Subject: Medical Image Volume Visualization Software FAQ
Supersedes: <42cqtt$14u@ousrvr3.oulu.fi>
Date: 5 Jan 1996 10:50:37 GMT
              Department of diagnostic radiology
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-96-01
====================

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if some of the text is out of date or too far off-topic as I don't want the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.

WWW-, FTP- gopher- and email-URLs are in a format that newsreaders like
Mac's NewsWatcher <ftp://ftp.acns.nwu.edu/pub/newswatcher/> can pass
automatically to helper-applications.

This file is formatted as ~setext~. Setext viewers for Mac, DOS/Windows and
UNIX can be found at <ftp://ftp.bilkent.edu.tr/pub/Local/setext/>. For more
information on setext, the structure-enhanced text format check
<http://hospex.icm.edu.pl/hospex/setext-clients.html> or send email to
<mailto:setext@tidbits.com>. A file will be returned shortly.

The latest version of this file is available at:

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

This file is also available at:

<http://www.smartpages.com
/faqs/medical-image-faq/volume-visualization/faq.html>

<http://www.cis.ohio-state.edu
/hypertext/faq/usenet/medical-image-faq/volume-visualization/faq.html>

<http://www.cs.ruu.nl
/wais/html/na-dir/medical-image-faq/volume-visualization.html>

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

Contents
========

**Software packages**: Progams relating to medical volume visualization and
imaging as well as users's notes.

**Some medical sites**: Some medicine-related WWW-, Gopher-, FTP- and other
Internet-sites worth knowing.

**DICOM info, software and example image files**

**Other interesting FAQs**

Changes
=======

Changes since 95-09
-------------------
**Software packages:**
IAP updated
ImportACCESS updated
IPLab Spectrum added
Khoros updated
Mvox added
NIH Image www-page added

**Some medical sites**
Mallinckrodt musculoskeletal www-page added

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

3DVIEWNIX
---------
3DVIEWNIX has 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.

Demo (SUN, SGI, and PC) available at <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.

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, <mailto:Vhelp@mipgsun.mipg.upenn.edu>.
<http://mipgsun.mipg.upenn.edu>.

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.

Alice
-----
DIPStation has been obsoleted by Alice. Alice is 3D oriented analysis
software for medical and scientific imaging. Alice brings you ROI and VOI
tools for region and volume analyses, plug-in file import/export extensions
to support a variety of scanner file formats and a modular architecture.
Available for the Macintosh, PowerMac, Windows and Windows NT, Alice was
created by Hayden Image Processing Group.

Features - Regional analyses, spatial measurements, calibration and
annotation of images. Multiple view, including Single Image, Multi Image,
Graph and Cine. 16 bit window/level. Alice supports non-integer image
values and units so that quantitative studies can have meaningful values
such as 0.25 uC/ml rather than uncalibrated integer values. Alice can
process both real and complex image datasets. Arithmetic operators can
create composite studies, such as subtraction studies. Statistical analyses
calculate image, region and volume statistics in tabular spreadsheet or
graph formats. "Hot" analyses update the reported values automatically when
an image or ROI changes. The Alice modular architecture allows you to
expand the product capabilities by adding standard plug-in extensions or
contract with HIPG to create custom extensions for a solution tailored
precisely to your requirements.

Details - Standard Tools: Pan, Zoom, LOI, ROI, VOI, Measure, Annotation,
Auto Segment. Standard File Formats: DIPStation, TIFF, vff, Sun Raster,
Binary w/ Descriptor, HDF, FITS, PICT, HVision, Visilog, Kodak PhotoCD,
PICS, EPS. Optional File Formats: DICOM3, ACR/NEMA-2, Siemens, Toshiba, GE,
Picker. Analysis: Statistics, Statistics vs. Column, Statistics vs. Row,
Statistics vs. Slice (3D), Histogram, Cross Section. Morphological:
Dilation, Erosion, Opening, Closing, Alternating Filter, OS Filters, Local
Extrema, Regional Extrema, Gradient, Contrast Filter, Geodesic Operators,
Distance Functions, AutoMedian, Watershed. Arithmetic: +, -, *, /,
Threshold, Modulo, Max, Min, CHS, Abs Val, Square, SQRT, Log, Exp, Sine,
Cos, Tan, Int, Frac, ASin, ACos, ATan, Rect to Polar, Polar to Rect,
Complex Conjugate. ROI/VOI Analysis: Fill In, Fill Out, Shrinkwrap,
Adaptive Propagate, ROI Morphology. Image Processing: Geometric (Flip,
Rotate, Translate, Roll), Linear Filters/Convolutions (Pad, Sobel,
Laplacian, Sharpen, Unsharpen, Gaussian, User Defined), FFTs.

Pricing - $1495.00 single license, $4495 5-pack, academic discounts
available.

Questions regarding Alice can be sent to: <mailto:sales@perceptive.com> or
Hayden Image Processing Group, P.O. Box 654, Boulder, CO 80306-0654. User
contributed code as well as updates to plug-in modules at
<ftp://perceptive.com/pub/>.

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.

For further information call CNSoftware: In Europe: Phone +44 403 733607,
FAX +44 403 733609, <mailto: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
<mailto: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, <mailto:support@avs.com>,
<mailto:info@avs.com>.

Biological Detection Systems
----------------------------
Biological Detection Systems imaging group was acquired by Oncor, Inc. They
can still be reached at 301-990-0100 or 800-237-7706. Anyone interested in
this Macintosh software (which is written in the TCL libraries from Delft)
can e-mail Scott Ireland <mailto:74673.314@compuserve.com>. Oncor Imaging
Systems: Voice 617-666-0775, Fax 617-666-8816.

>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
-----------------------------
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 Malcolm's work at Interval.
Programs include: 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). <ftp://ftp.interval.com/pub/papers/malcolm/ct.tar>

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 author is interested in supporting as many file formats as possible.
Please contact him if you have specific file format information. C language
header files are especially appreciated. He is 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
<mailto:razz@u.washington.edu>. Inquiries to the author should be sent to
<mailto: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).

EVAL3DPET
---------
EVAL3DPET - Programs for the Evaluation of 3D PET Reconstruction Algorithms
are available from the Medical image processing group, Department of
radiology - University of Pennsylvania.

EVAL3DPET is a set of programs designed to statistically evaluate 3D PET
reconstruction algorithms. It comprises of tools for 3D phantom and
projection data generation, evaluation and statistical comparison, and it
includes some fully 3D reconstruction algorithms.

The EVAL3DPET programming system is designed to be capable of:

Generating phantom and projection data based on a realistic 3D PET scanner
model. The phantoms are random samples from a statistically described
ensemble of 3D images with 69 ellipsoid features (cold, normal and hot)
ranging from small (4 mm) to large (40 mm). The projection data generation
takes into account detector field-of-view blurring and a realistic 3D PET
noise model.

Evaluating for structural accuracy, hot spot detectability and cold spot
detectability. The evaluation program also calculates a training
figure-of-merit, that can be used for optimizing reconstruction techniques.

Statistically comparing the efficacy of a pair of reconstruction techniques
using the t-test.

Included, as examples, are the ART and EM reconstruction techniques, both
implemented using traditional voxels and also using the so-called "blob"
basis functions. Our implementations of ART use a special data-access
ordering (of projection rays) to achieve fast convergence. The EM
algorithms support both attenuated and non-attenuated projection data.

EVAL3DPET will be made available to all who request it at the cost of
reproduction and mailing of the C source code (on a UNIX tar tape) and the
manual. The programs were developed using the C language (K&R), under a
UNIX operating system, and they have been tested on SPARCstations (SUN) and
Silicon Graphics machines. The software and the manual may also be received
via ftp (in which case we will require a login ID and a password). There is
a charge of $150.00 (checks only) for providing this service. (For overseas
mailing add another $50.00 if air mail delivery is required.) Please make
the check payable (in US currency) to RADIOLOGY ASSOCIATES and send it with
your order to:

Ms. Mary Blue, Medical Image Processing Group, Department of Radiology -
University of Pennsylvania, Blockley Hall, 4th Floor, 418 Service Drive,
Philadelphia, PA 19104--6021, Tel:(215) 662--6780, fax:(215) 898--9145,
e-mail: <mailto:mary@opus.mipg.upenn.edu>.

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,
<mailto:service@cossack.cosmic.uga.edu>. To join the FAST user group and
receive tips and important announcements about FAST, send your email
address to: <mailto:fast-users-request@nas.nasa.gov>. Email questions,
comments and suggestions to: <mailto: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: <mailto: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.

ISG supplies visualization software from MR scanners through PACS
workstations, to image-guided surgical systems. ISG customers include
diagnostic imaging companies, such as GE Medical Systems, Philips Medical
Systems, Siemens MR, Siemens CT, Siemens PACS, Hitachi and DuPont, as well
as surgical equipment companies, such as Elekta Instruments, Inc. and
Aesculap AG. <http://www.isgtec.com/>

IBM Data Explorer
-----------------
IBM, HP, Sun, SGI, DG. Contact: <mailto: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-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.

ICC
---
Imaging Control Center for Windows is designed for monochrome image
display, processing and analysis. One of the many unique features is that
it uses 16 bit integer pixels as the default internal data format.

Image display: Zoom, Squeeze and Pan multiple image displays. 8 functional
image display scaling modes. Display image sequences as movies. Create
image montages and text overlays. Gray-level and Pseudo-color image display
palettes. Realtime image display palette control.

