Path: senator-bedfellow.mit.edu!bloom-beacon.mit.edu!newsspool.sol.net!newshub.tc.umn.edu!fu-berlin.de!newsfeed.tli.de!newsfeed1.swip.net!swipnet!masternews.telia.net!news.algonet.se!newsfeed1.telenordia.se!newsfeed1.funet.fi!verkko.uwasa.fi!mhaveri From: mhaveri@walli.uwasa.fi (Matti Haveri) Newsgroups: alt.image.medical,alt.sci.nmr,comp.graphics.visualization,comp.sys.mac.scitech,sci.image.processing,sci.med.radiology,sci.techniques.mag-resonance,alt.answers,comp.answers,sci.answers,news.answers Subject: Medical Image Volume Visualization Software FAQ Supersedes: Followup-To: poster Date: Mon, 23 Nov 1998 01:41:02 +0200 Organization: i me mine Lines: 3738 Approved: news-answers-request@MIT.EDU Message-ID: Reply-To: Matti Haveri NNTP-Posting-Host: pm-51.walli.uwasa.fi Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 Xref: senator-bedfellow.mit.edu alt.image.medical:8232 alt.sci.nmr:314 comp.graphics.visualization:16119 comp.sys.mac.scitech:12698 sci.image.processing:34378 sci.med.radiology:12562 sci.techniques.mag-resonance:2646 alt.answers:38163 comp.answers:33981 sci.answers:9256 news.answers:144962 Archive-name: medical-image-faq/volume-visualization Posting-Frequency: when needed med-volviz-faq-98-11 ==================== 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. I don't anymore actively update the faq so please let me know if you wish to make corrections and additions to it. Also send me a note if some of the text is out of date or too far off-topic as I don't want the faq to grow too much with irrelevant info. Yes, some parts of the faq are showing their age but I think a little obsolete faq is better than no faq at all. This file is formatted as ~setext~. Setext viewers for Mac, DOS/Windows and UNIX can be found at . For more information on setext, the structure-enhanced text format check or send email to . A file will be returned shortly. The latest version of this file is available at: This file is also available at: Matti Haveri Seinäjoki 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. **Example image files** **Other interesting FAQs** Changes ======= Changes since 96-11 ------------------- **Software packages:** 3D-Doctor added ACR-NEMA acquisition plug-in for Mac updated ACRNview and PACSview added dicom2 added Dicom2Pict added DICOMaccess Photoshop plug-in added DICOmate added DicomEye added DICOM to TIFF & PGM converter sources added Digital Jacket added Dr Razz updated DxWin added Easymage added Image/J added InSight added Java and DicomApplet DICOM viewer added NeuroModeller added NIH Image mailing list updated Nuages updated Rubo Medical Imaging DICOM viewer added Slicer/Dicer updated Scion Image added T3D added TomoVision and sliceOmatic added Vis5D updated VisAD updated VOX-BASE Netscape Navigator DICOM Plug-in added VOXEL-MAN Junior added XEVA-VisualStudio updated Software packages ================= 3D-Doctor --------- For Windows 95/NT. Works with DICOM, as well as TIFF and BMP files (both 3D and 2D). You can use it as a viewer, but it also has 3D volume and surface rendering, restoration and more advanced image processing functions for CT, MRI, US and other 3D imaging applications. 1. Supports DICOM, TIFF, BMP and other 3D formats. Exports 3D rendering data in DXF and other 3D graphics file formats. Supports: 8-bit and 16-bit gray scale, 4-Bit, 8-bit and 24-bit color, 1-bit Black/White, complete image type conversion functions. 2. Display functions: Automatic mosaic view to display all image planes in one window. Image planes or slices can be animated. Quickly jump to a slice by double clicking on a pane in the mosaic view. Palette control, log scale, square root display histogram correction, image pixel interpolation. 3. Fully automatic and interactive 3D image segmentation. 4. Editing for image, boundaries, point markers and annotation. 5. Automatic 3D surface rendering: solid surface, wire frame, and direct voxel casting. 6. Direct 3D volume rendering: maximum voxel casting, direct object volume. 7. 3D image reconstruction by deconvolution. 8. Measurements: area, volume, distance, profile. 9. Automatic pattern recognition and feature extraction. 10. Other image processing functions: image enhancement, contrast adjustment, background removal, image combination, linear feature extraction, pattern recognition, segmentation, classification. There is a fully functioning trial version. Contact: Able Software Co, Tel: 781-862-2804, Fax: 781-862-2640 and . 3DVIEWNIX --------- 3DVIEWNIX has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. Demo (SUN, SGI, and PC) available at . The package sells for $1000 and comes with the source code, both the Silicon Graphics and SUN versions, and a couple of data files. Contact: Dr. J.K. Udupa, Medical Image Processing Group, University of Pennsylvania, Department of Radiology, 418 Service Drive - 4th Floor Blockley Hall, Philadelphia, PA 19104-6021, Phone: (215)-662-6780, Fax: (215)-898-9145, . . 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. ACR-NEMA acquisition plug-in for Mac ------------------------------------ ACR-NEMA Acquire is a plug-in module for Photoshop and other programs like NIH Image that allow the use of PhotoShop acquisition modules. Once the ACR-NEMA menu item is selected, you will be presented with a standard file open dialog box. Only files of type "ANMM" and "ANVM" will be presented in the dialog. If you have files that you suspect to be in ACR-NEMA format, but don¹t have either of these filetypes, you may by-pass the filtering of only these types by holding the option key down before selecting the ACR-NEMA menu item. This will allow you to attempt to open any file as if it were in ACR-NEMA format. The acquisition module has been tested with 8 and 12 bit gray-scale images in big-endian (Motorola) and little-endian (Intel) byte order. (There is no need to convert to one or the other, as both byte orders are handled automatically.) Color images are NOT supported. If the bit-depth is greater than 8, the raw pixel values must be scaled down to 8 bits: The "Top" value is the value that will be represented as white, the "Bottom" value will be represented as black, with all values between these spread evenly across the gray spectrum. The initial values presented are derived from information provided in the header of the ACR-NEMA image file. The "Largest Value" indicates the range of raw pixel values supplied in the file. >Matti Haveri: I've had excellent success opening both GE and Siemens CT and MRI files with this plug-in. If the files you regularly open don't be of type "ANMM" or "ANVM" you may want to make the following changes to the plug-in with ResEdit: open "8BAM" resource and "ACR NEMA" within it, find ASCII "ANMM" or "ANVM" and change either or both strings to the desired type (I changed them to "BINA" and "DICM" because my ftp client gives "BINA" for untyped binary data and Dr Razz changes them to "DICM"). ACRNview and PACSview --------------------- ACRNview is a viewer software for Windows 95/NT 4, displaying radiological images stored in DICOM Part10 file format or as ACR/NEMA 2.0 dump (without DICOM File Meta Information). Basic image processing features like zooming and windowing (brightness/contrast) are available. You can export images via the clipboard into other Windows applications. It is possible to list all DICOM elements in the file. PACSview inherits its basic functionality from ACRNview, but accesses not to single image files, but to image boxes, which content complete image sets of studies. Additional features of PACSview are related to the fact that PACSview operates with whole studies - in opposite to ACRNview, that only knows singles images. 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: 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 . ANALYZE ------- Provides an environment for the interactive visualisation and manipulation of 2-D, 3-D and 4-D biomedical images. An integrated set of tools is provided to allow data to be interrogated in both two and three dimensions. Three dimensional rendering tools are integrated with two dimensional orthogonal displays to allow real time reconstruction of conventional 2D. ANALYZE provides all the tools, including image registration, to truely support multi-modal image analysis. Tissue characterisation from multiple MRI, CT X-ray, and Nuclear medicine data is available as an interactive tool. Filtration program allow data preconditioning from statistical spatial filtering to minimise noise, and advanced 3D frequency domain deconvolution of the point spread function of a confocal microscopy system. ANALYZE has been deliberately developed to run on standard computer hardware. This allows for maximum value to be gained from the continual development of computer hardware. All supported customers receive unlimited hotline support and and an annual two day training course. ANALYZE is available to clinical and academic users for $16,000. Annual support contracts are $2,000. Contact CNSoftware for further details and evaluation. Computers supported: Sun Sparc stations (Solaris 1 & Solaris 2); Silicon Graphics; HP 9000/700 series; DEC station 5000; DEC alpha; IBM RS 6000; Apple Mac Quadra. X-Windows supported on all platforms. 