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From: mhaveri@cc.oulu.fi (Matti Haveri)
Newsgroups: alt.image.medical,alt.sci.nmr,comp.graphics.visualization,comp.sys.mac.scitech,sci.image.processing,sci.med.radiology,sci.techniques.mag-resonance,alt.answers,comp.answers,sci.answers,news.answers
Subject: Medical Image Volume Visualization Software FAQ
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Date: 2 Dec 1994 17:54:49 GMT
Organization: Oulu university central hospital
              Department of diagnostic radiology
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Summary: List of software packages, user's notes, references and other
         information relating to medical volume visualization and imaging.
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med-volviz-faq-94-12
====================

The following is a list of software packages, user's notes and other
information relating to medical volume visualization and imaging that I
have collected over the past from Usenet newsgroups, mailing lists, www
and other places. Many thanks to V.C. Arun Kumar and Lance Ladic for their
lists on 3D visualization software. I have NOT tried all of the packages
mentioned in this list, and therefore cannot attest to the quality of some
of them. Please let me know if I have misquoted someone's posting and if
you wish to make corrections and additions to the faq. Also send me a note
if some of the text is out of date or too far off-topic as I don't want
the faq to grow too much with irrelevant info.

I would be interested to hear other user's experiences concerning 2D and
3D-reconstruction of CT, MRI and US-data.

This file is formatted as ~setext~. For more information on setext, the
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This file is also available at:

<ftp://rtfm.mit.edu
/pub/usenet-by-group/news.answers/medical-image-faq/volume-visualization>

Matti Haveri <mhaveri@cc.oulu.fi>
Oulu university central hospital
Department of diagnostic radiology

Changes since 94-11
-------------------
**Software packages:**

PV-WAVE updated

VROOM updated

**Some medical sites**

UMDS Image Processing Group added

National Library of Medicine Visible Human Project updated

Changes since 94-10
-------------------
**Software packages:**

Dr Razz added

IRIS Explorer updated

ImageVolumes updated

**Some medical sites**

DICOM info, software and example image files added

National Library of Medicine Visible Human Project updated

Software packages
=================

3DVIEWNIX
---------
Demo (SUN, SGI, and PC) available at (130.91.180.111)
<ftp://mipgsun.mipg.upenn.edu/pub/>. The package sells for $1000 and comes
with the source code, both the Silicon Graphics and SUN versions, and a
couple of data files. You can get some MRI images in ACR-NEMA 2.0 format
at /pub/3DVIEWNIX1.0/DATA.

Contact: Dr. J.K. Udupa, Medical Image Processing Group, University of
Pennsylvania, Department of Radiology, 418 Service Drive - 4th Floor
Blockley Hall, Philadelphia, PA 19104-6021, Phone: (215)-662-6780, Fax:
(215)-898-9145, e-mail: <Vhelp@mipgsun.mipg.upenn.edu>.
<http://mipgsun.mipg.upenn.edu>.

3DVIEWNIX is a transportable, very inexpensive software system developed
by the Medical Image Processing Group, Department of Radiology, University
of Pennsylvania, Philadelphia. It has state-of-the-art capabilities for
visualizing, manipulating, and analyzing multidimensional, multimodality
image information. It is designed to run on Unix machines under X-windows.
It uses a data protocol that is a multidimensional generalization of the
ACR-NEMA standards. We have tested it extensively on SGI and Sun
workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a
variety of platforms including IBM RS6000s, HP700s, DEC machines, and
Stardent, all from a single source code version. 3DVIEWNIX has been picked
up as the TOP 10 GRAPHICS SOFTWARE PRODUCT OF THE YEAR by IEEE Computer
Graphics and Applications (January 1994, pp. 87). We charge $1000.00 for
the software which comes with source code and manuals. You can modify and
do whatever else you want as long as it is for your own noncommercial use.

3DVIEWNIX can handle rigid, non-rigid, static, and dynamic objects and
object assemblies. Can handle object information from multiple modalities
and longitudinal acquisitions. Multitudes of visualization, manipulation,
and analysis methods incorporated.

Preprocessing: 1. Volume-of-Interest: *To specify subset of the
n-dimensional (nD) volume image *To specify an
intensity-interval-of-interest for reducing the number of bits. 2.
Interpolation: *To create isotropically sampled data of lower or higher
resolution than input *Many interpolating functions *Interpolation in n
dimensions *Both grey-level and shape-based methods. 3. Filtering: *A
variety of forms of enhancing and smoothing filters *Used for filtering
surfaces, for normal estimation, for interpolation, and volume rendering.
4. Masking: *For assisting segmentation *Quick operation using "paint
brushes". 5. Thresholding: *Multiple intervals can be specified
*Iso-surface generation at any resolution. 6. Segmentation: *2-feature
cluster partitioning *Quick gesture-controlled (user-guided) boundary
segmentation. 7. Classification: *1-feature multiple material
classification for opacity assignment *2-feature multiple material
classification for opacity assignment. 8. Boundary Formation: *Connected,
oriented, closed 3D surfaces are formed *Surfaces may have any resolution.
9. Image Algebra: *Image addition, subtraction, logical operations.

Visualization: 1. Slice: *Sophisticated form of slice display *Multiple
input volumes of any dimensionality can be handled simultaneously
*Multiple color maps *Static montage viewing and dynamic cine viewing of
slices *Arbitrary magnification. 2. Reslice: *Guided by 3D display
*Reslicing through multidimensional volumes. 3. Surface Rendering:
*Multitudes of methods *Multiple objects with translucency and color
*Based on the notion of a structure system: A structure system may be a
collection of static objects, dynamic rigid objets, dynamic non-rigid
objects or any of these coming from multiple modalities *Structure systems
are visualized in their natural form, e.g., a beating heart is displayed
in that manner *Viewing properties of objects can be changed
independently. 4. Volume Rendering: *A new very fast method called shell
rendering *Interactive rendering *Interactive opacity and color
modification *Interactive measurement of fuzzy surfaces.

Manipulation: *One of the most sophisticated set of operations in
3DVIEWNIX *A variety of complex operations including cut away, reflect,
separate, move, surface marking, measure, animation *Complex surgical
procedures can be simulated.

Analysis: 1. Measurement: *A variety of inter and intra structure
morphometry *A variety of image intensity-based measurements such as
density profile, time density curves, region-of-interest statistics and
their variation with time. 2. Registration: *Based on matching homologous
features - points, curves, entire surfaces *For merging information from
multiple modalities *For motion description and analysis. 3. Motion
Analysis: *Rigid object assemblies *Animation of motion and its
quantification *Comparison of motion of two assemblies of objects such as
two joints *Relationship between moving surfaces.

Ongoing Work: *Fuzzy connected component object segmentation *A variety of
user-steered quick segmentation strategies: live-wire, live-band,
live-region methods *Fast volume rendering of fuzzy structure assemblies
with digital perspective *Manipulation of shells (fuzzy objects) and shell
algebra *Registration of shells (fuzzy objects) and their motion analysis
*Portable system integration.

ANALYZE
-------
Provides an environment for the interactive visualisation and manipulation
of 2-D, 3-D and 4-D biomedical images. An integrated set of tools is
provided to allow data to be interrogated in both two and three
dimensions. Three dimensional rendering tools are integrated with two
dimensional orthogonal displays to allow real time reconstruction of
conventional 2D. ANALYZE provides all the tools, including image
registration, to truely support multi-modal image analysis. Tissue
characterisation from multiple MRI, CT X-ray, and Nuclear medicine data is
available as an interactive tool. Filtration program allow data
preconditioning from statistical spatial filtering to minimise noise, and
advanced 3D frequency domain deconvolution of the point spread function of
a confocal microscopy system. ANALYZE has been deliberately developed to
run on standard computer hardware. This allows for maximum value to be
gained from the continual development of computer hardware. All supported
customers receive unlimited hotline support and and an annual two day
training course. ANALYZE is available to clinical and academic users for
$16,000. Annual support contracts are $2,000. Contact CNSoftware for
further details and evaluation.

Computers supported: Sun Sparc stations (Solaris 1 & Solaris 2); Silicon
Graphics; HP 9000/700 series; DEC station 5000; DEC alpha; IBM RS 6000;
Apple Mac Quadra. X-Windows supported on all platforms. 24 bit colour
supported where available.

Interactive 2-D image display: Display of multiple images with variable
size control; Mouse driven intensity windowing; Rapid generation of
orthogonal images from 3-D volumes; Display of 3-D volume as a cube with
control of size, intensity, range, angle-of-view and interactive
dissections along orthogonal planes; Generation and display of arbitrary
oblique planar images through 3-D volumes; Interactive generation of
"curved" images and/or radial image sections through images traced on
orthogonal images; Rapid display of images in cine movie loops.

3-D Image segmentation: Semi-automatic segmentation using advanced
morphology operations; Manual editing and automatic connection/deletion of
multiple objects using region growing; 3D image editing and object
definition; Multi-modal image classification and object definition.

Advanced 3-D image manipulation: Volume rendering using ray casting to
display 3-D images from volumetric data. A complete suite of facilities is
provided: Depth, depth gradient, grey scale and gray scale gradient shaded
surfaces; Maximum intensity projection with optional depth weighting.
Variable illumination and angle of view; Dynamic viewpoint manipulation;
Transparency for overlying surface structures; 3D interaction between
objects and orthogonal 2D slices; Multiple rendering parameters on
different regions of the same display; Combined display of multiple
segmented objects using different rendering parameters and colours.

Interactive surface labelling: Surface rendering for display of shaded
surfaces from contours extracted from segmented image data; Surface
smoothing and enhancement based on local neighbour characteristics within
the data; Display and output of surface contour profiles; ASCII file
output of surface normals for export to CAD/CAM or other design or
prosthetic applications.

Multi-modal Image Analysis: Geometric image registration across multiple
modalities using object surfaces or point files. Multi-modal image
analysis and segmentation. Fused image generation and display. Cross modal
object display - Bone from CT X-ray with soft tissue MRI.

Image & Data Manipulations: Linear combinations of images using algebraic
operators; Pseudo transparent addition of multimodal data; Spatial and
frequency domain image processing using standard and user defined filter
functions. Histogram operations. Manual object segmentation using
thresholding, tracing and erasing. Semi-automated, interactive boundary
detection for object segmentation. Automatic edge contour extraction. 2-D
and 3-D math morphology operators. 2-D and 3-D image transformation
compression using wavelets.

Image measurement: Plotting of line and trace profiles including 3-D
tracing. Region growing and spline region definitions. 2D and 3D region of
interest definition. Selection and automatic sampling of regions of
interest with image parameters. Interactive regional volume calculation.
Regional shape and texture analysis. Data plotting and statistical
analysis. 2-D and 3-D shape measurement tools. Multi spectral image
classification tools for multimodal data characterisation.

Operators toolbox: Escape and return to UNIX shell to run user developed
programs. Macro facility to record and rerun display and analysis
sessions. Magnifying glass for magnification of different areas of the
screen at different sizes. Full control of colour palette. Tex generation.

Image review: B/W & Colour postscript printer support. Multi panel cine
movie. Save facility for 24 bit RGB images for review or advanced
printing.