Image processing: Internal pixel data type is 16 bit signed integer. Binary
Operations: THRESHOLD, DILATE, ERODE, OUTLINE. Pixel Operations: SHIFT,
ROTATE, NEGATE, INVERT, ABS. Monadic Operations: ROTATE, FLIP, SHIFT, COPY,
SUBIMAGE, INSERT. Constant Operations: COPY, ADD, SUB, MUL, DIV, AND, OR,
XOR, MIN, MAX. Dyadic Operations: COPY, ADD, SUB, MUL, DIV, AND, OR, XOR,
MIN, MAX. Convolution Filters: SOBEL, LAPLACE, MIN, MAX, MEDIAN, OUTLINE,
USER. FFT Filters: LOW / BAND / HIGH PASS, BAND REJECT. FFT Data
Visualization: REAL, IMAGINARY, AMP, logAMP, PHASE. Geometric image
transformations: ROTATE, SCALE, TRANSLATE, SKEW. Integral row and column
resolution reduction: REDUCE. 16 to 8 bit data scaling: 8 scaling modes.
Correct image data using Bias, Dark Current, or Flat Field images

Image analysis: Pixel minimum, maximum, average, standard deviation, mean
deviation. Optionally restricted to rectangular or polygonal region of
interest. Plot area histogram, pixel row, column, or line, 3D surface. Plot
image analysis results or user defined data arrays. Analysis data and
subimages can be transferred to external programs. Measure point intensity
or euclidean distance and angle.

Image import and export: Read/Write native image files (16 bit). Read/Write
FITS image files (16 bit). Read/Write TIFF 8 bit gray scale image files.
Read TIFF 16 bit gray scale image files (both byte orders). Write Windows
DIB (8 bit with Color Palette). Read IPlab image files (16 bit). Read Star1
image files (16 bit). Read raw binary data files (8/16 bit). Write raw
binary data files (16 bit).

Command line interface: Command line interpreter, more than 150 commands.
Access more than 100 internal variables and structure elements. Expression
analysis similar to "C". Save complex command sequences in macro files.
Execute user defined macros from User menus or Icon toolbar. User defined
commands can be added (requires ICC SDK).

Miscellaneous functions: Interrupt driven serial I/O support. Access to
external I/O ports and physical memory. Read and Write external ASCII
files. Transfer images or subimages to the Windows Clipboard. Transfer
image plot data to the Windows Clipboard. Windows DDE command line and
internal variable access. TCP/IP network interface (requires ICCnet).

Cost Q1/95 $999. Contact: GKR Computer Consulting, 130 Huron Ct., Boulder,
CO 80303, Tel: (303) 543-0774, Fax: (303) 543-0775, CompuServe: 76346,26,
Internet: <mailto:gkrcc@gkrcc.com>. Demo at
<ftp://gkrcc.com/pub/gkrcc/iccdemo.zip>.

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,
<mailto: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).

>Melissa A. Hines: I have compiled a brief summary of what seems to be the
net-consensus. The general consensus is that IDL is an excellent package
_if_ you realize what you are getting. From the IDL Readme file: "IDL,
Interactive Data analysis Language, is a complete package for the
interactive reduction, analysis, and visualization of scientific data and
images." General notes:
o IDL is an interpreted language that has its roots in the PDP world. In
other words, this program predates the Mac (and mice) by many years.
Nevertheless, it is a very impressive package.
o IDL makes extensive use of a command line interface -- more than any
other Mac program in common use. You can program a GUI using "widgets."
From the responses to my post, it would seem that many people DO NOT do
this; however, the people who have attempted it say that it is not too
difficult to use.
o IDL runs on many different platforms -- workstations, mainframes and
personal computers. A number of replies indicate that the Mac version has a
higher density of bugs. Apparently, the manufacturers are aware of this and
trying to recruit a true Mac programmer.
o Technical support for IDL is excellent, but you have to pay for it
(approx. $200/yr.) On the other hand, there is a newsgroup devoted to IDL
(and its cousin, pvwave) -- comp.lang.idl-pvwave. There are also a number
of repositories of IDL code scattered about the net. See the IDL FAQ on
comp.lang.idl-pvwave for more info.
o IDL costs big bucks (on the order of $1500 I have heard). On the other
hand, there is a demo version available.

>Amara Graps: IDL is a vector-based language that makes it easy to
manipulate arrays and matrices. If A and B are arrays, then you can
multiply them together without a FOR loop, letting IDL worry about
accessing each index: C = A*B. However FOR loops are available if you need
them. (Because it is an interpreted language, some actions slow down the
computation, and using FOR loops is a biggie. I've done testing comparing
IDL speed to Fortran in various actions, and IDL was as fast as a Fortran
program in many cases.)
The scientific functions and procedures that come with IDL are often all
that scientists need, at least when you first start out. And if you need to
do some computation where a function doesn't exist, users over the years
have contributed a lot of routines to various archives all over the world
(the two at John Hopkins and at Goddard are especially good). The language,
for the most part is "open", i.e. you can see the text of any particular
procedure or function, in case you doubt the technique, or want to modify
it. Some functions and procedures are black-box, intrinsic functions or
procedures, but not nearly as many as Matlab (see below) are.
Keep in mind that you are in a scientific data analysis environment whose
roots are *not* in the Mac world, so you don't have nice user-interface
items to lead you through every step of the data analysis process, like you
might have with Igor Pro (I have't used Igor Pro, just Igor 1.2, and didn't
like it that much.)
Matlab? It's a similar scientific data-analysis environment, with
capabililties to build GUI programs, and it costs about the same: ~$1500.
Since I've spent the last 4 months converting Matlab wavelets code to IDL,
let me tell you some of the differences. IDL is more of a true programming
language. Matlab has scripts and functions and no way to explicitly type a
variable. IDL has programs, procedures, and functions and a language syntax
sort of like a cross between Fortran, Pascal, and APL. Matlab's syntax is
much more compact than IDL's. (For example: x = transpose(y) in IDL is x=y'
in Matlab.) Matlab has many more built-in, intrinsic functions than IDL.
MathWorks, the company that makes MatLab, has a thriving business selling
Toolkits, such as a Signal Processing Toolkit, which are libraries of more
intrinsic functions, for a fairly steep cost (I think).
>>First, IMHO Khoros and either IDL and MATLAB are complimentary rather
than duplicative as I first thought. >Yes, Yes, Yes! RSI, makers of IDL
realized this too, and so they have built a set of routines to link IDL
with AVS, a boxes-and-wires type of visualization system similar to Khoros.
I've seen and heard alot about Khoros- it seems to have far more useful
data-analysis routines than SGI's Explorer, IBM's Data Explorer or AVS.

>Mike Schienle: Just to follow-up to a much earlier suggestion of mine
regarding using IDL for the PowerMac. I tested the speed of the built-in
demo on a PMac 7100 (66 MHz) vs. a Sun SPARCStation 10 (50 MHz). The Mac
had 24 MB RAM. The Sun had 256 MB RAM. The IDL demo does quite a bit of
FFT, blurring, line plotting, etc. In short, I feel it is a decent test of
Int, FP and video speed for a system. Anyway, a single pass on the PMac
took six minutes. The same demo running on the Sun SS-10 took 4.5 minutes.
Roughly, a 6:1 price ratio and a 4:3 performance ratio between the Sun and
PMac (for running IDL only). The demo was less than half-way done on a Mac
IIci when the 10 minute demo license expired.

>John C. Schultz: Khoros provides one of the best sets of image processing
algorithms I have seen plus adequate 2 and 3D visualization tools and it
seems to have a large "installed" base. It is also easy to use with a neat
graphical "data flow" interface. It is lacking in interactive quantative
features (interactive ROI, displaying numeric values, profiles, etc) and
has limited data analysis features.
IDL has very good interactive image display features and has good data
analysis tools though not nearly so many high level image processing
routines as Khoros or as many data analysis routines as MATLAB. The command
line syntax is REALLY bad IMHO.
I have not yet found out about MATLAB's interactive display features (part
of an on-going evaluation) but MATLAB has zillions of data analysis
algorithms with many neat and useful ones in the toolboxes. The image
processing toolbox is very bad IMHO since images are stored as DOUBLE (64
bit precision) in the range [0.0, 1.0]. As with IDL the command line syntax
is bad news IMHO. The user base is huge however meaning that lots of neat
program (M-files I guess) are available.
Both IDL and MATLAB run on Windoze, Mac, Unix and probably NT which pretty
much covers everyone's favorite OS-tipple. Khoros is only Unix/X but does
run with Linux.

>Richard Olsen: If you want to do image analysis, IDL would have been an
automatic choice over MATLAB until recent times. Since IDL has firm roots
in the imaging world, vs signal processing, it is very adept at
manipulating images (or any array of information). Now MATLAB has an image
processing toolbox, and neural net toolbox that help balance out the
origins of the packages. IDL can read virtually any data structure known to
man, using existing io-procedures. You can also set up your own. My
students had trouble using MATLAB to read oddly formatted data sets...

>Chris Ruckman: The topic of comparing Matlab to IDL comes up often in
comp.soft-sys.matlab, although it's not in the Matlab FAQ. If you want more
detail, you might post there to request a recap of the last go-round.

Image-Pro Plus
--------------
Image-Pro Plus ($2499) is a Windows based scientific image analysis
software package made by Media Cybernetics, L.P. of Silver Spring,
Maryland.

IPP is used in applications ranging from auto crash tests and fingerprint
analysis, to automatic metallurgy measurements, biological research and
medical imaging diagnostics.

v1.3 includes new features including multiple Area of Interest (AOI)
processing, interactive manual object tagging and classifying, multiple
intensity thresholds for easy percent area calculation, precision 16-bit
gray scale image support, new optimal "Gaussian shaped" sharpening filters,
additional framegrabber and digital camera drivers and various application
specific tutorials.

There is also a microscope stage control module and a gel analysis module
for Image-Pro. Modules for latent fingerprint processing and material
science analysis will be introduced later 95.

Media Cybernetics can be contacted at 1-800-992-4256 (US & Canada) or
+301-495-3305. (Fax: +301-495-5964). <http://www.mediacy.com>

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,
<mailto:scivis@mndata.com>. Demo versions of ImageVolumes are available at
<gopher://gopher.mndata.com:2074/1>.

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 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. You can make
measurements on 3D models such as distances, numbers of objects, surface
areas and volumes. ImageVolumes now includes tools for quantification and
classification of 3D models, such as the distance field and 3D model
intersection tool, DField.

