3D Reconstruction

Software

This is a list of software (both commercial and otherwise) available for 3D reconstruction of MRI, CT, confocal, and serial-section data for medical/life-sciences imaging.

3-D-E

Windows-based contour editor and visualizer from Data Cell Ltd. (Platforms: PC; Cost: ~$1500)

3-D-E Visualiser and Contour Editor 3-D-E, supplied by Data Cell, is a Windows based software product designed to take 2D image data and reconstruct to a 3-D surface rendered object. It allows the user to view, rotate and zoom under mouse control in real time on a 486 PC.

Applications:

  • Confocal Microscopy
  • Cell Analysis
  • MRI and CT Scanning
  • Sequence Tracking
  • Laser Profiling
  • Research and Development

3-D-E comes with a contour editor used to generate a wire frame data set from 2-D images and a Visualiser which takes the wire frame data and renders it using lighting, camera and shading parameters.

Visualiser Features:

  • Accepts 3-D data from the Contour Editor or ASCII file.
  • Real Time Zooming and Rotating under mouse control
  • Ability to view inside by interactively changing cut plane.
  • External and internal Rendering

More than one object can be viewed at once and rotated independently while objects of different colours maybe defined within an object to show internal workings. The image window can be copied into the clipboard and pasted into word-processing and graphical packages for report generation.

The Contour Editor is used to load a set of image slices and define them as a sequence with a Z distance between each slice. The contour of each image is drawn around the perimeter using the mouse in a point and click fashion. Contours are then repeated and edited for subsequent images until all contours have been drawn. The constructed object can be seen in the Viewer by launching it from the editor.

As well as manually drawing contours, boundary points can be loaded in from packages like Optimas where they are generated automatically. An Optimas macro is available which generates boundary points of a chosen segment length and converts the data to a contour file. In addition, the macro can be linked to the Sequence Extension available with Optimas to automate the complete image set.

Contour Editor Features:

  • Uses Industry Standard file formats including tif, bmp and jpg
  • Contours can be re-edited at any stage
  • Contours can be pasted between slices and shifted, rotated and zoomed.
  • Generates ASCII files for loading into the 3-D Viewer
  • Several files can be pasted together to generate objects within objects

Both the Editor and Visualiser come with full on-line help and a manual that explains the technical aspects of the software.

  • Platforms: PC (Windows).
  • Cost: £995, (~$1500).
  • Email: imaging@datacell.co.uk
  • Contact: Data Cell Ltd., (tel)01628 415415, (fax)01628 415400

3DVIEWNIX

3DVIEWNIX is a transportable, very inexpensive software system developed by the Medical Image Processing Group, Department of Radiology, University of Pennsylvania, Philadelphia. It has state-of-the-art capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. (Platforms: SGI, Sun, PC; Cost: unknown)

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

  • Preprocessing:
    • 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.
    • 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.
    • Filtering:
      • A variety of forms of enhancing and smoothing filters
      • Used for filtering surfaces, for normal estimation, for interpolation, and volume rendering.
    • Masking:
      • For assisting segmentation
      • Quick operation using "paint brushes".
    • Thresholding:
      • Multiple intervals can be specified
      • Iso-surface generation at any resolution.
    • Segmentation:
      • 2-feature cluster partitioning
      • Quick gesture-controlled (user-guided) boundary segmentation.
    • Classification:
      • 1-feature multiple material classification for opacity assignment
      • 2-feature multiple material classification for opacity assignment.
    • Boundary Formation:
      • Connected, oriented, closed 3D surfaces are formed
      • Surfaces may have any resolution.
    • Image Algebra:
      • Image addition, subtraction, logical operations.
  • Visualization:
    • 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.
    • Reslice:
      • Guided by 3D display
      • Reslicing through multidimensional volumes.
    • 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 objects, 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.
    • 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:
    • 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.
    • Registration:
      • Based on matching homologous features - points, curves, entire surfaces
      • For merging information from multiple modalities
      • For motion description and analysis.
    • 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.
  • Platforms: Sun, SGI, PC.
  • Contact:
    	Dr. J.K. Udupa
    	Medical Image Processing Group
    	Univeristy of Pennsylvania
    	Department of Radiology
    	418 Service Drive - 4th Floor Blockley Hall
    	Philadelphia, PA 19104-6021.
    	Phone : (215)-662-6780
    	Fax   : (215)-898-9145
    	e-mail: Vhelp@mipgsun.mipg.upenn.edu.	
    
  • WWW Server: http://mipgsun.mipg.upenn.edu
  • FTP: demo version available at mipgsun.mipg.upenn.edu/pub/3DVIEWNIX1.1
  • Comments:
    • Krishna Iyer: You may also want to check out some of the new surface rendering algorithms from the 3dviewnix group. They can be reached at Vhelp@mipgsun.mipg.upenn.edu. You can get some MRI images in ACR-NEMA 2.0 format at /pub/3DVIEWNIX1.0/DATA.

Amira

Interactive segmentation and visualisation package for biomedical images. (Platforms: SGI, Sun, Windows; Cost: $$$$)

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. (Platforms: SGI, Sun, HP, DEC; Cost: $$$)

Analyze from Mayo clinic . 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.

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 anddisplay of arbitrary oblique planar images through 3-D volumes; Interactive generation of "curved" images and/or radial image sections through images traced on orthogonal images; Rapid display of images in cine movie loops.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • WWW: http://www.mayo.edu/bir/home.html
  • Platforms: Sparc (Sun- Solaris 1+2), SGI, HP 9000/700, DEC 5000 and Alpha, IBM RS6000, Apple Mac Quadra.
  • Cost: $16000 for clinical and academic users. Support available for $2000/year.
  • Contact:
    Daniel Broderick
    Mayo Medical Ventures, 200 First Street SW Rochester, MN 55905
    "tel"(507)-284-8452, "fax"(507)-284-5410

Comments:

  • Alex Milshteyn: Analyze would do pretty neat 3D recons (and different kinds of segmentation, too) but for the reason of some dumb internal constraints, its 3D tool (whatever its name is, I do not recall) it would scale any size 3D image to just about 3x3 in on a standard Sparc 5 screen, hence the real value of this 3D rendering is kind of questionable.
  • Julian Guffogg: We use "Analyze" (so do quite a few others in the Medical imaging sphere) and havent had any problems like that. We run it on an IPX without any hassle. I find the user interface rather dated, its not very user friendly, but you get some neat 3D recons!
  • Vinayak Dutt: Volume rendering tool of Analyze is frankly quite good.

AutoDeblur

AutoDeblur performs blind deconvolution for 3d data. (Platforms: SGI; Cost: unknown)

Platforms and Cost

Platforms Cost
Silicon Graphics Please call (518)276-2138
or e-mail sales@aqi.com

Features

AutoDeblur supports confocal flourescence, transmitted light brightfield, and widefield flourescence microscopes. It offers accelerated maximum likelihood based blind deconvolution and a faster less noise-immune method. Visulatization capabilities include maximum and summed intensity, orthogonal projections, voxel gradient shading, and orthogonal cross sectional views.

For More Information

AVS

AVS - commercial visualization package from Advanced Visual Systems, Inc. (Platforms: SGI, Sun, HP, DEC; Cost: unknown)

AVS - commercial visualization 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.

  • WWW: http://www.mayo.edu/bir/home.html
  • Platforms: Sparc (Sun- Solaris 1+2), SGI, HP 9000/700, DEC 5000 and Alpha, IBM RS6000, Apple Mac Quadra.
  • Cost: $16000 for clinical and academic users. Support available for $2000/year.
  • Contact:
    Daniel Broderick
    Mayo Medical Ventures, 200 First Street SW Rochester, MN 55905
    "tel"(507)-284-8452, "fax"(507)-284-5410
  • Platforms: Sparc (Sun- Solaris 1+2), SGI, HP 9000/700, DEC 5000 and Alpha, IBM RS6000, Apple Mac Quadra.
    • AVS3- Convex, Cray, DEC, Evans&Sutherland, HP, IBM, Kubota, SGI, Stardent, Sun, Wavetracer.
    • AVS4- all Unix workstations.
  • Contact: avs@avs.com.
  • Ftp: avs.ncsc.org.
  • Usenet: comp.graphics.avs
  • Web: http://www.avs.com or, for the International AVS Group: http://iac.ncsc.org
  • Comments: Excellent functionality, excellent video tape training available, bit costly.