Software development: Support of developments of Analyze program
extensions simple user defined menu builder. Within the Analyze
documentation you will receive a sample 'C' code program to help you
develop your own utilities. Access to Analyze shared memory from external
program and interface building tools.

Data types and structures: As an inherently modality independent
environment Analyze naturally allows the comparison and the fusion of data
collected from different sites or scanners, or from different modalities.
CNSoftware can assist you with porting data into Analyze by developing
additional file conversion utilities. File import facility for: IGE Signa,
Advantage windows, 9000 & 9800; Siemens Magnatom; ACR/NEMA; Interfile;
Papyrus; TIFF included. Within the Analyze documentation you will receive
a sample 'C' code program to develop your own import file utilities.
Analyze is fully compatible, for file import, with the widely accepted
ACR-NEMA file structure and the Papyrus format. These have been adopted by
many scanner manufactures including IGE; Phillips and Siemens and which
the majority of scanners will support as a file downloading format.
Analyze will support a wide range of data resolutions including binary; 8
bit; 16 bit; 32 bit; and 64 bit data. All measurements are made at full
data resolution irrespective of the display resolution which may be
adopted. Import/export from standard image formats, TIFF; Sunraster; PCX;
GIF; PPM etc.

Confidence: Developed at the MAYO FOUNDATION'S Biomedical Imaging
Resource, Analyze allows you to benefit from more than 15 years experience
in visualisation of biomedical data and to have a software team of 15
members behind your imaging applications.

Value: The independent workstation approach offered by Analyze allows for
more productive use of scanner systems by allowing data analysis and
research to be carried out without requiring access to the scanner
console. Where not all modalities are present at a single site Analyze
allows the maximum value from externally contracted studies by allowing
referring clinicians full access to the data on their patients. Staff can
also develop and maintain their skills in the full range of data
modalities even when these are not directly available.

Training: All new purchasers receive a two day training course.

Research and Collaboration: Training of new staff with new data modalities
and new imaging approaches such as 3-D, is a realistic proposition with
Analyze. For senior clinicians the independence offered by Analyze means
that data collected over the years of clinical study and research can move
with the clinician from hospital to hospital. Collaboration between
clinicians and scientists at different institutions is greatly facilitated
by the harmonisation of data display which can be achieved by using a
standard resolution and colour palette in Analyze.

Upgradability: Analyze is supplied as an upgradable product. Entry into
the upgrade program, at the time of purchase, is available for an annual
payment of $2000. Including a further 2 day training course. Analyze is
available to Clinical and Scientific sites for $16,000.

For further information call CNSoftware: In Europe: Phone +44 403 733607,
FAX +44 403 733609, email <analyze@cnsltd.co.uk>, CNSoftware Ltd, The Old
Post Office, Worthing Road, Southwater, W.Sussex, RH13 7DT. In North
America: Phone +1 507 252 8304, FAX +1 507 252 8315, email
<analyze@cnsoft.com>, CNSoftware Inc, 201 1st Avenue SW, Rochester, MN
55902.

AVS
---
Commercial package from Advanced Visual Systems, Inc. AVS is a
visualization application software and development environment. AVS
accepts data and attempts to create a visual display of the data in a
variety of forms using different visualization techniques. AVS is
structured around their concept of a module. A module is an independent
computing element (C or FORTRAN) which is represented by a rectangular
icon on the AVS screen. AVS comes with 110 modules, and the International
AVS Center provides access to a much larger set of modules contributed by
the AVS user community. A range of data input, filter, mapper and data
output modules are also included in AVS. Filters transform data into data,
e.g. contrast stretch or edge detect. Mappers transform data into
geometry, e.g isosurface or arbitrary slice. And data output modules write
data to files, send data to peripheral devices, or render data, e.g
displaying geometry, images and volumes on the screen.

Convex, DEC, Hewlett-Packard, IBM, Sun, Wavetracer.

<http://sslab.colorado.edu:2222/projects/AVS_toc.html>.
<ftp://avs.ncsc.org/>. Usenet: comp.graphics.avs. Contact: Advanced Visual
Systems Inc, 300 Fifth Avenue, Waltham, MA 02154, USA, Tel:
1-800-428-7001, 617-890-4300, Fax: 617-890-8287, Email: <support@avs.com>,
<info@avs.com>.

Biological Detection Systems
----------------------------
15200 Omega Drive #105, Rockville, MD 20850, Phone: 800-BDS-7706, Fax:
301-990-8391. Macintosh.

>Pete Clinch: They are a company that has been around in one form or
another for the last 5 years or so. It was formed to capitalize on
technology developed at Carnegie-Mellon's Center for Fluorescence Studies.
The package they sell is a turnkey system that comes with a computer. The
main product is the software, however, and includes such niceties as
removal of out-of-focal-plane light to de-blur images and 3-D
reconstruction of a spatial series of images. Their software is at least
$10,000 for the basic package, and it can be much more than that depending
on how many of their add-ons you buy.

Bioquant
--------
Low-end 3D reconstruction and quantitative histochemistry system.
Platforms: PC. Contact: R&M Biometrics, 5611 Ohio Ave, Nashville, TN
37209, Phone: 800-221-0549.

CT programs by Malcolm Slaney
-----------------------------
<ftp://ftp.apple.com/pub/malcolm/ct.tar>

>Doug Merritt: This is a package of code that accompanies the book
"Principles of Computerized Tomographic Imaging" by A. C. Kak and Malcolm
Slaney (IEEE Press, 1988). It has nothing to do with my work at Apple.
Programs included: back - Back Projection, bgr - Insert Black Cross Hatch
on the Comtal, cen - Find the Center of CRC Scanner Data, disn - Quantize
an N x N picture, filt - Filter Projection Data, fmm - Find Minimum and
Maximum of Data, g128 - Generate 128 x 128 Picture from Quadrants, gen -
Generate Simulated Data for CT Scanners, hf - Homorphic Filter Waveforms,
hist - Find Histogram of Eight Bit Binary Data, kakman - Print Help Files
for CRC Tomography Software, median - One Dimensional Median Filter, merge
- Add Two 128 x 128 Images together, path - Generate multipath data,
pdsname - Extract PDS Name Information, radon - Plot the Radon Space of
the Scans, scan - Massage Raw Data from the CRC Scanner, sim - Simulate
Ellipse Field Images, tof - Calculate Time of Flight vs. Threshold Value.,
tv - Extract True Values from Comtal Images, window - Convolve an image
with a square window (averaging).

DIP Station
-----------
Macintosh. Contact: whc@po.cwru.edu.

>Pete Clinch: I'm pretty happy with a package called DipStation. I think
you can also make user code modules that are basically written in c.

Dr Razz
-------
Dr Razz is a 16 bit image display and analysis program for Macintosh color
computers. The program has been optimized for display of radiographic CT
and MRI images, although any 16 bit image stored in a raster file format
(with or without a header) can in principle be viewed. Features include
near real-time window width and window level adjustments on the full 16
bit image data on standard Macintosh graphic hardware. Images can be
viewed individually, or a series of images (eg, a CT or MRI exam) can be
viewed in an image stack. Most non-compressed CT and MRI images can be
opened automatically, without entering any image parameters. In the 'Auto'
open mode, the program attempts to automatically determine image type (CT
vs. MRI), presence of a header and byte order (little endian vs. big
endian). However, a 'Custom' open mode allows complete adjustment of these
and other parameters. Images created with the General Electric 'ximg'
image extraction tool can be opened directly, even if compressed. The
window width and window level setting can be interactively changed via the
window/level control, or by the arrow keys. Most of the image processing
and image analysis tools are not yet implemented. Images can be saved as
16 bit raster files, or 8 bit grayscale PICTs. TIFF and 8 bit raster
formats should be included by the first official release.

The application supports the core AppleEvents (except for printing, which
is not yet implemented) and stationary pad documents.

System 7.x and a color Macintosh with a 68020 or greater CPU are required.
A math co-processor is NOT required. A Power Macintosh version will be
released after the first non-beta version is posted for 680x0 Macintoshes.

Dr Razz is a "freeware" application. You are free to distribute this
program for non-commercial use. Please include all doucmentation that came
with the program. However, the copyright is retained by the author,
Thurman Gillespy III.

I am interested in supporting as many file formats as possible. Please
contact me if you have specific file format information. C language header
files are especially appreciated. I am also interested in collecting as
many examples of different image file formats as possible for a test
suite.

Bugs reports, and any general comments about the program should be sent to
<razz@u.washington.edu>. Inquiries to the author should be sent to
<tg3@u.washington.edu>. Thurman Gillespy III, Department of Radiology,
SB-05, University of Washington, Seattle, WA 98195, voice: 206-543-3320,
FAX: 206-543-6317.

<ftp://ftp.u.washington.edu/pub/user-supported/razz/>

EutecticSSRS
------------
Low-end 3D reconstruction, mapping, and analysis system. Contour-based
using a digitizing tablet. Platform: PC. Contact: Eutectic Electronics,
Inc, 8608 Jersey Court, Raleigh, NC 27613, Phone: 800-942-4480 (also:
919-782-3000).

FAST
----
Currently under development by members of the Numerical Aerodynamics
Simulation (NAS) Division at NASA Ames Research Center, Moffett Field, CA
94035-1000. It is a software environment for analyzing Computational Fluid
Dynamics data. FAST consists of a collection of separate programs
(modules) that run simultaneously and allow the user to examine the
results of numerical simulations by loading data files, performing
calculations on the data, visualizing the results of these calculations,
and constructing scenes of 3D graphical objects that may be animated and
recorded. SGI.

<http://www.nas.nasa.gov/FAST/fast.html>. User Guide $72, Source code for
commercial customers $2000, for educational institutions $200. Contact
COSMIC, phone (706) 542-3265, fax (706) 542-4807, email
<service@cossack.cosmic.uga.edu>. To join the FAST user group and receive
tips and important announcements about FAST, send your email address to:
<fast-users-request@nas.nasa.gov>. Email questions, comments and
suggestions to: <fast@nas.nasa.gov>.

GVLware
-------
Bob - An interactive volume renderer for the SGI.

Raz - A disk based movie player for the SGI.

Icol - Motif color editor.

Contact: <gvlware@ahpcrc.umn.edu>. Free. The Army High Performance
Computing Research Center (AHPCRC) has been developing a set of tools to
work with large time dependent 2D and 3D data sets. In the Graphics and
Visualization Lab (GVL) we are using these tools along side standard
packages, such as SGI Explorer and the Utah Raster Toolkit, to render 3D
volumes and create digital movies. A couple of the more general purpose
programs have been bundled into a package called "GVLware".

The most interesting program is probably Bob, an interactive volume
renderer for the SGI. Some Bob features: Motif interface, SGI GL
rendering. Renders 64 cubed data set in 0.1 to 1.0 seconds on a VGX. Alpha
Compositing and Maximum Value rendering in perspective (only Maximum Value
rendering on Personal Iris). Data must be a "Brick of Bytes" on a
regularly spaced grid. Animation, subvolumes, subsampling, stereo. Raz
streams raster images from disk to an SGI screen enabling movies larger
than memory to be played. Icol is a color map editor that works with Bob
and Raz. Source and pre-built binaries for IRIX 4.0.5 are included.