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

ImportACCESS Plug-In for Mac
----------------------------
Written as an Adobe Photoshop plug-in for the Macintosh, ImportACCESS can
read ACR-NEMA 2.0, DICOM 3.0, Interfile, Papyrus and proprietary formats
from GE, PHILIPS, PICKER, SIEMENS, and SOPHA among others. The built-in
format editor dialog can be used to create fixed file formats for most
other vendors' files. Files can be brought into programs such as Adobe
Photoshop, Adobe PageMaker, QuarkXPress, Deneba Canvas, Fractal Painter or
NIH-Image.

With integrated TCP/IP support, ImportACCESS allows raw medical files to be
imported over the Internet and other TCP/IP networks.

A display settings editor dialog is provided in which window level
conversion from 12, 16-bit integer and 32, 64-bit floating point values can
be performed with a real-time preview and allows the window to be set
directly on the slice or whole file histograms of the original data. For
the purpose of absolute quantification, the values will still be converted
into 8-bit data usable by NIH Image, but one has the option with
ImportACCESS of adding an annotated colorbar from which the underlying
values can be drawn.

Support is included for window level manipulation, template creation for
formatting single and multi-slice files, and tools for consistent
production of publication quality output. An integrated format editor with
real-time file preview is used for fixed file format creation, and a
drop-in reader interface is provided for tagged formats such as DICOM 3.0,
and other newly emerging industry standards.

ImportACCESS works with any Macintosh running System 7.0 or later. The
programs costs US$389, with external code readers for DICOM 3.0, ACR-NEMA
2.0, Interfile 3.3 and Papyrus costing US$75 per reader.

Contact: Hugh Lyshkow, Chief Technical Officer, DesAcc, 702 Wrightwood
Avenue, Chicago, IL 60614, <mailto:daccess@interaccess.com>, Phone: (312)
404-7888, FAX: (312) 472-8834. <http://www.desacc.com/>.

IPLab Spectrum
--------------
Requirements: Power Macintosh, Quadra, Macintosh II or Centris, with FPU, 8
MB of RAM, System 7.0 or later, 8-bit display (24-bit display preferred).

File Formats: Read and write PICT, TIFF (8- and 16-bit integer as well as
color), FITS and Text file formats. Import images in nearly arbitrary
"foreign" binary file formats.

Data Processing with >8-bit Accuracy: Processes and displays high dynamic
range data with 16-bit, 32-bit and floating point data.

Visualization: Perspective view displays a 3-dimensional plot. Text view
displays pixel values at each (x,y) location. Animate cycles through a
movie sequence.

Image Enhancement: Interactive Contrast Adjustment, Histogram Equalization
and Pseudocoloring.

Filtering and Convolutions: Built-in filters for Linear, Median and Edge
filtering of grayscale and 24-bit color images. Design custom linear
filters.

Geometric Operations: Fractional rotation and scaling. Align images with
the registration command.

Particle Analysis: Count and measure particles identified by intensity
thresholding in an overlay. A binary morphology command is included to
modify the overlay.

Image Transformations: Extract histograms, row and column average plots,
graph pixel values along a slice, perform Fourier analysis and measure
angles and lengths.

Color Image Analysis: Split a 24-bit color image into components, like RGB
or HSV and analyze components separately. Or Merge components into a new
color image.

Advanced Processing: Flat Fielding to correct for lighting and sensor
non-uniformities. Point functions to apply mathematical operations to
individual pixels. Grayscale Morphological operators. Arithmetic operations
between images.

Customization: With IPlab Scripting you build Scripts by selecting commands
from the menus just as you would do interactively. Write IPLab Extensions
to add your own procedures to IPLab Spectrum.

Contact: Signal Analytics Corporation. Phone: (703) 281-3277, fax; (703)
281-2509, <mailto:D6196@applelink.apple.com>.

IRAF
----
Image Reduction and Analysis Facility. National Optical Astronomy
Observatory (NOAO) Contact: <mailto: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, <mailto:helpdesk@iec.co.uk> and
<mailto: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,
<mailto: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,
<mailto: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 is a data exploration and software development environment. Over 300
Image processing and visualization programs are available via the visual
programming language. Khoros 2.0.2 is supported on Sun (SunOS 4.1.3), Sun
(Solaris 2.3), SGI (Irix 5.3), DEC (OSF1/3.0), PC/486/P5 (Linux), Cray
(UNICOS 8.0.3).

Contact: <mailto:info@khoral.com>, comp.soft-sys.khoros,
<http://www.khoral.com/>. Khoros is available in source form from
<ftp://ftp.khoral.com//pub/khoros/>. Before installing retrieve the file
/pub/khoros/khoros2.0/release/install.

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://ftp.funet.fi//pub/mac/info-mac/sci/mac-cube-view-16.hqx>

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.

Contact: Doug Norton, Otter Solution, 10 Limekiln Road, Whitesboro, NY
13492-2338, USA, Phone: (315) 768-3956, Fax: (315) 736-4371, Internet:
<mailto:ottersol@aol.com>, American Online: OtterSol, AppleLink: ottersol.

<ftp://ftp.funet.fi//pub/mac/info-mac/sci/mac-phase-20-demo.hqx>
<ftp://ftp.funet.fi//pub/mac/info-mac/sci/mac-phase-20-nofpu-demo.hqx>
<ftp://ftp.funet.fi//pub/mac/info-mac/sci/mac-phase-207-ppc-demo.hqx>
<ftp://ftp.funet.fi//pub/mac/info-mac/sci/mac-phase-extras.hqx>

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.

MedVision
---------
MedVision Viewer for Mac (with color QuickDraw) and Windows (386 up) for
$765. Supports 24-bit video cards. You can view and manipulate CT, MR, PET,
SPECT etc. Proxy view offers an overview of the slices in the dataset.
Single-, multi- and cine-views. Magnification, interpolative scaling,
palette controls, window / level for 12- or 16-bit images. Allows also
patient data to be viewed. Supports Evergreen's Store & Forward
teleradiology PC-package. Additional modules access DICOM, Interfile, DEFF
and many proprietary medical formats. Exports files in standard formats.
For another $655 you can have GE Starcam Starlink or Interfile interfaces.
Demos available for $10-15.

Evergreen Technologies, Inc., Main Street, PO Box 795, Castine, Maine
04421, (207) 326-8300, fax: (207) 326-8333. Jeffrey Siegel
<mailto:jsiegel@lunis.nucmed.luc.edu>.

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, <mailto:rob@retina.anatomy.upenn.edu>.

Mvox
----
Mvox is a general purpose tool for visualization and manipulation of a wide
range of 2-4D grey level/colour images and 3D surface graphics. 

Mvox can handle images with different depths, number of colours, number of
time instances and has been successfully used in the past to visualize 3D
medical images with stacks of slices (CT, MR, etc.), 2D remote sensing
images with many channels and 2D colour images (Red, Green and Blue). In
addition Mvox can also display and manipulate 3D surface graphics (as used
in CAD programs). 3D graphics can be exported in VRML format for use on
WWW.

Keywords: *Image browser, *Fast slicing, *Volume rendering using the
VolPack library, *Iso-surface rendering (result similar to Marching Cubes),
*3D surface graphics, *Interactive thresholding, *Drawing, *Histogram,
*Statistics, *Histogram stretch, *Enlarge, *Colormaps, *Contours, *3D shape
from contours using Nuages, *Overview window, *Advanced command line
interface, *User-defined functions.

Image formats: *ANALYZE, *TIFF, *SGI, *TGA, *BMP, *Inrimage, *HIPS, *BRIMG.

3D formats: Import: *OFF, *Flex3D - Export: *VRML, *DXF, *Inventor,
*Flex3D.

Mvox is only supported on Silicon Graphics platforms, but can run on HP and
IBM RS/6000 as well. A free demo version and test images are available from
the Mvox homepage. The demo version will only work with the test images.
Licenses are available for approx. $550 (DKK 3000 excl. VAT).

For further information please contact: BNI Software, c/o Morten
Bro-Nielsen <mailto:mvox@imm.dtu.dk>, Institute of Mathematical Modelling,
Building 321, Technical University of Denmark, DK-2800 Lyngby, DENMARK.

<http://www.imm.dtu.dk/documents/users/mvox/>

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
<mailto: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 <mailto:viewit@ncsa.uiuc.edu> to request a subscription. Clint Potter
(the original author and pricipal contact) is at
<mailto:cpotter@ncsa.uiuc.edu>.

NIH Image
---------
NIH Image reads and writes TIFF, PICT, PICS and MacPaint files. 16-bit
images can be imported and scaled to 8-bits. The 16-bit (up to 65536 gray
levels) to 8-bit (256 gray levels) scaling can be controlled by the user or
performed automatically based on the minimum and maximum gray values in the
16-bit image. The Rescale command allows the user to redo the 16-bit to
8-bit scaling at a later time. The Import and Export commands allow images
with arbitrary binary and tab-delimited (spreadsheet) formats to be read
and written. The Import command can be used to convert 16-bit images from
medical scanners to the 8-bit format. For example, to import raw MRI-scans
from a GE SIGNA scanner, set width and height to 256, select 16-bit Signed
and set Offset to 14336. Swap Bytes if you are importing 16-bit images from
"little-endian" systems, such as the IBM-PC, PDP-11 or VAX. Image supports
Data Translation and Scion frame grabber cards for capturing images or
movie sequences using a TV camera. Acquired gray scale images can be
shading corrected and frame averaged. Measurement results can be exported
to a text file compatible with spreadsheet and statistical analysis
programs.

DICOM import routine. In addition to DICOM-3 images, it now reads many
ACR/NEMA images. This requires a DICOM dictionary to decode the DICOM or
ACR/NEMA header. The dictionary is available from
<ftp://zippy.nimh.nih.gov/pub/nih-image/documents/>. Hold the option key
down to get a full dump of the DICOM header.

Image supports the organization and manipulation of a series of 2D images
as a 3D array called a stack. A stack contains set of related 2D images,
such as a movie loop or serial sections from a volume. Animate animates the
images in a stack at a rates up to 100 frames per second. Reslice
reconstructs a new 2D image perpendicular to the plane of the slices in a
stack. Project does volume rendering, which is useful for visualizing the
internal structures of 3D images.