24 bit colour supported where available. Interactive 2-D image display: Display of multiple images with variable size control; Mouse driven intensity windowing; Rapid generation of orthogonal images from 3-D volumes; Display of 3-D volume as a cube with control of size, intensity, range, angle-of-view and interactive dissections along orthogonal planes; Generation and display of arbitrary oblique planar images through 3-D volumes; Interactive generation of "curved" images and/or radial image sections through images traced on orthogonal images; Rapid display of images in cine movie loops. 3-D Image segmentation: Semi-automatic segmentation using advanced morphology operations; Manual editing and automatic connection/deletion of multiple objects using region growing; 3D image editing and object definition; Multi-modal image classification and object definition. Advanced 3-D image manipulation: Volume rendering using ray casting to display 3-D images from volumetric data. A complete suite of facilities is provided: Depth, depth gradient, grey scale and gray scale gradient shaded surfaces; Maximum intensity projection with optional depth weighting. Variable illumination and angle of view; Dynamic viewpoint manipulation; Transparency for overlying surface structures; 3D interaction between objects and orthogonal 2D slices; Multiple rendering parameters on different regions of the same display; Combined display of multiple segmented objects using different rendering parameters and colours. Interactive surface labelling: Surface rendering for display of shaded surfaces from contours extracted from segmented image data; Surface smoothing and enhancement based on local neighbour characteristics within the data; Display and output of surface contour profiles; ASCII file output of surface normals for export to CAD/CAM or other design or prosthetic applications. Multi-modal Image Analysis: Geometric image registration across multiple modalities using object surfaces or point files. Multi-modal image analysis and segmentation. Fused image generation and display. Cross modal object display - Bone from CT X-ray with soft tissue MRI. Image & Data Manipulations: Linear combinations of images using algebraic operators; Pseudo transparent addition of multimodal data; Spatial and frequency domain image processing using standard and user defined filter functions. Histogram operations. Manual object segmentation using thresholding, tracing and erasing. Semi-automated, interactive boundary detection for object segmentation. Automatic edge contour extraction. 2-D and 3-D math morphology operators. 2-D and 3-D image transformation compression using wavelets. Image measurement: Plotting of line and trace profiles including 3-D tracing. Region growing and spline region definitions. 2D and 3D region of interest definition. Selection and automatic sampling of regions of interest with image parameters. Interactive regional volume calculation. Regional shape and texture analysis. Data plotting and statistical analysis. 2-D and 3-D shape measurement tools. Multi spectral image classification tools for multimodal data characterisation. Operators toolbox: Escape and return to UNIX shell to run user developed programs. Macro facility to record and rerun display and analysis sessions. Magnifying glass for magnification of different areas of the screen at different sizes. Full control of colour palette. Tex generation. Image review: B/W & Colour postscript printer support. Multi panel cine movie. Save facility for 24 bit RGB images for review or advanced printing. Software development: Support of developments of Analyze program extensions simple user defined menu builder. Within the Analyze documentation you will receive a sample 'C' code program to help you develop your own utilities. Access to Analyze shared memory from external program and interface building tools. Data types and structures: As an inherently modality independent environment Analyze naturally allows the comparison and the fusion of data collected from different sites or scanners, or from different modalities. CNSoftware can assist you with porting data into Analyze by developing additional file conversion utilities. File import facility for: IGE Signa, Advantage windows, 9000 & 9800; Siemens Magnatom; ACR/NEMA; Interfile; Papyrus; TIFF included. Within the Analyze documentation you will receive a sample 'C' code program to develop your own import file utilities. Analyze is fully compatible, for file import, with the widely accepted ACR-NEMA file structure and the Papyrus format. These have been adopted by many scanner manufactures including IGE; Phillips and Siemens and which the majority of scanners will support as a file downloading format. Analyze will support a wide range of data resolutions including binary; 8 bit; 16 bit; 32 bit; and 64 bit data. All measurements are made at full data resolution irrespective of the display resolution which may be adopted. Import/export from standard image formats, TIFF; Sunraster; PCX; GIF; PPM etc. For further information call CNSoftware: In Europe: Phone +44 403 733607, FAX +44 403 733609, , 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 , 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. . . 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, , . Biological Detection Systems ---------------------------- Biological Detection Systems imaging group was acquired by Oncor, Inc. They can still be reached at 301-990-0100 or 800-237-7706. Anyone interested in this Macintosh software (which is written in the TCL libraries from Delft) can e-mail Scott Ireland . Oncor Imaging Systems: Voice 617-666-0775, Fax 617-666-8816. >Pete Clinch: They are a company that has been around in one form or another for the last 5 years or so. It was formed to capitalize on technology developed at Carnegie-Mellon's Center for Fluorescence Studies. The package they sell is a turnkey system that comes with a computer. The main product is the software, however, and includes such niceties as removal of out-of-focal-plane light to de-blur images and 3-D reconstruction of a spatial series of images. Their software is at least $10,000 for the basic package, and it can be much more than that depending on how many of their add-ons you buy. BioQuant -------- BioQuant/True Color Windows is a computer system for image analysis, topographic morphometry and 3D specimen visualization. The program and accompanying hardware provide for measurement and automatic outlining of multiple specimen structures on serial sections. Each specimen feature can be individually processed at an appropriate level of magnification and assigned its own graphic overlay color. By storing the X, Y and Z coordinates of all feature outlines, BioQuant/TCW provides for continuous measurement and outlining of objects over multiple fields of view and controls for possible overlapping or double counting at the edges of adjoining fields of view. Each feature being evaluated is assigned a color with which it will be displayed in the 3D view. As each section in the series is measured, the user specifies a pair of control points for registration of the successive sections in the 3D view. When all sections have been processed, the color overlays may be displayed in their 3D organization as a graphic that may be viewed from different orientations. Various orientation views can be redisplayed rapidly as an animation. Platform: Windows. Contact: Andrew W. Ragland , Product Support Manager, R & M BioMetrics / BioQuant, 5611 Ohio Ave, Nashville, TN 37209, Phone: 800-221-0549. Champollion and 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). 