<ftp://ftp.arc.umn.edu/pub/gvl.tar.Z>
To use GVLware:
mkdir gvl ; cd gvl
zcat gvl.tar.Z | tar xvf -
more README

IAP
---
Imaging Applications Platform is a commercial package for medical and
scientific visualization. It does volume rendering, binary surface
rendering, multiplanar reformatting, image manipulation, cine sequencing,
intermixes geometry and text with images and provides measurement and
coordinate transform abilities. It can provide hardcopy on most medical
film printers, image database functionality and interconnection to most
medical (CT/MRI/etc) scanners. It is client/server based and provides an
object oriented interface. It runs on most high performance workstations
and takes full advantage of parallelism where it is available. It is
robust, efficient and will be submitted for FDA approval for use in
medical applications. Cost: in the $5K range.

Available from: ISG Technologies, 6509 Airport Road, Mississauga, Ontario,
Canada, L4V-1S7, (416) 672-2100.

IBM Data Explorer
-----------------
IBM, HP, Sun, SGI, DG. Contact: <stein@watson.ibm.com>.

>Keith Sams: Data Explorer is used in the following commercial industries:
CFD, Earth Sciences, Environmental Modeling, Power Generation (ie
Utilities), Financial Modeling, Petroleum Exploration, Virtual Reality ,
Computer Graphics Education, Medical Imaging, ECAD (Electronic component
design), Site Remediation, Chemistry/Molecular Modeling. To get another
view of how Data Explorer is being used you might want to look at
<http://www.tc.cornell.edu/DX/dx.html> and
<http://www-i.almaden.ibm.com/dx/>. There are some great application
examples there and some example mpeg animations done by students in the
computer graphics program at Cornell.

IDL
---
Interactive Data Language is a package for the interactive reduction,
analysis, and visualization of scientific data and images. IDL integrates
a responsive array oriented language with numerous data analysis methods
and an extensive variety of two and three dimensional displays into a
powerful tool for researchers. IDL supports an extensive data import
capability, publication quality hard copy output, and user-defined
Windows, Macintosh, or Motif graphical user interfaces. IDL is useful in
physics, astronomy, image and signal processing, mapping, medical imaging,
statistics, and other technical disciplines requiring visualization of
large amounts of data. Environments: Macintosh, Unix, VMS and Windows.
Cost: $1500 to $3750, Educational and quantity discounts available.

Contact: Research Systems Inc., 2995 Wilderness Place, Suite 203, Boulder,
CO 80301, USA, Phone: 303-786-9900, FAX: 303-786-9909, E-Mail:
<info@rsinc.com>.
<http://sslab.colorado.edu:2222/projects/IDL/idl_ssl_home.html>. Demos:
<ftp://ftp.rsinc.com/pub/idl/> (all OSs),
<ftp://boulder.colorado.edu/pub/rsi/idl/> (all OSs),
<ftp://ftp.Germany.EU.net/shop/CreaSo/IDL/>. Usenet: comp.lang.idl-pvwave.

>Joe Biegel: [about commercial packages] ...I'd recommend looking into IDL
from Research Systems in Boulder CO. It does many things (including volume
rendering now) real well. It is also very programmable & extensible
(unlike some more turnkey packages).

Image Pro
---------
From Media Cybernetics ($3,500).

ImageSpace
----------
Software environment for confocal imaging. Integrated acquisition,
processing, and visualization for 3D datasets. Platforms: SGI. Contact:
Molecular Dynamics, 880 East Arques Avenue, Sunnyvale, CA 94086.

ImageVolumes
------------
Interactive image processing, contour editing, 3D reconstruction and
volumetric analysis for confocal, EM, X-ray tomography, and MRI.
Platforms: SGI. Price: $4,500, software maintenance is $950/yr. (10/94).
Contact: Minnesota Datametrics Corporation, 1000 Ingerson Road, St. Paul,
MN 55126-8146, Phone: 612-482-7938, Fax: 612-490-9717, E-mail:
<scivis@mndata.com>. Demo versions of ImageVolumes are available at the
Gopher site gopher.mndata.com 2074 (look in the US/Minnesota listings
under Minnesota Regional Network).

SOFTWARE DESCRIPTION

The ImageVolumes system for the Silicon Graphics IRIS workstation provides
a complete software environment for three-dimensional (3D) reconstruction,
visualization and quantification of volumetric data. Input can be
digitized gray scale images, or two-dimensional (2D) graphics data that
describe contours and points. You can interactively process either form of
data to produce sophisticated 3D shaded surface models. An image
processing module, Image, lets you enhance and analyze serial section gray
scale images using several different classes of functions, including
radiometric, filtering, algebraic, geometric and morphologic. A 3D
graphical editing module, ContourEdit, lets you edit and align serial
section contours and point data taken from digitizing tablets or
microscope stage digitizers such as the MD2 Microscope Digitizer from
Minnesota Datametrics. The 3D display and analysis modules, Display and
Metrics, make full use of the visualization features of the IRIS
workstations including their surface materials and light source modeling
capabilities and their fast hidden surface removal and polygon rendering.
Most importantly, you can make measurements on 3D models such as
distances, numbers of objects, surface areas and volumes. In addition,
ImageVolumes now includes new advanced analytical tools for quantification
and classification of 3D models, such as the distance field and 3D model
intersection tool, DField.

OVERVIEW

You control actions in ImageVolumes using an interactive, screen oriented
DataFlow Manager. By simply clicking the mouse on one or more icons you
define the sequence of operations on your data and the results to be
displayed and stored. At each step of the process the DataFlow Manager
assists you in the selection of appropriate input and output data files.
The major programs within ImageVolumes are:

Image - An interactive image processor that operates on digitized gray
scale images.

ContourEdit - A screen oriented 3D database editor.

Cubes - A polygon and voxel generator that processes your serial section
data and stores a 3D geometry database of surface polygons and voxel
densities.

Display - Displays your reconstruction with user defined surface materials
properties, Phong shading and multiple light sources.

Metrics - A volumetric analysis program for measuring sizes and numbers of
objects and their surface areas and volumes.

DField - Computes distance fields of 3D surface models and quantifies
intersections between 3D surface models. Distance fields can also be used
to interpolate iso-surfaces between two 3D models.

Image Processing

Image is an interactive 2D image display and processing program. Images
can be displayed singly, as movie loops or as a mosaic. You can choose
from among radiometric, algebraic, geometric, filtering , morphological
and graphical overlay functions. The program supports region-of-interest
processing and can be run using scripts or macros that are learned by the
software during your processing operations. Major image processing
categories in Image include:

Radiometric operations - Gray level scaling, histogram normalization,
histogram equalization, binary level slice, piecewise linear
transformation, local adaptive histogram equalization (LAHE) and local
adaptive histogram normalization (Wallis).

Algebraic operations - Add, subtract, multiply, divide, square root and
logarithm of gray scale images.

Geometric operations - Image translation, rotation and scaling. A
registration feature allows interactive alignment of pairs of images.

Filtering operations - Smoothing and median filtering. Kirsch, Laplace,
Roberts, sharpening, sigma and Sobel edge detection operators. Special
line detect filter for enhancing thin fibrous structures.

Morphological operators - Area fill, dilate, erode, boundary track and
medial axis operators for delineating boundaries, identifying objects and
creating overlay masks to be used for region-of-interest operations during
radiometric and filtering operations.

Interactive Graphics Editing

ContourEdit lets you edit graphics data in the form of points, lines and
closed contours. Data can come from a variety of sources including a
digitizing tablet, boundaries of objects extracted from images by the
Image program or the MD2 Microscope Digitizer from Minnesota Datametrics.
You can view your data interactively in 3D from any vantage point using
orthographic or perspective projection. Individual vertices, points, lines
or contours can be selected using hardware picking and then visually
translated, rotated or scaled and saved in their new position. Vertices
can be deleted from or added to line and contour elements. Lines and
contours can be copied or created as interpolations of adjacent lines or
contours. Set operations are one of the most powerful features of
ContourEdit. Elements can be added to or removed from named sets of
elements and each set treated as a single geometric object. Set name
information is preserved in the database and individual sets can be
written to their own disk files.

Isosurface Extraction and 3D Rendering

Cubes analyzes your serial section data, be it digitized gray scale images
or processed contour and point data, and writes a 3D geometry file
containing a winged-edge, linked list of surface polygons and vertex
normal vectors. Voxel values can also be extracted from image data and
saved in the geometry file.

The Display program renders your 3D model using sophisticated graphics
techniques:

Ambient, diffuse, specular, transparency and emissive properties by simply
choosing a material from a supplied library of materials - or design your
own materials.

Multiple, colored light sources.

Phong shading for seamless rendering of surfaces.

Smoothing of surfaces.

Interactive translation, rotation, scaling and spinning of 3D models.

Automated animation of rotation sequences with frame-by-frame screen
capture to disk files.

Volumetric Analysis

The Metrics program allows you to measure the numbers of objects, surface
areas and volumes of all or a portion of a 3D model using a bounding box.
The bounding box can also be used to create cutaway views.

DField computes distance fields of 3D surface models and intersections
between 3D surface models.

Utility Functions

The full-featured version of ImageVolumes is supplied with a number of
utilities for image format conversion, 3D geometry file format conversion
and for capturing screen images to disk in tagged-image-file-format
(TIFF). Image conversions include TIFF, PCX, sample-scanline and PIC.
Geometry file conversions include AutoCAD DXF.

Imagist2
--------
From Princeton Gamma Tech-integrated microscope and analysis systems.
Platforms: Sun. Contact: Princeton Gamma Tech, 1200 State Road, Princeton,
NJ 08540.

IRAF
----
Image Reduction and Analysis Facility. National Optical Astronomy
Observatory (NOAO) Contact: <iraf@noao.edu>.

IRIS Explorer
-------------
IRIS Explorer was originally developed by Silicon Graphics for their
workstations. It is a modular visualisation environment - you create your
application interactively by connecting modules together using a
point-and-click interface. IRIS Explorer comes with about 150 modules
(more are available) which perform tasks such as reading in data,
filtering it, transforming it; creating graphical objects like line
graphs, histograms, contours, surfaces, isosurfaces, volumes, vector
plots, etc; and displaying them together in a window with full 3D
interaction. A number of modules are built using Silicon Graphics'
ImageVision library, and provide a large amount of image processing
functionality.

You can create your own modules to read or translate data using a
point-and-click tool called the DataScribe, or use the Module Builder -
another tool bundled with the system - to transform your existing routines
(in the form of C, C++ or FORTRAN source, or even as pure executables)
into modules for use from within IRIS Explorer. Finally, IRIS Explorer
provides the application developer with the ability to customise the look
and feel of the application before handing it over to the end-user.

Recently, SGI licenced IRIS Explorer to the Numerical Algorithms Group
(NAG), who are porting it to Sun, IBM RS/6000, HP and DEC platforms. The
Sun and RS/6000 ports are available 10/94; the others will follow soon.
Please contact the IRIS Explorer Centers for more details.