Oncor

Biomedical image measurement and analysis system. (Platforms: Mac, PC; Cost: $$)

  • Platforms: Macintosh.
  • Contact:
    Oncor Imaging
    200 Perry Parkway, Suite 1, Gaithersburg, MD 20877
    "Phone"1-800-77-ONCOR
  • WWW: http://www.oncorinc.com/home Software starts at ~$6000, package cost rises with peripherals. Macintosh and Power Mac supported for 3D reconstruction, PC support for acquisition and color processing. More information available at their Web site.
  • Comments:
    • 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.
    • Kevin Ryan: Biological Detection Systems has sold their instrument technology to Oncor, Inc.. The sales and service is still handled from the same office, but will be moving shortly. The phone number is 301-990-0100, fax the same as before.
    • Kevin Ryan: As an update to your Web page on Reconstruction; I wanted to correct some information about Oncor. Your reference is to Biological Detection Systems/Oncor, which is no longer correct - BDS exists as a separate entity, selling mainly fluorescent dyes, and it is legally inappropriate for Oncor to be referred to as BDS. The company is Oncor Imaging, the reconstruction product is "Oncor Image"
    • Software starts at ~$6000, package cost rises with peripherals. Macintosh and Power Mac supported for 3D reconstruction, PC support for acquisition and color processing. More information available at their Web site.

Bioquant

3D reconstruction and quantitative histochemistry system. (Platforms: PC; Cost: unknown)

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.

  • Platforms: PC (Win3.1).
  • Email: bioquant@usa.pipeline.com .
  • Contact:
    R&M Biometrics
    5611 Ohio Ave., Nashville, TN 37209
    "Phone"800-221-0549

BOB (GVLware)

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. (Platforms: SGI; Cost: 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.

C_Images 3D

3D Image analysis package by Foster-Findlay Associates (UK). (Platforms: PC (DOS, Windows), Unix (IBM, Sun, SGI); Cost: unknown)

3D Version of C_Images by Foster-Findlay Associates (UK).

CELLscan

A system for high-resolution 3D fluorescence microscopy. Provides image acquisition, deconvolution, and analysis capabilities. (Platforms:PC; Cost: Unknown)

The CELLscan System is a computer-based instrument which enhances your existing fluorescence microscope allowing visualization and analysis of living or fixed specimens in 2D or 3D with unprecedented resolution and under extremely gentle imaging conditions.

The Exhaustive Photon Reassignment (EPR) algorithm (developed and patented by the Biomedical Imaging Center at the University of Massachusetts Medical School in Worcester), when applied to a through-focus stack of images acquired from any conventional fluorescence microscope or confocal micorscope, reassigns all out-of-focus photons back to their proper place of origin, producing very "thin" optical sections. These images which are of very high contrast, reveal fine small structures which are not visible in the unprocessed image set and are ideal for the 3D rendering functions included with the CELLscan System. Importantly, only Scanalytic's EPR algorithm has been proven to retain the quantitative accuracy of the image set, permitting accurate studies on intensity level to be conducted on highly-resolved 3D images.

  • Email: scan_info@scanalytics.com
  • WWW: www.scanalytics.com/cellscan.htm
  • Mail:
    Scanalytics, A Division of CSPI
    40 Linnell Circle, Billerica, MA 01821
    Phone:(800)882-6247 (508)663-8161 Fax:(508)663-0150

CT

CT programs by Malcolm Slaney. (Platforms: Many; Cost: free)

CT programs by Malcolm Slaney.

  • Platforms: Most platforms (requires old (K&R) C compiler).
  • FTP: ftp.interval.com/pub/papers/malcolm/ct.tar
  • Contact: malcolm@interval.com
  • Comments:
    • Doug Merritt: This is a package of code that accompanies the book "Principles of Computerized Tomographic Imaging" by A. C. Kak and Malcolm Slaney (IEEE Press, 1988).

Programs included:

  • back... Back Projection
  • bgr ... Insert Black Cross Hatch on the Comtal
  • cen ... Find the Center of CRC Scanner Data
  • disn ... Quantize an N x N picture
  • filt ... Filter Projection Data
  • fmm ... Find Minimum and Maximum of Data
  • g128 ... Generate 128 x 128 Picture from Quadrants
  • gen ... Generate Simulated Data for CT Scanners
  • hf ... Homorphic Filter Waveforms
  • hist ... Find Histogram of Eight Bit Binary Data
  • kakman ... Print Help Files for CRC Tomography Software
  • median ... One Dimensional Median Filter
  • merge ... Add Two 128 x 128 Images together
  • path ... Generate multipath data
  • pdsname ... Extract PDS Name Information
  • radon ... Plot the Radon Space of the Scans
  • scan ... Massage Raw Data from the CRC Scanner
  • sim ... Simulate Ellipse Field Images
  • tof ... Calculate Time of Flight vs. Threshold Value.
  • tv ... Extract True Values from Comtal Images
  • window ... Convolve an image with a square window (averaging)

DeltaVision

Image acquisition and deconvolution software for 5-dimensional microscopy. (Platforms: SGI; Cost: unknown)

DeltaVision is a microscope system designed to acquire and deconvolve multi-dimensional images of fluorescently-labeled specimens. The software provides true, 3-dimensional iterative deconvolution for high resolution microscopy of fixed or living cells.

Dicer

Slicer/Dicer is a volumetric visual data analysis package. (Platforms: Mac; Cost: $)

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

  • Platforms: Macintosh (256 color display, 4MB RAM, FPU), PC (Windows, 8MB RAM), Unix (256 color display, 16MB RAM).
  • Cost: $695 (Mac), $495 (PC).
  • Email: info@fortner.com
  • Phone: 703-478-0181
  • Fax: 703-689-9593
  • Contact:
    Fortner Research
    100 Carpenter Drive, Sterling, VA 20164
  • James Sneyd: I've used Spyglass for many years, and found it to be excellent. Especially when combined with the HDF format libraries. Animation is excellent, and Mac-Unix coordination is seamless. It's not nearly as powerful as some visualisation systems (Explorer, AVS, Wavefront) but is a LOT cheaper and I have never needed anything more expensive. I use it mostly for numerical solutions of PDEs in two and three dimensions. One problem is the absence of Dicer for Unix.
  • Scott Likens: We no longer create or support the line of Visual Data Analysis tools. (Slicer/Dicer, Plot, and Transform). While successful, we now concentrate solely on web technology. Last year we sold the software to Fortner Research, which is headed up by one of the founders of Spyglass. It's in good hands, and fully supported.

DIP Station

Macintosh-based reconstruction package. (Platforms: Mac; Cost: unknown)

  • Platforms: Macintosh.
  • Contact: whc@po.cwru.edu.
    • Pete Clinch: I'm pretty happy with a package called DipStation. I think you can also make user code modules that are basically written in C.

Dr. Razz

CT/MR display and analysis program for Macintosh color computers. (Platforms: Mac; Cost: free)

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

System 7.x and a color Macintosh with a 68020 or greater CPU are required. A math co-processor is NOT required. A Power Macintosh version will be released after the first non-beta version is posted for 680x0 Macintoshes. The application supports the core AppleEvents (except for printing, which is not yet implemented) and stationary pad documents.

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

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

  • Platforms: Apple Mac (System 7.x w/ color).
  • Cost: free for non-commercial use.
  • Contact:
    Thurman Gillespy III
    Department of Radiology, SB-05
    University of Washington
    Seattle, WA 98195
    Phone: 206-543-3320 Fax: 206-543-6317, Email: tg3@u.washington.edu
  • FTP ftp://ftp.u.washington.edu/pub/user-supported/razz/

EM3D

Electron microscopy reconstruction software package from Stanford. (Platforms: Win, UNix; Cost: free)

Visit the EM3D site

EutecticSSRS

Low-end 3D reconstruction, mapping, and analysis system. Contour-based using a digitizing tablet. (Platforms: PC; Cost: $24-28k (NTS), $8-10k (NTSV))

The Eutectic NTS (Neuron Tracing System) is a 3D reconstruction and analysis system for computer-aided tracing of branching structures from tissue slices viewed through a light microscope. The NTS includes custom hardware and software. The software offers an extensive range of publication-ready neuron-specific morphometric analysis. Cost: $24,000 - $29,000 (U.S.)

The Eutectic NTSV (Neuron Tracing System for Video) is a 3D reconstruction and analysis system for computer-aided tracing of branching structures from a collection of image files. The NTSV supports any 255 grey level image file format. The user can "focus" through a stack of images in real time simulating a microscope environment. The NTSV includes custom hardware and software. The software offers an extensive range of publication-ready neuron-specific morphometric analysis. Cost: $8,000 - $10,000 (U.S.)

FAST

It is a software environment for visualizing and analyzing Computational Fluid Dynamics data. (Platforms: SGI; Cost: free)

FAST is currently under development by members of the Numerical Aerodynamic Simulation Division (NAS) at the NASA Ames Research Center. 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.