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, Fax: (+41 22) 346 11 97, Compuserve: 100277,164. C_Images 3D ----------- C_Images 3D is available for PCs under 32-bit DOS and Windows, and for UNIX on IBM RS6000's, Sun and Silicon Graphics workstations, using a variety of compilers. The code has no restrictions in dimensionality and images of 4 or more dimensions may be processed. You can process images that are larger than the memory available on your computer, without the performance loss associated with virtual memory paging. C_Images 3D splits images into suitable sized blocks for processing in RAM. ROI processing allows operations to be performed on objects, or lists of objects. You can localise processing of the image data to detected objects. The use of ROI processing results in faster operation, as the amount of data to be processed is reduced. C_Images 3D provides image processing functions such as image enhancement algorithms, Fouriers, segmentation techniques, binary morphology, and object detection and measurement. Texture processing using neural network and advanced segmentation techniques are also included. The library uses AVS for visualisation. No programming is required as the modules provided can be linked together. Function Listing: Image Formats: Analyze format (all data types), Voxel View (slices and volumes), Raw (all data types), AVS (all data types), BioRad (PIC). Pointset Manipulation: Connected component labelling, Pointset to gray image, Binary image pointset, Delete small objects. Utility Functions: Copy, Move, Draw, Convert (user defined, autoscale, max strech), Blank Pad, Strip, Global max/min, Local max/min. Fourier: Block transforms, High/Low pass filter. Linear Filters: 3X3X3 Edge detector - Sobel, Prewitt, Frei & Chen. Box-car derivative: Canny (1st derivative Gaussian), Deriche (1st and 2nd derivatives, Laplacian), Gaussian (1st, 2nd and 3rd derivatives, Laplacian), Laplacian of Gaussian, Mean, User defined, Zucker-Hummel (edge). Non-linear Filters: Local adaptive histogram normalisation, Median/Rank, Multiplicative rank, Global histogram normalisation, Distance transform, Watershed, Kuwahara. Measurement: Histogram, Average grey-level, Number of objects, Surface area, Volume, Feret dimensions, Maximum length, length/breadth projections, Orientations, Centroid - moments, Grey centroid - moments. Mathematical Morphology: Erode, Dilate, Open, Close, Alternating sequential filters, Skeletonise (Thinning, to Sheet, to Line), Arithmetic, Math (offset, add, subtract, multiply, divide), Threshold, Trig-cos, sin, tan, arccos, arcsin, arctan, arctan 2, Arithmetic parser. Textural Classification: Visualisation: Display Histogram, Display Image, Display Measurements. Contact: Dominique Miller , Marketing Executive, Foster Findlay Associates, Newcastle Technopole, Kings Manor, Newcastle upon Tyne, NE1 6PA, UK. Phone: National (0191) 201 2180, International +44 191 201 2180. Fax: National (0191) 201 2190, International +44 191 201 2190. . CT programs by Malcolm Slaney ----------------------------- This is a package of code that accompanies the book "Principles of Computerized Tomographic Imaging" by A. C. Kak and Malcolm Slaney (IEEE Press, 1988). It has nothing to do with Malcolm's work at Interval. Programs include: back - Back Projection, bgr - Insert Black Cross Hatch on the Comtal, cen - Find the Center of CRC Scanner Data, disn - Quantize an N x N picture, filt - Filter Projection Data, fmm - Find Minimum and Maximum of Data, g128 - Generate 128 x 128 Picture from Quadrants, gen - Generate Simulated Data for CT Scanners, hf - Homorphic Filter Waveforms, hist - Find Histogram of Eight Bit Binary Data, kakman - Print Help Files for CRC Tomography Software, median - One Dimensional Median Filter, merge - Add Two 128 x 128 Images together, path - Generate multipath data, pdsname - Extract PDS Name Information, radon - Plot the Radon Space of the Scans, scan - Massage Raw Data from the CRC Scanner, sim - Simulate Ellipse Field Images, tof - Calculate Time of Flight vs. Threshold Value., tv - Extract True Values from Comtal Images, window - Convolve an image with a square window (averaging). David Clunie's dicom tools -------------------------- . 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 . dicom2 ------ dicom2 is a free command-line driven program which allows you to convert medical images and DICOM files to various other formats, while optionally performing some rudimentary image processing tasks. Reads DICOM file, or raw data-sets (ACR/NEMA). Converts non-encapsulated (native) syntax to PNG, BMP, TARGA, raw, DICOM (any syntax). Lists DICOM tags in a human-readable form. Allows batch conversion. Extracts multiple-frame files. Renames destination files using user-defined pattern based on DICOM tags. Accumulates set of files into one image (to generate masks). Provides some image processing functions: mask, crop, halve, flip, window. Is small and easy to install. dicom2 is actually available for: Windows 95/NT (x86), Linux (x86) and SunOS/Solaris ([Ultra]Sparc). Image samples page might be useful to test everyone's converter. Every entry describes a file by its name, its graphical contents and some of its main features: type, modality, manufacturer, photmetric interpretation, size, and binary structure. Dicom2Pict ---------- Freeware Macintosh drag 'n drop application that converts images from DICOM into two differently windowed PICT images using W/L info in the headers. It is distributed with the sources so you can adapt it to your own needs. >Matti Haveri: Note that you have to change some long filenames like "1.3.12.2.1107.5.998080709183295" to something shorter like "1" to prevent error messages. DICOMaccess Photoshop plug-in ----------------------------- DICOMaccess for Windows 95/98/NT4 (Macintosh version should also be coming) enables Adobe Photoshop, ImageReady, PhotoDeluxe and Illustrator read and write DICOM 3.0 compatible files. DICOM images are saved as Secondary Capture Image Objects, where patient and study information can be added to the files prior to saving them. One file can be used as a template, such that patient information doesn't need to be entered multiple times. DICOMaccess can also transparently open 8 & 16-bit grayscale data, as well as indexed and RGB Color data, even multi-frame and encoded data. Demo version at . DICOmate -------- DICOM reader for Windows 95/98/NT4. It is able to realize many DICOM 3.0 service classes. At the same time, as a User / Provider. Its Application Profile support means that it is also able to support a transfer function for such storage media as MO and CD ROM. DICOMBMP -------- DICOMBMP runs under Windows 3.1 or later. It should handle any DICOM image and convert it to a standard Windows bitmap thus converting from 12-16 bit to 8 bit data. DICOMBMP.INI contains the preset window & level settings; you can put in your favorite values. 0 HU is set at 1024, if you are converting with 0 HU set at a different point then adjust the values accordingly. When undefined window & level is selected, a simple 16 to 8 bit conversion is performed which is probably the best choice for MRI. The last line of the .INI-file should contain a path to your favorite image viewing program so that the converted image will be displayed automatically. With batch conversion only the last image will be displayed. Contact: James B. Haswell, M.D. . DicomEye -------- General purpose DICOM viewer including some original features as: "dicomization" as secondary capture of images coming from TWAIN compliant scanners, paste operations or file imports, DICOM storage as SCU and SCP, multiframe images to AVI conversion. DICOM to TIFF & PGM converter sources ------------------------------------- To extract the dicom header info from a part 10 file: Digital Jacket -------------- Digital Jacket (DICOM SCP, a DICOM Storage Service Class provider) allows you to receive files from MR, CT, CR, Nuclear Medicine, X-Ray, Ultrasound, PACS and other DICOM devices directly on your Macintosh or PC. It can accept multiple simultaneous incoming connections from DICOM compliant scanners on an Ethernet network. Incoming files are hierarchically stored to patient, study and series specific folders created using information extracted from each incoming file. Files can be stored to any device connected to the computer running Digital Jacket, including RAID drives, removeable media devices and even to other computers on your LAN. You can specify the application which will be used to review incoming files, making viewing an image from your desktop only a double-click away. Security features are available allowing different ports to be configured for either anonymous connections or for connections from only specific IP addresses and remote devices. Drop-in Agents have been developed for post-processing DICOM files. A DICOM-to-Papyrus agent is included which automatically allows single image DICOM files to be appended into a multi-slice series for easy review with OSIRIS. Fully functional Macintosh and Windows 95/NT demo versions at the www site. Contact: DesAcc, 2502 N. Clark St., Suite 204, Chicago, IL 60614, phone: (773) 404-7888, fax: (773) 472-8834, email: , . >Matti Haveri: I tried the demo and it worked right out of the box (after our Siemens tech configured the scanner's parameters). I'd recommend Dr Razz as a viewer. 