WWW: <http://www.nag.co.uk:70/1h/Welcome_IEC>. Usenet: comp.sys.sgi,
comp.graphics.explorer. <ftp://ftp.epcc.ed.ac.uk/pub/explorer/> or
<ftp://swedishchef.lerc.nasa.gov/explorer/>.

IRIS Explorer Center (Europe): PO Box 50, Oxford OX2 8JU, UK, Tel: +44
(0)1865 516377, Fax: +44 (0)1865 516388, email: <helpdesk@iec.co.uk> and
<infodesk@nag.co.uk>.
IRIS Explorer Center (North America): 1400 Opus Place, Suite 200, Downers
Grove IL 60551-5702, USA, Tel: +1 708 971 2367, Fax: +1 708 971 2706,
email: <infodesk@nag.com>.
IRIS Explorer Center Japan (IECJ): Nagashima Building 2F, 2-24-3 Higashi,
Shibuya-ku, Tokyo, Japan, Tel: +81 3 5485 2901, Fax: +81 3 5485 2903,
email: <help@IRIS.explorer.co.jp>.

KBVision
--------
Software environment for creating image understanding applications-
automatic detection, classification, and statisticas generation.
Platforms: Sun, IBM (RS6000s), DEC, SGI. Contact: Amerinex Artificial
Intelligence, 39135 Walnut Terrace, Fremont, CA 94536, Phone:
510-794-7853, Fax: 510-794-1406.

Khoros
------
KHOROS version 1.0 does not do 3D visualization, version 2.0, scheduled to
be released 8/94 might have 3D Tools. The small contributed toolbox in
KHOROS v 1.0 does very nice surface thresholding using image gradient
technique and produced grayscale renderings of surfaces. Sun, SGI, DEC,
HP, IBM, NeXT. The three major requirements for Khoros are: X11R4, a
UNIX-type operating system, and lots of space (min. 120-150 Meg). Only if
your PC has these three prerequisites can you consider doing a port of
Khoros to your PC. Successful ports of Khoros have been done for the Mac
II and various 386/486 machines that meet these requirements. Talk to
Donna Koechner <donna@khoros.unm.edu>. Contact:
khoros-request@chama.eece.unm.edu. Usenet: comp.soft-sys.khoros.

<ftp://ftp.eece.unm.edu/pub/khoros/>
<ftp://ftp.uu.net/pub/window-sys/khoros/>
<ftp://popeye.genie.uottawa.ca/pub/khoros/>
<ftp://ftp.rrz.Uni-Koeln.DE/graph/khoros/>
<ftp://ftp.lrz-muenchen.de/local/khoros/>
<ftp://ipifidpt.difi.unipi.it/pub/khoros/>
<ftp://ftp.waseda.ac.jp/pub/khoros/>
<ftp://ftp.mcc.ac.uk/pub/cgu/khoros/>
<ftp://unix.hensa.ac.uk/pub/uunet/window-sys/khoros/>
Pull back the file $KHOROS_FTP/release/install.ftp and read it first.

>Alex Milshteyn: The toolbox written by that guy from Italy works fine for
me. Khoros is able to output data in .rs format, therefore Sunview would
handle it just fine as well.

MacCubeView
-----------
Designed to display a texture map image of three-dimensional (3-D) data.
In this release, three simple ray-tracing techniques have been added. The
data in mind is typically generated by medical imaging techniques such as
CT, MRI, and nuclear medicine. Some geophysics techniques also produce
suitable 3-D image data. Hardware Requirements: MacCubeView will probably
run on any Colour Macintosh Computer that is running System 7 or newer.
The software will be at its best when used with a large eight-bit colour
monitor. The Macintosh should have at least eight megabytes of memory
installed. It will not run on a Mac Plus, SE, Classic, etc. Two versions
of the programme are supplied - one for machines with a FPU, the other is
for machines without a FPU, such the LC475 and Quadra 605. There is a demo
file of a slice of the author's head.
<ftp://mac.archive.umich.edu
/mac/graphics/graphicsutil/maccubeview1.50.sit.hqx> and the mirrors around
the world.

MacPhase
--------
2D data analysis and visualization application for the Macintosh. Data
sets can be byte, integer, longint, or real and can be as large as memory
allows. MacPhase has an extensive collection of processing tools ranging
from simple math operators to fourier transforms. You can use simple tools
to filter in the frequency domain. There are 3x3 and 5x5 configurable
convolution filters and much more. MacPhase can also display your data
using raster, contour, 3D wireframe, 3D surface, 3D rendered surface,
vector, 3D contour, 3D line, line, and combination plots. There is an easy
to use color look up table editor. Use it to put the colors where they
best show your data. MacPhase has a Data Tool palette which allows you to
draw in the data layer of your data window. MacPhase has also has a Draw
Tool palette which draws in an drawing layer of your data window. Use the
draw tools to annotate your data with text, simple shapes, placed
pictures, color look up table legends, and even sound objects. Just about
every function or operation can be called using a pascal-like macro
language. Macros are a great way to extend some of the already great
features in MacPhase. You can also write external code modules, Add-ons,
for MacPhase. These Add-ons can be an excellant way to extend MacPhase's
capablities. Add-ons will be made available to support the QuickCapture
and SCION frame grabbers, GPIB interface, serial ports, QuickTime, video
digitization (AV-vdig), Photoshop plug-ins, color channels, image
restoration, and more. Add-ons are callable from the macro language.
Add-ons can be used to add new file formats as well. MacPhase has a large
number of supported formats some of which are PICT, TIFF, MatLab, HDF,
FITS, binary, text, EPS, Mathematica, Photoshop, polygon files, sound,
color tables, and others. MacPhase supports AppleEvents through the
DoScript event and several custom events. Use the DoScript event to send
macro commands to MacPhase. Use the custom events to pass data between
applications.

<ftp://sumex-aim.stanford.edu/info-mac/sci/mac-phase-20-nofpu-demo.hqx>
and /mac-phase-20-demo.hqx (and the mirrors around the world). Contact:
Doug Norton, Otter Solution, 10 Limekiln Road, Whitesboro, NY 13492-2338,
USA, Phone: (315) 768-3956, Fax: (315) 736-4371, Internet:
<ottersol@aol.com>, American Online: OtterSol, AppleLink: ottersol.

MacStereology
-------------
Demo version is available at
<ftp://zippy.nimh.nih.gov/pub/nih-image/programs/>. MacStereology is a
package designed to make measurements of images and to make 3-D
reconstructions. Input to MacStereology is either from a digitising tablet
or from Pict files. The boundaries of the objects of interest can
therefore be drawn by hand on the tablet or traced automatically on a
binary image. From these boundaries and the magnification, parameters such
as area, perimeter and centre of gravity are calculated. If the
co-ordinates of each boundary are also saved, together with the section
thicknesses then 3-D reconstructions can be displayed, printed or plotted,
using a wireframe (for pen plotter), layers or surface plot. MacStereology
should work with any Macintosh with at least 1 Mbyte memory. It was
designed for a MacII with 8-bit colour, but is OK in grey tones or black
and white.

>Stephen M Echteler: [...]MacStereology to do some 3D reconstructions of
developing sensory neurons. The program is rather expensive ($750) and the
Mac interface is a bit buggy. I'd really appreciate comments from anyone
who:1) has used this program or 2) could suggest an alternative
application with similar features.

>John Russ: Well, I've been a MacStereology user for several years now. We
use it in our research (3D reconstructions from all kinds of imaging
including TEM, confocal light, and x-ray microtomography), as well as in
teaching courses to grad students, and like it a lot. There are only three
basic approaches to 3D reconstruction: a) volumetric (transparency)
imaging like VoxelView or VoxBlast, which shows all of the data, but can
be VERY time consuming to fiddle with all of the transparency, lighting,
etc., parameters to reveal the important aspects of structure (they really
require you to already know what is there, and just use the program to
show it to others); b) resectioning approaches like Spyglass Dicer, which
allows you to examine arbitrary sections but cannot show the important
topological characteristics present in the 3D volume; and c) surface
rendering, as in MacStereology, which is very efficient (small files and
fast displays), shows the topology and presents images that appear natural
because we are all used to seeing surfaces, but accomplishes this by
hiding other detail including internal structures behind the surfaces. The
three approaches are complementary and we use them all, but if I had to
choose, I would take Macstereology first, Spyglass Dicer a very close
second, and Voxelview (or Voxblast) a distant third, based on the amount
they are used, and the response of students and researchers to the images
(how much they can learn from them, how difficult it is to interact with
them, etc.).
As to the two specific complaints: I don't agree that the interface is
"buggy." It does have a few peculiarities that are not totally Mac-like,
like fiddling with the display LUT and taking over the whole window, but
you can turn that off if you like. Whenever I've found a bug (usually when
Apple releases a system upgrade or new hardware), the author has fixed it
pretty quickly, and he is also very good about giving advice via e-mail.
And the complaint about the price is really sort of annoying. Photoshop
costs nearly as much, but consider the number of copies they sell? What do
you think Spyglass' set of programs cost? Or how about Voxelview which is
considerably more expensive? How much did you spend for your computer+
camera+ interface+ microscope+ printer+... - well you get the idea. $750
for a program that has taken man-years to develop and has a very
specialized market is hardly high-priced. You are just spoiled because
Image is free (well, unless you count that we all pay taxes to support
Wayne). In the PC world, you would spend $2K or more for a program
equivalent to Image. Expensive? No, expensive is trying to do without a
tool you need.

MCID
----
Image analysis and quantification mainly for fluorescence imaging.
Platform: PC. Contact: Imaging Research Inc, Brock University, 500
Glenridge Ave, St. Catharines, Ontario, Canada L2S-3A1, Phone:
905-688-2040, Fax: 905-685-5861.

MetaMorph
---------
Integrated microscope image capture, enhancement, reconstruction, and
visualization system. Platform: PC. Contact: Universal Imaging
Corporation, 502 Brandywine Parkway, West Chester, PA 19380.

MicroVoxel
----------
OS/2 v2.1. Indec Systems, Inc. 820, Bay Avenue #212, Capitola, CA 95010,
(408) 479-8285.

>Jeff Ingeman: MicroVoxel is a 3D imaging package that imports data from
BioRad MRC-600 files, TIFF files, or raw 8-bit data. You can visually
examine any slice made at any angle or plane through the 3D volume. You
can render your 3D data in 3 different modes of volume rendering. You can
also extract objects from your data and render them in shaded-surface
mode. There are also a number of 2D and 3D image processing tools included
in the program. Animated movies can be rendered and shared with others
using an included, public-domain viewer program. Multiple volumes of 3D
data can also be merged into a tricolor shaded rendering. Markers can be
placed anywhere in 3D space and numerous measurements taken. We have been
using it here at UCI for over a year now and are quite happy with it.

Montage
-------
One of the first complete serial-section reconstruction packages and was
produced at the University of Pennsylvania. It includes component programs
for 2D data entry from digitizer, 3D reconstruction and display, and
surface area/volume analysis. Platforms: PC (Linux w/ VGA or X11), Unix
workstation (Sun, IBM, SGI, etc.). Cost: Free (scientific community), $ if
extended support required.
<ftp://retina.anatomy.upenn.edu/pub/mont.linux.tgz>. Refs: Journal of
Neuroscience Methods v21, pp 55-69, 1987. Contact: Robert G. Smith,
Department of Neuroscience, University of Pennsylvania, Philadelphia, PA
19104-6058, email: <rob@retina.anatomy.upenn.edu>.