  • Platforms: SGI.
  • Contact: fast@nas.nasa.gov.
  • Server: http://www.nas.nasa.gov/FAST/fast.html

HVEM 3D

PC-based serial section reconstruction program for microscopy created by Kinnamon/Young at UColorado. (Platforms: PC; Cost: unknown)

PC-based serial section reconstruction program for microscopy created by Kinnamon/Young at UColorado. The last version was 1.2 and was released in 1988.

  • Platforms: PC (Dos).
  • Contact: Dr. John C. Kinnamon
  • References:
    • Kinnamon, J C, S J Young, and T J Sherman, "3DEd, Recon. and Show.," (Laboratory for High Voltage Electron Microscopy. University of Colorado, Boulder.: 1986).
    • Young, S. J., et al., "Three-dimensional reconstructions from serial micrographs using the IBM PC," Journal of Electron Microscopy Technique 6 (1987): 207-17.

IAP

Imaging Applications Platform is a commercial package for medical and scientific visualization. (Platforms: Most workstations; Cost: $$)

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.

  • Platforms: Most workstations?
  • Cost: in the $5K range.
  • Contact:
    ISG Technologies
    6509 Airport Road
    Mississauga, Ontario, Canada, L4V-1S7
    Phone: (416) 672-2100

IBM Data Explorer

IBM Data Explorer. (Platforms: IBM, SGI, Sun, HP, DG; Cost: unknown)

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

IDL

IDL (Interactive Data Language) is a package for the interactive reduction, analysis, and visualization of scientific data and images. (Platforms: IBM, SGI, Sun, HP, DEC, PC, Mac; Cost: $$)

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.

  • Platforms: DEC (VMS/Ultrix), HP, IBM, SGI, Sun, MS Windows, Mac.
  • Cost: $1500-$3750 (Educational and quantity discounts available)
  • Contact:
    Research Systems, Inc.
    2995 Wilderness Place
    Boulder, CO 80301
    Phone: 303-786-9900, Fax: 303-786-9909
    Email: info@rsinc.com
  • Usenet: comp.lang.idl-pvwave
  • Comments:
    • 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). I think it costs about $1500 for PC & MAC and about $2500 for Unix.

Image Pro

Image Pro from Media Cybernetics ($2,999). (Platforms: PC (Win3.1, NT, 95); Cost: $$$)

Image Pro from Media Cybernetics ($2,999).

  • Platforms: PC (Windows 3.1, 95, NT), Mac (avail 6/96).
  • WWW: http://www.mediacy.com
  • Email: sales@mediacy.com
  • Usenet: comp.lang.idl-pvwave
  • Phone: 301-495-3305
  • Fax: 301-495-5964
  • Contact:
    Media Cybernetics, L.P.
    8484 Georgia Avenue
    Silver Spring, MD 20910

ImageSpace

Software environment for confocal imaging. (Platforms: SGI; Cost: unknown)

Software environment for confocal imaging. Integrated acquisition, processing, and visualization for 3D datasets.

  • Platforms: SGI.
  • WWW: http://www.mdyn.com
  • Contact:
    Molecular Dynamics
    880 East Arques Avenue
    Sunnyvale, CA 94086

Image Volumes

Interactive image processing, contour editing, 3D reconstruction for confocal, EM, X-ray tomography, and MRI. (Platforms: SGI; Cost: unknown)

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

Overview

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

  • Image - An interactive image processor that operates on digitized gray scale images.
  • ContourEdit - A screen oriented 3D database editor.
  • Cubes - A polygon and voxel generator that processes your serial section data and stores a 3D geometry database of surface polygons and voxel densities.
  • Display - Displays your reconstruction with user defined surface materials properties, Phong shading and multiple light sources.
  • Metrics - A volumetric analysis program for measuring sizes and numbers of objects and their surface areas and volumes.
  • DField - Computes distance fields of 3D surface models and quantifies intersections between 3D surface models. Distance fields can also be used to interpolate iso-surfaces between two 3D models.

Image Processing

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

  • Radiometric operations - Gray level scaling, histogram normalization, histogram equalization, binary level slice, piecewise linear transformation, local adaptive histogram equalization (LAHE) and local adaptive histogram normalization (Wallis).
  • Algebraic operations - Add, subtract, multiply, divide, square root and logarithm of gray scale images.
  • Geometric operations - Image translation, rotation and scaling. A registration feature allows interactive alignment of pairs of images.
  • Filtering operations - Smoothing and median filtering. Kirsch, Laplace, Roberts, sharpening, sigma and Sobel edge detection operators. Special line detect filter for enhancing thin fibrous structures.
  • Morphological operators - Area fill, dilate, erode, boundary track and medial axis operators for delineating boundaries, identifying objects and creating overlay masks to be used for region-of-interest operations during radiometric and filtering operations.

Interactive Graphics Editing

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

Isosurface Extraction and 3D Rendering

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

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

  • Ambient, diffuse, specular, transparency and emissive properties by simply choosing a material from a supplied library of materials - or design your own materials.
  • Multiple, colored light sources.
  • Phong shading for seamless rendering of surfaces.
  • Smoothing of surfaces.
  • Interactive translation, rotation, scaling and spinning of 3D models.
  • Automated animation of rotation sequences with frame-by-frame screen capture to disk files.

Volumetric Analysis

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

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

Utility Functions

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

  • Platforms: SGI.
  • Price: $8000 (12/92)
  • Contact:
    Minnesota Datametrics Corporation
    1000 Ingerson Road
    St. Paul, MN 55126-8146
    Phone: 612-482-7938, Fax: 612-490-9717
  • Comments: Charles K. Knox [scivis@mndata.com]: Minnesota Datametrics now has its ImageVolumes scientific visualization software available in demo form at the Gopher site: gopher.mndata.com, port 2074

Imagist

Imagist2 from Princeton Gamma Tech- integrated microscope and analysis systems. (Platforms: Sun; Cost: unknown)

Imagist2 from Princeton Gamma Tech- integrated microscope and analysis systems.

  • Platforms: Sun.
  • Contact:
    Princeton Gamma Tech
    1200 State Road
    Princeton, NJ 08540

IMOD

Image modeling package used for EM tomography and serial section reconstruction. (Platforms: unknown; Cost: unknown)

IMOD Image modeling program package.

View 3-D Graphic Data

IMOD reads and displays 3-dimensional graphic data in the MRC file format. Tools are provided for translating raw images, RGB files, and simple TIFF files into the MRC format.

The main window of IMOD shows slices of a 3-dimensional graphic volume along the X,Y and Z axis in three linked views. Selecting a point in one view will automaticlly find the point in the two other views. Each of the three views can be movied forwards or backwords.

Additional views include: a view of the selected point in a tilt series, a view of a slice through the 3-D graphic data, a view of a small sub volume of the 3-D graphic data, projected in real time. Image intesity graphs can be opened for the x, y and z axis.

Modeling

Models can be created manually using the mouse or segmented by using thresholding. Models are structured into objects for easy editing. Model files can be transfered to NFF, Wimp or SYNU data formats.

Models can be viewed in real time wire frame rendering with hidden line removal. Models can also be viewed in cross-eyed or wall eyed stereo. Control of rotation, translation, magnification and transparentcey is interactive. Image data inside of the contours can be colored and rendered into a movie rotating about the x, y or z axis. Volume and surface area calculations can be calculated from the model.

Presentation

A seperate viewing program allows easy slide and movie making cababilities. Titles and multiple text fonts can be added to images.

Requirements

IMOD has been tested on a Personal Iris 4D/20 and an Indigo R4000. Most of the programs require 24 bit graphics. There should also be enough memory to load the entire contents of a 3-D graphics file for best performance.

Availability

IMOD excecutable is available free to anyone who wants it.

IMOD source will be available free with certain restrictions.

Credits

IMOD is Copyright (C) 1994 Boulder Laboratory for 3-Dimensional Fine Structure, University of Colorado. ("3DFS").

This work is supported by NIH biotechnology resources grant #RR00592, for the Boulder Laboratory for 3-Dimensional Fine Structure.

IRAF

IRAF (Image Reduction and Analysis Facility). (Platforms: unknown; Cost: unknown)

IRAF (Image Reduction and Analysis Facility). National Optical Astronomy Observatory (NOAO).

  • Contact: iraf@noao.edu.

KBVision

Software environment for creating image understanding applications. (Platforms: Sun, IBM, DEC, SGI; Cost: $$)

Software environment for creating image understanding applications- automatic detection, classification, and statistics 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

Very large, general image processing toolkit. (Platforms: Sun, SGI, IBM, DEC, HP; Cost: free)

KHOROS version 1.0 does not do 3D visualization, version 2.0, scheduled to be released 8/94 might have 3D Tools. The small contributed toolbox in KHOROS v 1.0 does very nice surface thresholding using image gradient technique and produced grayscale renderings of surfaces.

