med-volviz-faq-95-05
====================

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 Also send me a note if some of the text is out of date or too far off-topic as I don't want the faq to grow too much with irrelevant info.

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

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

This file is also available at:

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

<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 95-04
-------------------
**Software packages:**
Alice added
NIH Image updated

**Some medical sites**
University Hospitals of Cleveland added
Marching Through the Visible Man [General Electric] added
MIAS Digital Mammogram Database added
SCAR added
The whole brain atlas added

**DICOM info, software and example image files**
CHAMPOLLION [PAPYRUS] added

Changes since 95-03
-------------------
**Software packages:**
VIDA added
MedVision added

**Some medical sites**
National Library of Medicine Visible Human Project updated
PPG's newsletters added

**DICOM info, software and example image files**
Atlas of MRI Foot added
NIH Image stacks added

Changes since 95-02
-------------------
**Software packages:**
IDL updated
XEVA-VisualStudio added

**Some medical sites**
Radiology Teaching Files on the Web added

**DICOM info, software and example image files**
David Clunie's dicom tools updated

Changes since 95-01
-------------------
**Software packages:**
OSIRIS added
NIH Image DICOM import routine added

**Some medical sites**
Penn State University updated
University Hospital of Geneva - Digital Imaging Unit (OSIRIS & PAPYRUS) added
General Electric added
RSNA added
CRS4 added

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

Changes since 94-12
-------------------
**Personal info**
I am a proud father of a girl born 9th of December 1994!

**Software packages:**
EVAL3DPET added
SNARK93 added

**Some medical sites**
National Library of Medicine Visible Human Project updated
WWW news.answers archive added

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

For further information call CNSoftware: In Europe: Phone +44 403 733607, FAX +44 403 733609, <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
----------------------------
15200 Omega Drive #105, Rockville, MD 20850, Phone: 800-BDS-7706, Fax: 301-990-8391. Macintosh.

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

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

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

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

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

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

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

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

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

Bugs reports, and any general comments about the program should be sent to <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>.

By purchasing the EVAL3DPET software, the recipient agrees to abide by the following terms:

1. EVAL3DPET shall not be redistributed in any way.
2. EVAL3DPET is not a patient-care tool and it is not approved by the United States Food and Drug Administration.
3. While every effort has been to correct all known bugs, EVAL3DPET is provided "as is" with no warranty whatsoever. As such, the recipient agrees not to hold the authors responsible for any problems they may encounter with the software.
4. The recipient agrees to purchase EVAL3DPET with the explicit knowledge that the authors do not offer technical support.

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.

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.tc.cornell.edu/DX/dx.html> and <http://www-i.almaden.ibm.com/dx/>. There are some great application examples there and some example mpeg animations done by students in the computer graphics program at Cornell.

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

Contact: Research Systems Inc., 2995 Wilderness Place, Suite 203, Boulder, CO 80301, USA, Phone: 303-786-9900, FAX: 303-786-9909, <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
--------------
From Media Cybernetics ($2499).

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 the Gopher site gopher.mndata.com 2074 (look in the US/Minnesota listings under Minnesota Regional Network).

SOFTWARE DESCRIPTION

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

OVERVIEW

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

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

ContourEdit - A screen oriented 3D database editor.

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

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

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

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

Image Processing

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

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

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

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

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

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

Interactive Graphics Editing

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

Isosurface Extraction and 3D Rendering

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

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

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

Multiple, colored light sources.

Phong shading for seamless rendering of surfaces.

Smoothing of surfaces.

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

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

Volumetric Analysis

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

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

Utility Functions

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

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

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

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

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

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

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

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

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

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

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

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

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>.

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).

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. Geomview is available at geom.umn.edu. Conversion tools to other file formats and several contour sets can be found at <ftp://avalon.chinalake.navy.mil/>. How to get input data: The input format is a simple ascii file (see man prepros for a format description).

