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

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Aoki-S, Sasaki-Y, Machida-T, Ohkubo-T, Minami-M, Sasaki-Y. Cerebral
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Brink-J-A, Heiken-J-P, Balfe-D-M, Sagel-S-S, DiCroce-J, Vannier-M-W.
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Burk DL, Mears DC, Kennedy WH, Cooperstein LA, Herbert DL.
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Castillo M. Diagnosis of disease of the common carotid artery
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Cline HE, Lorensen WE, Souza SP et al. 3D surface rendered MR images
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Dillon EH, Leeuwen MS, Fernandez MA, Eikelboom BC, Mali WP. CT
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Gillespie JE, Adams JE, Isherwood I. Three-dimensional computed
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Gillespie JE, Isherwood I, Barker GR, Quayle AA. Three-dimensional
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Horrocks JA, Speller RD. Short communication: Helical computed
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Kalender WA, Seissler W, Klotz E et al. Spiral volumetric CT with
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Levy-R-A, Rosenbaum-A-E, Kellman-R-M, Bailey-G-L, Aravapalli-S-R.
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Magid D, Fishman EK. Imaging musculoskeletal trauma in three
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Magid-D, Michelson-J-D, Ney-D-R, Fishman-E-K. Adult ankle fractures:
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Marks MP, Napel S, Jordan JE, Enzmann DR. Diagnosis of carotid artery
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Masaryk AM, Ross JS, DiCEllo MC et al. 3DFT MR angiography of the
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Parisi M, Mehdizadeh HM, Hunter JC, Finch IJ. Evaluation of
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Pommert A, Bomans M, Riemer M, Tiede U, H=F6hne KH. 3-D imaging in
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Ray-C-E-Jr, Mafee-M-F, Friedman-M, Tahmoressi-C-N. Applications of
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Radiol-Clin-North-Am 1993 Jan, VOL: 31 (1), P: 181-94, ISSN:
0033-8389.

Robertson DD, Walker PS, Granholm JW, et al. Design of custom hip
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Tomogr 1987; 11:804-809.

Rubin-G-D, Dake-M-D, Napel-S-A, McDonnell-C-H, Jeffrey-R-B-Jr.
Three-dimensional spiral CT angiography of the abdomen: initial
clinical experience. Radiology 1993 Jan, VOL: 186 (1), P: 147-52,
ISSN: 0033-8419.

Rubin GD, Dake MD, Napel SN, Jeffrey RB Jr, McDonnel CH, Sommer FG,
Wexler L, Williams DM. Spiral CT of renal artery stenosis: Comparison
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Schmid UD, Steiger HJ, Huber P. Accuracy of high resolution computed
tomography in direct diagnosis of cerebral aneyrysms. Neuroradiology
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Schwartz RB, Kendall MJ, Chernoff DM et al: Common carotid artery
bifurcation: Evaluation with spiral CT. Radiology 92; 185:513-519.

Soyer-P, Roche-A. Three-dimensional imaging of the liver. Acta-Radiol
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