  • Platforms: Sun, SGI, DEC, HP, IBM, NeXT.
  • Contact: khoros-request@chama.eece.unm.edu.
  • Web http://www.khoros.unm.edu
  • FTP:
    • USA - ftp.eece.unm.edu - 129.24.24.119 - /pub/khoros
    • USA - ftp.uu.net - 192.48.96.9 - /pub/window-sys/khoros
    • CANADA - popeye.genie.uottawa.ca - 137.122.20.3 - /pub/khoros
    • GERMANY - ftp.rrz.Uni-Koeln.DE - 134.95.80.5 - /graph/khoros
    • GERMANY - ftp.lrz-muenchen.de - 129.187.10.35 - /local/khoros
    • ITALY - ipifidpt.difi.unipi.it - 131.114.8.130 - /pub/khoros
    • JAPAN - ftp.waseda.ac.jp - 133.9.1.32 - /pub/khoros
    • UK - ftp.mcc.ac.uk - 130.88.203.12 - /pub/cgu/khoros
    • UK - unix.hensa.ac.uk - 129.12.21.7 - /pub/uunet/window-sys/khoros
    • Pull back the file $KHOROS_FTP/release/install.ftp and read it first.
  • Usenet: comp.soft-sys.khoros
  • Comments:
    • Alex Milshteyn: The toolbox written by that guy from Italy works fine for me. Khoros is able to output data in .rs format, therefore Sunview would handle it just fine as well.
    • Steven Jorgensen: We are happy to announce that a Khoral Research Web Server is functioning, and has links to various bits of information about KRI and Khoros. See the below or our home page for more detail.
      • Information about the company
      • General information about Khoros, including:
        • FAQs, Documentation, and Bugs
        • Training Courses
        • Software Licencing
        • Free Access Distribution
        • Consortium
        • History
        • Mailing list and Newsgroup
        • Other sites' use of Khoros
      • Getting Khoros and Other Goodies
      • Bibliography of Papers related to Khoros
      • KRI Staff Home Pages.
    • URL: http://www.khoros.unm.edu Khoral Research, Inc (KRI) is a New Mexico company founded by the creators of Khoros, the buildable software. Khoros, distributed via a free access licence over the internet, is a flexible software environment ideally suited for scientific data exploration and software development. The KRI home page provides links to all Khoros resources on the internet, as well as other sites of general interest.

      Information available from the Khoral Research Home Page:

MacCubeView

Designed to display a texture map image of three-dimensional (3-D) data. (Platforms: Mac; Cost: shareware)

Designed to display a texture map image of three-dimensional (3-D) data. In this release, three simple ray-tracing techniques have been added. The data in mind is typically generated by medical imaging techniques such as CT, MRI, and nuclear medicine. Some geophysics techniques also produce suitable 3-D image data.

MacPhase

2D data analysis and visualization application for the Macintosh. (Platforms: Mac; Cost: unknown)

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 application

MacStereology

MacStereology is package designed to make measurements of images and to make 3-D reconstructions. (Platforms: Mac; Cost: unknown)

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 application

  • Platforms: Macintosh.
  • FTP: A demo version is available at zippy.nimh.nih.gov:/pub/nih-image/programs.
  • Comments
    • Stephen M Echteler: [...]MacStereology to do some 3D reconstructions of developing sensory neurons. The program is rather expensive ($750) and the Mac interface is a bit buggy. I'd really appreciate comments from anyone who: 1) has used this program or 2) could suggest an alternative application with similar features.
    • John Russ: Well, I've been a MacStereology user for several years now. We use it in our research (3D reconstructions from all kinds of imaging including TEM, confocal light, and x-ray microtomography), as well as in teaching courses to grad students, and like it a lot.

      There are only three basic approaches to 3D reconstruction: a) volumetric (transparency) imaging like VoxelView or VoxBlast, which shows all of the data, but can be VERY time consuming to fiddle with all of the transparency, lighting, etc., parameters to reveal the important aspects of structure (they really require you to already know what is there, and just use the program to show it to others); b) resectioning approaches like Spyglass Dicer, which allows you to examine arbitrary sections but cannot show the important topological characteristics present in the 3D volume; and c) surface rendering, as in MacStereology, which is very efficient (small files and fast displays), shows the topology and presents images that appear natural because we are all used to seeing surfaces, but accomplishes this by hiding other detail including internal structures behind the surfaces. The three approaches are complementary and we use them all, but if I had to choose, I would take Macstereology first, Spyglass Dicer a very close second, and Voxelview (or Voxblast) a distant third, based on the amount they are used, and the response of students and researchers to the images (how much they can learn from them, how difficult it is to interact with them, etc.).

      As to the two specific complaints: I don't agree that the interface is "buggy." It does have a few peculiarities that are not totally Mac-like, like fiddling with the display LUT and taking over the whole window, but you can turn that off if you like. Whenever I've found a bug (usually when Apple releases a system upgrade or new hardware), the author has fixed it pretty quickly, and he is also very good about giving advice via e-mail.

      And the complaint about the price is really sort of annoying. Photoshop costs nearly as much, but consider the number of copies they sell? What do you think Spyglass' set of programs cost? Or how about Voxelview which is considerably more expensive? How much did you spend for your computer+ camera+ interface+ microscope+ printer+... - well you get the idea. $750 for a program that has taken man-years to develop and has a very specialized market is hardly high-priced. You are just spoiled because Image is free (well, unless you count that we all pay taxes to support Wayne). In the PC world, you would spend $2K or more for a program equivalent to Image. Expensive? No, expensive is trying to do without a tool you need.

MCID

Image analysis and quantification mainly for fluorescence imaging. (Platforms: PC; Cost: unknown)

Image analysis and qunatification 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

MEDx

Medical image visualization and analysis program for MRI, CT, PET, and SPECT. (Platforms: SGI; Cost: unknown)

MEDx is a medical image visualization and analysis program capable of processing multidimensional data from various imaging modalities, including MRI, CT, PET, and SPET. Volume visualization tools allow viewing of fused functional and anatomical images. Compatibility with other present and future imaging modalities is provided with a DICOM 3.0 import facility. MEDx provides an industry-standard image processing development environment, including image processing tasks. Based on familiar hypertext concepts, the MEDx user interface is both powerful and easy-to-use.

  • Platform: SGI (IRIX 5.x and 6.x).
  • Cost: $6500 (academic discount)
  • Contact:
    Thomas Zeffiro
    Vice President Sensor Systems, Inc.
    103A Carpenter Drive
    Sterling, VA 20164-4423 USA
    Phone: 703-437-7651, Fax: 703-437-0039
    Email: zeffiro@sensor.com

MetaMorph

Integrated microscope image capture, enhancement, reconstruction, and visualization system. (Platforms: PC; Cost: unknown)

Integrated microscope image capture, enhancement, reconstruction, and visualization system.

  • Platform: PC (Win95).
  • Contact: Neal Glicksman
  • Company Website: http://www.image1.com
  • Company email: sales@image1.com
  • Phone: 610-344-9410
  • Fax: 610-344-9515

MicroMorph

MicroMorph is the software aid in learning the mathematical morphology techniques of image analysis. (Platforms: PC; Cost: Varies)

MicroMorph is the software aid in learning the mathematical morphology techniques of image analysis.

It was developed at the Center of Mathematical Morphology (CMM) of the Ecole des Mines de Paris. MicroMorph implements the latest algorithmic innovations. Through exercises of increasing difficulty, it provides the user with the know-how resulting from more than 20 years' experience of image processing in CMM.

Fast by implementation, as compared to other similar systems, MicroMorph not only serves as course support, but often can be the good solution for real-world problems.

  • Platforms: PC (Windows 3.1, Win95, NT)
  • Cost: Varies- see web site.
  • WWW: http://cmm.ensmp.fr/~gorokhov/mmorph.html
  • Phone: (33 1) 64 69 47 06
  • Fax: (33 1) 64 69 47 07
  • Email: beucher@cmm.ensmp.fr
  • Contact:
    35 rue Saint Honore
    F-77305 Fontainebleau, FRANCE

MicroVision II

MicroVision II can be used for for visualising point-sampled data volumes. produced by 3D scanning devices such as MRI, PET, CT-scanners and confocal microscopes. (Platforms: PC; Cost: unknown)

MicroMorph is the software aid in learning the mathematical morphology techniques of image analysis.