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 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. Optional overlay of patient demographics. Images can be saved as 16 bit raster files, or 8 bit grayscale PICTs, TIFFs, JPGs etc. The author is interested in supporting as many file formats as possible. Please contact him if you have specific file format information. C language header files are especially appreciated. He is also interested in collecting as many examples of different image file formats as possible for a test suite. Bugs reports, and any general comments about the program should be sent to . Inquiries to the author should be sent to . Thurman Gillespy III, Department of Radiology, SB-05, University of Washington, Seattle, WA 98195, voice: 206-543-3320, FAX: 206-543-6317. >Matti Haveri: This is the best medical image viewer I know, it even beats many commercial products. If you work in radiology this is a must-have application together with NIH Image and ACR-NEMA acquisition plug-in. DxWin ----- DxWin is a Windows 95/NT4 DICOM client and viewer by MEDASYS. DxWin performs the following features: DICOM query/retrieve (even on internet), read DICOM and INTERFILE files, support lossy and lossless JPEG and RLE compression, display simultaneously still and dynamic images. Functionalities include magnifier, roaming, save image in PC standard format and DICOM format, interactive video LUT adjustment, annotation. a free demo CD is available at: about medical department : Easymage -------- Easymage DV - DICOM image viewer for Windows 95/98/NT. Compliant with DICOM 3.0, ACR-NEMA 2.0 and a number of sub-versions. Study, hospital and patient information displayed on screen, printable or exportable in office documents. Level/window, Zoom-in and zoom-out. Adjustable thumbnails, navigation and digital player. Export of image sequences in AVI or static RAWs. Demo version (all enabled but savings features). Easymage RT - 3D image processing. Loading, viewing and manipulating stacks of image files (most common formats supported, including DICOM). Slice-by-slice image registration. 3D reconstruction with multi-planar reformatting. 2D and 3D image segmentation. Surface rendering. Volume measurements. Advanced Engineering Technology Srl, Viale Mosto 4 ph. (39) 10 377 4810, 16146 Genoa - Italy, fax (39) 10 377 6518. 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: . The Explorer ------------ Macintosh. UCLA. 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. . User Guide $72, Source code for commercial customers $2000, for educational institutions $200. Contact COSMIC, phone (706) 542-3265, fax (706) 542-4807, . To join the FAST user group and receive tips and important announcements about FAST, send your email address to: . Email questions, comments and suggestions to: . GVLware ------- Bob - An interactive volume renderer for the SGI. Raz - A disk based movie player for the SGI. Icol - Motif color editor. Contact: . 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. To use GVLware: mkdir gvl ; cd gvl zcat gvl.tar.Z | tar xvf - more README HIPS ---- Image transformations, image arithmetic, filtering, convolution, Fourier and other transform processing, edge detection and line drawing manipulation, digital image compression and transmission methods, noise generation, halftoning, image statistics computation etc. HIPS features images that are self-documenting. Each image stored in the system contains a history of the transformations that have been applied to that image. HIPS includes a small set of subroutines which primarily deal with a standardized image sequence header (including subroutines and programs which allow the user to customize and extend the header resulting in a general database capability within each stored image), a large library of image processing subroutines at a variety of levels of abstraction and a large library of image transformation tools in the form of UNIX "filters". It comes complete with source code, on-line manual pages, and on-line documentation. HIPS is in use on a variety of computers including Vax and Microvax, Sun, Apollo, Masscomp, NCR Tower, Iris, IBM AT etc. For image display and input, drivers are supplied written by SharpImage or contributed by our users for X11, XView, Sun-View and a variety of other framestores and windowing packages (Sun gfx, Sun console, Datacube MaxVideo, Adage, Matrox VIP-1024, ITI IP-512, Lexidata, Macintosh II and Iris). It is a simple matter to interface HIPS with other framestores. HIPS can be adapted for other image display devices because 98% of HIPS is machine independent. HIPS has been described in Computer Vision, Graphics, and Image Processing (Vol. 25, 1984, pp. 331-347) and in Behavior Research Methods, Instrumentation and Computers (Vol. 16, 1984, pp. 199-216). Contact: Michael Landy, SharpImage Software, P.O. Box 373, Prince Street Station, New York, NY 10012-0007, Voice: (212) 998-7857, Fax: (212) 995-4349 (NOTE: address fax messages c/o Michael Landy, New York University), . IAP --- Imaging Applications Platform is a commercial package for medical and scientific visualization. It does volume rendering, binary surface rendering, multiplanar reformatting, image manipulation, cine sequencing, intermixes geometry and text with images and provides measurement and coordinate transform abilities. It can provide hardcopy on most medical film printers, image database functionality and interconnection to most medical (CT/MRI/etc) scanners. It is client/server based and provides an object oriented interface. It runs on most high performance workstations and takes full advantage of parallelism where it is available. It is robust, efficient and will be submitted for FDA approval for use in medical applications. Cost: in the $5K range. Available from: ISG Technologies, 6509 Airport Road, Mississauga, Ontario, Canada, L4V-1S7, (416) 672-2100. ISG supplies visualization software from MR scanners through PACS workstations, to image-guided surgical systems. ISG customers include diagnostic imaging companies, such as GE Medical Systems, Philips Medical Systems, Siemens MR, Siemens CT, Siemens PACS, Hitachi and DuPont, as well as surgical equipment companies, such as Elekta Instruments, Inc. and Aesculap AG. IBM Data Explorer ----------------- IBM, HP, Sun, SGI, DG. Contact: . >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 . There are some great application examples there and some example mpeg animations done by students in the computer graphics program at Cornell. ICC --- Imaging Control Center for Windows is designed for monochrome image display, processing and analysis. One of the many unique features is that it uses 16 bit integer pixels as the default internal data format. Image display: Zoom, Squeeze and Pan multiple image displays. 8 functional image display scaling modes. Display image sequences as movies. Create image montages and text overlays. Gray-level and Pseudo-color image display palettes. Realtime image display palette control. Image processing: Internal pixel data type is 16 bit signed integer. Binary Operations: THRESHOLD, DILATE, ERODE, OUTLINE. Pixel Operations: SHIFT, ROTATE, NEGATE, INVERT, ABS. Monadic Operations: ROTATE, FLIP, SHIFT, COPY, SUBIMAGE, INSERT. Constant Operations: COPY, ADD, SUB, MUL, DIV, AND, OR, XOR, MIN, MAX. Dyadic Operations: COPY, ADD, SUB, MUL, DIV, AND, OR, XOR, MIN, MAX. Convolution Filters: SOBEL, LAPLACE, MIN, MAX, MEDIAN, OUTLINE, USER. FFT Filters: LOW / BAND / HIGH PASS, BAND REJECT. FFT Data Visualization: REAL, IMAGINARY, AMP, logAMP, PHASE. Geometric image transformations: ROTATE, SCALE, TRANSLATE, SKEW. Integral row and column resolution reduction: REDUCE. 16 to 8 bit data scaling: 8 scaling modes. Correct image data using Bias, Dark Current, or Flat Field images Image analysis: Pixel minimum, maximum, average, standard deviation, mean deviation. Optionally restricted to rectangular or polygonal region of interest. Plot area histogram, pixel row, column, or line, 3D surface. Plot image analysis results or user defined data arrays. Analysis data and subimages can be transferred to external programs. Measure point intensity or euclidean distance and angle. Image import and export: Read/Write native image files (16 bit). Read/Write FITS image files (16 bit). Read/Write TIFF 8 bit gray scale image files. Read TIFF 16 bit gray scale image files (both byte orders). Write Windows DIB (8 bit with Color Palette). Read IPlab image files (16 bit). Read Star1 image files (16 bit). Read raw binary data files (8/16 bit). Write raw binary data files (16 bit). Command line interface: Command line interpreter, more than 150 commands. Access more than 100 internal variables and structure elements. Expression analysis similar to "C". Save complex command sequences in macro files. Execute user defined macros from User menus or Icon toolbar. User defined commands can be added (requires ICC SDK). Miscellaneous functions: Interrupt driven serial I/O support. Access to external I/O ports and physical memory. Read and Write external ASCII files. Transfer images or subimages to the Windows Clipboard. Transfer image plot data to the Windows Clipboard. Windows DDE command line and internal variable access. TCP/IP network interface (requires ICCnet). Cost Q1/95 $999. Contact: GKR Computer Consulting, 130 Huron Ct., Boulder, CO 80303, Tel: (303) 543-0774, Fax: (303) 543-0775, CompuServe: 76346,26, Internet: . Demo at . 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, . . Demos: (all OSs), (all OSs), . 