Each open image has a look-up table (LUT) associated with it. The LUT for
the currently active image is used to map, at video rates, pixels (in the
range 0-255) to screen colors. Various commands allow you to invert the
current LUT, to specify the number of gray levels or colors it uses, or to
switch to one of several built-in color tables. LUTs are automatically
stored with an image when it is saved to disk, or they can also be saved
separately.

Image supports many standard image processing functions, including contrast
enhancement, density profiling, smoothing, sharpening, edge detection,
median filtering and spatial convolution with user defined kernels up to
63x63. Make Binary command converts grayscale images to images consisting
of only black and white pixels and includes commands to process such
images. Arithmetic to add or multiply an image (or selection) by a
constant. Addition or subtraction of two images.

Image provides MacPaint-like editing of color and gray scale images,
including the ability to draw lines, rectangles, ovals and text. It can
flip, rotate, invert and scale selections. It supports multiple windows and
8 levels of magnification. All editing, filtering and measurement functions
operate at any level of magnification and are undoable.

Image can be used to measure area, average, minimum and maximum gray value,
center and angle of orientation of a user defined regions of interest. It
also performs automated particle analysis and can be used to measure path
lengths and angles. Measure distances by making a straight, freehand or
segmented line selection. The wand tools automatically outlines structures
isolated using thresholding. Analyze Particles automatically counts and
measures features of interest. This requires thresholding to discriminate
objects of interest from surrounding background based on their gray values.
Image has two thresholding methods. In thresholding mode all pixels equal
to or greater than a single threshold level are displayed in black and all
other pixels (the background) are displayed in white. In Density Slicing
mode all pixels between a lower and upper threshold are highlighted in red.
Measurement results can be printed, exported to text files, or copied to
the Clipboard.

Spatial calibration is supported to provide real world area and length
measurements. Density calibration can be done against radiation or optical
density standards using user specified units. The user can select from any
of eight different curve fitting methods for generating calibration curves.

Image can be extended using a Pascal-like macro programming language and
Photoshop compatible plug-ins. Acquisition plug-ins are used to support
scanners or frame grabbers, or to read images in file formats that Image
does not normally support. Export plug-ins are used to output to printers
that do not have a Chooser selectable driver or to save images in file
formats not normally supported by Image. Filter plug-ins perform filtering
operations on images. Image is written using Think Pascal from Symantec
Corporation and the complete source code is freely available.

Image requires a Macintosh with at least 8MB of memory, but 16MB or more
are recommended for working with 3D images, 24-bit color or animation
sequences. Image directly supports, or is compatible with, large monitors,
flatbed scanners, film recorders, graphics tablets, PostScript laser
printers, photo typesetters and color printers.

Image is free and available from <ftp://zippy.nimh.nih.gov/pub/nih-image/>
or on floppy disk from NTIS, 5285 Port Royal Rd., Springfield, VA 22161,
part number PB93-504868. <http://rsb.info.nih.gov/nih-image/>.

Mailing list: <mailto:nih-image@soils.umn.edu>, subscriptions to the
mailing list: <mailto: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
<mailto:listserv@soils.umn.edu>. These files can then be retrieved by means
of a "get nih-image filename" command.

NIH Image Macro to import ACR-NEMA 2.0 and DICOM 3.0 images by Tunc Iyriboz
<mailto: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>

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. How to get input
data: The input format is a simple ascii file (see man prepros for a format
description).
<ftp://ftp-sop.inria.fr//prisme/NUAGES/Nuages/>
<ftp://geom.umn.edu//pub/software/geomview/>

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.

>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.

OSIRIS
------
OSIRIS has been designed as a general medical image manipulation and
analysis software. The design is mainly based on the following criteria:
portability, extendibility and suitability for any imaging modality. OSIRIS
is designed to deal with images provided by any type of digital imaging
modality to allow physicians to easily display and manipulate images from
different imaging sources using a single generic software program.
Portability ensures the software implementation on different types of
computers and workstations. Thus, the user can work in the same way, with
exactly the same graphical user interface, on different stations. Also by
supporting standard file formats, the OSIRIS software provides access to
images from any imaging modality. The OSIRIS program was developed as part
of the Geneva PACS project and is intended for physicians and non
computer-oriented users allowing them to display and manipulate medical
images. Its standard original version included only basic image
manipulation tools accessible through a convenient and user-friendly
graphic interface. In addition to being used at the University Hospital of
Geneva, it was widely distributed around the world and was adjusted
according to user's comments and suggestions. This program was also
designed to serve as a development of more advanced image processing and
analysis tools.

Portability: The initial development of OSIRIS program was undertaken
simultaneously on UNIX based X/window graphic environment as well as Apple
Macintosh native platform. The UNIX version was further tested on a variety
of workstations namely SUN Sparc series, DEC alpha series, HP 7000 series,
IBM Risc-6000 series and SGI machines. Recent evolution in the desktop
computing environment lead us to develop a new kernel of the OSIRIS
software to be compatible with Windows 4 graphic interface for PC
compatible computers. This new version is also directly compatible with
Windows NT and may be used on Windows 3.1 with some restrictions in
performance. Finally we also ported our code to run native on the PowerPC
RISC computers to fully benefit from the enhanced performance of this new
generation of processors.

OSIRIS provides (just a few characteristics): Interactive graphic user
interface, Customizable display modes for images sets, Zoom, rotation,
flipping of image sets, Color adjustment on full dynamic range, Magnifying
glass, Annotations, Regions of interest (polygons, ...), Measurements
(distance, angle, surface, volume, ...), Filters, Multiplanar sections of
tomographic images, Region growing for automatic image segmentation,
Histogram equalization.

OSIRIS software can be obtained free of charge from: Digital Imaging Unit,
University Hospital of Geneva, 24 Micheli du Crest, 1211 Geneva 14 -
Switzerland. Fax: (+41 22) 372 61 98, <mailto:osiris@cih.hcuge.ch>. A
special developer license is available for the full source code.
<http://expasy.hcuge.ch/www/UIN/osiris.html>,
<ftp://expasy.hcuge.ch/pub/Osiris/>.

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.

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

RMN
---
>Philip Grandinetti <mailto: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,
<mailto:ross@biocomp.arc.nasa.gov>.
<http://biocomp.arc.nasa.gov/ross/.index.html>

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.

SNARK93
-------
SNARK93 - a programming system for 2-D image reconstruction from
projections for the UNIX/Sun environment, is available from the Medical
image processing group, Dept. of radiology - University of Pennsylvania.

SNARK93 is a programming system designed to help researchers interested in
developing and evaluating reconstruction algorithms for image
reconstruction from projections. It is the latest in a series of releases
of SNARK. One of these, SNARK77, is described in some detail in the book by
G.T. Herman, "Image Reconstruction from Projections: The Fundamentals of
Computerized Tomography," Academic Press, New York, 1980. In fact, all
illustrations of two dimensional reconstructions (by a large variety of
algorithms) in that book were produced by SNARK77. Additional
reconstruction algorithms can be found in SNARK93, such as the linogram
method of Edholm, Herman, and Roberts (IEEE Trans. on Med. Imaging, vol. 7,
pp. 239-246, 1987), the maximum likelihood EM algorithm of Shepp and Vardi
(IEEE Trans. Med. Imaging, vol. 6, pp. 113-122, 1982), and the maximum a
posteriori probability algorithm of Herman, De Pierro, Gai (J. Visual Comm.
and Image Proc., vol. 3, pp. 316-324, 1992). SNARK93 also provides a
methodology for testing for statistically significant task-specific
performance differences between algorithms, as illustrated in the papers by
Herman and Odhner (IEEE Trans. Med. Imaging, vol. 10, pp. 336-346, 1991)
and Herman and Meyer (IEEE Trans. Med. Imaging, vol. 12, pp. 600-609,1992).
It also extends the capability of previous SNARK releases (which simulate
data collection in X-ray computed tomography) to emission tomography.
SNARK93 has been designed to be flexible and transportable, in places at
the expense efficiency. While it may also be used to reconstruct repeatedly
from data collected by a particular device, a special purpose program for
that device is likely to be much more efficient.

The SNARK93 programming system is designed to:

(a) be capable of generating mathematically described phantoms
realistically representing various cross-sections of the human body;

(b) be capable of generating mathematically simulated projection data of
such cross-sections reflecting the characteristics (geometrical
arrangements of sources and detectors, spectra, noise properties, etc.) of
various possible tomographic data-collection devices;

(c) contain many of the published reconstruction algorithms;

(d) contain subroutines to carry out work which appears to be common to
many reconstruction algorithms, so as to facilitate the incorporation of
additional (user-defined) algorithms;

(e) contain routines for the evaluation of single reconstructions and
provide a methodology for testing for statistically significant differences
between reconstruction algorithms;

(f) be capable of displaying the reconstructed images and plotting several
distance measures between the original object and the reconstructed image.

SNARK93 will be make available to all who request it at the cost of
reproduction and mailing of the FORTRAN source code (on a UNIX tar tape)
and the manual. The software and the manual may also be received via ftp
(in which case we will require a login ID and a password). We charge US$200
(checks only; drawn on a U.S. bank) for providing this service. For
overseas mailing add another US$50.00 if air mail delivery is required.
Please make the check payable to RADIOLOGY ASSOCIATES and send it with your
order to:

Ms. Mary Blue, Medical Image Processing Group, Dept. of Radiology - Univ.
of Pennsylvania, Blockley Hall, 4th Floor, 418 Service Drive, Philadelphia,
PA 19104-6021, U.S.A., Tel. (215) 662-6780, Fax (215) 898-9145,
<mailto:mary@mipg.upenn.edu>.

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 <mailto: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
---------

VIDA
----
VIDA (Volumetric Image Display and Analysis). Cost: $5,000.