MicroVision II can be used for for visualising point-sampled data volumes. produced by 3D scanning devices such as MRI, PET, CT-scanners and confocal microscopes. Wherever you have a point sampled volume, MicroVision can be used. This includes Finite Element Analysis, CFD, Non destructive testing, Chemisty, Astrophysics, and many other areas. For more information, check out our web pages or e-mail: info@fairimag.co.uk We also deal in other products related to visualisation, image capture, and image analysis, for more information, look at our home page at: http://www.fairimag.co.uk/fairfield/

MicroVoxel

MicroVoxel is a 3D imaging package that imports data from BioRad MRC-600 files, TIFF files, or raw 8-bit data. (Platforms: PC; Cost: unknown)

  • Platforms: PC (OS/2 v2.1).
  • Contact:
    Indec Systems, Inc.
    820 Bay Avenue #212
    Capitola, CA 95010
    Phone: 408-479-8285
  • Comments:
    • 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

Montage is one of the first complete serial-section reconstruction packages and was produced at the University of Pennsylvania. (Platforms: Sun, SGI, IBM, PC; Cost: free)

Montage is 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.
  • WWW: http://retina.anatomy.upenn.edu/montage.html
  • FTP: retina.anatomy.upenn.edu:/pub/mont.linux.tgz.
  • Refs:
    • Journal of Neuroscience Methods v21, pp 55-69, 1987
  • Contact:
    Robert G. Smith
    Department of Neuroscience
    University of Pennsylvania,
    Philadelphia, PA 19104-6058
    email: rob@retina.anatomy.upenn.edu

Mvox

Mvox is a general purpose tool for visualization and manipulation of a wide range of 2-4D grey level/colour images and 3D surface graphics. (Platforms: SGI, HP, IBM; Cost: $$)

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

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

The wide range of data types that can be handled by Mvox makes it a very flexible tool and it is especially well suited for users with changing or widespread needs.

Keywords:

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

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

Mvox is only supported on Silicon Graphics platforms, but can run on HP and IBM RS/6000 as well. A free demo version and test images are available from the Mvox homepage: http://www.imm.dtu.dk/documents/users/mvox/

The demo version will only work with the test images. Licenses are available for approx. $550 (DKK 3000 excl. VAT).

  • Platforms: SGI, HP, IBM RS6000.
  • Cost: $550.
  • WWW: http://www.imm.dtu.dk/documents/users/mvox/
  • Contact:
    BNI Software
    c/o Morten Bro-Nielsen
    Institute of Mathematical Modelling, Building 321
    Technical University of Denmark, DK-2800 Lyngby, DENMARK
    email:mvox@imm.dtu.dk

NCSA Tool Suite (DataSlice, Viewit, Tiller)

3D Visualization tools from the NCSA. (Platforms: Sun, SGI, DEC, IBM, Cray, Mac; Cost: free)

Viewit is a memory hog which can do array manipulations on entire 3d datasets, some limited format conversions, and 3D volumetric projections. Tiller is an SGI viewer for viewit displays.

A viewit electronic newsletter is distributed on an irregular basis - email to viewit@ncsa.uiuc.edu to request a subscription. Clint Potter (the original author and pricipal contact) is at cpotter@ncsa.uiuc.edu.

  • Platforms: DEC, IBM, SGI, Sun, Cray, Mac.
  • Cost: Free.
  • Contact:
    National Center for Supercomputing Applications
    Computing Applications Building
    605 E. Springfield Ave.
    Champaign, IL 61820
    Email: viewit@ncsa.uiuc.edu.
  • FTP (ftp.ncsa.uiuc.edu)/WWW:
  • Comments:
    • 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.
    • 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.

Neuro_Echo, Neuro_SPGR, Neuro_Lobe

Neuro_Echo aids analysis of double-echo MR brain scans from the GE Signa imager. The program uses axial scans to segment the brain scans into gray matter, white matter and CSF. (Platforms: Sun; Cost: unknown)

Neuro_Echo
Neuro_Echo aids analysis of double-echo MR brain scans from the GE Signa imager. The program uses axial scans to segment the brain scans into gray matter, white matter and CSF. (Platforms: Sun Sparcstation 10 or 20) Neuro_Echo aids analysis of double-echo MR brain scans from the GE Signa imager. The program uses axial scans to segment the brain scans into gray matter, white matter and CSF. The product offers a number of advantages:

  • Downloads images from network or tape.
  • Provides two types of standardization for the image format by reslicing the image stack either
    • parallel to the modified canthomeatal plane (defined with the help of the lenses of the eye and the internal auditory canals) or
    • parallel to the bicommissural plane, which contains the anterior and posterior commissures and is perpendicular to the interhemispheric fissure.
  • Finds the intracranial contours automatically.
  • Segments the brain automatically into gray/white matter and CSF.
  • Provides output that is downloadable for further statistical analysis.
  • Facilitates manual tracing of selected features.

Neuro_SPGR
Neuro_SPGR can analyze thin-slice (1.5mm) SPGR images of the brain. The program provides the same features as Neuro_Echo, but it does reslicing only in the bicommissural mode.

Neuro_Lobe
Neuro_Lobe separates an SPGR image stack into the hemispheres; the frontal, parietal,temporal and occipital lobes; the cerebellum; and the area containing the basal ganglia. Demarcation of the brain into lobes follows our computerization of a protocol developed by the BU Neuroanatomy group. This package is expected to be available for dissemination in the second half of 1996.

Neurolucida

Interactive image analysis software for neuron tracing and anatomical mapping. (Platforms: PC; Cost: unknown)

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: 802-655-5245

NIH Image

NIH Image has painting and image manipulation tools, a macro language, tools for measuring areas, distances and angles, and for counting things. (Platforms: Mac; Cost: free)

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

  • Platforms: Macintosh.
  • Cost: free.
  • Ftp: zippy.nimh.nih.gov/pub/nih-image
  • Email list: nih-image@soils.umn.edu (email 'listserv@solis.umn.edu' with subject "subscribe nih-image" to subscribe)

Nuages

This is Bernhard Geiger's (INRIA) reconstruction package. (Platforms: Sun, SGI, DEC; Cost: free)

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

  • Platforms: Sun, SGI, DEC.
  • WWW: http://www.inria.fr/prisme/personnel/geiger/nuages.html
  • FTP: Nuages 4.0 betelgeuse.inria.fr (138.96.16.91) /pub/Nuages
    • NUAGES_SUN4.tar.Z sun sparc 2 (sun4OS4)
    • NUAGES_SGI.tar.Z sgi (iris4d)
    • NUAGES_DEC.tar.Z decstation (ultrix)
  • 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.
  • Comments:
    • Matthew T. Adams : I wanted to let you know about a little utility I just wrote and posted as ftp.uwa.edu.au:/pub/povray/utilities/vera2pov-1.1.tar.gz. 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. (Platforms: Sun, DEC; Cost: unknown)

On-Line Pattern Analysis and Recognition System from the PAR Government Systems Corporation. Statistical pattern recognition system that can be applied to analyzing information derived from reconstructions.

  • Platforms: Sun (Unix), DEC (VAX/VMS).
  • Contact:
    Amber Technologies
    47 Junction Square Drive, Concord, MA 01742
    Phone: 508-369-0515, Fax: 508-371-9642

Pixar

High-end visualization and rendering for movies, but also for the medical community. (Platforms: SGI; Cost: $$$)

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

Pixcell from Sandia Labs. (Platforms: Sun; Cost: free)

Pixcell ($1,500) from Sandia Labs.

PV-Wave

PV-WAVE from Visual Numerics. (Platforms: unknown; Cost: unknown)

PV-WAVE from Visual Numerics. It is commonly used for creating 3D renderings of voxel based data, and stacks of MRI images as you describe could be displayed with PV-WAVE, using the Z-Buffer, Ray tracer, or iso-surface renderer.

  • Contact:
    Visual Numerics, Inc.
    6230 Lookout Rd., Boulder, CO 80301
    Phone: 303-530-9000, Fax: 303-530-9329

RMN

A Nuclear Magnetic Resonance (NMR) data processing program for the Macintosh. (Platforms: Mac; Cost: unknown)

A Nuclear Magnetic Resonance (NMR) data processing program for the Macintosh.

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. RMN runs on PowerPC Macs (no longer on 68k versions). 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 some bugs can be fixed. The same is true for Simulate under the Acquire menu.

  • Platforms: Macintosh PPC.
  • Cost: Free.
  • Web Page
  • Contact: Philip Grandinetti

Reconstruction Of Serial Sections (ROSS)

Serial-section based reconstruction and visualization system for microscopy. (Platforms: SGI; Cost: free)

Serial-section based reconstruction and visualization system for microscopy. Interactive and automated mosaicking, contour extraction, and registration with advanced visualization capabilities. More details on the functionality and release restrictions is available.