Neurolucida
-----------
Low-end interactive image analysis software for neuron tracing and
anatomical mapping. Platforms: PC (Windows). Contact: MicroBrightField,
Inc, 75 Hegeman Ave, Colchester, VT 05446, Phone: 802-655-9360, Fax:
802-655-4031.

NCSA Tool Suite
---------------
Unix Workstations (DEC, IBM, SGI, Sun), Macintosh, Cray. Contact: National
Center for Supercomputing Applications, Computing Applications Building,
605 E. Springfield Ave., Champaign, IL 61820. Cost: Free. The suite
includes tools for 2D image and 3D scene analysis and visualization. The
code is actively maintained and updated. <ftp://ftp.ncsa.uiuc.edu/>.

NCSA Data Slice (XDataSlice). Supports X11. /UNIX/XDataSlice.

Viewit in /misc/viewit/. Viewit is a memory hog which can do array
manipulations on entire 3d datasets, some limited format conversions, and
3D volumetric projections. This program includes facilities for
constructing animated sequences of 3D volumetric views through various
volumes. Viewit has been ported to a number of machines including Crays
under UNICOS, Sun Workstations, Silicon Graphics Workstations, Alliant and
Convex Minisupercomputers, and a variety of other machines. Public domain.
Contact: viewit@ncsa.uiuc.edu.

Tiller in /misc/tiller/. Tiller is an SGI viewer for viewit displays.

>Patrick Moran: Viewit has a command line interface and is not the
friendliest software that you can use. On the other hand it does have a
large number of built-in functions that are useful for image processing,
including functions for MR reconstruction. Viewit is used by researchers
doing work in MR here.

>Joe Biegel: I never said Viewit had a great User I/F - in fact it
doesn't! However, it does MANY things including volume rendering quite
well. If you read the documentation, it's not that hard to get results.
It's also free. I've been using it for a few years - it's not NIH Image,
but it DOES do things like depth cued volume rendering. I've used it quite
a bit for brain imaging visualization - it works - there is a learning
curve, but it works. If you want more info on ViewIt, send email to
cpotter@ncsa.uiuc.edu (Clint Potter).

>Alexander-James Annala: Check out the code for NCSA viewit (if you have
an unix/x11 platform) -- requires 'tons' of memory for any reasonable size
volume -- and it is not exactly GUI based code (uses Tk command line
tools) -- but it does have a huge manual, 'tons' of functionality, and it
is fast when run on systems with fast processors and 'tons' of memory.

>Alexander-James Annala: If you have a SUN SPARC workstation/server with
>250M free memory available (that's free memory -- not available disk
space) then you can use NCSA's Viewit (NMR Imaging and Spectroscopy
Package) to do 3d volumetric imaging at full resolution of the UNC CHVRTD
datasets.
The following SUN SPARC recipe displays multiple views of a 3D head: get
any X11R5 (or maybe X11R4) server running on myhost - this is where you
are going to display images -- rlogin to bighost - this is where you will
need the free memory for storing intermediate results during the volume
rendering.
myhost(96): rlogin bighost -l myusername
bighost(1): ftp -i ftp.ncsa.uiuc.edu
ftp> cd misc/viewit/viewit.v3.13
ftp> binary
ftp> get viewit.sparc-version.Z
ftp> get viewit.help
ftp> quit
bighost(2): zcat viewit.sparc-version.Z >viewit
bighost(3): chmod 755 viewit
bighost(4): ftp -i omicron.cs.unc.edu
ftp> cd pub/softlab/CHVRTD/volI
ftp> binary
ftp> get 3dhead
ftp> quit
bighost(5): dd if=3dhead of=3dhead.s conv=swab
bighost(6): viewit
viewit(tcl)> -dim 3 256 256 109 -iformat RAW -itype USHORT -i 3dhead.s
viewit(tcl)> -scale 1.0 1.0 2.3486 -reorder 2 0 1 -push
viewit(tcl)> -dim 1 90 -ramp -1 1 -linscl 0 356 -xchg
viewit(tcl)> -movie 0.0 add no_erode
viewit(tcl)> -linscl 0 255
viewit(tcl)> -displ X myhost
bighost(7): exit
myhost(97): logout
If you have a smaller workstation you can still do some limited volume
rendering - but you will have to subsample the original 3D dataset to
reduce swapping to disk to a reasonable level.
A viewit electronic newsletter is distributed on an irregular basis -
email to <viewit@ncsa.uiuc.edu> to request a subscription. Clint Potter
(the original author and pricipal contact) is at <cpotter@ncsa.uiuc.edu>.

NIH-Image
---------
Has painting and image manipulation tools, a macro language, tools for
measuring areas, distances and angles, and for counting things. Using a
frame grabber card, it can record sequences of images to be played back as
a movie. It can invoke user-defined convolution matrix filters, such as
Gaussian. It can import raw data in tab-delimited ASCII, or as 1 or 2-byte
quantities. It also does histograms and even 3-D plots. It is limited to
8-bits/pixel, though the 8 bits map into a color lookup table. It runs on
any Mac that has a 256-color screen. Free.

<ftp://zippy.nimh.nih.gov/pub/nih-image/>. Mailing list:
<nih-image@soils.umn.edu>, subscriptions to the mailing list:
<listserv@soils.umn.edu> (subscribe nih-image "your name") (set nih-image
mail digest). The best way to search the archived messages is to use
<gopher://saturn.soils.umn.edu:151/77/wais-sources/nih-image-archive> to
search the archived messages for keywords, or
<gopher://saturn.soils.umn.edu/11/email-lists/nih-image> for the actual
archived messages. The archived messages are also available at
<ftp://ftp.soils.umn.edu/pub/info/email-lists/nih-image/>. The archived
messages are also in <ftp://zippy.nimh.nih.gov/pub/nih-image/documents/>
but some of the more recent ones may be missing. You can also obtain a
list of the available archive files by sending an "index nih-image"
command to <listserv@soils.umn.edu>. These files can then be retrieved by
means of a "get nih-image filename" command.

Nuages
------
Input: a set of simple closed polygons on parallel planes. There may be
several (nested) polygons per plane. Output: A set of triangles
representing the surface of a 3D polyhedra, and/or a set of tetrahedra
filling the 3D polyhedra. The program adds vertices onto and inside the
contours. How to display the output: The program currently supports
wavefront .obj format, DXF format and Object File Format (.off) format.
The latter can be visualized with geomview on sgi and NeXT. Geomview is
available at geom.umn.edu. Conversion tools to other file formats and
several contour sets can be found at <ftp://avalon.chinalake.navy.mil/>.
How to get input data: The input format is a simple ascii file (see man
prepros for a format description).

Platforms: Sun, SGI, DEC. Refs: "Three-dimensional modeling of human
organs and its application to diagnosis and surgical planning.", Technical
Report 2105, Institut National de Recherche en Informatique et
Automatique, (France), Dec 1993. <ftp://betelgeuse.inria.fr/pub/Nuages/>
(138.96.16.91).

NUAGES_SUN4.tar.Z     sun sparc 2 (sun4OS4)
NUAGES_SGI.tar.Z      sgi         (iris4d)
NUAGES_DEC.tar.Z      decstation  (ultrix)

>Matthew T. Adams: I wanted to let you know about a little utility I just
wrote and posted to <ftp://ftp.uwa.edu.au/pub/povray/incoming/utilities/>.
It converts Bernhard Geiger's Nuages' "vera" file format into the PoV 2.x
file format, suitable for inclusion into a PoV scene file.

OLPARS
------
On-Line Pattern Analysis and Recognition System from the PAR Government
Systems Corporation. Statistical pattern recognition system that can be
applied to analyzing information derived from reconstructions. Platforms:
Sun (Unix), DEC (VAX/VMS). Contact: Amber Technologies, 47 Junction Square
Drive, Concord, MA 01742, Phone: 508-369-0515, Fax: 508-371-9642.

Pixar
-----
High-end visualization and rendering for movies, but also for the medical
community. Contact: Pixar, 3240 Kerner Blvd, San Rafael, CA 94901, Phone:
415-258-8100, Fax: 415-459-4297.

Pixcell
-------
$1,500 from Sandia Labs. A demo version of Pixcell, complete with manuals
and images from Sandia Labs <ftp://ecto.ca.sandia.gov/pub/Pixcell/>.

PV-WAVE
-------
PV-WAVE is a comprehensive software environment that integrates
state-of-the-art graphical and numerical analysis techniques into an easy
to use, easy to extend, easy to apply, and easy to learn system for
quickly finding solutions to, and building applications for, complex
technical problems.

PV-WAVE uses an intuitive fourth-generation language (4GL) that analyzes
and displays data as you enter commands.  With it you can perform complex
analysis, visualization, and application development quickly and
interactively.

PV-WAVE provides hundreds of routines for representing, importing,
exporting, filtering, transforming, analyzing, visualizing, and
communicating data, as well as constructing widget-based applications with
this technology.

PV-WAVE is available for UNIX and OpenVMS workstations and for PCs running
MicroSoft Windows or Windows NT.

Cost: $995 to $6995.  Education and quantity discounts available.

Contact: Visual Numerics, Inc., 6230 Lookout Rd, Boulder, CO 80301, Phone:
800-447-7147 (outside the US: 303-530-9000), Fax: 303-530-9329.

<cwine@boulder.vni.com>, <http://doc:8118/vnihome.html>, Usenet:
comp.lang.idl-pvwave.

RMN
---
>Philip Grandinetti <grandinetti@osu.edu>: RMN - A Nuclear Magnetic
Resonance (NMR) data processing program for the Macintosh. Free.
<ftp://ftp.funet.fi/pub/sci/chem/nmr/>.

Various types of one- and two-dimensional NMR data processing. It can read
in text files (single column of data), and data files from most
Chemagnetics and Varian spectrometers. It should also read in Tecmag data
files. As far as Bruker data files are concerned, I could never figure out
what their format is. If anyone has specific details, please let me know.

There are two versions: "RMN" - for Macs with a math coprocessor, and "RMN
(no 881)" - for those without. "RMN (no 881)" will run on a PowerPC,
however, it is certainly not native mode.

There is no manual for this program. Most menu items should be obvious.
Just try it and see what happens. The menu Analyze is disabled until I
have time to fix some bugs. The same is true for Simulate under the
Acquire menu.

ROSS
----
Reconstruction Of Serial Sections. Serial-section based reconstruction and
visualization system for microscopy. Interactive and automated mosaicking,
contour extraction, and registration. Platforms: SGI. Cost: free.
Availability: late `94. Contact: Dr. Muriel Ross, Biocomputation Center,
MS239-11, NASA Ames Research Center, Moffett Field, CA 94035-1000, Email:
<ross@biocomp.arc.nasa.gov>.