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/J ------- A Java based system that can import DICOM datasets. Image-Pro Plus -------------- Image-Pro Plus ($2499) is a Windows based scientific image analysis software package made by Media Cybernetics, L.P. of Silver Spring, Maryland. IPP is used in applications ranging from auto crash tests and fingerprint analysis, to automatic metallurgy measurements, biological research and medical imaging diagnostics. v1.3 includes new features including multiple Area of Interest (AOI) processing, interactive manual object tagging and classifying, multiple intensity thresholds for easy percent area calculation, precision 16-bit gray scale image support, new optimal "Gaussian shaped" sharpening filters, additional framegrabber and digital camera drivers and various application specific tutorials. There is also a microscope stage control module and a gel analysis module for Image-Pro. Modules for latent fingerprint processing and material science analysis will be introduced later ´95. Media Cybernetics can be contacted at 1-800-992-4256 (US & Canada) or +301-495-3305. (Fax: +301-495-5964). 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. ImageTool --------- UTHSCSA ImageTool (IT) is a free image processing and analysis program for Windows 95 or NT. IT can read and write over 22 common file formats including BMP, PCX, TIF, GIF and JPEG. Support for 8, 10, 12, 14, 16 bit grayscale, 8 bit color and 24 bit color images. Image analysis functions include dimensional (distance, angle, perimeter, area) and gray scale measurements (point, line and area histogram with statistics). ImageTool supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection, median filtering and spatial convolutions with user-defined convolution masks. IT also has built-in macro capabilities. Support for image acquisition using either Photoshop plug-ins or Twain scanners. Geometric transformations such as rotate, flip vertical, flip horizontal and magnification up to four levels. All analysis and processing functions are available at any magnification factor. Spatial and density calibration. ImageVolumes ------------ * Interactive image processing, contour editing, 3D reconstruction and volumetric analysis for light microscope, EM, X-ray tomography and MRI. * Platforms: SGI. Price: $6,900, software maintenance is $950/yr. Educational discounts available. (1/96). * Contact: Minnesota Datametrics Corporation, 1000 Ingerson Road, St. Paul, MN 55126-8146, Phone: 612-482-7938, Fax: 612-490-9717, . Demo versions of ImageVolumes are available at . * Input: Can be digitized images or two-dimensional (2D) graphics data that describe contours and points. You can interactively process either form of data to produce 3D shaded surface models. An image processing module, Image, lets you enhance and analyze serial section gray scale images using several different classes of functions, including radiometric, filtering, algebraic, geometric and morphologic. A 3D graphical editing module, ContourEdit, lets you edit and align serial section contours and point data taken from digitizing tablets or microscope stage digitizers such as the MD2 Microscope Digitizer from Minnesota Datametrics. * Output: The 3D display and analysis modules, Display3 and Metrics, make full use of the visualization features of the IRIS workstations including surface materials and light source modeling capabilities, fast hidden surface removal and polygon rendering. Display3 can render shaded surfaces, lines and point data, and provides functions for surface smoothing, coordinate transformation and animation. With Metrics you can make measurements on 3D models such as distances, numbers of objects, surface areas and volumes. * Distance Fields: ImageVolumes now includes tools for quantification and classification of 3D models, such as the distance field and 3D model intersection tool, DField. Applications for DField have included: Studies of synaptic connections between nerve cells; Association of nerves and blood vessels with sweat glands; and, 3D morphing and shape interpolation. * Stereolithography: ImageVolumes geometry files can be imported into common stereolithography systems (.STL files) for applications such as rapid prototyping of mechanical parts. * Utilities: Numerous conversion utilities are provided for common image formats (TIFF, GIF, DICOM3) and for geometry formats such as AutoCAD DXF and stereolithography (STL). The Pcut, polygon reduction utility lets one reduce numbers of surface polygons in a flat portions of 3D models, often by as much as 50%, with minimal effects on regions of high curvature. Imagist2 -------- From Princeton Gamma Tech-integrated microscope and analysis systems. Platforms: Sun. Contact: Princeton Gamma Tech, 1200 State Road, Princeton, NJ 08540. IMGF2TIF -------- IMGF2TIF DOS converts GE IMGF 16-1 bit grayscale image files into TIFF 8 bit grayscale image files. The automatic byte swapping feature allows image file format conversion to take place without the need to swap the bytes prior to using the IMGF2TIF program. The intelligent ranging feature tries to retain the pixel value range of the image so that very little or none of the original pixel information is lost. The fast conversion feature makes converting of one or more GE image files extremely fast. A 138K GE image file can be converted to a noncompressed 65K TIFF image in 3 seconds or less depending on the CPU used. The batch conversion feature (list file mode) is an extremely fast and efficient method to automate the conversion process of many GE images. The TIFF packbits compression features allows the TIFF image file to be reduced in size. The amount of compression achieved is dependent on the original GE image file. When converting from a 12 bit GE image file to a 8 bit TIFF image file the file is automatically reduced by 50% and more savings may be achieved by using the TIFF compression feature. The TIFF image description tag feature allows for certain GE header fields to be incorporated into the TIFF image file by automatically placing the information into the TIFF image description tag. This allows the user to uniquely identify the converted image when an eight character filename will not do. Since most TIFF viewers either don't or only partially display the image description tag this program will also dump the image description tag of the TIFF image file to the display whenever the user wants to identify the TIFF image file do so. To optimize the image for slide photography using a graphics program such as Microsoft PowerPoint or Lotus Freelance Graphics, the image can be resized in a bitmap editor from its native 256 x 256 pixels up to 384 x 384 pixels. Resizing minimizes the pixel effect on slides. The need to resize the image is not related to IMGF2TIF but reflects the acquisition matrix. The MR console does this resizing and smoothing automatically when the images are displayed or photographed. Cost of IMGF2TIF is $90.00 tax included with 10% discounts when ordering quantities of 2 or more. Send e-mail to for more information. ImportACCESS Plug-In for Mac ---------------------------- Written as an Adobe Photoshop plug-in for the Macintosh, ImportACCESS can read ACR-NEMA 2.0, DICOM 3.0, Interfile, Papyrus and proprietary formats from GE, PHILIPS, PICKER, SIEMENS, and SOPHA among others. The built-in format editor dialog can be used to create fixed file formats for most other vendors' files. Files can be brought into programs such as Adobe Photoshop, Adobe PageMaker, QuarkXPress, Deneba Canvas, Fractal Painter or NIH-Image. With integrated TCP/IP support, ImportACCESS allows raw medical files to be imported over the Internet and other TCP/IP networks. A display settings editor dialog is provided in which window level conversion from 12, 16-bit integer and 32, 64-bit floating point values can be performed with a real-time preview and allows the window to be set directly on the slice or whole file histograms of the original data. For the purpose of absolute quantification, the values will still be converted into 8-bit data usable by NIH Image, but one has the option with ImportACCESS of adding an annotated colorbar from which the underlying values can be drawn. Support is included for window level manipulation, template creation for formatting single and multi-slice files, and tools for consistent production of publication quality output. An integrated format editor with real-time file preview is used for fixed file format creation, and a drop-in reader interface is provided for tagged formats such as DICOM 3.0, and other newly emerging industry standards. ImportACCESS works with any Macintosh running System 7.0 or later. The programs costs US$389, with external code readers for DICOM 3.0, ACR-NEMA 2.0, Interfile 3.3 and Papyrus costing US$75 per reader. Contact: Hugh Lyshkow, Chief Technical Officer, DesAcc, 702 Wrightwood Avenue, Chicago, IL 60614, , Phone: (312) 404-7888, FAX: (312) 472-8834. . InSight ------- InSight workstation is based on Windows NT and performs realtime volume rendering. It also provides interactive surface