  • Platforms: SGI.
  • Cost: free.
  • Availability: Released 3/15/95.
  • WWW server: http://biocomp.arc.nasa.gov
  • References:
    • Montgomery, K, and M D Ross, "A method for semiautomated serial section reconstruction and visualization of neural tissue from TEM images," (San Jose, CA: SPIE, 1993), 69.
    • Montgomery, K, and M D Ross, "Improvements in semiautomated serial section reconstruction and visualization of neural tissue from TEM images," (San Jose, CA: SPIE, 1994),
    • Ross, M D, et al., "High Performance Computing Applications in Neurobiological Research," (San Diego, CA: Society for Computer Simulation, 1994), 120-125.
  • Contact:
    Biocomputation Center, MS239-11
    NASA Ames Research Center
    Moffett Field, CA 94035-1000

SciAn

Florida State University scientific visualization package. (Platforms: SGI, IBM; Cost: free)

Semper6

General image Processing and acquisition system. (Platforms: PC, DEC, Sun; Cost: unknown)

General image Processing and acquisition system.

  • Platforms: PC, DEC (VAX), Sun.
  • Cost: Free.
  • Contact:
    Synoptics Ltd
    Paragon Towers
    233 Needham St, Newton, MA 02164
    Phone: 617-527-4461, Fax: 617-527-4084

SGI Explorer

SGI Iris Explorer. (Platforms: SGI, Cray, DEC, HP, IBM, Sun; Cost: unknown)

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.

  • Platforms: SGI Iris, Cray, DEC, IBM, HP, SPARC.
  • Usenet: comp.sys.sgi, comp.graphics.explorer
  • Ftp: ftp.epcc.ed.ac.uk or swedishchef.lerc.nasa.gov.
  • Contact: infodesk@nag.com or helpdesk@iec.co.uk.
  • WWW: http://nags2.nag.co.uk/Welcome_IEC.html

Sunview

Sunview - available from SunSoft. (Platforms: Sun; Cost: unknown)

Sunview - available from Sun.

  • Platforms: Sun.
  • WWW Server: http://www.sun.com
  • Contact:
    Sun Microsystems
    2550 Garcia Avenue
    Mountain View, CA 94043
    Phone: 415-960-1300

SunVision

Sun Visualization software, providing SunIPLib (Image Processing), SunVoxel (volume rendering), SunART (high-quality rendering), SunGV (interactive 3D graphics). (Platforms: Sun; Cost: unknown)

Sun Visualization software, providing SunIPLib (Image Processing), SunVoxel (volume rendering), SunART (high-quality rendering), SunGV (interactive 3D graphics).

  • Platforms: Sun (SunOS under X).
  • WWW Server: http://www.sun.com
  • Availability: Released 3/15/95.
  • Contact:
    Sun Microsystems
    2550 Garcia Avenue
    Mountain View, CA 94043
    Phone: 415-960-1300
  • Comments:
    • 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.
      • easily customizable (interactive GUI editor)
      • volume renderings (SunVoxel) you can hook in your own C code to the GUIs
      • 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

UCSD reconstruction/visualization program. (Platforms: SGI; Cost: free)

Non-interactive components run on some Unix-based systems.

  • Platforms: SGI.
  • Contact: spl@dim.ucsd.edu.
  • Comments:
    • 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 San Diego, under the direction of Mark Ellisman. It runs on a Silicon Graphics machine, and produces gorgeous images of serial sections, with variable transparency, stereo pairs, etc. I think it may be available for just the cost of the media. An example of the product is shown on the front cover of the November issue of J. Neurosciences by Martone. The current problem with it (when I last spoke with the Ellisman group about this) was that it takes a bit of doing to import files into it from Image or Canvas or other programs, and it does need a Silicon Graphics to run the program.

The Explorer

Macintosh-based package from UCLA. (Platforms: Mac; Cost: free)

from UCLA.

  • Platforms: Macintosh.

TIM

Tomographic Imaging- PC Software for 3D image processing of pixel planes. (Platforms: PC; Cost: unknown)

TIM, Tomographic Imaging Version 2.0 - PC Software for 3D image processing of pixel planes. It is a software package for three-dimensional image processing of volume data. The main area of application is the work with tomographical data of MRI and CT scanners, but the software can handle all data witch is strucured in pixel planes. TIM runs on ordinary PC (>=3D486).

Theraview

No information available. (Platforms: unknown; Cost: unknown)

V

Public-domain software package for magnetic resonance imaging and spectroscopy data. (Platforms: Unix; Cost: free)

The Beckman Institute for Advanced Science and Technology has recently made available a public-domain software package for multidimensional signal processing, especially for magnetic resonance imaging and spectroscopy data. This software has routines for transformation, geometric manipulation, constrained reconstruction, parameter estimation, and baseline correction, among others.

Vida

Commercial volumetric display and analysis tool for Unix. (Platforms: Sun, HP, SGI; Cost: $$$)

VIDA: (Registered Trademark of and Copyrighted to VIDA Technologies L.L.C) Since the first dynamic volumetric studies were done in the early 1980's on the Dynamic Spatial Reconstructor (DSR), there has been a surge of interest in volumetric and dynamic imaging using a number of tomographic techniques. Knowledge gained in handling DSR image data has readily transferred to the current use of a number of other volumetric and dynamic imaging modalities including cine and spiral CT, MR, and PET. This in turn has lead to our development of an image display and quantitation package which we have named VIDATM (Volumetric Image Display and Analysis). 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. A shared memory structure has been designed which allows for the manipulation of multiple volumes simultaneously. VIDA utilizes a windowing environment and allows execution of multiple processes simultaneously. Available programs include: oblique sectioning, volume rendering, surface display with movie scripting, region of interest analysis, interactive image segmentation/editing, algebraic image manipulation, conventional cardiac mechanics analysis, homogeneous strain analysis, tissue blood flow evaluation, etc. VIDA is built modularly, allowing new programs to be developed and integrated easily. An emphasis has been placed upon image quantitation for the purpose of physiological evaluation.

  • Refs:
    • Hoffman, E.A., D. Gnanaprakasam, K.B. Gupta, J.D. Hoford, S.D. Kugelmass, and R.S. Kulawiec: VIDA: An environment for multidimensional image display and analysis. SPIE Proceedings, 1660: 694-711, 1992
  • WWW: http://everest.radiology.uiowa.edu/DPI/nlm/vida/vidahome.html
  • Platforms: Sparc (SunOS 4.1.2, Solaris), HP/Apollo, SGI (coming soon).
  • Cost: $5000
  • Contact:
    Eric Hoffman, Ph.D.
    VIDA Technologies L.L.C.
    3128 Rapid Creek Wood, N.E., Iowa City, IA 52240
    E-mail: eric@everest.radiology.uiowa.edu

View

SGI-based program from UNC. (Platforms: SGI; Cost: unknown)

  • Platforms: SGI (4D, Indigo, Crimson).
  • Ftp: ftp.cs.unc.edu /pub/VIEW.
  • Contact: bergman@cs.unc.edu or ward@cs.unc.edu.

Vis5D

Visualization program for time-varying multi-variate 3-D gridded data. (Platforms: SGI, IBM, Sun, HP, DEC; Cost: unknown)

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

  • Platforms: SGI, IBM, Sun, HP, DEC.
  • Ftp: iris.ssec.wisc.edu:/pub/vis5d.
  • Contact: whibbard@macc.wisc.edu or bpaul@macc.wisc.edu.

VisAD

Visualization program for interactively steering and visualizing scientific computation. (Platforms: SGI; Cost: unknown)

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

  • Platforms: SGI.
  • Ftp: iris.ssec.wisc.edu:/pub/visad.
  • Contact: whibbard@macc.wisc.edu or bpaul@macc.wisc.edu.

VolPack

VolPack is a portable software library for volume rendering. (Platforms: SGI, Sun, HP, DEC; Cost: unknown)

VolPack is a portable software library for volume rendering. It is based on a new family of fast volume rendering algorithms (see Philippe Lacroute and Marc Levoy, Fast Volume Rendering Using a Shear-Warp Factorization of the Viewing Transformation, Proc. SIGGRAPH '94, pp. 451-458).

    Here is a brief list of features:
  • Renders data sampled on a regular, three-dimensional grid.
  • Supports user-specified transfer functions for both opacity and color.
  • Provides a shading model with directional light sources, multiple material types with different reflective properties, and depth cueing.
  • Produces color (24 bits/pixel) or grayscale (8 bits/pixel) renderings.
  • Supports arbitrary affine view transformations.
  • Supports a flexible data format that allows an arbitrary C structure to be associated with each grid point.
  • Achieves very fast rendering times without specialized hardware.