VIDA is written in C, runs under the UNIX operating system, and uses the
XView toolkit to conform to the Open Look graphical user interface
specification. Available programs include: orthogonal sectioning, oblique
sectioning, volume rendering, surface rendering, region of interest
analysis, conventional cardiac mechanics analysis, homogeneous strain
analysis, tissue blood flow evaluation, interactive image segmentation and
editing, algebraic image manipulation, and more. VIDA is built modularly,
allowing new programs to be developed and integrated easily. An emphasis
has been placed upon image quantitation for the purpose of physiological
evaluation.

The Visualization modules are used for viewing image data sets in 2-D, 3-D,
or dynamically (movies). One can view a volumetric data set in a
transverse, sagittal, coronal, or oblique orientation. In particular, the
Orthogonal Sections Display (OSD) allows you to display images on top of
one another, side by side, or within a region of the screen for comparison.
Oblique Sections Display (OBL) allows you to extract slices at any
arbitrary orientation. You can create 3-dimensional displays of organs such
as the heart, lungs,and brain with Volume Render (VR) or Surface Render
(SR). Both VR and SR also allow you to make movies rotating and magnifying
the organ. You can rapidly display images and movies created with the
Volume Render and Surface Render programs using the Movie Viewer.

The Analysis modules can be used for making various regional and global
measurements. For instance, Region of Interest (ROI) is designed for
interactive image quantization, one of the current strong points of VIDA.
Several regions of various types can be created on a slice by using the
mouse buttons and the cursor. Each region type has statistics and graphics
options associated with it. Once regions have been defined, regional
statistics (mean intensity, area, pixel count, length, etc.) can be
extracted and stored as text files. Time-intensity plots and other graphs
can also be generated for single or multiple regions. All defined regions
can be saved to hard disk as .roi files and can be recalled later. Some
VIDA modules, such as Contour-Based Cardiac Mechanics, Homogeneous Strain
Analysis, and Imatron Blood Flow, can read .roi files directly to aid
further analysis.
Contour-Based Cardiac Mechanics computes regional ejection fractions,
regional wall thickness, % wall thickening, etc. Homogeneous Strain
Analysis was developed specifically to evaluate regional myocardial strain
non-invasively through a magnetic imaging technique known as SPAMM by
calculating the distortion of triangles generated from nodal points
embedded within the myocardium. Tube Geometry Analysis (TGA) can be used
for making 3-D geometric measurements, such as regional cross-sectional
area, regional anterior-posterior length and lateral length of
pre-segmented vessels or tubes. Image Based Perfusion Analysis (IBPA)
automates the analysis of cine x-ray CT images, thereby allowing one to
rapidly compute physiologic data such as regional blood flow, regional
tissue, blood and air contents, mean transit times, etc. Color coded images
of all physiologic parameters are generated and may be saved to disk.

The Image Manipulation modules are used for processing and manipulating
image data. Included are various segmentation methods, interactive image
editors, and automated analysis libraries. 2-D Segmentation makes manual
image segmentation as flexible as possible. One can use 2-D Segmentation to
distinguish particular structures from others within the same slice, such
as the right vs. the left chambers of the heart. Segmentation is
accomplished by altering the gray levels of structures so as to uniquely
identify them. Algebraic Image Manipulation (AIM) can be used for
performing image algebra by treating images as simple variables in an
equation. Impromptu ( IMage PROcessing Module for Prototyping, Testing, and
Utilizing image-analysis processes) provides a graphical user interface
system for constructing, testing and executing automatic image analysis
processes. Complex image analyses can be performed by constructing a
sequence of simpler image processing and analysis functions.

Shape-Based Interpolation (MSBI) is used to form cubic voxels to maximize
preservation of an organ's apparent original shape. Cubic-Voxel
Interpolation (CVI) performs a similar task as Shape-Based Interpolation,
while preserving an image's gray level information. By using MSBI or CVI
before Surface Render or Volume Render, one reduces the stair step effect
associated with thick slices. Vessel Segmentation can be used to segment
connected vessels, such as airways or other major conduits, from three
dimensional images.

The File Manipulation modules provide tools for creating ANALYZE header
files (.hdr) and reorganizing image data within a disk file. These modules
may be needed before proceeding to use image data sets in VIDA. For example
an image data set cannot be loaded into VIDA without an accompanying .hdr
file and a header file needs to be created before proceeding. In other
cases, it may be necessary to reorganize the sequence in which image slices
are stored on hard disk, or flip the orientation of the slices.

For historic reasons, we currently support the same file format used by
another image processing packaged known as ANALYZE. Since this file format
only supports four dimensional data, VIDA's Load ANALYZE Format module does
not take full advantage of the 5 dimensional nature of the shared memory.
We have plans to support ACR-NEMA and Interfile compatible file formats to
take full advantage of shared memory capabilities. Tape to Disk translates
vendor specific image formats into the ANALYZE file format currently used
by VIDA. This translation occurs while transferring the image data from
tape to hard disk. Currently supported file formats include: Imatron, GE
8800 CT, GE 9800 CT, GE Signa MR, Siemens CT, and Siemens MR.

Color Scales allows you to select a color scheme for displaying images in
VIDA modules. This module also allows you to window and level your image
display and customize the colors used in various overlays in some VIDA
modules. The color scheme, window, and level can be changed at any time.

Contact: Eric Hoffman <mailto:eric@everest.radiology.uiowa.edu>

<http://everest.radiology.uiowa.edu/>
<http://everest.radiology.uiowa.edu/DPI/nlm/nlm.home.html>
<http://everest.radiology.uiowa.edu/DPI/nlm/vida/vida.home.html>
<http://everest.radiology.uiowa.edu/DPI/nlm/apps/aneur/aneurysm.html>

VIDX
----
VIDX Scan Imaging Software by Evex Analytical Instruments (908) 874-3800.
System Requirements: Microsoft Windows 3.1 or later. PC compatible 386+387,
486, Pentium or better. Minimum 4 MB memory. Full installation requires 5
MB hard disk space.

Typical Applications: Optical and electron microscopy. Biological video
microscopy. Forensic investigation, including fingerprint enhancement,
document examination, ballistics, photograph enhancement. Astronomical
image processing. Medical image analysis, including x-ray, CAT-scan, MRI
and digital angiography. Satellite and spacecraft imaging. Aerial photo
enhancement and analysis. Archaeological document restoration and
microscopy. Quality control and automated inspection systems.

Image Types: Binary, byte, signed 16-bit, unsigned 16 bit, signed 32-bit,
single precision real (32 bits), double precision real (64-bits), single
precision complex (64-bits) and double precision complex (128-bits) images
with unlimited dimensions. Conversion between all image types.

Display: All image types are displayed with automatic on-screen scaling and
format control. Automatic formatting may be overridden using various manual
options. Display settings are local to each image.

Contrast Processing: Linear stretching and intensity range remapping for
contrast enhancement. Inversion. Shading measurement and correction.
Logarithmic and gamma corrections.

Histograms and Profiles: Plot and analyze histograms of any image type.
Plot intensity profiles of any length, along a simple or complicated path.
Copy plots to the clipboard. Image statistics.

Color Support: Generate smoothly interpolated false color sequences using
any number of intermediate colors. Process and render composite color
images.

Geometric Operations: Image resizing with non-integer scale factors and
separate horizontal and vertical scaling. Rotation through any angle.
Horizontal and vertical reflection. Skew correction. Image warping for
rectification and registration. Image transpose. Nearest neighbor or
bilinear intensity interpolation.

Arithmetic Operators: Addition, subtraction, multiplication and division of
images including images of different types, and between images and
constants.

Logical Operators: AND, OR, XOR, NOT, NAND, NOR, and XNOR operations
between images, and between images and constants. SHL, SHR, ROL, ROR
operations.

Relational Operators: Comparisons (>, <, , , , MIN, MAX) between images
and between images and constants.

Extended Mathematics: Logarithm, exponential, absolute value, negative,
square, square root, scaling, real part, imaginary part, complex conjugate,
phase and rectangular / polar conversions.

Filters: Linear edge detection, smoothing and sharpening filters.
User-defined linear filters (2X2, 3X3, and 5X5). Selectable boundary
conditions. Minimum, maximum, rank, median, conditional median, range and
top-hat filters.

Fast Fourier Transform: Forward and reverse Fast Fourier Transform (FFT) of
images using single or double precision. Enhancement and manipulation in
the frequency domain with spectrum editing.

Morphology and Set Operations: Erosion, dilation, opening, closing, edge
trace. Cross, square and disk structure elements in various sizes.
Euclidean distance transform. Set union, intersection, complement and
difference.

Object Analysis and Counting: Thresholding, segmentation, counting,
acceptance / rejection criteria, area, perimeter, centroid, principle axes
and orientation, moments. Point-to-point distance measurement.

Image Acquisition and Correction: Acquire images from a wide variety of
frame grabbers. Live focus window. Support for 16-bit cooled CCD cameras.
Reference subtraction, flat-field correction. CCD pixel, row and column
defect correction.

Scripting Language: Multiple text editors. Variables and constants, for
loops, while loops, repeat until loops, if-then-else, expression
evaluation, procedures and functions. Full support for complex numbers.
More than 150 built-in imaging functions.

Image File Formats: TIFF 6.0 binary, monochrome and palette color images
(includes 1, 2, 4, 8, 16, 32, 64, and 128 bits per pixel). Flexible Image
Transport System (FITS). Windows device independent bitmap (BMP).
Encapsulated PostScript (EPS). Import feature for other file formats and
unformattted files.

Time-saving speedbar, undo previous operation, on-line help system,
drag-and-drop client, clipboard support, user preferences set-up. Software
Development Kit (SDK) available.

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

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

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 [-]

<http://www.uni-hamburg.de/~medizin/imdm>

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 <mailto:userserv@vitalimages.com>. Email: <mailto: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 <mailto: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, <mailto: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: <mailto: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.

XEVA-VisualStudio
-----------------
XEVA-VisualStudio is an interactive system running on most Unix
workstations, supporting visualization of volume data sets from image
slices (acquired by CAT, NMR, Ultrasound, microscopy, confocal laser
systems). The program runs on SGI IRIX 4.5.1, SunOs 4.1.3_U1, HP HPUX
A.09.01, IBM Risc6000 AIX 3.2.5 (shared X11 libraries only)..

