Date: Thu, 15 Dec 1994 14:45:29 GMT ====== Public domain data sets ----------------------- aerial stereo image pair are available by anonymous ftp: ftp.tu-graz.ac.at pub/images/ References ========== Other useful newsgroups ----------------------- comp.sys.sun comp.graphics.avs comp.sys.sgi comp.infosystems.gis comp.graphics sci.image.processing Books ----- Convert to refer: E. Tufte, The Visual Display of Quantitative Information Cleveland, William: "The Elements of Graphing Data" Wadsworth Advanced Books and Software. Tukey, John: "Exploratory Data Analysis" Addision Weseley, pub. "Graphics and Graphic Information Processing" - Translated by William J. Berg and Paul Scott, Walter De Gruyter, Publisher. %A Edward Huff %T How to Lie with Statistics %A Mark Monmonier %T How to Lie with Maps %I Univ. of Chicago Press %C Chicago %D 1991 %X Ch. 2 Elements of the Map Ch. 3 Map Generalizations: Little White Lies and Lots of Them Ch. 4 Blunders that Mislead Ch. 5 Maps that Advertise Ch. 6 Development Maps (or, How to Seduce the Town Board) Ch. 7 Maps for Political Propaganda Ch. 8 Maps, Defense, and Disinformation: Fool Thine Enemy Ch. 9 Data Maps: Making Nonsense of the Census Ch. 10: Color: Attraction and Distraction %A Thomas D. Davies %Z R. Adm. USN, (ret.) %T New Evidence Places Peary at the Pole %J National Geographic %V 117 %N 1 %D January 1990 %P 44-61 %K photogrammetry, surveying, angles, protractor, trigonometry %X Full report: $15 to Navigation Foundation, Box 1126, Rockville, MD 20850. See also the page before the index of this issue entitled, "Sun angle anyone?" Jacques Bertin's "The Semiology of Graphics" ? - it's what Tufte should have been (although it predates both books). @book{Earnshaw:92, editor = {Earnshaw, R.A. and Wiseman, N.}, title = {An Introductory Guide to Scientific Visualization}, publisher = {Springer-Verlag}, year = 1992, month = {September}, note = {ISBN 3-540-54664-2, ISBN 0-387-54664-2} note = {Out of print and may never reprint. --steve} } @book{Brodlie:92, editor = {Brodlie, K.W. and Carpenter, L.A. and Earnshaw, R.A. and Gallop, J.R. and Hubbold, R.J. and Mumford, A.M. and Osland, C.D. and Quarendon, P.}, title = {Scientific Visualization --- Techniques and Applications}, publisher = {Springer-Verlag}, year = 1992, month = {January}, note = {ISBN 3-540-54565-4, ISBN 0-387-54565-4} } Better than average papers @INPROCEEDINGS{Insel90a, AUTHOR = "Alfred Inselberg and Bernard Dimsdale", TITLE = "Parallel Coordinates: A Tool for Visualizing Multi-dimensional Geometry", BOOKTITLE = "Proceedings of the First IEEE Conference on Visualization, San Francisco, 23-26 October 1990", EDITOR = "Arie Kaufman", PUBLISHER = "IEEE Computer Society Press", PAGES = "361-377", YEAR = 1990} Papers not checked for quality but suggested -------------------------------------------- @ARTICLE{Dick91a, AUTHOR = "Robert R. Dickinson", Title = "Interactive Analysis of the Topology of 4d Vector Fields", JOURNAL = "IBM Journal of Research and Development", MONTH = Jan, VOLUME = 35, NUMBER = 1, PAGES = "59-66", YEAR = 1991 ANNOTE = "tracing curves through the direction fields of the major and minor eigenvectors of 2nd order tensor fields. His application was also stress and strain, and the method appeared quite effective." } @INPROCEEDINGS{Delm92, AUTHOR = "Thierry Delmarcelle and Lambertus Hesselink", TITLE = "Visualization of Second Order Tensor Fields and Matrix Data", BOOKTITLE = "Visualization'92", ORGANIZATION = "IEEE Computer Society", YEAR = 1992, MONTH = Oct, PAGES = "316--323" } Nicolas Capaldi, "The art of deception", Prometheus Books, 1987 Journals -------- IEEE Computer Graphics & Applications ACM Transactions on Graphics The Journal of Visualization and Computer Animation published by John Wiley & Sons Ltd, ISSN 1049-8907 Scientific Programming: A Wiley-Interscience Publication Subscription: In the US: Scientific Programming: A Wiley-Interscience Publication John Wiley and Sons Periodicals Division P.O. Box 7247-8491 Philadelphia, PA 19170-8491 Outside the US: Scientific Programming: A Wiley-Interscience Publication John Wiley and Sons Journals Administration Dept. Baffins Lane, Chichester Sussex PO19 1UD England Magazines --------- Pixel Conferences & workshops (see also the proceedings from years