To give an idea of the performance of the library, a 256 by 256 by 256 voxel volume can be rendered in roughly one second on an SGI Indigo R4000, running entirely in software.

The VolPack distribution includes source code, a tutorial user's manual, man pages for all library routines, and some sample programs with one sample dataset. A simple Tcl/Tk application based on VolPack is also available.

  • Platforms: any UNIX workstation (tested on SGI, DEC Ultrix, Sun, HP)
  • Contact: volpack@graphics.stanford.edu
  • WWW Server: http://www-graphics.stanford.edu/software/volpack
  • FTP: graphics.stanford.edu /pub/volpack

VolVis

Volume Visualization package from SUNY. (Platforms: SGI, Sun, HP; Cost: unknown)

  • Platforms: SGI, HP (Starbase), Sun SPARC (X11R5).
  • FTP: sbcs.sunysb.edu:/pub/volvis.
  • Contact: volvis@cs.sunysb.edu.
  • Comments:
    • Dave Wyble: While I'm sure VolVis is a very impressive package, it does not appear to run on Sun OpenWindows (I know, is this a bug or a feature). I understand the Sun/OW3 may not be the preferred tool for many of you imaging folks out there, but does anyone know of a decent 3d visualization package that I can use?

Vox-L

MR and CT visualizer. (Platforms: unknown; Cost: unknown)

There is an extensive archive at ftp.near.net /member/dataspace. The demo subdirectory has several demo disks of the Vox-L Visualizer which can run under Windows NT (for Intel, Mips and Alpha) as well as Windows 3.1. The Vox-L Visualizer demo can only operate on an included 128^3 file, but the actual application is quite comfortable with 256x256x128 sized volume data of MR and CT scans (see GIF format images in the images subdirectory). The software is also available with drivers for Stereographics' CrystalEyes. For a complete visualization environment, check out the Vox-L Workstation line which can provide a 150mhz Alpha AXP workstation tuned for volume rendering which start under $19,000.

  • Platforms: PC (MS Windows NT, MS Windows 3.1), Unix/Motif.
  • Contact: info@dataspace.com.

More Information from the PPG:
PARALLEL PERFORMANCE GROUP
IMAGING/MEDICAL IMAGING NEWSLETTER

Volume 1, Number 2 | July, 1994

THIS ISSUE's TOPIC:

The Vox-L Stereoscopic Workstation: Stereoscopic lnteractive Volume Visualization for Medical Data

The combination of an intuitive graphical interface, interactive stereoscopic rendering, and powerful volume manipulation algorithms proyides an environment for efficient interpretation of data generated by modern medical imaging hardware (confocal microscopes, MRl, PET and CAT-scanners). This increased in- terpretive power has the potential to streamline diagnosis and patient care, creating significant opportunities for enhanced data utilization and reduced cost.

A majority of volume data is currently viewed as a series of static cross- sections which have been output to film. While this provides a direct representation of the data, the slices are fixed in their orientation, significantly restricting the doctor's view of the complete volume.

An improved environment for visualizing three-dimensional medical image data must include preserving the accuracy of the original data, while providing information to the user in a more efficient manner, and insuring that the new environment would be easily accessible by doctors and radiologists. Interactive slicing, for example, would be a significant improvement over a series of static slices, as it establishes a feedback loop between the user and the data.

The usefulness of any new modality for viewing volume data may be limited by the accessibility of the new technology. If there is only one machine in a hospital which can generate the new images, while static films remain significantly more accessible, then a majority of users will tend to make active use only of representations to which they feel they have the best access.

In defining an improved system for visualizing volume data, Vox-L sought to develop a solution which would not only provide a new angle on the data, but one which would be easily accessible to the user. The Vox-L system has been developed to address these considerations. It provides a highly graphical user interface which can be used directly by a physician without the assistance of a computer technician. Because the software components were developed to work with open systems, Vox-L was able to realize a reduction in the overall cost of its solution compared with related, dedicated technologies. This makes it possible for a hospital to provide a greater number of stations where the information can be reviewed using the new environment.

THREE-DIMENSIONAL RECONSTRUCTIONS

A useful, intuitive representation of volume data is provided by a three-dimensional reconstruction. The most commonly used representation is based on a polygonal abstraction of the volume data. These iso-surface representations are generated either by hand, a time consuming process, or by a surface extraction algorithm such as Marching Cubes. Either approach may fail to accurately reflect the underlying data. A significant loss of information will always result from any attempt to convert discrete, three- dimensional raster data into a vector representation.

A ray-traced volume rendering creates images which accurately reflect the value of the model at each voxel (VOlume piXEL). Despite the obvious advantages of working directly with the voxel data, this approach has often been overlooked due to the computational expense of generating an image from a voxel dataset, which may range from sixteen to sixty-four megabytes in size, as as compared with the expense of working with polygonal datasets, which are often no more than a megabyte or two in size. Recent advances in the speed of general purpose computers combined with developments in the field of discrete ray-tracing algorithms have enabled Vox-L to maintain interactive ray-tracing rates even when working with full voxel datasets on desktop workstations.

STEREOSCOPIC VIEWING

Stereoscopic viewing of a volume provides a more complete representation of the data by taking advantage of the visual system's ability to discern depth information from binocular disparities. Even the best rendering algorithms may create images which, when displayed two-dimensionally, may be ambiguous to the user.

By providing a stereoscopic view of the data, ambiguities are reduced and the amount of information conveyed simultaneously to the user is increased. This effect is most prominent when the three-dimensional reconstruction is translucent in nature, making visible structures within structures. The spatial relationships of these structures is then emphasized through stereopsis. The finer the detail of the model, the greater the gain realized when going to a full stereoscopic representation. While a polygonal model can be made translucent, there are often no more than a handful of surfaces within the model. In tracing a single ray through a voxel model, several hundred surfaces may be traversed, one for each voxel along the ray. All of the fine detail encountered during the ray-tracing process is then rapidly conveyed to the user by making full use of the human visual system.

THE VOX-L STEREOSCOPlC WORKSTATlON

The environment integrates a complete range of volume viewing capabilities, including interactive orthogonal and oblique slicing, surface rendering with variable thresholding, and true, stereoscopic ray traced volume rendering. When used in conjunction with traditional methods of viewing volume data, these new tools allow a user to comprehend and explore a volume data set in new ways, adding valuable insight to clinical diagnosis and medical research.

The Vox-L system integrates stereoscopic viewing hardware and a high-speed, general-purpose workstation. StereoGraphics' CrystalEyes were chosen over other means of stereo viewing as they combine better resolution and convenience when compared with mirror based or head- mounted units. The workstation is build around Digital Equipment's Alpha AXP chip, which provides the level of compute power necessary for rapid interactive volume visualization at a competitive price/performance ratio. Although the Vox-L discrete ray-tracing software used is portable to a variety of operating systems, Windows NT was used due to its ease of use and the availability of a wide range of complementary products that can make use of the same platform. This solution is extremely cost effective. The Vox-L approach can provide at least three complete viewing stations for a one thousand dollar investment that would purchase only one viewing station with a dedicated graphics hardware approach.

Stuart Bar-On or Tom Beshaw of Parallel Performance Group, at (602) 282-6300, or E-mail at ppg@ppgsoft.com, will be glad to answer any questions and provide information about Medical Imaging and Vox-L hardware and software. To get a free e-mail Newsletter subscription, send "Subscribe Imaging Newsletter" message to subscribe@ppgsoft.com.

Voxblast

Voxel-based 3d volume rendering system developed by Randall Frank at the University of Iowa Image Analysis Facility. (Platforms: SGI, Sun, DEC, HP, IBM, Mac, PC; Cost: unknown)

Voxel-based 3d volume rendering system developed by Randall Frank at the University of Iowa Image Analysis Facility.

    Some of its advantages include:
  • Multiple platform support
  • Software based renderer - the faster the cpu the faster the renderer
  • Motif/X-windows GUI
  • Command line interface - macro definition possible
  • Unix Version allows external modules to be added via TCP/IP links
  • True 3D analysis tools built into software
  • Several segmentation algorithms built into software
  • Displays polygonal data in addition to Voxel data
  • Powerful built-in Palette editor for color and opacity definition
  • Contains Brainvox tracing for correlating 3D views with cross sectional views
  • Several support tools exist for Unix and Windows versions, including volumetric math calculations and image analysis.
  • Platforms: Unix (SGI, Sun, DEC, HP, IBM RS6000), Macintosh, PC (Windows).
  • FTP: Demo available- contact for username/password.
  • Contact:
    Vaytek Inc.
    305 West Lowe
    PO Box 732, Fairfield, Iowa 52556
    Phone: 515-472-2227, Fax: 515-472-8131
  • Comments:
    • Alex Colburn: PC options may be slower than other hardware options, but our version of Voxblast running under Windows, will render at about 800,000 voxels per second on a 486 DX2, w/ 16M RAM. Granted it takes about 3 seconds to render the standard hogheart volume (202x132x144) and larger volumes take longer...