XEVA-VisualStudio volume rendering system is available for free at
<http://www.dsi.unimi.it/Users/imaging/eva.html>

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
<mailto:zmode@callamer.com>.

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

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.

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/>.

Chapel Hill Volume/Ray Tracing Datasets
---------------------------------------
<ftp://omicron.cs.unc.edu/pub/softlab/CHVRTD/>. Chapel Hill Volume/Ray
Tracing Dataset. 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.

University Hospitals of Cleveland
---------------------------------
University Hospitals of Cleveland and Case Western Reserve University's web
server contains images from different diagnostic modalities. As the server
grows we will add more images in many different subspeciality areas, such
as MRI, PET, SPECT, CT, Pediatrics. We will also in the future add CME
credits for questions answered on the various cases in the archives. Since
the server contains many images, it is a good idea to have your Web browser
set to at least 256 colors. <http://chaos.uh.cwru.edu/uhweb1.html>

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 <mailto:chorus@mcw.edu>.

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.

CRS4
----
Center for Advanced Studies, Research and Development in Sardinia.
Interactive Volume Visualization CT/MRI Data Tools, Medical Imaging Movies,
Semi-Trasparent Direct Volume Rendering, Fuzzy Gradient Shading Methods,
Simple 2D Visualization Methods.

<http://www.crs4.it/~france/vvis.html>

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.

3D confocal microscopy page & Free/shareware graphics apps link
---------------------------------------------------------------
Introduction/overview of how to obtain 3-D reconstructions from confocal
data. There is also a freeware/shareware graphics software section which
lists packages for all major computer platforms (SGI/UNIX, Mac/PowerMac,
and PC (DOS/Windows). There are also sections on file formats, colour
quantization, and general image processing links and tips.

Programs for these lists have the following features: Image Display/Format
Conversion, Image Processing (image filtering, colour management, etc.),
Image Manipulation (scaling, rotation, etc.), 3-D Reconstruction (volume
rendering, surface rendering, etc.), Animation (creation, display, etc.),
Source Code/Libraries. Contact: Lance Ladic <mailto:ladic@cs.ubc.ca>.

<http://www.cs.ubc.ca/spider/ladic/confocal.html>
<http://www.cs.ubc.ca/spider/ladic/software.html>

General Electric
----------------
<http://www.ge.com/>
<http://www.ge.com/crd/ivl/three_dim_medical.html>

For the purpose of example image sets, GE images are provided in two
formats: DICOM Part 10 format and Central Test Node (CTN) v2.2
(Mallinckrodt Institute of Radiology) format. The GE DICOM images are
available solely for the purpose of providing examples and do not represent
a complete set of every image type. These images are not meant for
exhaustive testing purposes.

<ftp://ftp.med.ge.com/pub/DICOM/IMAGES/CT/>
<ftp://ftp.med.ge.com/pub/DICOM/IMAGES/CT/HiLgtHsp/PART10/>

DICOM conformance statements:
<ftp://ftp.med.ge.com/pub/DICOM/CONFSTMT/>

Marching Through the Visible Man: The National Library of Medicine is
creating a digital atlas of the human body. This project, called the
Visible Human, has already produced computed tomography, magnetic resonance
imaging and physical cross-sections of a human male cadaver. This paper
describes a methodology and results for extracting surfaces from the
Visible Male's CT data. We use surface connectivity and isosurface
extraction techniques to create polygonal models of the skin, bone, muscle
and bowels. Early experiments with the physical cross-sections are also
reported. <http://www.ge.com/crd/ivl/vm/vm.html>

University Hospital of Geneva - Digital Imaging Unit
----------------------------------------------------
<http://expasy.hcuge.ch/www/UIN/UIN.html>. Unit d'Imagerie Numrique.
Provides new perspectives for physicians and medical staff in allowing them
to manipulate images from their workstations. The OSIRIS
<http://expasy.hcuge.ch/www/UIN/osiris.html> software has been designed for
the manipulation and analysis of digital medical images stored in a
standard format called PAPYRUS
<http://expasy.hcuge.ch/www/UIN/papyrus.html>. These images can be
retrieved from the PACS database through the ISIS software.

Images and Related Processing at www.santel.lu
----------------------------------------------
<http://www.santel.lu/SANTEL/imgrel/imagproc.html>

Indiana University
------------------
<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>.

MAG-NET
-------
Magnetic resonance internet resources
<http://atlas.chemistry.uakron.edu:8080/cdept.docs/nmrsites.html>.

Mallinckrodt musculoskeletal www server
---------------------------------------
Each week a case will be presented highlighting a specific magnetic
resonance imaging pathology which radiologists may expect to encounter in
daily practice. Initially our focus will be on musculoskeletal MRI with an
intended audience of practicing radiologists and radiology residents.
<http://kayla.wustl.edu/>

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.

MIAS Digital Mammogram Database
-------------------------------
The Mammographic Image Analysis Society (MIAS) is a organisation of UK
research groups interested in the understanding of mammograms and has
generated a database of digital mammograms. This is a NON-PROFIT making
venture. Income is used for materials and further expansion of the
database.

Films taken from the UK National Breast Screening Programme have been
digitised to 50 micron pixel edge with a Joyce-Loebl scanning
microdensitometer, a device linear in the optical density range 0-3.2 and
representing each pixel with an 8-bit word. The database contains 320
digitised films and is available on 2.3GB 8mm (ExaByte) tape. It also
includes radiologist's "truth"-markings on the locations of any
abnormalities that may be present.

The MIAS miniMammographic Database is available by anonymous FTP via the
Pilot European Image Processing Archive (PEIPA) at the University of Essex.
The dataset is the same as the original except that it has been reduced to
a 200 micron pixel edge and padded/clipped so that all the images are 1024
x 1024. <ftp://peipa.essex.ac.uk/ipa/pix/mias/>.

All enquires/orders to: Dr John Suckling, MIAS Mammographic Database, c/o
Department of Physics, Royal Marsden Hospital, Fulham Road, London, SW3
6JJ, UK. <mailto:john@skye.icr.ac.uk>.

<http://skye.icr.ac.uk/miasdb/miasdb.html>

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.

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
<mailto: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!

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

National Library of Medicine Visible Human Project
--------------------------------------------------
>Michael J Ackerman: 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.

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.

The License Agreement for use of the male Visible Human Project data set is
now available. It can be retrieved from NLM's gopher site,
<gopher://gopher.nlm.nih.gov>. The agreement will be found in the section
entitled Visible Human Project as a text file and as a downloadable
WordPerfect file. It is also available from NLM's FTP site,
<ftp://nlmpubs.nlm.nih.gov>. The agreement will be found in section
"visible" as a WordPerfect file, "vhpagree.wp", or as a text file,
"vhpagree.txt". Please make two copies of the agreement and have both
copies signed as originals by your appropriate officials. The agreement
requires that you include a statement explaining your intended use of the
data set. Send both signed copies of the agreement and the statement of how
you intend to use the data set to me at:

Dr. Michael J. Ackerman, Visible Human Project, National Library of
Medicine, 8600 Rockville Pike, Bethesda, MD 20894.

We will have the agreement signed here at NLM and one of the originals will
be returned to you. At that time you will be sent your account and password
to the Visible Human Project FTP site if you wish to download all or part
of the data set via the internet and information on where you may purchase
the data set on 8 mm or 4 mm DAT tape. The data set will be distributed on
6 DAT tapes in UNIX TAR format corresponding to 6 body regions. At this
time each tape is estimated to cost $150. A 7th, "sample", tape which
contains the entire body at 1 cm increments will also be available. The set
of 7 tapes should cost $1,000. The size of the data set is about 14
gigabytes.

Sample images are also available at this time via the NLMPubs FTP site. Six
full color anatomical images and an explanatory README file can be found in
<ftp://nlmpubs.nlm.nih.gov/visible/bitmaps/color24/> as "*.raw". Please be
careful as each of these images is over 6 megabytes in size. Ten CT scan
images and an explanatory README file can be found in
<ftp://nlmpubs.nlm.nih.gov/visible/bitmaps/ct/> as "*.fre" (5 images
captured while the cadaver was fresh) and "*.fro" (5 images captured after
the cadaver was frozen). Six MRI scan images and an explanatory README file
can be found in <ftp://nlmpubs.nlm.nih.gov/visible/bitmaps/mri/> as "*.ti".

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,
<mailto:ackerman@lhc.nlm.nih.gov>.

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

<gopher://public.nlm.nih.gov/11/visible>

->Research Systems' Visible Human CD is available on Windows 3.1 & NT,
Macintosh 68k & ppc, Sun, Hewlett Packard, Silicon Graphics. Research
Systems acquired and enhanced the axial images (removed the gel), derived
new images (coronal and sagittal views), developed a graphical browser to
navigate and display the images and put the 10,000+ images on a CD-ROM. The
modalities include: digital photographs, CT and MR images. The images have
been compressed using JPEG.
The graphical Navigator application lets you: browse and display images in
multiple resolutions, See inside the body in axial, coronal, or sagittal
orientations, Annotate and set bookmarks on notable images, Adjust
brightness and gamma corrections for MR and CT images, Create animations
through a range of images. In addition you can export the images in TIFF,
PICT, GIF, Postscript, EPS and BMP formats.
The product requirements will be 16 MB of RAM and 15 MB of hard disk, along
with a CD-ROM reader. The product is scheduled to be released 4/95. Cost
$495 USD (plus shipping), purchase order or Visa or Mastercard. Contact:
<mailto:human@rsinc.com>

->Visual Man contains over 1800 actual cross-section images of a
cryosectioned male cadaver. The images are in 24 bit JPEG format.
<http://www.winc.com/commerce/expomed/visblman.html>
System requirements: 386 CPU (486 recommended), 4MB RAM,(8MB recommended),
256 color VGA display (true color video recommended) DOS 5.0 or later, MS
Windows 3.1, Macintosh version due out late 1995.
Cost: MSRP $39.95, Expomed price $29.95USD plus $5 for shipping and
handling (domestic), $15.00USD (International) per CD-ROM. Contact Marty
Thomas or Charles Eup at Expomed Inc. <mailto:expomed@interramp.com>.