passed): --------------------------------------------------------------------- Visualization '9x - Annual visualization conference SIGGRAPH - Annual ACM graphics conference Eurographics '9x - Annual European graphics conference of the Eurographics association ------------------------------------------------------------------------------ Subject: med.volviz.faq Followup-To: alt.image.medical Organization: University of Oulu Date: Mon, 14 Mar 1994 20:22:46 GMT med.volviz.faq.3/94 The following is a list of software packages _and user's notes_ relating to medical volume visualization (I'm mainly interested in CAT and MRI) that I have collected over the past from Usenet newsgroups and mailing lists. Many thanks to V.C. Arun Kumar and Lance Ladic for their lists on 3D visualization software. Please let me know if I have misquoted someone's posting and if you wish to make corrections and additions to the faq. I have NOT tried all of the packages mentioned in this list, and therefore cannot attest to the quality of some of them. Matti Haveri-------------------------------------- ... MacCubeView 1.1.0. on comp.binaries.mac. There is a demo file of a slice of the author's head. MacCubeView is designed to display a texture map image of three-dimensional (3-D) data. 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. Analysis & Visualization Application for the Macintosh. Operates on 1D and 2D data arrays. Import/Export several different file formats. Several different plotting options such as gray scale, color raster, 3D Wire frame, 3D surface, contour, vector, line, and combinations. FFTs, filtering, and other math functions, color look up editor, array calculator, etc. Shareware, available at sumex-aim.stanford.edu /info-mac/app. For other information contact Doug Norton (e-mail: 74017.461@compuserve.com). MacStereology. A demo version is available at zippy.nimh.nih.gov /pub/nih-image/programs. >Stephen M Echteler: [...]MacStereology to do some 3D reconstructions of developing sensory neurons. The demo available from zippy.nimh.nih.gov has lots of nice features but 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. ... *3D Skull (brain) images generated from CT or MR slices: omicron.cs.unc.edu (128.109.136.159) /pub/softlab/CHVRTD. *The Chapel Hill Volume Rendering Test Data Sets are available at ftp.cs.unc.edu /pub/softlab/CHVRTD. There is an MRI scan of a human skull (256x256x109) and a CT scan of a skull of a human cadaver (256x256x113). Note that these are not images but volumes, but the slices could be treated as images if you can extract them. >Alexander-James Annala: CHVRTD (Chapel Hill Volume/Ray Tracing Dataset) which you should be able to find somewhere around omicron.cs.unc.edu /pub/softlab - this points to several tens of megabytes of 3D images (MRI scan of knee and head, CT scan of head, a few other datasets - something like 109 slices of 256 x 256 pixels x 16 bit integer per pixel for one of the datasets). >Patrick Kane: [...]where can I get the 3D model at FTP sites? ftp to avalon.chinalake.navy.mil /pub/objects. 3D object files subdirectories exist for different formats. Avalon was created to be a 3D object "repository" for the net. You'll find 3D datasets in various formats, utilities to convert between the different formats, and documents explaining the file formats. There is a pub/incoming directory for uploads, so if you have anything to contribute, please upload it! If you have any problems connecting to avalon, try its mirror site Kubota Pacific at ftp.kpc.com (144.52.120.9) /pub/mirror/avalon. *WWW server with a scientific visualization home page: http://web.msi.umn.edu/WWW/SciVis/umnscivis.html. Contact: hughes@s1.msi.umn.edu. ... MacCubeView 1.1.0. ftp://sumex-aim.stanford.edu/info-mac/ and its mirrors around the world. There is a demo file of a slice of the author's head. MacCubeView is designed to display a texture map image of three-dimensional (3-D) data. 