rendering, MIP, MinIP, radiographic projection, curvilinear MPR, patient information management and built-in mini PACS. Contact: Tina Young, Neo Imagery Technologies, Inc., Tel: 626-333-3633, Fax: 626-961-0080, email: , . InterFormat ----------- InterFormat is a medical image format conversion program for industry standard UNIX workstations. Using a Motif interface, users can specify lists of input files, directories, and tape devices, specify an output directory and an output format, specify parameters to be displayed on the image list (patient name, study ID, etc.) and their order of placement, specify the output file naming convention and save or recall these settings as configurations. The user can then scan the list of inputs for medical image files, which are automatically identified and parsed into 3D image sets. The user then selects the desired 3D images for conversion. A character mode is available for use at a terminal or shell, with list-only and convert-all modes for use in scripts and database or spreadsheet input preparation. Input formats include ACR-NEMA 1.0, ACR-NEMA 2.0, DICOM 3.0, AAPM, GE Advantage MR and CT (ximg or Image Extract formats), GE Signa MR, GE 9800 CT, GE 8800 CT, Siemens Magnetom MR and Somatom CT, Picker Q800 MR and CT, Philips 300 Series CT, Technicare 2000 CT, Positron PET, Trionix Triad SPECT and Varian Ximatron CT Simulator. Siemens CTI PET and Elscint SPECT are planned for the near future. Output formats include AAPM, Interfile (including ADAC), DICOM 3.0, Vital Images VoxelView and Varian Ximatron. We will be pleased to quote on adding custom input and output formats. Availability will be October 1, 1994 for SUN computers running SunOS and Solaris and November 1, 1994 for HP, SGI, and IBM AIX systems. Initially distribution will be on 1/4" cartridge tapes, but will shift to writable CD in the near future. Planned pricing for InterFormat is $4495US (L3000UK) for three input formats, $995US (L665UK) for each additional input format. The software is node locked, with no limit on the number of copies which can run simultaneously and additional formats can be enabled by obtaining license keys. Some input formats may require additional royalty payments to the manufacturers, the cost of which will be passed on to the users. These charges have not been determined at the present time. Contact: In North and South America: Radio Logic, Incorporated, P O BOX 9665, NEW HAVEN CT 06536-0665, USA, Tel: 203-245-4664, . In EC countries and the Mid-East: Bartec Medical Systems, Ltd., Impression House, Invincible Road, Farnborough, Hampshire, GU14 7NP England, Tel: (+44) 252 376737, Fax: (+44) 252 376737, . IPLab Spectrum -------------- Requirements: Power Macintosh, Quadra, Macintosh II or Centris, with FPU, 8 MB of RAM, System 7.0 or later, 8-bit display (24-bit display preferred). File Formats: Read and write PICT, TIFF (8- and 16-bit integer as well as color), FITS and Text file formats. Import images in nearly arbitrary "foreign" binary file formats. Data Processing with >8-bit Accuracy: Processes and displays high dynamic range data with 16-bit, 32-bit and floating point data. Visualization: Perspective view displays a 3-dimensional plot. Text view displays pixel values at each (x,y) location. Animate cycles through a movie sequence. Image Enhancement: Interactive Contrast Adjustment, Histogram Equalization and Pseudocoloring. Filtering and Convolutions: Built-in filters for Linear, Median and Edge filtering of grayscale and 24-bit color images. Design custom linear filters. Geometric Operations: Fractional rotation and scaling. Align images with the registration command. Particle Analysis: Count and measure particles identified by intensity thresholding in an overlay. A binary morphology command is included to modify the overlay. Image Transformations: Extract histograms, row and column average plots, graph pixel values along a slice, perform Fourier analysis and measure angles and lengths. Color Image Analysis: Split a 24-bit color image into components, like RGB or HSV and analyze components separately. Or Merge components into a new color image. Advanced Processing: Flat Fielding to correct for lighting and sensor non-uniformities. Point functions to apply mathematical operations to individual pixels. Grayscale Morphological operators. Arithmetic operations between images. Customization: With IPlab Scripting you build Scripts by selecting commands from the menus just as you would do interactively. Write IPLab Extensions to add your own procedures to IPLab Spectrum. Contact: Scanalytics Incorporated. Phone: 703-208-2230, fax; 703-208-1960, , . IRAF ---- Image Reduction and Analysis Facility. National Optical Astronomy Observatory (NOAO) Contact: . 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: . Usenet: comp.sys.sgi, comp.graphics.explorer. or . IRIS Explorer Center (Europe): PO Box 50, Oxford OX2 8JU, UK, Tel: +44 (0)1865 516377, Fax: +44 (0)1865 516388, and . 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, . 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, . Java and DicomApplet DICOM viewer --------------------------------- Written in Java, you can see your Dicom files with a web browser, make some image processing and save your Dicom files in GIF format, provided you disable the java securities of your browser. KBVision -------- Software environment for creating image understanding applications- automatic detection, classification, and statisticas generation. Platforms: Sun, IBM (RS6000s), DEC, SGI. Contact: Amerinex Artificial Intelligence, 39135 Walnut Terrace, Fremont, CA 94536, Phone: 510-794-7853, Fax: 510-794-1406. Khoros ------ Khoros is a data exploration and software development environment. Over 300 Image processing and visualization programs are available via the visual programming language. Khoros 2.0.2 is supported on Sun (SunOS 4.1.3), Sun (Solaris 2.3), SGI (Irix 5.3), DEC (OSF1/3.0), PC/486/P5 (Linux), Cray (UNICOS 8.0.3). Contact: , comp.soft-sys.khoros, . Khoros is available in source form from . Before installing retrieve the file /pub/khoros/khoros2.0/release/install. MacCubeView ----------- Designed to display a texture map image of 3D 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 3D image data. MacCubeView will probably run on any 8MB colour Macintosh that is running System 7 or newer. There is a demo file of a slice of the author's head. MacPhase -------- 2D data analysis and visualization application for the Macintosh. Data sets can be byte, integer, longint, or real and can be as large as memory allows. MacPhase has an extensive collection of processing tools ranging from simple math operators to fourier transforms. You can use simple tools to filter in the frequency domain. There are 3x3 and 5x5 configurable convolution filters and much more. MacPhase can also display your data using raster, contour, 3D wireframe, 3D surface, 3D rendered surface, vector, 3D contour, 3D line, line, and combination plots. There is an easy to use color look up table editor. Use it to put the colors where they best show your data. MacPhase has a Data Tool palette which allows you to draw in the data layer of your data window. MacPhase has also has a Draw Tool palette which draws in an drawing layer of your data window. Use the draw tools to annotate your data with text, simple shapes, placed pictures, color look up table legends, and even sound objects. Just about every function or operation can be called using a pascal-like macro language. Macros are a great way to extend some of the already great features in MacPhase. You can also write external code modules, Add-ons, for MacPhase. These Add-ons can be an excellant way to extend MacPhase's capablities. Add-ons will be made available to support the QuickCapture and SCION frame grabbers, GPIB interface, serial ports, QuickTime, video digitization (AV-vdig), Photoshop plug-ins, color channels, image restoration, and more. Add-ons are callable from the macro language. Add-ons can be used to add new file formats as well. MacPhase has a large number of supported formats some of which are PICT, TIFF, MatLab, HDF, FITS, binary, text, EPS, Mathematica, Photoshop, polygon files, sound, color tables, and others. MacPhase supports AppleEvents through the DoScript event and several custom events. Use the DoScript event to send macro commands to MacPhase. Use the custom events to pass data between applications. Contact: Doug Norton, Otter Solution, 10 Limekiln Road, Whitesboro, NY 13492-2338, USA, Phone: (315) 768-3956, Fax: (315) 736-4371, Internet: , American Online: OtterSol, AppleLink: ottersol. MacStereology ------------- Demo version is available at . 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 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, 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 $695. 