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

Penn State University
---------------------
<http://www.xray.hmc.psu.edu/>
<http://www.xray.hmc.psu.edu/dicom/dicom_home.html> DICOM home page

Electronic versions of the ACR-NEMA DICOM standard in the directories:
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/dicom_3.0/frame/> framemaker
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/dicom_3.0/word_hqx/> Macintosh Word
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/dicom_3.0/postscript/> postscript

There is also a user conformance profile for DICOM 3.0 written by dr. Fred
Prior of Penn State in the files:
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/UCP.ps>
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/UCP.ps.Z>
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/UCP.txt>
<ftp://ftp.xray.hmc.psu.edu/dicom_docs/UCP.txt.X>

We also offer access to the Mallinckrodt Institute of Radiology's DICOM
implementation in the directory:
<ftp://ftp.xray.hmc.psu.edu/dicom_software/Mallinckrodt/>

We are also pleased to announce the availability of the European
CEN/TC251/WG4 version of DICOM software in the directory:
<ftp://ftp.xray.hmc.psu.edu/dicom_software/European/>

Interactive Computing Resource of the Magnetic Metabolic Research Resource
Computing Center: <ftp://nmrsg.biophys.upenn.edu/pub/>. New developments in
this FTP site are documented in the electronic newsletter, WavePacket. You
can subscribe to WavePacket by sending e-mail to
<mailto:letter@nmrsg.biophys.upenn.edu> and putting "subscribe" in the
first line of the text.
/pub/data         interesting MR and optical data sets
/pub/education    technical documents of educational nature
/pub/programs     programs for MR related analysis, display, ...
/pub/sequences    pulse sequence programs for various MR systems
/pub/wavepacket   editions of WavePacket, the electronic newsletter

PPG's newsletters
-----------------
Parallel Performance Group (PPG) is a provider of Unix- and PC-based
scientific, engineering and graphics software. PPG publishes a free monthly
email Newsletter for each of the categories below. Each Newsletter covers
material on the market/industry niches served by these categories and
tutorial information on the technologies involved. By sending an e-mail
letter to any mailbox shown below, you will obtain by return e-mail sample
Newsletters for the particular area(s) of your interest. You will not be
put on any mailing list unless you specifically ask to be.

Category                    Software Products         Auto-Resp email Box
-------------------------   -----------------------   -------------------
RealTime DSP                Rippen, Hypersignal       <dsp@ppgsoft.com>
Image Proc'g/Medicl Imgng   IAP                       <img@ppgsoft.com>
Fuzzy Logic/Fuzzy Control   Fuzzy Control Manager     <fuz@ppgsoft.com>
Neural Networks             NeuroCom, NeuroGraph      <neu@ppgsoft.com>
Project Management          Accent, ACOS PLUS 1       <prm@ppgsoft.com>
Volume Visualization        Vox-L, IAP                <vis@ppgsoft.com>

RealTime Multiprocessing/   Rippen, Express,          <mpr@ppgsoft.com>
 Parallel Processing/        Strand88, HyperC,
 Distributed Processing      Load Balancer,
                             MUSIC, Pulsus

Solid Modelling/CADD/       Prelude, Pytha, Unicad,   <sol@ppgsoft.com>
 Mech. Design/Animation      Point Line, 3DGO

Obj.-Oriented CASE Tools    Wizdom Pro, Oberon/F,     <obj@ppgsoft.com>
                            case/4/0, objectiF,
                            Innovator

Simulation                  SIMPLE++, SystemSpecs,    <sim@ppgsoft.com>
                             GPSS

Graphical Application       LOOX GAI Design Tool      <gai@ppgsoft.com>
 Interfaces

To regularly receive any Newsletter, reply to
<mailto:subscribe@ppgsoft.com> with the message "Subscribe <category>". For
example, "Subscribe Multiprocessing". <http://www.ppgsoft.com/ppgsoft>

Radiology Teaching Files on the Web
-----------------------------------
There are many sites offering Radiology teaching files on the Web.
Unfortunately, each site is completely independent of the others and there
is no common search method to find all the radiology teaching files. As a
temporary solution in time for board review we offer the following list of
Radiology Teaching files by subject. Note that none of the files below
reside here at Penn State, rather we have visited each site in our list of
colleges and universities, extracted those that offer teaching files and
organized the links by subject rather than by institution. Enjoy! (perhaps
someday we can organize a registry service for teaching files).

Anyone know of any radiology related teaching files to add??? If yes,
please send pointers to David S. Channin, <mailto:dsc@xray.hmc.psu.edu>.

<http://www.xray.hmc.psu.edu/public/tf.html>

RSNA
----
<http://www.rsna.org/>
<http://www.rsna.org/edu/publications/pub.html> includes recent table of
contents of Radiology and Radiographics.

<ftp://rsna.org/pub/>

RSNA maintains a public mailing list about DICOM. To subscribe send mail
with the command "add" in the text of your message to
<mailto:dicom93-server@rsna.org>. To send mail to the group, mail to
<mailto:dicom93@rsna.org>.

SCAR
----
The Society for Computer Applications in Radiology (SCAR) is an
organization of professionals who realize that computers have become an
indispensable part of our daily activities in medical imaging.
Computer-generated and enhanced images, image transmission and display,
radiology information management, and decision support systems are already
important components of state-of-the-art practice.

Today, all of us must be familiar with computers in radiology, whether we
are comfortable working with them or find them frustrating. SCAR is for you
if you are employed in the medical imaging field, interpret medical images,
conduct research in medical imaging, teach in the medical imaging
environment, are a radiology administrator, manufacture or market
computer-based medical imaging equipment, purchase computer-based medical
imaging equipment or are interested in medical informatics. SCAR will help
you to stay abreast of what's new, help you to understand existing
computer-based technology, and acquaint you with a network of people who
share your appreciation for the importance of computers in radiology.

Membership Benefits of SCAR: Subscription to The Journal of Digital
Imaging, Receipt of the society newsletter, SCAR News, Complimentary copies
of the educational handbook series such as Understanding PACS 1992 and
Understanding Teleradiology 1994, Discount on published proceedings of SCAR
conferences, Reduced registration fees for selected conferences,
Participation in specific projects and special interest groups,
Opportunities to network with colleagues.

To join SCAR please fill out the application form from the www-page and
mail, FAX or email to: SCAR, 4750LindleRoad, P.O.Box8800,
HarrisburgPA17105-8800, Voice:717-561-5266, FAX:717-561-5360,
E-Mail:<mailto:73531.1173@compuserve.com>.

Regular membership is available to individuals associated with the medical
imaging field. ($125 USA and Canada, $155 all other countries). Student
membership is available to individuals enrolled in an academic program in
medical imaging. A letter from the student's director is required. ($50).
Industrial sponsors receive 10 subscriptions of the Journal of Digital
Imaging for distribution to key accounts or VIPs. Industrial sponsors are
recognized in the Journal and Society newsletter and have access through
the membership to leaders in this field. ($1,250).

For further information, contact the SCAR office or:
ThurmanGillespyIII,MD, SCARTreasurer, DepartmentofRadiology,SB-05,
UniversityofWashington, Seattle,WA98195, voice:(206)543-3320,
fax:(206)543-6317, email:<mailto:tg3@u.washington.edu>.

<http://www.scar.rad.washington.edu/>

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

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.

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

The whole brain atlas
---------------------
This is an information resource for central nervous system imaging which
integrates clinical information with magnetic resonance (MR), x-ray
computed tomography (CT), and nuclear medicine images. We welcome
submission of Atlas entries. The Atlas project is made possible by the
Departments of Radiology and Neurology at Brigham and Women's Hospital,
Harvard Medical School, the Countway Library of Medicine, Digital Equipment
Corporation, and the American Academy of Neurology.

<http://www.med.harvard.edu/AANLIB/home.html>
<http://www.med.harvard.edu/BWH/Education.html>

WWW news.answers archive
------------------------
>Henk Penning <mailto:henkp@cs.ruu.nl>: Take a look at our new WWW
news.answers archive at <http://www.cs.ruu.nl/cgi-bin/faqwais>. The archive
supports full-text search by keyword (WAIS), access by archive-name/subject
and access by news.group.

Each article contains a link to the archive-name directory where the
article resides, and link(s) to overviews of the newsgroup(s) where the
article was posted.

This means that when you do a keyword search, you can jump from any
matching article to other related articles in the same archive-name
directory and to other articles posted in the same news.group(s).

Articles are left intact, but things that look like URLs are activated
(made selectable).

The archive is generated daily from our news.answers ftp-archive by two
small Perl programs. It takes about 1.5 hours (sparc-2).

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.med.vision
sci.techniques.mag-resonance
sci.techniques.microscopy

DICOM info, software and example image files
============================================

ACR Nema acquisition Plug-In for Mac
------------------------------------
ACR Nema acquisition Plug-In (Macintosh) for Photoshop and NIH Image.

<ftp://ftp.funet.fi//pub/mac/info-mac/gst/grf/pshp/acr-nema-12.hqx>

Atlas of MRI Foot
-----------------
Contains 15 sagittal and 16 coronal slices (TIFF-stacks) of foot. Pointing
at anatomy hilites the name in the list. Clicking on the name shows a
pointer at anatomy. A full description of the program will be published in
Acta Radiologica in spring 1995.

<ftp://ftp.funet.fi//pub/mac/info-mac/sci/foot-mri.hqx>

David Clunie's dicom tools
--------------------------
<ftp://ftp.rahul.net/pub/dclunie/dicom3tools_0.08.tar.gz>. Tools and
libraries for handling files of DICOM 3 attributes, and conversion of
proprietary formats to DICOM 3. Can handle older ACR/NEMA format data, and
some proprietary versions of that such as SPI. Also handles Part 10
Metaheaders. VERY limited X display capability.