VoxelBox

3D Volume renderer for Windows. (Platforms: PC; Cost: $)

3D Volume renderer for Windows. Features include direct ray-traced volume rendering, color and alpha mapping, gradient lighting, animation, reflections and shadows.

  • Platforms: PC (MS Windows).
  • Cost: $495.
  • Contact:
    Jaguar Software Inc.
    573 Main St. Suite 9B
    Winchester, MA 01890
    Phone: (617) 729-3659, Email: jwp@world.std.com

VoxelMan 3D

Interactive atlas of skull and brain. (Platforms: unknown; Cost: unknown)

Interactive atlas of skull and brain.

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

VoxelView

VoxelView software from Vital images for 3D reconstruction of images. (Platforms: SGI, Mac; Cost: unknown)

VoxelView software of Vital images for 3D reconstruction of images.

  • Platforms: SGI, Mac.
  • WWW: http://www.vitalimages.com/vv.html
  • Refs:
    • Voxels: Data in 3D", Byte, May 1992 issue, pp177-182.
  • Contact:
    Vital Images
    Fairfield, Iowa
    Phone: 515-472-7726, Email: bvz@vitalimages.com
  • Comments:
    • Mustafa Khokha: Vital Images writes its software so that it goes to the graphics hardware in the machine to do its voxel renderings. On machines like the SGI, this is great since SGI machines have fast graphics engines for just this sort of thing. The renderings are fast. I mean really fast. I was really amazed the first time that I saw it. This is a key part of both of these programs. If you have to wait many minutes for a rendering to occur, then a lot of the manipulations like opacity, lighting, and such become a lot (I mean a LOT) less useful. You learn so much more by being able to change these parameters on the fly. If you have to wait, forget it. I just don't have the patience to play with it, and I think you really lose a lot of "feeling" for what is going on in your datset. Therefore make sure that you get to try out a datset that is representative of the ones that you would be doing in terms of size and complexity. Then see if you can manipulate the settings (like lower the rendering quality) so that it renders before your eyes. Then when you see something interesting, up the quality and see if it really pans out. I know VoxBlast allows you to do this but I am not sure about VoxelView. This is because VoxBlast goes through the operating system when it makes its calls so they can "cheat" and render every other voxel or so. VoxelView doesn't because of its dependence on the hardware. On the other hand perhaps this is only true for the Unix versions? Anyway something to be aware of.

      Also one problem that we have with VoxelView is that you cannot have fractional spacing in the Z direction. In other words interpolations are purely whole numbers in the Z direction. This is a real drag since most of my datasets do not have aspect ratios that are whole number multiples in the z compared with x and y. Things may not look right then. Again this is because VoxelView depends on the graphics architecture and VoxBlast does not.

      Personally, for the short time that I tried VoxBlast, I thought it was quite nice. Everything is menu driven although you can if you want write your own scripts. Ease of use is not a problem. I would still compare with the Mac version that Vital Images makes though so be sure to get your hands on the demos.

    • Michael Cammer: VoxelView does do up to 16 bit renderings where bits can be grouped. We have tried the new color merging function for double immunofluorescence which allows for each dataset to be full eight bits.
    • Dietmar Reiter: I've got some minor experience on VoxelView Ultra on SGI, as well as on the Macintosh Version of VoxelView (which I know better, since our lab has got one). Three basic points are remarkable:
      1. Speed (and therefore interactivity) is minimal on the Macintosh release. It should be somewhat of an indication, what volume rendering SHOULD be on a graphics computer as the SGI. Speed lacks tremendously, what makes interacitve working with datasets (volumes) larger than 1 million voxels (a cube of 100x100x100 voxels) nearly impossible. It can be helpful to threshold out most of the voxels, in other words to keep the rendering task as minor as possible.
      2. Nearly no parameters of the VoxelView Mac can be given by numbers, but by fancy scroll bars. This inhibits for example an exact setting of the opacity for discrete voxel values. A manually cursor-drawn curve is the approximation.
      3. According to sources at Vital Images, the Macintosh version will not be developed further, what is understandable, because of hardware limitations of the 680x0 and the Mac PC system as a whole. This may probably change with the upcoming of the PowerPC. William VanZandt at Vital Images will give give more information.
    • Greg Gillen: It appears that NIH Image will open Voxel View PICS animation files and run them at a much faster rate than Voxel View. The only problem seems to be the LUT is messed up.
    • John Russ: [how you might be annotating your animations and if anyone has transferered animations to video for presentation at meetings] Yes - I use the mac version, which is a bit slow but OK on a Quadra. I save the animations as PICS files which I then convert to MooV format using ConvertToMovie. This lets me play them as Quicktime movies. I play them directly from a powerbook using an LCD overhead panel, not through videotape.

Voxtool

Voxtool from General Electric. (Platforms: PC, Unix; Cost: unknown)

Voxtool from General Electric.

  • Platforms: Sun (Advantage Windows).
  • Comments:
    • Matti Haveri : We use Voxtool 1.0.4 in a Sparcstation (64MB of RAM) connected via Ethernet to General Electric's High Speed Advantage and GE Sytec CAT-scanners. Segmentation is done through lower and higher HU-thresholds. Shaded surface display, MIP, RaySum, Integral and Multiplanar reformatting (MPR) as well as movie loop (if memory permits full 360 degree rotation with 6 degree intervals is sometimes possible). Select/remove object, filter floaters (user-definable size), scalpel (user-definable cut depth), erosion, dilation, open bridges and close gaps-functions. Intersection, union, difference and delta-functions between manipulated models. Seems to be quite stable - I've crashed it only a few times. Restarting the program or rebooting clears occasional memory-problems. Can save only two models at a time and the program sometimes loses link to the original slices which is _very_ annoying. 3D-images can be saved as individual still-images to disk in GE's image-format (hope we will be able to open and view this format in the other platforms as well). In the current version area-measurements require at least two contiguos slices which is also annoying. If the 3D-model has to use more than 60 512x512 image's space as virtual memory the program is too slow to use interactively.

VROOM

VROOM (Vol. Rendering by Object Oriented Meth.). C++ Library. (Platforms: unknown; Cost: unknown)

VROOM (Vol. Rendering by Object Oriented Meth.). C++ Library (PC?).

  • Contact: karel@cv.ruu.nl.

Wavefront

Wavefront Data Visualizer. (Platforms: SGI, Sun, IBM, HP, DEC; Cost: unknown)

Wavefront Data Visualizer.

  • Platforms: SGI, SUN, IBM, HP, DEC.
  • Contact: mike@wti.com.

WHIP

General purpose image processing software from GW Hannaway & Associates. (Platforms: SGI; Cost: unknown)

General purpose image processing software from GW Hannaway & Associates. Also has automated stage control and acquisition capabilities.

  • Platforms: SGI.
  • Contact:
    GW Hannaway & Associates
    839 Pearl Street, Boulder, CO 80302
    Phone: 303-440-9631, Fax: 303-440-4421

XCOSM

X-Windows interface to Computational Optical Sectioning Microscopy. (Platforms: SGI, DEC, Sun; Cost: Free)

X-Windows interface to Computational Optical Sectioning Microscopy.

xcosm is an X-Windows interface to two Computational Optical Sectioning Microscopy (COSM) algorithms for removing out-of-focus light in 3-D volumes collected plane by plane. The interface allows users to view and process multiple 3-D datasets within a simple mouse-driven environment.

It was created at the Biomedical Computer Laboratory (BCL), a component of the Institute for Biomedical Computing (IBC) at Washington University in St. Louis, MO.

Zmode

Software/hardware that can convert a series of parallel MRI/CT scan images to a 3D reconstructive model in a CAD system. (Platforms: unknown; Cost: unknown)

Software/hardware that can convert a series of parallel MRI/CT scan images to a 3D reconstructive model in a CAD system.

  • Contact: zmode@callamer.com
  • Comments:
    • John Noel: Zmode has developed the ability to manufacture models representing patient anatomy. The models are produced using medical imaging software and rapid prototyping technology. Zmode provides this modeling as a service and can also provide custom software solutions such as translation into CAD entities.