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. IMNET/Evergreen, Main Street, PO Box 795, Castine, Maine 04421, phone: (207) 326-8300, fax: (207) 326-8333. Jeffrey Siegel , . MetaMorph --------- Integrated microscope image capture, enhancement, reconstruction, and visualization system. Platform: PC. Contact: Universal Imaging Corporation, 502 Brandywine Parkway, West Chester, PA 19380. MicroVision II -------------- For visualising point-sampled data volumes produced by 3D scanning devices such as MRI, PET, CT and confocal microscopes. This includes Finite Element Analysis, CFD, Non destructive testing, Chemisty, Astrophysics etc. System requirements: you need a computer running UNIX with X11 and Motif. Contact: FairField Imaging Limited, 8 Lonsdale Gardens, Tunbridge Wells, Kent England TN1 1NU. Phone: +44 (0)1892 539588, Fax: +44(0)1892 539488. , . 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. . Refs: Journal of Neuroscience Methods v21, pp 55-69, 1987. Contact: Robert G. Smith, Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104-6058, . Mvox ---- General purpose tool for visualization and segmentation of a wide range of 2-4D medical images and graphics. Mvox has a user interface based on software standards such as Unix, X/Motif and OpenGL. Mvox can handle images with different numbers of slices, colours and time steps. It has been used to visualize and segment: *2-3D medical images with stacks of slices (CT, MR, etc.), *2D remote sensing images with many channels and *2-3D colour images (Red, Green and Blue). In addition Mvox can also display and manipulate *3D surface graphics (as used in CAD programs). 3D graphics can be exported in *VRML format for use on WWW. In Mvox, image segmentation can be performed manually using *editing and *contour drawing facilities. For semi-automatic segmentation, Mvox has interactive/automatic *thresholding and statistical *classification using discriminant analysis, both with multiple classes. Segmented images can be visualized in 3D along with the original images using either *iso-surfacing, *volume rendering, or fast display of *slices. Also *stacked contours can be turned into 3D structures and visualized. Additional features include image *registration, computation and manipulation of *histograms, computation of image *statistics, *volume and *angle mesurements, *colormap alterations, etc. User-developed C programs can use Mvox as a front-end through a *shared memory interface by including as little as two lines of extra user code. Image formats: *ANALYZE, *TIFF, *SGI, *TGA, *BMP, *Inrimage, *HIPS, *BRIMG. 3D formats: Import: *Cyberware, *OFF, *Flex3D - Export: *VRML, *DXF, *Inventor, *Flex3D. Mvox is only supported on Silicon Graphics platforms, but can run on HP, DEC, and IBM RS/6000 as well. A free demo version and test images are available from the Mvox homepage. Licenses are available for approx. $2500 (DKK 15.000 excl. VAT). Contact: Mware / Morten Bro-Nielsen , Groentoften 4, 3.tv., DK-2860 Soeborg, DENMARK. Navigator-win ACR-NEMA plugin ----------------------------- Free half-a-year-running plugin module for Netscape Navigator & 32-bit Windows to display ACR-NEMA images 8 to 12 bit: 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. NeuroModeller ------------- Free medical image 3D visualization software for Windows 95/NT by Cornell University/Division of Neurosurgery. It supports software rendering & hardware 3D accelerated graphics, as well as file support for DICOM, BMP and RAW formats. NeuroModeller offers realtime 3D visualization and manipulation of surface iso-contours. Some of the features include: scrolling through multiple contours, superposition of contours, rotating, zooming, moving, lighting, texture mapping, coloring with transparency and toggling on or off the visibility of contiguous regions. Image processing features of NeuroModeller include: window/level control, thresholding, pixel island removal, masking and anisotropic diffusion. 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. . 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: , . 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 (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 to request a subscription. Clint Potter (the original author and pricipal contact) is at . 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 . 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 or on floppy disk from NTIS, 5285 Port Royal Rd., Springfield, VA 22161, part number PB93-504868. . To subscribe to a digested version of the mailing list, send email to , the subject of the message should contain "subscribe". NIH Image Macro to import ACR-NEMA 2.0 and DICOM 3.0 images by Tunc Iyriboz : >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. Nuages ------ Nuages is a tool that reconstructs 3D surfaces and volumes from a stack of contours on parallel 2D images. 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 vrml, inventor, STL, wavefront .obj format, DXF format and Object File Format (.off) format. How to get input data: The input format is a simple ascii file (see man prepros for a format description). A few data sets are available at the site. Platforms: Sun, SGI, DEC, HP. Refs: "Three-dimensional modeling of human organs and its application to diagnosis and surgical planning.", Technical Report 2105, Institut National de Recherche en Informatique et Automatique, (France), Dec 1993. >Matthew T. Adams: I wanted to let you know about a little utility I just wrote and posted to . 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. Includes statistical and neural network classifiers, feature data visualization, feature ranking and selection (by utility for classification), and unsupervised clustering. Platforms: PC (Windows 3.1; Windows 95 and NT under emulation); Sun (SunOS and Solaris); SGI (IRIX); VAX (VMS). Contact: PAR Government Systems Corp., 1010 Prospect St., Suite 200, La Jolla, CA 92037, Phone: 619-551-9880, Fax: 619-551-0257, , . OSIRIS ------ OSIRIS has been designed as a general medical image manipulation and analysis software. The design is mainly based on the following criteria: portability, extendibility and suitability for any imaging modality. OSIRIS is designed to deal with images provided by any type of digital imaging modality to allow physicians to easily display and manipulate images from different imaging sources using a single generic software program. Portability ensures the software implementation on different types of computers and workstations. Thus, the user can work in the same way, with exactly the same graphical user interface, on different stations. Also by supporting standard file formats, the OSIRIS software provides access to images from any imaging modality. The OSIRIS program was developed as part of the Geneva PACS project and is intended for physicians and non computer-oriented users allowing them to display and manipulate medical images. Its standard original version included only basic image manipulation tools accessible through a convenient and user-friendly graphic interface. In addition to being used at the University Hospital of Geneva, it was widely distributed around the world and was adjusted according to user's comments and suggestions. This program was also designed to serve as a development of more advanced image processing and analysis tools. Portability: The initial development of OSIRIS program was undertaken simultaneously on UNIX based X/window graphic environment as well as Apple Macintosh native platform. The UNIX version was further tested on a variety of workstations namely SUN Sparc series, DEC alpha series, HP 7000 series, IBM Risc-6000 series and SGI machines. Recent evolution in the desktop computing environment lead us to develop a new kernel of the OSIRIS software to be compatible with Windows 4 graphic interface for PC compatible computers. This new version is also directly compatible with Windows NT and may be used on Windows 3.1 with some restrictions in performance. Finally we also ported our code to run native on the PowerPC RISC computers to fully benefit from the enhanced performance of this new generation of processors. OSIRIS provides (just a few characteristics): Interactive graphic user interface, Customizable display modes for images sets, Zoom, rotation, flipping of image sets, Color adjustment on full dynamic range, Magnifying glass, Annotations, Regions of interest (polygons, ...), Measurements (distance, angle, surface, volume, ...), Filters, Multiplanar sections of tomographic images, Region growing for automatic image segmentation, Histogram equalization. OSIRIS software can be obtained free of charge from: Digital Imaging Unit, University Hospital of Geneva, 24 Micheli du Crest, 1211 Geneva 14 - Switzerland. Fax: (+41 22) 372 61 98, . A special developer license is available for the full source code. , . Photoshop-mac dicom plugin -------------------------- Platform: Macintosh. This is pretty quick and dirty and no substitute for real programs like Dr Razz, NIH Image and Osiris but it may be helpful. It has been tested with Macintosh Photoshop 3.0.5, requires 16 bit grayscale