Proprietary image conversions from General Electric CT 9800, General
Electric CT High Speed Advantage (Genesis), General Electric MR Signa
3X/4X, General Electric MR Signa 5X (Genesis), General Electric CT Sytec,
Siemens Somatom CT DR family, Siemens Somatom Plus family (SPI version of
ACR/NEMA), Siemens Magnetom Impact (SPI version of ACR/NEMA), Siemens
Magnetom SP (SPI version of ACR/NEMA), Philips Gyroscan MR S5 (native &
exported SPI(ANI)).

Image format support: DICOM 3 offline file format as per draft Part 10,
Parsing/validating DICOM 3 data sets as modules and IODs, Pbmplus extended
16 bit raw format, Raw binary images.

Archive retrieval from General purpose 9-track and DAT file extraction,
General Electric CT 9800 9-track, General Electric Genesis DAT, Philips
Gyroscan MR S5 native format (ANSI format tapes).

Miscellaneous image format utilities: Dump (octal / hex / decimal / byte /
short / long / ieee float), Patch, Swap bytes, Word to byte shift, Vax VMS
DUMP output to binary (poor man's uudecode).

Frequent Answers: Yes, many of the tools compile on a Mac (Symantec) but
there are no screen based utilites yet. No, I haven't tried compiling on a
PC under DOS or Windows, though it works under Linux if you have enough
memory for the compile. Yes, I will write a viewer for the Mac (and maybe
even Windows if I ever succumb and by a PC), but it is a low priority ...
try the Photoshop ACR/NEMA plugin. No, the tools are not a network DICOM
package, they just convert things to offline file formats (for now). Yes,
if you don't care about dicom (!) but want to translate from a proprietary
format to something else, the tools will help. No I don't know the format
of the GE Genesis optical disks. Yes, I do want to hear from ANYONE who
knows ANYTHING about any medical image format that is not included, or can
provide sample images to reverse engineer.

Comments, criticism and general abuse are greatly appreciated and should be
directed to <mailto:dclunie@flash.us.com>.

IMGF2TIF
--------
IMGF2TIF DOS converts GE IMGF 16-1 bit grayscale image files into TIFF 8
bit grayscale image files.

The automatic byte swapping feature allows image file format conversion to
take place without the need to swap the bytes prior to using the IMGF2TIF
program.

The intelligent ranging feature tries to retain the pixel value range of
the image so that very little or none of the original pixel information is
lost.

The fast conversion feature makes converting of one or more GE image files
extremely fast. A 138K GE image file can be converted to a noncompressed
65K TIFF image in 3 seconds or less depending on the CPU used. The batch
conversion feature (list file mode) is an extremely fast and efficient
method to automate the conversion process of many GE images.

The TIFF packbits compression features allows the TIFF image file to be
reduced in size. The amount of compression achieved is dependent on the
original GE image file. When converting from a 12 bit GE image file to a 8
bit TIFF image file the file is automatically reduced by 50% and more
savings may be achieved by using the TIFF compression feature.

The TIFF image description tag feature allows for certain GE header fields
to be incorporated into the TIFF image file by automatically placing the
information into the TIFF image description tag. This allows the user to
uniquely identify the converted image when an eight character filename will
not do. Since most TIFF viewers either don't or only partially display the
image description tag this program will also dump the image description tag
of the TIFF image file to the display whenever the user wants to identify
the TIFF image file do so.

To optimize the image for slide photography using a graphics program such
as Microsoft PowerPoint or Lotus Freelance Graphics, the image can be
resized in a bitmap editor from its native 256 x 256 pixels up to 384 x 384
pixels. Resizing minimizes the pixel effect on slides. The need to resize
the image is not related to IMGF2TIF but reflects the acquisition matrix.
The MR console does this resizing and smoothing automatically when the
images are displayed or photographed.

Cost of IMGF2TIF is $90.00 tax included with 10% discounts when ordering
quantities of 2 or more. Send e-mail to <mailto:tom@wbs.roc.servtech.com>
for more information.

InterFormat
-----------
InterFormat is a medical image format conversion program for industry
standard UNIX workstations. Using a Motif interface, users can specify
lists of input files, directories, and tape devices, specify an output
directory and an output format, specify parameters to be displayed on the
image list (patient name, study ID, etc.) and their order of placement,
specify the output file naming convention and save or recall these settings
as configurations. The user can then scan the list of inputs for medical
image files, which are automatically identified and parsed into 3D image
sets. The user then selects the desired 3D images for conversion. A
character mode is available for use at a terminal or shell, with list-only
and convert-all modes for use in scripts and database or spreadsheet input
preparation.

Input formats include ACR-NEMA 1.0, ACR-NEMA 2.0, DICOM 3.0, AAPM, GE
Advantage MR and CT (ximg or Image Extract formats), GE Signa MR, GE 9800
CT, GE 8800 CT, Siemens Magnetom MR and Somatom CT, Picker Q800 MR and CT,
Philips 300 Series CT, Technicare 2000 CT, Positron PET, Trionix Triad
SPECT and Varian Ximatron CT Simulator. Siemens CTI PET and Elscint SPECT
are planned for the near future.

Output formats include AAPM, Interfile (including ADAC), DICOM 3.0, Vital
Images VoxelView and Varian Ximatron. We will be pleased to quote on adding
custom input and output formats.

Availability will be October 1, 1994 for SUN computers running SunOS and
Solaris and November 1, 1994 for HP, SGI, and IBM AIX systems. Initially
distribution will be on 1/4" cartridge tapes, but will shift to writable CD
in the near future.

Planned pricing for InterFormat is $4495US (L3000UK) for three input
formats, $995US (L665UK) for each additional input format. The software is
node locked, with no limit on the number of copies which can run
simultaneously and additional formats can be enabled by obtaining license
keys. Some input formats may require additional royalty payments to the
manufacturers, the cost of which will be passed on to the users. These
charges have not been determined at the present time.

Contact: In North and South America: Radio Logic, Incorporated, P O BOX
9665, NEW HAVEN CT 06536-0665, USA, Tel: 203-245-4664,
<mailto:reddy@nucmed.med.nyu.edu>. In EC countries and the Mid-East: Bartec
Medical Systems, Ltd., Impression House, Invincible Road, Farnborough,
Hampshire, GU14 7NP England, Tel: (+44) 252 376737, Fax: (+44) 252 376737,
<mailto:bob@bartec.demon.co.uk>.

Misc stuff
----------
**Alice** [look under software packages]

**Dr Razz** [look under software packages]

**General Electric** [look under some medical sites]

**NIH Image** [look under software packages]

**Penn State University** [look under some medical sites]

**RSNA** [look under some medical sites]

NIH Image stacks
----------------
Animation sequences and 3D images as TIFF-stacks:

<ftp://zippy.nimh.nih.gov/pub/nih-image/stacks/CT_Head_Movie.cpt.bin>

127-slice sagittal MRI data set of a human knee:
<ftp://zippy.nimh.nih.gov/pub/nih-image/stacks/3D_Knee.cpt.bin>

124-slice axial MRI data set of a human head:
<ftp://zippy.nimh.nih.gov/pub/nih-image/stacks/MRI.Axials_1.5mm.bin>

27-slice axial MRI data set of a human head:
<ftp://zippy.nimh.nih.gov/pub/nih-image/stacks/MRI_Axials_5mm.bin>

PAPYRUS
-------
PAPYRUS 3.0 file format is based on the new DICOM 3.0 Standard. Although
version 3.0 of PAPYRUS is absolutely compliant with DICOM Part 10, it does
reinforce a few rules. It provides a way to group several images in a file
in a "PAPYRUS-File object". There are certainly other ways to regroup
images in a single file while remaining compliant with DICOM part 10
specifications . PAPYRUS is also restricted to keep images of a same
patient and of a same series together. PAPYRUS is not intended to stores
images from different patients (teaching files for example) or from
different modalities or even from different acquisition series. These
restrictive rules allow a better file management in a PACS environment.
PAPYRUS 3.0 is presented as a "profile" of DICOM possible implementations.
While PAPYRUS specification focuses on the image files it still relies on
the directory structure defined in Part 10 to keep these files linked
together on a given storage media (DICOMDIR file).

<http://expasy.hcuge.ch/www/UIN/papyrus.html>
<ftp://expasy.hcuge.ch/pub/Osiris/Images/>

CHAMPOLLION is a software package developed on Macintosh platform for the
conversion of a variety of image file format into PAPYRUS format. It
currently supports: INTERFILE (tested for variation of different vendors
such as GE, Picker and Elscint), MATRIX (file format used on Siemens/CTI
PET scanners), GE proprietary nuclear medicine format on Starcam systems,
Siemens SPI format and PICT format. The software also supports converting
data from PAPYRUS to PICT or QuickTime formats. It also includes a special
tool for resizing images to different resolutions using interpolation
algorithms with options for cropping the images interactively.

For additional information as well as possible developments of new
"plug-ins" for any other format, please contact the author: Antoine Rosset,
Digital Imaging Unit, University Hospital of Geneva, 1211 Geneva 14,
Switzerland, <mailto:ROSSET@dial.eunet.ch> Fax: (+41 22) 346 11 97,
Compuserve: 100277,164..

<ftp://expasy.hcuge.ch/pub/Osiris/ChampollionDemo.sea.hqx>

Example DICOM image files at wuerlim.wustl.edu
----------------------------------------------
This directory contains example DICOM image files that were created for the
DICOM demonstration held at the annual meeting of the Radiological Society
of North America, December, 1994. These images are stored in Little-Endian
byte order as a stream of bytes. This file format is not the format that is
defined in Part 10 of the Standard. These image files are readable with the
MIR CTN software.

<ftp://wuerlim.wustl.edu/pub/dicom/images/version3/>

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]

<ftp://ftp.rahul.net/pub/dclunie/medical-image-faq/> Text, html or
postscript versions.

<http://www.rahul.net/dclunie/medical-image-faq/html/>

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/> [part 1-2]

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-96-01-