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. Analysis & Visualization Application for the Macintosh. Operates on 1D and 2D data arrays. Import/Export several different file formats. Several different plotting options such as gray scale, color raster, 3D Wire frame, 3D surface, contour, vector, line, and combinations. FFTs, filtering, and other math functions, color look up editor, array calculator, etc. Shareware. ftp://sumex-aim.stanford.edu/info-mac/app and the mirrors around the world. For other information contact Doug Norton (e-mail: 74017.461@compuserve.com). MacStereology. A demo version is available at ftp://zippy.nimh.nih.gov/pub/nih-image/programs. MacStereology is a package designed to make measurements of images and to make 3-D reconstructions. Input to MacStereology is either from a digitising tablet or from Pict files. The boundaries of the objects of interest can therefore be drawn by hand on the tablet or traced automatically on a binary image. From these boundaries and the magnification, parameters such as area,perimeter and centre of gravity are calculated. If the co-ordinates of each boundary are also saved, together with the section thicknesses then 3-D reconstructions can be displayed, printed or plotted, using a wireframe (for pen plotter), layers or surface plot. MacStereology should work with any Macintosh with at least 1 Mbyte memory. It was designed for a MacII with 8-bit colour, but is OK in grey tones or black and white. >Stephen M Echteler: [...]MacStereology to do some 3D reconstructions of developing sensory neurons. The program is rather expensive ($750) and the Mac interface is a bit buggy. I'd really appreciate comments from anyone who:1) has used this program or 2) could suggest an alternative application with similar features. >John Russ: Well, I've been a MacStereology user for several years now. We use it in our research (3D reconstructions from all kinds of imaging including TEM, confocal light, and x-ray microtomography), as well as in teaching courses to grad students, and like it a lot. There are only three basic approaches to 3D reconstruction: a) volumetric (transparency) imaging like VoxelView or VoxBlast, which shows all of the data, but can be VERY time consuming to fiddle with all of the transparency, lighting, etc., parameters to reveal the important aspects of structure (they really require you to already know what is there, and just use the program to show it to others); b) resectioning approaches like Spyglass Dicer, which allows you to examine arbitrary sections but cannot show the important topological characteristics present in the 3D volume; and c) surface rendering, as in MacStereology, which is very efficient (small files and fast displays), shows the topology and presents images that appear natural because we are all used to seeing surfaces, but accomplishes this by hiding other detail including internal structures behind the surfaces. The three approaches are complementary and we use them all, but if I had to choose, I would take Macstereology first, Spyglass Dicer a very close second, and Voxelview (or Voxblast) a distant third, based on the amount they are used, and the response of students and researchers to the images (how much they can learn from them, how difficult it is to interact with them, etc.). As to the two specific complaints: I don't agree that the interface is "buggy." It does have a few peculiarities that are not totally Mac-like, like fiddling with the display LUT and taking over the whole window, but you can turn that off if you like. Whenever I've found a bug (usually when Apple releases a system upgrade or new hardware), the author has fixed it pretty quickly, and he is also very good about giving advice via e-mail. And the complaint about the price is really sort of annoying. Photoshop costs nearly as much, but consider the number of copies they sell? What do you think Spyglass' set of programs cost? Or how about Voxelview which is considerably more expensive? How much did you spend for your computer+ camera+ interface+ microscope+ printer+... - well you get the idea. $750 for a program that has taken man-years to develop and has a very specialized market is hardly high-priced. You are just spoiled because Image is free (well, unless you count that we all pay taxes to support Wayne). In the PC world, you would spend $2K or more for a program equivalent to Image. Expensive? No, expensive is trying to do without a tool you need. **sites** *3D Skull (brain) images generated from CT or MR slices: (128.109.136.159) ftp://omicron.cs.unc.edu/pub/softlab/CHVRTD. *>AJ Annala: If you might be interested in viewing a 36 frame