SciAn
-----
SGI 4D, IBM (req. GL, Z-buff). <ftp://ftp.scri.fsu.edu/pub/SciAn/> or
<ftp://monu1.cc.monash.edu.au/pub/SciAn/>.

>Bob Lipman: [where to get red-blue 3D glasses] So far I've heard about 3
places: Reel-3D, Culver City, CA 310-837-2368, American Paper Optics,
800-767-8427 and Cygnus Graphic, Phoenix, AZ. Some of you asked about the
software that displayed the red-blue image. The software is called SciAn.

Semper6
-------
General image Processing and acquisition system. Platforms: PC, DEC (VAX),
Sun. Contact: Synoptics Ltd, Paragon Towers, 233 Needham St, Newton, MA
02164, Phone: 617-527-4461, Fax: 617-527-4084.

Spyglass Slicer/Dicer
---------------------
Volumetric visual data analysis package that allows users to create 3D
color images in seconds. It can display isosurfaces, cut through data with
oblique slices, and scale, annotate and label the display of data. Slicer
for Windows also has contains translucency and lighting options.

Availability: Macintosh, Windows. List: $495 for Windows, $695 for
Macintosh. Requirements: Macintosh: 256 color display, 4MB RAM; Windows:
256 color display, 8MB RAM, FPU; UNIX: 256 color display, 16MB RAM.

Contact: Spyglass, Inc, P.O. Box 6388, Champaign, IL 61826, USA (or 1800
Woodfield Drive, Savoy, IL 61874?), Phone: (217) 355-6000, FAX: (217)
355-8925. Spyglass Technical Support at <info@spyglass.com>.
<http://www.spyglass.com/>.

>James Sneyd: I've used Spyglass for many years, and found it to be
excellent. Especially when combined with the HDF format libraries.
Animation is excellent, and Mac-Unix coordination is seamless. It's not
nearly as powerful as some visualisation systems (Explorer, AVS,
Wavefront) but is a LOT cheaper and I have never needed anything more
expensive. I use it mostly for numerical solutions of PDEs in two and
three dimensions. One problem is the absence of Dicer for Unix.

Sunview
-------
From SUN. <http://www.sun.com>. Contact: Sun Microsystems, 2550 Garcia
Avenue, Mountain View, CA 94043, Phone: 415-960-1300.

SunVision
---------
Sun (SunOS under X). <http://www.sun.com>. Contact: Sun Microsystems, 2550
Garcia Avenue, Mountain View, CA 94043, Phone: 415-960-1300.

>Matthew T. Adams: I have a SparcStation 2 (SunOS 4.1.3) with OpenWindows
3, and I use SunVision 1.1 to do MRI volume renderings.
Advantages: easily customizable (interactive GUI editor), you can hook in
your own C code to the GUIs, volume renderings (SunVoxel), lots of image
processing tools (SunIP), photorealistic rendering (SunART, using Pixar's
RenderMan), geometric renderings (SunGV), animation (SunMovie), C library
containing all tools in all the above modules, straightforward file format
(for volume & image data, at least). Drawbacks: SunVision 1.1 is the last
version -no new stuff. Sun recommends SunVideo, speed (I'm not sure if
it's slow because of sloppy coding or my slow machine): ~3 minutes to
render a 256x256x50 8-bit volume, ~12-15 minutes to render a 256x256x124 8
bit volume.

Synu
----
SGI. Contact: spl@dim.ucsd.edu. Non-interactive components run on some
Unix-based systems.

>Harvey Karten: There is an excellent new program, called SYNU, that does
elegant 3D reconstruction of neurons, written by the Imaging Group at the
University of California Sand Diego, under the direction of Mark Ellisman.
It runs on a Silicon Graphics machine, and produces gorgeous images of
serial sections, with variable transparency, stereo pairs, etc. I think it
may be available for just the cost of the media. An example of the product
is shown on the front cover of the November issue of J. Neurosciences by
Martone. The current problem with it (when I last spoke with the Ellisman
group about this) was that it takes a bit of doing to import files into it
from Image or Canvas or other programs, and it does need a Silicon
Graphics to run the program.

The Explorer
------------
Macintosh. UCLA.

Theraview
---------

View
----
SGI (4D, Indigo, Crimson). <ftp://ftp.cs.unc.edu/pub/VIEW/>. Contact:
<bergman@cs.unc.edu> or <ward@cs.unc.edu>.

VIS-5D
------
SGI, IBM, SUN, HP, DEC (volume rend. only on SGI).
<ftp://iris.ssec.wisc.edu/pub/vis5d/>.
Contact: <whibbard@macc.wisc.edu> or <bpaul@macc.wisc.edu>.

VIS-5D is primarily designed for interactive visualization of time-varying
multi-variate 3-D gridded data such as the output of numerical simulations
of the atmosphere and oceans.  It can be applied to a variety of other 3-D
gridded data.

Vis-AD
------
SGI only.
<ftp://iris.ssec.wisc.edu/pub/visad/>.
Contact: <whibbard@macc.wisc.edu> or <bpaul@macc.wisc.edu>.

VIS-AD is designed for interactively steering and visualizing scientific
computations.  The system includes a high-level interpreted programming
language with links to C and Fortran. Users define data types appropriate
for their applications. The system includes a novel and flexible way for
users to control how their data are displayed.

VolVis
------
<ftp://sbcs.sunysb.edu/pub/volvis/>. The major restriction is that you
have to have some sort of a Silicon Graphics workstation in order to run
it. If you do not have and SGI, there is a starbase version at that same
site that will run only on HP's with starbase. VolVis can be compiled on
SPARC and runs fine under SGI, HP (w/Starbase), Sun SPARC (X11R5).
Contact: <volvis@cs.sunysb.edu>.

>Dave Wyble: While I'm sure VolVis is a very impressive package, it does
not appear to run on Sun OpenWindows.

Vox-L
-----
MS Windows NT (Intel, Mips, DEC Alpha), MS Windows 3.1, Unix/Motif.

Contact: <info@dataspace.com>. There is an extensive archive at
<ftp://ftp.near.net/member/dataspace/>. The demo subdirectory has several
demo disks of the Vox-L Visualizer. The Vox-L Visualizer demo can only
operate on an included 128^3 file, but the actual application is quite
comfortable with 256x256x128 sized volume data of MR and CT scans (see GIF
format images in the images subdirectory). The software is also available
with drivers for Stereographics' CrystalEyes. For a complete visualization
environment, check out the Vox-L Workstation line which can provide a
150mhz Alpha AXP workstation tuned for volume rendering which start under
19,000.

Voxblast
--------
Voxel-based 3d volume rendering system. Macintosh, PC. They have a demo
available via FTP. Contact: Vaytek, Inc., 305 West Lowe, PO Box 732,
Fairfield, Iowa 52556, Phone: 515-472-2227, Fax: 515-472-8131.

>Alex Colburn: PC options may be slower than other hardware options, but
our version of Voxblast running under Windows, will render at about
800,000 voxels per second on a 486 DX2, w/ 16M RAM. Granted it takes about
3 seconds to render the standard hogheart volume ( 202x132x144) and larger
volumes take longer, but I not that old yet!!!

VOXEL-MAN 3D
------------

>Karl Heinz Hhne: Some weeks ago we had announced the availability of the
VOXEL-MAN 3D interactive atlas of skull and brain. Those who like to have
an impression of its functionality may get interactively generated sample
images via ftp at (134.100.96.5) <ftp://fokus.uke.uni-hamburg.de/>
[anonymous.voxelman.images]. All images are in CompuServe ".gif" format.
Be sure to use BINARY transfer mode! File sizes are in "blocks" of 512
bytes. A sample ftp session can be found in the file
ftp-sample-session.log in the anonymous home directory. The server is a
VAX/VMS system, so some aspects are somewhat special:

common UNIX FTP server     this FTP server
__________________________________________
cd voxelman                cd [.voxelman]
cd voxelman/images         cd [.voxelman.images]
cd ..                      cd [-]

Voxel View
----------
Vital Images (505 N. 4th St., Fairfield, Iowa 52556, tel: 515-472-7726,
fax: 515-472-1661) for 3D reconstruction of images. SGI, Mac. User service
at <userserv@vitalimages.com>. Email: <bvz@vitalimages.com>. Refs:
"Voxels: Data in 3D", Byte, May 1992 issue, pp177-182.

>Mustafa Khokha: Vital Images writes its software so that it goes to the
graphics hardware in the machine to do its voxel renderings. On machines
like the SGI, this is great since SGI machines have fast graphics engines
for just this sort of thing. The renderings are fast. I mean really fast.
I was really amazed the first time that I saw it. This is a key part of
both of these programs. If you have to wait many minutes for a rendering
to occur, then a lot of the manipulations like opacity, lighting, and such
become a lot (I mean a LOT) less useful. You learn so much more by being
able to change these parameters on the fly. If you have to wait, forget
it. I just don't have the patience to play with it, and I think you really
lose a lot of "feeling" for what is going on in your datset. Therefore
make sure that you get to try out a datset that is representative of the
ones that you would be doing in terms of size and complexity. Then see if
you can manipulate the settings (like lower the rendering quality) so that
it renders before your eyes. Then when you see something interesting, up
the quality and see if it really pans out. I know VoxBlast allows you to
do this but I am not sure about VoxelView. This is because VoxBlast goes
through the operating system when it makes its calls so they can "cheat"
and render every other voxel or so. VoxelView doesn't because of its
dependence on the hardware. On the other hand perhaps this is only true
for the Unix versions? Anyway something to be aware of.
Also one problem that we have with VoxelView is that you cannot have
fractional spacing in the Z direction. In other words interpolations are
purely whole numbers in the Z direction. This is a real drag since most of
my datasets do not have aspect ratios that are whole number multiples in
the z compared with x and y. Things may not look right then. Again this is
because VoxelView depends on the graphics architecture and VoxBlast does
not.
Personally, for the short time that I tried VoxBlast, I thought it was
quite nice. Everything is menu driven although you can if you want write
your own scripts. Ease of use is not a problem. I would still compare with
the Mac version that Vital Images makes though so be sure to get your
hands on the demos.

>Michael Cammer: VoxelView does do up to 16 bit renderings where bits can
be grouped. We have tried the new color merging function for double
immunofluorescence which allows for each dataset to be full eight bits.

>Dietmar Reiter: I've got some minor experience on VoxelView Ultra on SGI,
as well as on the Macintosh Version of VoxelView (which I know better,
since our lab has got one). Three basic points are remarkable: (1) Speed
(and therefore interactivity) is minimal on the Macintosh release. It
should be somewhat of an indication, what volume rendering SHOULD be on a
graphics computer as the SGI. Speed lacks tremendously, what makes
interacitve working with datasets (volumes) larger than 1 million voxels
(a cube of 100x100x100 voxels) nearly ipossible. It can be helpful to
threshold out most of the voxels, in other words to keep the rendering
task as minor as possible. (2) Nearly no parameters of the VoxelView Mac
can be given by numbers, but by fancy scroll bars. This inhibits for
example an exact setting of the opacity for discret voxel values. A
manually cursor-drawn curve is the approximation. (3) According to sources
at Vital Images, the Macintosh version will not be developed further, what
is understandable, because of hardware limitations of the 680x0 and the
Mac PC system as a whole. This may probaly change with the upcoming of the
PowerPC. William VanZandt at Vital Images will give give more information.