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

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

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

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

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 anytype 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>.

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>.

SNARK93 CONFIDENTIALITY AGREEMENT & DISCLAIMER

By purchasing the SNARK93 software, the recipient agrees to abide by the following terms:

1. SNARK93 shall not be redistributed in any way.
2. SNARK93 is not a patient-care tool and it is not approved by the United States Federal Drug Administration.
3. While every effort has been made to correct all known bugs, SNARK93 is provided "as is" with no warranty whatsoever. As such, the recipient agrees not to hold the authors responsible for any problems they may encounter with the software.
4. The recipient agrees to purchase SNARK93 with the explicit knowledge that the authors do not offer technical support.

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:8080/home.html>
<http://everest.radiology.uiowa.edu:8080/DPI/nlm/nlm.home.html>
<http://everest.radiology.uiowa.edu:8080/DPI/nlm/vida/vida.home.html>
<http://everest.radiology.uiowa.edu:8080/DPI/nlm/apps/aneur/aneurysm.html>

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 Hšhne: 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/>.

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

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.

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>. UnitŽ d'Imagerie NumŽrique. 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.

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

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>

>Denise Fields, Research Systems <mailto:denisef@rsinc.com>: We are working on a product called the Visible Human CD. It contains all the data from the National Library of Medicine (approximately 1800+ axial Slices) as images. Note, the data is available in both low and high resolution. Also included are sagittal and coronal slices that have been reconstructed. The modalities include: digital photographs, CT and MR images. The images have been compressed using JPEG.
There is also a Browser which is mouse driven - you just select a place on the body and click and it brings up the type of slice you selected. You can also do annotation, establish bookmarks throughout the body and create powerful animations.
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 platforms to be supported will include Unix, Windows and Macintosh. Each platform will be on a separate CD and will cost $495 USD (plus shipping). The product is scheduled to be released mid-April 95. We accept either a purchase order or Visa or Mastercard.

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

Penn State University
---------------------
<http://www.xray.hmc.psu.edu/>

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".

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, 4750ÊLindleÊRoad, P.O.ÊBoxÊ8800, HarrisburgÊPAÊ17105-8800, Voice:Ê717-561-5266, FAX:Ê717-561-5360, E-Mail:Ê<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: ThurmanÊGillespyÊIII,ÊMD, SCARÊTreasurer, DepartmentÊofÊRadiology,ÊSB-05, UniversityÊofÊWashington, Seattle,ÊWAÊ98195, voice:Ê(206)543-3320, fax:Ê(206)543-6317, email:Ê<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://zippy.nimh.nih.gov/pub/nih-image/plug-ins/ACRNema.hqx> or:
<ftp://ftp.funet.fi/pub/mac/info-mac/grf/util/photoshop-acr-nema.hqx>

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>.

ImportACCESS Plug-In for Mac
----------------------------
Designed Access of Chicago, IL announces the introduction of ImportACCESS, a commercially available product for importing medical and scientific files directly into a wide variety of software packages previously incapable of handling such data.

Written as an Adobe Photoshop plug-in for the Macintosh line of personal computers, ImportACCESS brings CT, MR, SPECT, PET, and other forms of digitally collected data to the desktop, regardless of the format in which the data has been saved. The progam has readers for variable sized tagged formats such as DICOM 3.0, ACR-NEMA 2.0, Interfile 3.3, Papyrus, Lumysis, and the newer GE and SIEMENS/CTI PET scanners. The built-in format editor dialog can be used to create fixed file formats for most other vendors' files. It allows software packages as Adobe Photoshop, NIH Image, and over twenty other programs to be used as viewboxs for visualization, presentation, and creation of various forms of B/W and color output.

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$449, 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, Designed Access, 702 Wrightwood Avenue, Chicago, IL 60614, Phone: (312) 880-2034, FAX: (312) 472-8834, <mailto:daccess@interaccess.com>.

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-95-05-