support from Photoshop which probably isn't in pre 3.0 versions. Source code is also available. Currently it handles: 8 and 16 bit grayscale, signed or unsigned data, uncompressed transfer syntaxes, DICOM part 10 style meta-information headers, older ACR/NEMA and SPI files in little or big endian byte order. It also only reads for now, and does not yet write. Furthermore, it is a file format plugin, not an acquire plugin, and hence is not useable with NIH Image. This has the advantage that DICOM files can be opened from the Open menu as any other file. There is automatic recognition of a FileType of "DICM" and file extensions of ".dc3" and ".dic". Any file type can be opened though, by selecting Show All in the Open dialog and choosing a file type of "Dicom File". To use, just drag the "DicomFile" file into the "Plug-ins:File Format" folder in the Photoshop home folder. When you open a 16 bit DICOM file such as a CT or MR from the Open menu using this plugin, you will get a 16 bit grayscale image in Photoshop, with which you can't do very much because it may look ugly as Photoshop tries to display the whole range of pixel values. Select Image/Levels/AutoLevels from the menu and all the used pixel values will be expanded to fill the available grayscale. You can use the manual levels adjustment to select the window level and width you want, and then change the mode to 8 bit grayscale to manipulate the image further, or save it as something "normal" you can import into other programs. Contact: David A. Clunie 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 . PV-WAVE ------- PV-WAVE integrates graphical and numerical analysis techniques for finding solutions to, and building applications for, complex technical problems. PV-WAVE uses fourth-generation language (4GL) that analyzes and displays data as you enter commands. With it you can perform complex analysis, visualization and application development interactively. PV-WAVE provides routines for representing, importing, exporting, filtering, transforming, analyzing, visualizing and communicating data, as well as constructing widget-based applications with this technology. Platforms: UNIX and OpenVMS workstations and PCs running 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, , , Usenet: comp.lang.idl-pvwave. RMN --- >Philip Grandinetti : RMN - A Nuclear Magnetic Resonance (NMR) data processing program for the Macintosh. Free. . 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, . Rubo Medical Imaging DICOM viewer --------------------------------- Wintel DICOM viewer of Rubo Medical Imaging . SciAn ----- SGI 4D, IBM (req. GL, Z-buff). or . >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. Scion Image ----------- Scion Image for MacOS/Windows is an extended version of NIH Image for MacOS. The modifications which Scion has made to NIH Image involve advanced capturing capabilities, video export abilities and the display of 24 bit color images. Complete support has been added for the Scion CG-7 RGB color frame grabber including high resolution capture, color frame averaging and frame summation and color on-chip integration. Scion Image supports video rate frame averaging, blank field shading correction and mathematical operations with the Scion AG-5 frame grabber. Exporting video images to video printers is supported on Scion frame grabbers with video outputs. Scion Image for MacOS requires a Macintosh with a PowerPC processor and at least 16 Mb of RAM. Those working with color images or frame sequences should have at least 32 Mb of RAM. Scion Image works best with display systems capable of supporting millions or thousands of colors. Scion Image for Windows requires a PC compatible computer with a Pentium processor. Windows 95/NT is required. Microsoft DirectX operating system extensions must be installed. At least 32 Mb of RAM in the computer is recommended. Scion Image works best with a display system that supports thousands or millions of colors. Scion Image is available free of charge. Frequent updates of Scion Image are made to keep it current with NIH Image. 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. Slicer/Dicer ------------ Volume data visualization program designed for scientists, medical professionals, engineers and other technologists involved with complex data defined in three or more dimensions. Examples of such data include seismic measurements (geophysics), output from MRI and CT scanners (biomedicine) and computational fluid dynamics results (aerodynamics, meteorology, etc.). With Slicer Dicer you can "slice and dice" a data volume, viewing arbitrary orthogonal and oblique cross sections, rectilinear blocks and cutouts, isosurfaces, and projected volumes. You can generate animation sequences featuring continuous rotation, moving objects (slices, blocks, etc.), time variation (or the variation of any non-spatial dimension), oblique slice rotation and varying transparency. The data volume can be scaled and rotated arbitrarily. Dicer was developed in the late '80s at Visualogic with sponsorship from The National Science Foundation and Apple Computer. It was originally code named "Slicer/Dicer" but was released commercially as "Dicer". Spyglass had an exclusive license from Visualogic to market Dicer until '95. One of the other Spyglass tools was called Slicer. Like Dicer, this program was a volume data visualizer. It was a Windows application, whereas Dicer ran only on Macintosh platforms. The two programs are similar in that both are designed to provide visual access to 3D data defined on regular cartesian grids. Both support the HDF and netCDF data formats, among others. Both offer capabilities for viewing arbitrary planar slices and isosurfaces. The two programs are also different in many ways. The user interfaces are completely different. Dicer's main strength is the ease with which a data volume can be "sliced and diced" for visualization purposes. In addition to arbitrary orthogonal and oblique slices, the user can also create arbitrary rectilinear blocks and cutouts. Slicer offers more rigorous 3D projection and rotational capabilities and relys primarily on a volume-rendering (ray-tracing) model. In '95, Spyglass sold its data visualization tools, Plot, Transform and Slicer, to Fortner Research. Fortner sells the current version of Slicer under the name "T3D". Visualogic ('97) has ported Dicer to Windows as Slicer Dicer v2.5 for Windows NT and 95. The new Windows product is similar to and includes all the functionality of the last Macintosh version (2.0). It now supports arbitrary scaling and rotation of the data volume and projected-volume rendering modes similar to ray tracing (but less rigorous) are available. A Macintosh version of Slicer Dicer is planned for release in '98. The price for Slicer Dicer v2.5 is $595, with discounts available for academic purchasers and for quantities greater than one. System requirements are Windows NT or 95, at least 8 MB RAM and a display with 256 or more colors. The standard distribution includes a CD-ROM with extensive sample data sets, most notably the National Library of Medicine Visible Man data. Contact: Visualogic, Inc., PO Box 3027, Bellevue WA 98009-3027, USA, Phone (425) 747-3305, Fax: (425) 644-8422, Sales: (888) 747-3305, email: , , . 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, . Sunview ------- From SUN. . Contact: Sun Microsystems, 2550 Garcia Avenue, Mountain View, CA 94043, Phone: 415-960-1300. SunVision --------- Sun (SunOS under X). No longer sold or supported by Sun. >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. T3D --- (See also Slicer/Dicer). Contact: Fortner Research, LLC, 100 Carpenter Dr., Sterling, VA 20164, Phone: (703) 478-0181 Support, (800) 252-6479 Sales, (703) 689-9593 Fax. Theraview --------- TomoVision and sliceOmatic -------------------------- TomoVision is a Windows 95/NT tool that allows you to display medical images and scale them, alter their colormap and access any pixel position and value. In addition, you can access details of the image header. Supported image formats include NEMA, DICOM, Interfile and Papyrus files. Many of the manufacturers proprietary formats are also supported. You can also read other image formats as raw data, TomoVision's interface help you select the correct parameters with its suggestions and its preview window. sliceOmatic helps you to visualize, segment and analyse data. The 3D options enable to reconstruct and visualize 3D surfaces extracted from the scans segmented in sliceOmatic. You can also take precise 3D measurements on these surfaces. The 3D options add these new tools to sliceOmatic: 3D surface creation, 3D measurements and 3D surface extraction. sliceOmatic runs on a Silicon Graphics WS. Supported image formats include NEMA, DICOM, Interfile and Papyrus files. Many of the manufacturers proprietary formats are also supported. sliceOmatic $5000, sliceOmatic with the 3D Options $7000. 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