animation loop of a series of views taken at 10 degree intervals around a 3D stack of 113 256x256 pixel CAT scan images of a human head then acquire the file ftp://camelot.usc.edu/pub/images/xmovie.skull.tar.Z, compile the xmovie program on your system (modify the makefile to use your local C compiler, X11 lib, and socket lib) -- then enter 'xmovie -height 256 -width 256 skull*' to view the animation loop on your X11R4 or X11R5 display station. If you have the ability to select your local X11 screen resolution (SUN's can't do this -- but most i386 unix systems can select their display resolution) you may enlarge the image by selecting an X11 display resolution of 640 x 480 x 8 bit color. Otherwise you will be viewing a 256 x 256 pixel animated image within whatever screen resolution is the default on your system. *The Chapel Hill Volume Rendering Test Data Sets are available at ftp://ftp.cs.unc.edu/pub/softlab/CHVRTD. There is an MRI scan of a human skull (256x256x109) and a CT scan of a skull of a human cadaver (256x256x113). Note that these are not images but volumes, but the slices could be treated as images if you can extract them. >Alexander-James Annala: CHVRTD (Chapel Hill Volume/Ray Tracing Dataset) which you should be able to find somewhere around ftp://omicron.cs.unc.edu/pub/softlab - this points to several tens of megabytes of 3D images (MRI scan of knee and head, CT scan of head, a few other datasets - something like 109 slices of 256 x 256 pixels x 16 bit integer per pixel for one of the datasets). >Patrick Kane: [...]where can I get the 3D model at FTP sites? ftp://avalon.chinalake.navy.mil/pub/objects. 3D object files subdirectories exist for different formats. Avalon was created to be a 3D object "repository" for the net. You'll find 3D datasets in various formats, utilities to convert between the different formats, and documents explaining the file formats. There is a /pub/incoming directory for uploads, so if you have anything to contribute, please upload it! If you have any problems connecting to avalon, try its mirror site Kubota Pacific at (144.52.120.9) ftp://ftp.kpc.com/pub/mirror/avalon. WWW server with a scientific visualization home page: http://web.msi.umn.edu/WWW/SciVis/umnscivis.html. Contact: hughes@s1.msi.umn.edu. [>Does anyone know where I could find 3-D images of a human brain in any common graphic format (GIF, JPEG, TIFF, etc...)]. gopher://gopher.austin.unimelb.edu.au/11/images/petimages/ **Newsgroups** of (possible) interest: alt.3d alt.graphics alt.graphics.pixutils alt.image.medical alt.sci.nmr bionet.neuroscience bionet.software comp.graphics comp.graphics.algorithms comp.graphics.avs comp.graphics.data-explorer comp.graphics.explorer comp.graphics.visualization comp.lang.idl comp.lang.idl-pvwave comp.protocols.dicom comp.soft-sys.khoros comp.soft-sys.wavefront comp.sys.mac.graphics comp.sys.sgi.graphics sci.answers sci.data.formats sci.image.processing sci.med sci.med.physics sci.med.radiology sci.med.telemedicine sci.techniques.mag-resonance sci.techniques.microscopy **references** Ali-Q-M, Ulrich-C, Becker-H. Three-dimensional CT of the middle ear and adjacent structures. Neuroradiology 1993, VOL: 35 (3), P: 238-41, ISSN: 0028-3940. 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AJR-Am-J-Roentgenol 1993 Jun, VOL: 160 (6), P: 1273-8, ISSN: 0361-803X. Dillon EH, Leeuwen MS, Fernandez MA, Eikelboom BC, Mali WP. CT angiography: application to the evaluation of carotid artery stenosis. Radiology 1993; 189:211-219. =46ishman EK, Drebin B, Magid D, Scott WW, Ney DR, Brooker AF, Riley LH, Ville JA, Zerhouni EA, Siegelman SS. Volumetric rendering techniques: applications for three-dimensional imaging of the hip. Radiology 1987; 163:737-738. =46ishman EK, Magid D, Ney DR, Drebin RA, Kuhlman JE. Three-dimensional imaging and display of musculoskeletal anatomy. J Comput Assist Tomogr 1988; 12:465-467. =46ishman-E-K, Magid-D, Ney-D-R, Chaney-E-L, Pizer-S-M, Rosenman-J-G, Levin-D-N, Vannier-M-W, Kuhlman-J-E, Robertson-D-D. Three-dimensional imaging (published erratum appears in Radiology 1992 Mar; 182(3):899). Radiology 1991 Nov, VOL: 181 (2), P: 321-37, ISSN: 0033-8419 89 Refs. Galanski M, Prokop M, Chavan A, Schaefer CM, Jandeleit K, Nischelsky JE. 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