suzuki@sai.vtt.fi (Makoto Suzuki) (11/07/90)
(Ok, I'll add one.) Dear readers of this newsgroup. Are there anyone who are interested in visualization in the biomedical field? I am studying about a 3D visualization of patients' organs for surgeons. But now I paused it because I am here(see below). I'll continue it after I back to Japan. I'd like to exchange some information. ******************************************************** Makoto Suzuki _ _ ___ ___ (SUZUKI@vtsai2.sai.vtt.fi) | / | | Technical Research Centre of Finland |/ | | Medical Engineering Laboratory ******************************************************** I will stay in Finland from this September to next June as a scholarship student. I am a REAL Japanese. So my English is not good. I hope all of you don't mind it. :) ********************************************************
toster@watson.bcm.tmc.edu (Tom Oster) (11/07/90)
In article <1470@vtsai2.sai.vtt.fi> suzuki@sai.vtt.fi (Makoto Suzuki) writes: > Are there anyone who are interested in visualization in the > biomedical field? I am studying about a 3D visualization of > patients' organs for surgeons. You don't specify what platform you would use for this visualization. Spyglass technologies has a new product called Dicer, which is based on work done at NCSA. It is very good, although slow, as it runs on the Macintosh, not a workstation. It is the best program I've seen on a micro for 3-D visualization of data sets. I'll be glad to provide more information if anyone is interested. Tom Oster - Computing Resource Center Baylor College of Medicine toster@watson.bcm.tmc.edu Opinions expressed here are mine alone.
stanh@meyerhof.iaims.bcm.tmc.edu (Stan Hanks) (11/08/90)
In article <2630@gazette.bcm.tmc.edu>, toster@watson.bcm.tmc.edu (Tom Oster) writes: |> In article <1470@vtsai2.sai.vtt.fi> suzuki@sai.vtt.fi (Makoto Suzuki) |> writes: |> > Are there anyone who are interested in visualization in the |> > biomedical field? I am studying about a 3D visualization of |> > patients' organs for surgeons. |> |> Spyglass technologies has a new product called Dicer...it runs on the |> Macintosh, not a workstation If you're interested in visualization on a larger scale, we're using AVS from Stardent Computer (and DEC, and Evans&Sutherland, and Tektronics, and Convex, and Cray, and ???) on a variety of platforms for our efforts in the W.M. Keck Center for Computational Biology. While it's not the best system in the world, it certainly has some large advantages, and it *DOES* provide an excellant "visual programming environment" for casual users (I classify anyone who doesn't write code as a casual user). Regards, -- Stanley P. Hanks Director, Information Technology Planning and Development Baylor College of Medicine, One Baylor Plaza, Houston TX 77030, Mail Stop: IR-3 e-mail: stanh@bcm.tmc.edu voice: (713) 798-4649 fax: (713) 798-3729
dunlop@wateol (Doug Dunlop) (11/08/90)
In article <2630@gazette.bcm.tmc.edu> toster@watson.bcm.tmc.edu (Tom Oster) writes: >In article <1470@vtsai2.sai.vtt.fi> suzuki@sai.vtt.fi (Makoto Suzuki) >writes: >> Are there anyone who are interested in visualization in the >> biomedical field? I am studying about a 3D visualization of >> patients' organs for surgeons. > >You don't specify what platform you would use for this visualization. >Spyglass technologies has a new product called Dicer, which is based on >work done at NCSA. It is very good, although slow, as it runs on the >Macintosh, not a workstation. It is the best program I've seen on a >micro for 3-D visualization of data sets. I'll be glad to provide more information if anyone is interested. > >Tom Oster - Computing Resource Center >Baylor College of Medicine >toster@watson.bcm.tmc.edu >Opinions expressed here are mine alone. There is also a Public Domain program which is very similar in function to Dicer but runs under XWindows on various Unix machines. A copy can be obtained from the FTP server of the National Center for SuperComputer Applications (NCSA). The program is called XDataSlice and can be retreived using FTP from: ftp.ncsa.uiuc.edu 128.174.20.50 There is source code to build from scratch or there are binaries for some common Unix platforms. XDataSlice has some common development lineage with Dicer but IMHO is even more powerful than Dicer. Regards, Doug ======================================================================== ______ ______ __ / ____/ / _ / / / Doug Dunlop (Research Scientist) / /_ / / / / / / Earth Observations Lab / __/ / / / / / / University of Waterloo / /___ / /_/ / / /___ (519) 885-1211 x2689 FAX 888-6768 /_____/ /_____/ /_____/ dunlop@wateol.uwaterloo.ca ======================================================================== --
andyrose@batcomputer.tn.cornell.edu (Andy Rose) (11/08/90)
