data Analysis

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

Khoros

Visualization software with an emphasis on image processing applications. Khoros uses a visual programming paradigm for its user interface (i.e., similar to AVS and Explorer). There are too many modules in Khoros to list here but a sample might include: a 2-D graphing module, a 3D surface/contour rendering module, dozens of 1-D and 2-D image processing modules, data importing modules, data exporting modules, etc. Khoros is based on the X Windows system (athena widgets).

Version: 1.0 p15
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations
Categories: Visualization, Isosurfaces, Contours, Graphs, Image Processing

NCAR Graphics

NCAR 4.1 is a library of C and FORTRAN 77 callable functions that allow applications to generate 2-D and 3-D graphics on a number of output devices, including X windows, PostScript, Tektronix 4010 and 4014 and 4107, and HP Pen Plotters and SunTools. The NCAR 4.0 library provides such functions as 2-D line and color-shaded contours with labeling, 2-D halftone contours, 2-D vector fields and streamlines, simple 2-D Cartesian graphs with linear or logarithmic scaling, histograms, 2-D and 3-D (plane projected) text in a number of fonts at any size or angle with superscripting and subscripting, 3-D mesh surfaces, 3-D contoured iso-surfaces with hidden lines removed, 3-D axes systems, 3-D curves, world-coastline, U.S. state, and world political map database, and ten cartographic projections. Contours, vector fields, streamlines, and grids can undergo map projections and can optionally be masked by continents, state, and world political boundaries (e.g., contours can be drawn over land masses only). This makes NCAR 4.1 well-suited for atmospheric applications. NCAR 4.1 also provides limited supported for animation and scrolled or stationary titles. In addition, NCAR 4.1 comes with a public domain software package called BIVAR that performs bivariant interpolation of random 2-D scalar data into a regular 2-D scalar grid. A number of man pages are available (man -k ncar ) and on line at http://ngwww.ucar.edu/ngdoc/ng4.0/ngdochome.html

Version: 4.1.1
Labs: IBM SP, Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): The IBM SP and all UNIX workstations in the SDVL and BSCL
Categories: Visualization, Isosurfaces, Contours, Graphs, Vector Fields

Raz/Xraz

Raz is a GL based program for animating a series of raster or byte based pseudo-colored images using a user supplied color map which can be edited interactively. Raz is controlled by commands in a script file or by the program xraz which offers a Motif based Graphical User Interface (GUI). Raz and xraz allow varying the frame rate for animation, zooming the images, and adding a variable size border to make live recordings of the animations look more professional. Raz can play from memory or off disk. Man pages are available (man raz and man xraz).

Version: 1.3
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations
Categories: Visualization, Image Display

Note: Xraz crashes on i8, i9, and i11 when the color map is edited.

Tecplot

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. Tecplot allows the user to create plots with contours, iso-surfaces, mesh lines, vectors, streamlines, light-source shaded surfaces, and scatter symbols. Tecplot manuals are available in the Institute's reference library, in /usr/local/tecplot8/doc (pdf format), and on line.

Tecplot has some built in animation capabilities which produces AVI movies or raster meta files. For raster metafiles, use rm2sun or rm2mpeg to convert these to sun image files or to a mpeg movie respectively (be sure to add the imageproc module, module add imageproc).

Version:10.0-0-7
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Scientific Development and Visualization Lab-sdvlapp1, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Altix, IBM Power4
System(s): all UNIX workstations, Unisys, PCs in SDVL and BSCL
License: Shared U site license
Categories: Visualization, Isosurfaces, Contours, Graphs, Vector Fields, Fluid Dynamics

For more information, see http://www.msi.umn.edu/software/tecplot/tutorial/index.html.

Transform

Transform is an easy to use visualization tools. The only somewhat confusing operation is reading in data files. Transform works best with Matrix data and accepts several types of data formats, including binary, ascii and hdf. Transform can create contours and surface plots.

Version: 3.02
Labs: Scientific Development and Visualization Lab
System(s): all SGI workstations, the Macintosh m2
License: SGI: 2 concurrent users.
Categories: Visualization, Isosurfaces, Contours

For more information, see http://www.msi.umn.edu/software/transform/tutorial/index.html.

Velocity

Velocity2 is a 3-D reconstruction system that's an image processor, surface reconstructor, render, editor, measurement and analysis tool. Produces highly accurate reconstructions from many forms of data including simulation data, computed tomography (CT) data and magnetic resonance (MR) data.

Version: 2
Labs: Scientific Development and Visualization Lab
System(s): i7
Categories: Visualization, Isosurfaces

For more information, see http://www.msi.umn.edu/software/velocity/tutorial/index.html.

Vis5D

Vis5D is a system for interactive visualization of large 5-D gridded data sets such as those produced by numerical weather models. One can make isosurfaces, contour line slices, colored slices, volume renderings, etc of data in a 3-D grid, then rotate and animate the images in real time. There's also a feature for wind trajectory tracing, a way to make text anotations for publications, support for interactive data analysis, etc.

The Vis5D system includes the vis5d visualization program, several programs for managing, analyzing and importing five-dimensional data grids, an API for supporting custom user interfaces, a TCL scripting language, complete source code, and documentation.

Vis5D is available from: http://www.ssec.wisc.edu/~billh/vis5d.html

Documentation is in /usr/local/vis5d-5.2/doc/README.ps (ghostview /usr/local/vis5d-5.2/doc/README.ps).

To run Vis5D, you must first load the module. Type

To run vis5d on a sample data file, type

Version: 5.2
Labs: IBM SP, Scientific Development and Visualization Lab, Basic Sciences Computing Lab
System(s): IBM SP and all SGI workstations
Categories: Visualization

Volocity

Description

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

Volocity access reservation

More Information

Xmgr

Xmgr is the interactive program of ACE/gr. ACE/gr is an XY plotting tool for workstations or X-terminals using X. Features include Linear regression, splines, running averages, DFT/FFT, and cross/auto-correlation Documentation is available on-line from within xmgr.

To run xmgr, first load the xmgr module ( module add xmgr), and then type xmgr.

Version: 4.1.2
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all UNIX workstations
Categories: Visualization, Graphs

iView Media Pro

Description

iView MediaPro is a media management and cataloguing application for Mac OS X. You can use iView to import images directly from a digital camera, view, calibrate, organize, annotate, or backup media files. iView creates web sites, slide show presentations and QuickTime movies with your images, animations and audio soundtracks.

Features:

• Import more than 120 Mac OS, PC and Web media formats
• Import and catalog images directly from digital cameras
• Create and view media files in customized catalogs
• Organize, classify and annotate media with indexable and searchable tags
• Fast access to media from disks, CD-ROMs and other unmounted volumes
• Automatically generate web pages; Customize web page templates
• Convert and repurpose image, sound and movie files into a variety of formats
• Instant playback of movies, QTVR, animations, sounds in any view
• Print reports, contact sheets as well as full images
• Watch slide shows with movies, sound, images; Select timing & transitions
• Create QuickTime movie presentations
• Store, backup and burn your files to CD-ROM and other removable disk
• Integrate workflow with the most popular applications

More Information

Tour of iView Media Pro features
iView MediaPro feature details

Version: iView MediaPro 1.5.5
Labs: Scientific Development and Visualization Lab
System(s): MacIntosh SDVL (m2.msi.umn.edu)
Categories: Animation, Image Display, Image Processing, Visualization, Miscellaneous

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