>Greg Gillen: It appears that NIH Image will open Voxel View PICS
animation files and run them at a much faster rate than Voxel View. The
only problem seems to be the LUT is messed up.

>John Russ: [how you might be annotating your animations and if anyone has
transferered animations to video for presentation at meetings] Yes - I use
the mac version, which is a bit slow but OK on a Quadra. I save the
animations as PICS files which I then convert to MooV format using
ConvertToMovie. This lets me play them as Quicktime movies. I play them
directly from a powerbook using an LCD overhead panel, not through
videotape.

Voxtool
-------
From General Electric. Runs on a Sun Sparcstation with Advantage Windows.

>Matti Haveri <mhaveri@cc.oulu.fi>: We use Voxtool 1.0.4 in a Sparcstation
(64Mt of RAM) connected via Ethernet to General Electric's High Speed
Advantage and GE Sytec CT-scanners.
Binary segmentation is done through lower and higher HU-thresholds. Shaded
surface display, MIP, RaySum, Integral and Multiplanar reformatting (MPR)
as well as movie loop (if memory permits full 360 degree rotation with 6
degree intervals is sometimes possible). Select/remove object, filter
floaters (user-definable size), scalpel (user-definable cut depth),
erosion, dilation, open bridges and close gaps-functions. Intersection,
union, difference and delta-functions between manipulated models.
Crashes occasionally the whole workstation. Restarting the program or
rebooting clears occasional memory-problems. Can save only two models at a
time and the program sometimes loses link to the original slices which is
very annoying. 3D-images can be saved as individual still-images to disk
in GE's image-format (hope we will be able to open and view this format in
the other platforms as well). In the current version area-measurements
require at least two contiguos slices which is also annoying. If the
3D-model has to use more than 100 512x512 image's space as virtual memory
the program is too slow to use interactively. The current version doesn't
support colors, transparency or simulated surgical interventions. There
are some demo-pictures at
<http://biocomp.arc.nasa.gov/3dreconstruction/movies>.
Contact: We get tech support and upgrades through local GE staff here but
when we have some questions they often consult GE anyway and it takes
time. I have heard that in the past it was possible to contact GE's
software-staff directly but now GE wants that the local staff must be
consulted first. ...wish we had tech support through the Internet, it
would be _much_ easier. GE - are you listening?

VROOM
-----
Contact: Karel Zuiderveld, Computer Vision Research Group, Utrecht
University Hospital, E02.222, Heidelberglaan 100, 3584 CX Utrecht, Phone:
+31-30-506711, e-mail: <karel@cv.ruu.nl>.

VROOM is an acronym for Volume Rendering using Object-Oriented Methods; it
is a C++ class library aimed at multi-modal visualization. A description
of the functionality can be found in: Zuiderveld KJ, Viergever MA. 
Multi-modal Volume Visualization using Object-Oriented  Methods.
Proceedings of the 1994 Symposium on Volume Visualization (Washington
D.C.), ACM SIGGRAPH 1994:59-66.

The VROOM class library runs on various platforms (including HP, IBM
RS/6000, Sun, SGI and Intel-based PC's running UnixWare or Linux) with a
wide variety of compilers (as cfront, g++, xlC, Symantec).

Unfortunately, we can not give VROOM source code to interested parties
(due to restrictions placed upon us by the sponsoring companies). We are
currently working on a Tcl/Tk binding for VROOM; this will allow us to
provide others with a major part of VROOM's functionality since we then
can place TclVroom binaries on our ftp server.

For more information on the Computer Vision Research Group, see our WWW
page.  <http://www.cv.ruu.nl>.

Wavefront Data Visualizer
-------------------------
SGI, SUN, IBM, HP, DEC. Contact: <mike@wti.com>.

WHIP
----
General purpose image processing software from GW Hannaway & Associates.
Also has automated stage control and acquisition capabilities. Platforms:
SGI. Contact: GW Hannaway & Associates, 839 Pearl Street, Boulder, CO
80302, Phone: 303-440-9631, Fax: 303-440-4421.

Zmode
-----
>John Noel [Software/hardware that can convert a series of parallel MRI/CT
scan images to a 3D reconstructive model in a CAD system?]: Zmode has
developed the ability to manufacture models representing patient anatomy.
The models are produced using medical imaging software and rapid
prototyping technology. Zmode provides this modeling as a service and can
also provide custom software solutions such as translation into CAD
entities. You can get more information by mailing <zmode@callamer.com>.

Some medical sites
==================

NASA Reconstruction Home Page
-----------------------------
<http://biocomp.arc.nasa.gov/3dreconstruction>

>Kevin Montgomery: I'd like to point everyone to a new World-Wide Web
server devoted to 3D reconstruction that I've recently created. It
contains information about software packages (commercial and
researchware), data sets (including pointers to image formats), output
(images/movies), references (bibliographical), and pointers to other
locations over the Internet that contain relevant information (Web, FTP,
news, etc) for CT, MRI, confocal, and serial-section reconstruction. If
you have any additions or modifications to the information contained
therein, please send email to <www@biocomp.arc.nasa.gov> and please format
any new information in HTML if at all possible. This service is being
provided by the NASA Ames Biocomputation Center in order to aid other
researchers in the field and we hope you find the pages useful,
informative, and enjoyable!

Blood flow in intracranial arteries and aneurysms
-------------------------------------------------
<http://www.neuronet.pitt.edu:8910/~georgef> or
<http://www.pitt.edu/~gnfst1>

Finite Element Modeling of Intracranial Arterial Blood Flow and Saccular
Aneurysm Formation. Efficient Segmentation and 3-D Reconstruction of
Intracranial Vascular Structures from Magnetic Resonance Angiography Data.

>George Foutrakis (University of Pittsburgh, Department of Neurological
Surgery): I've put together a WWW Home Page describing my past and current
research. The main focus is on the computational modeling of blood flow in
intracranial arteries and aneurysms.

National Library of Medicine Visible Human Project
--------------------------------------------------
>Michael J Ackerman <ackerman@nlm.nih.gov>: The initial aim of the Visible
Human Project is to create a digital image data set of a complete human
male and female cadaver in MRI, CT and anatomical modes.

The imaging of the male cadaver has been completed. The data set consists
of axial MRI images of the head and neck taken at 5 mm intervals and
longitudinal sections of the rest of the body also at 5 mm intervals. The
MRI images are 256 pixel by 256 pixel resolution. Each pixel has 12 bits
of grey tone resolution.

The CT data consists of axial CT scans of the head and neck taken at 1 mm
intervals at a resolution of 512 pixels by 512 pixels where each pixel is
made up of 12 bits of grey tone. The axial anatomical images are 2048
pixels by 1216 pixels where each pixel is defined by 24 bits of color,
about 7.5 megabytes. The anatomical cross-sections are at 1 mm intervals
and coincide with the CT axial images. About 1880 cross-sections were
obtained from the male cadaver for each mode, i.e., CT and anatomy.

The male Visible Human Data Set will be available via FTP on the Internet
and via DAT tape on November 1, 1994. FTP is free. There will be a
duplication fee for the DAT tape. The fee is expected to be under $1,000.
The size of the data set is about 14 gigabytes.

Please remember that this is a "raw" data set. No rendering tools will be
provided with the initial distribution. The data format is a
non-interlaced RGB format read by most advanced rendering systems. Each
anatomical cross-section is over 6 megabytes in size.

A licensing agreement with NLM will be required in order for you to gain
access to the data set. This is a non-financial agreement which states
that neither NLM nor the government has any financial interest in your
product. We want to know who you are and what you propose to do with the
data set. You must agree to protect the integrity of the data set and to
credit NLM and the Visible Human Project(tm) as the source of the pictures
in any derived product. We would like a copy of any derived product. And
we would like you to help us by critiquing our work so that if NLM
continues to produce further anatomical data sets, we correct in those
data sets any deficiencies which may be present in the current data set.
The agreement should become available via FTP and Gopher at the beginning
of October 94. You will be notified via e-mail of the addresses.

The data set from the female cadaver will have the same characteristics as
the male cadaver with one exception. The axial anatomical images will be
obtained at 0.33 mm intervals instead of 1.0 mm intervals. This will
result in over 5,000 anatomical images. The data set is expected to be
about 40 gigabytes in size. Distribution is anticipated during the Summer
of 1995. We are decreasing the spacing in the "Z" direction to 0.33 mm in
order to match the pixel spacing in the "XY" plane which is 0.33 mm. This
will enable developers who are interested in three-dimensional
reconstructions to work with cubic voxels.

If you have further questions, please don't hesitate to ask. Your interest
in NLM's Visible Human Project is greatly appreciated.

Contact: Michael J. Ackerman, Ph.D. Project Officer
<ackerman@lhc.nlm.nih.gov>.

<http://www.nlm.nih.gov/extramural_research.dir/visible_human.html>

University of Indiana
---------------------
<http://foyt.indyrad.iupui.edu/HomePage.html>. Radiology Home Page -
Indiana University. Many CT and MRI-series transferred to gif-format in
<http://foyt.indyrad.iupui.edu/medres/iurad2.html>.

UMDS Image Processing Group
---------------------------

<http://www-ipg.umds.ac.uk/>. The Image Processing Group [IPG] is an
interdisciplinary research group based at UMDS, the United Medical &
Dental Schools of Guy's and St Thomas' Hospitals.

We are developing image processing and computer vision techniques, with a
particular emphasis on medical applications. This WWW has information
about The Image Processing Group, including staff, publications and
project pages, the IPG's Medical Image Archive, the IPG's Teaching
Archive, Biomedical Imaging Conference Database, Radiological Sciences
Services, Radiological Sciences newsletter, Job Vacancies. Includes an
example of combining MR, CT, and MR angiographic images for planning skull
base surgery.

<ftp://boris.umds.ac.uk/pub/images/>

ct01_raw.Z	6073k	24.5.1994
mr01_raw.Z	3197k	24.5.1994
mr02_raw.Z	6099k	24.5.1994
mr03_raw.Z	4862k	30.8.1994
pet02_raw.Z	1097k	24.5.1994

Comparison of Visualization Techniques and Packages
---------------------------------------------------
<http://www.sara.nl/Consumer.Report/Report.html>. We have made a
comparison of visualization techniques and packages. It consists of a
general part with descriptions of AVS, IRIS Explorer, Data Explorer (DX)
and Data Visualizer. The other part contains a study about how these
visualization packages have been used in visualizing plasmaphysical
processes.

AVS and IDL in medical treatment planning
-----------------------------------------
<http://archive.xrt.upenn.edu/0h/buhle/manuscripts/avs94_paper.html>.
Hypertext version of paper on using AVS and IDL in medical treatment, by
E. Loren Buhle, Jr. Ph.D.

Scientific visualization home page
----------------------------------
<http://web.msi.umn.edu/WWW/SciVis/umnscivis.html>. Scientific
visualization home page. Contact: <hughes@s1.msi.umn.edu>.

Collaborative Hypertext of Radiology and Ultrasonography
--------------------------------------------------------
<http://chorus.rad.mcw.edu/chorus.html>. CHORUS (Collaborative Hypertext
of Radiology and Ultrasonography) is a multi-author, multi-institution
hypertext that contains more than 1100 documents on radiologic anatomy,
differential diagnoses ("gamuts"), and related diseases and syndromes.
CHORUS will incorporate facilities for distributed authoring, peer review,
and publication via the World Wide Web. It's based on Fact/File, a
radiology hypertext that has been integrated with a clinical radiology
information system since 1990. Comments or questions about CHORUS are
welcome at <chorus@mcw.edu>.

NASA URLs
---------
<http://www.nas.nasa.gov/RNR/Visualization/annotatedURLs.html>. A great
resource for general information about visualization related weblets.

NMR software
------------
<gopher://gopher.nmrfam.wisc.edu>

Austin.au PET-Digital Image Library
-----------------------------------
<gopher://gopher.austin.unimelb.edu.au/11/images>. Austin Hospital,
Australia: 3-D PET-images of a human brain etc.

DICOM info, software and example image files
--------------------------------------------
<ftp://wuerlim.wustl.edu/pub/dicom/>
<ftp://wuerlim.wustl.edu/pub/dicom/images/>
---
<ftp://rsna.org/pub/>
---
<ftp.rahul.net:/pub/dclunie/dicom3tools_0.06.tar.gz>
---
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/>
<ftp://ftp.xray.hmc.psu.edu/dicom_software/>

Mallinckrodt Institute of Radiology's DICOM implementation:
<ftp://ftp.xray.hmc.psu.edu/dicom_software/Mallinckrodt/>

European CEN/TC251/WG4 version of DICOM software:
<ftp://ftp.xray.hmc.psu.edu/dicom_software/European/>
---
Dr Razz, a 16 bit image display and analysis application for Macintosh
computers. Most non-compressed CT and MRI images can be opened
automatically, without entering any image parameters. In the 'Auto' open
mode, the program attempts to automatically determine image type (CT vs.
MRI), presence of a header and byte order (little endian vs. big endian).
However, a 'Custom' open mode allows complete adjustment of these and
other parameters.
<ftp://ftp.u.washington.edu/pub/user-supported/razz/>
---
ACR Nema acquisition Plug-In (Macintosh) for Photoshop and NIH-Image:
<ftp://zippy.nimh.nih.gov/pub/nih-image/plug-ins/ACRNema.hqx> or:
<ftp://ftp.funet.fi/pub/mac/info-mac/grf/util/photoshop-acr-nema.hqx>
---
NIH-Image Macro to import ACR-NEMA 2.0 and  DICOM 3.0 images by Tunc
Iyriboz <iyriboz@dialup.francenet.fr>: >I tried it with a various ACR-NEMA
and some DICOM 3.0 images, coming from Internet archives, from various
manufacturers like Elscint, Picker, and third-party developers like
Evergreen Technologies. I had problems importing KODAK PDS 2.5 storage
files, using an inversed byte order and separate header file. It certainly
should not work with many other semi-proritary format files. It doesn't
work yet either with part 10 complient DICOM 3.0 files unfortunately. I am
working on part 10 compatible images from GE.
<ftp:zippy.nimh.nih.gov:/pub/nih-image/user-macros/import_ACR_NEMA.txt>
---
RSNA maintains a public mailing list about DICOM. To subscribe send mail
with the command "add" in the text of your message to
<dicom93-server@rsna.org>. To send mail to the group, mail to
<dicom93@rsna.org>.

sci.image.processing archive
----------------------------
<ftp://ruby.oce.orst.edu/pub/sci.image.processing/> or
gopher://skyking.oce.orst.edu, on port 71 "Information from the Coastal
Imaging Lab". sci.image.processing archive.

medical.resources
-----------------
<ftp://ftp.sura.net/pub/nic/> [medical.resources.xx-xx]. It's updated it
4-5 times a year. For the most recent files telnet or Gopher to KUFacts,
(ukanaix.cc.ukans.edu) and login as kufacts. Look under Internet ToolBox
>>> Internet Health Science Resources.

MRI
---
<ftp://nmrsg.biophys.upenn.edu/>. Specifically devoted to magnetic
resonance.

MRI MonkeyHead dataset
----------------------
<ftp://ftp.nc.nihon-u.ac.jp/pub/data/MRIMonkeyHead/>. Image sets of a
brain map on Japanese monkey by using MRI are available which were created
by Dr.Masato Taira of Department of Physiology, Nihon University, School
of Medicine. These image set were anatomically correct. Please use them
for a research on physiology or medical image processing.

xmovie.skull.tar.Z
------------------
<ftp://camelot.usc.edu/pub/images/xmovie.skull.tar.Z>

>AJ Annala: If you might be interested in viewing a 36 frame animation
loop of a series of views taken at 10 degree intervals around a 3D stack
of 113 256x256 pixel CAT scan images of a human head then acquire the
file, compile the xmovie program on your system (modify the makefile to
use your local C compiler, X11 lib, and socket lib) -- then enter 'xmovie
-height 256 -width 256 skull*' to view the animation loop on your X11R4 or
X11R5 display station. If you have the ability to select your local X11
screen resolution (SUN's can't do this -- but most i386 unix systems can
select their display resolution) you may enlarge the image by selecting an
X11 display resolution of 640 x 480 x 8 bit color. Otherwise you will be
viewing a 256 x 256 pixel animated image within whatever screen resolution
is the default on your system.

Chapel Hill Volume/Ray Tracing Datasets
---------------------------------------
<ftp://omicron.cs.unc.edu/pub/softlab/CHVRTD/>. (Chapel Hill Volume/Ray
Tracing Dataset) 3D Skull (brain) images generated from CT or MR slices.
Several tens of megabytes of 3D images (MRI scan of knee and head, CT scan
of head, a few other datasets - something like 109 slices of 256 x 256
pixels x 16 bit integer per pixel for one of the datasets).

<ftp://ftp.cs.unc.edu/pub/softlab/CHVRTD/>. The Chapel Hill Volume
Rendering Test Data Set. There is an MRI scan of a human skull
(256x256x109) and a CT scan of a skull of a human cadaver (256x256x113).
Note that these are not images but volumes, but the slices could be
treated as images if you can extract them.

Avalon 3D object files
----------------------
<ftp://avalon.chinalake.navy.mil/pub/objects/>. 3D object files
subdirectories exist for different formats. Avalon was created to be a 3D
object "repository" for the net. You'll find 3D datasets in various
formats, utilities to convert between the different formats, and documents
explaining the file formats. There is a /pub/incoming directory for
uploads, so if you have anything to contribute, please upload it! If you
have any problems connecting to avalon, try its mirror site Kubota Pacific
at (144.52.120.9) <ftp://ftp.kpc.com/pub/mirror/avalon/>.

Newsgroups of (possible) interest
---------------------------------
alt.3d
alt.graphics
alt.graphics.pixutils
alt.image.medical
alt.sci.nmr
bionet.neuroscience
bionet.software
comp.graphics
comp.graphics.algorithms
comp.graphics.avs
comp.graphics.data-explorer
comp.graphics.explorer
comp.graphics.visualization
comp.lang.idl-pvwave
comp.protocols.dicom
comp.soft-sys.khoros
comp.soft-sys.wavefront
comp.sys.mac.graphics
comp.sys.sgi.graphics
sci.answers
sci.data.formats
sci.image.processing
sci.med
sci.med.physics
sci.med.radiology
sci.med.telemedicine
sci.techniques.mag-resonance
sci.techniques.microscopy

Other interesting FAQs
======================

Medical Image Format FAQ
------------------------
From: dclunie@flash.us.com (David A. Clunie)
Newsgroups: alt.image.medical,comp.protocols.dicom,sci.data.formats,
            alt.answers,comp.answers,sci.answers,news.answers
Subject: Medical Image Format FAQ
Summary: This posting contains answers to the most Frequently Asked
         Question on alt.image.medical - how do I convert from image
         format X from vendor Y to something I can use ? In addition
         it contains information about various standard formats.

<ftp://rtfm.mit.edu
/pub/usenet-by-group/news.answers/medical-image-faq/> [part1-3]

comp.graphics.vis FAQ
---------------------
From: eugene@amelia.nas.nasa.gov (Eugene N. Miya)
Newsgroups: comp.graphics.visualization
Subject: comp.graphics.vis FAQ c.g.v.FAQ
Organization: NASA Ames Research Center, Moffett Field, CA

comp.compression Frequently Asked Questions
-------------------------------------------
From: jloup@chorus.fr (Jean-loup Gailly)
Newsgroups: comp.compression,comp.compression.research,
            news.answers,comp.answers
Subject: comp.compression Frequently Asked Questions

<ftp://rtfm.mit.edu
/pub/usenet-by-group/news.answers/compression-faq/> [part1-3]

JPEG image compression: Frequently Asked Questions
--------------------------------------------------
From: tgl@netcom.com (Tom Lane)
Subject: JPEG image compression: Frequently Asked Questions
Newsgroups: comp.graphics,alt.graphics.pixutils,
            alt.binaries.pictures.utilities,
            alt.binaries.pictures.d,
            alt.binaries.pictures.erotica.d,comp.answers,
            alt.answers,news.answers
Summary: Useful info about JPEG (JPG) image files and programs

<ftp://rtfm.mit.edu/pub/usenet-by-group/news.answers/jpeg-faq>

comp.graphics Frequently Asked Questions
----------------------------------------
From: grieggs@netcom.com (John T. Grieggs)
Newsgroups: comp.graphics,comp.answers,news.answers
Subject: comp.graphics Frequently Asked Questions (FAQ)

<ftp://rtfm.mit.edu/pub/usenet-by-group/news.answers/graphics/faq>

Computer Graphics Resource Listing
----------------------------------
From: nfotis@theseas.ntua.gr (Nick C. Fotis)
Subject: Computer Graphics Resource Listing
Newsgroups: comp.graphics,comp.answers,news.answers

<ftp://rtfm.mit.edu
/pub/usenet-by-group/news.answers/graphics/resources-list/> [part1-6]

Macintosh Image Processing Information Sources (FAQ)
----------------------------------------------------
From: huff@mcclb0.med.nyu.edu (Edward J. Huff)
Newsgroups:
sci.image.processing,comp.sys.mac.scitech,sci.answers,news.answers
Subject: Macintosh Image Processing Information Sources (FAQ)
Summary: Macintosh Image Processing Information available via gopher, FTP,
         Usenet, e-mail, telephone, and snail mail.
X-Last-Updated: 1993/10/26

<ftp://rtfm.mit.edu
/pub/usenet-by-group/news.answers/image-processing/Macintosh>

Scientific Data Format Information FAQ
--------------------------------------
From: ilana@kiowa.scd.ucar.edu (Ilana Stern)
Newsgroups: sci.data.formats,news.answers,sci.answers
Subject: Scientific Data Format Information FAQ

<ftp://rtfm.mit.edu/pub/usenet-by-group/news.answers/sci-data-formats>

-end of med-volviz-faq-94-12-