<Pardon the rambling nature of this note, consider this some free think> With the news that Tektronix will no longer play a role in high end workstations a number of issues come to mind. If a seemingly strong commitment to graphics, if judged by the size of Tek's booth at SIGGRAPH, can vanish, where do graphics people put their "beans"? IBM (RS6000), Silicon Graphics, Stardent,souped up apples? I would be interested in hearing how buyers/developers deal with the changing market. Let's consider a few points of view... 1) Big Co. wants to set up a visualization lab. Let's say Big owns a few Convexen or some Crays. They are producing enormous amount of, let's say, pressure and temperature data in a three D irregular mesh of points using some boundary solving thingy. They have been using Big's inhouse cad system to build the meshes and design the objects. a. Big does not wish to develop a product for sale, rather it wants to visualize the data so that the scientists can better understand there science (Big is a big believer in sci vis). In these tight times, Big doesn't mind kicking down $$$ but wants a system to last into the future. Performancewise, Big wants to see its models rotate in realtime and see the colors change in realtime. Big also wants to interact with the science as it displays the graphics. True sci viz. Big definitely needs a good deal of processing power (tens of thousands of polygons shaded a second). Big can a. Buy a Stardent ($60-150K) and bang out graphics with AVS in a few weeks. b. Buy Silicon Graphics (same price), write custom code (assuming programming talent), and be groovy in a few months. c. Buy silicon graphics and some software (Wavefront Data Visualizer?) and maybe be happy in less than a few months (may also assume programming talent). d. Lease hardware (avoiding inevitable obselescence) and rent talent. What is Big to do? Can he be secure in his choice of SGI or Stardent, or should he go BIG BLUE and relax (???). Can he find programming talent? What software can he get off-the-shelf which will do this stuff? What about output? Does he need to record the animation? Digital or analog video? Can he get this kind of service out-of-house? 2. Small Co. develops graphics software. Small got in the game a few years ago writing plotting packages and supporting Telegraf for some Fortune 500s. Small just hired talent and wants to break into "scientific visualization." Small knows Big needs a package to display 3D models and data interactively with feedback to the science program (i.e. widgets). Small knows about AVS, apE, Khoros, Serpent, IKP, UIMX, Motif, X, etc... Small hates reinventing the wheel. Can Small add to an existing software product (AVS, apE) and repackage it along with support, training, doc, etc. for resale to Big? Small needs a machine, which one? Right now I don't think either of these guys can build a system which will sail them into the 21st century. It is painfully clear how quickly this stuff is changing (Tektronix XD88). SO. What is it about scientific visualization that is not changing? Besides all the inevitable goings ons in the hardware realm where is sci vis going? Since guys in suites are going to decide which platform to buy anyway, the software will be platform independent to protect the software vendors (ala Wavefront). Just how expensive is sci viz anyway? Rather than rambling on here are some figures. Dept. Vis. Cornell Theory Center serves supercomputer users with lots of data. In order to do this we rely on 2 full time animators cranking frames with Wavefront Tech Model/Preview/Image (Professional Visualizer) on Tek XD88 (2). Both are facile with c and write readers and other filters for each job. This setup is great for batch type animation but insufficient for interactive vis. For this we use a Stardent GS1000 ($140K 2 years ago) running AVS 2.0. This setup has successfully visualizaed 4,000 particles represented as spheres updated 2-4 times a second while the simulation ran (parameters effecting the science could be adjusted "on the fly"). This requires custom coding also to read science data and to design an interface for the scientist, however, with training the process of building AVS modules is on the order of weeks rather than months for building X or Motif interfaces. Color encoders allow output of Wavefront frames to an Abekas frame store for editing onto 3/4" video tape. Video setup costs $$$. Would like to convert the whole thing to digital soon. In many ways this is representative of setups at NCSA, SDSC, and other "production" facilites. Big, self-contained, labor intensive. As platforms become less expensive and everyone uses 24bit color and blasts 100,000 polygons/second, more mature software tools will be needed to take advantage of the resource. Video prices won't (read will but slower) come down so how does the small user output (one answer is shared resources or automated video dumping across the net)? enough for now... How do you vis? -- Andrew Newkirk Rose '91 Department of Visualization CNSF/Theory Center 632 E & T Building, Hoy Road Ithaca, NY 14583 607 254 8686 andy@cornellf.tn.cornell.edu
hhe@ifi.uio.no (Hans Henrik Eriksen) (11/08/90)
In article <2630@gazette.bcm.tmc.edu> toster@watson.bcm.tmc.edu (Tom Oster) writes: > Spyglass technologies has a new product called Dicer, which is based on > work done at NCSA. It is very good, although slow, as it runs on the > Macintosh, not a workstation. It is the best program I've seen on a > micro for 3-D visualization of data sets. I'll be glad to provide more > information if anyone is interested. I think DEC sells a system called AVS (Advanced Visualization System?) for 3D vis. which is based on PHIGS+. It runs nicely on their ds5000/200. Hans Henrik Eriksen hhe@ifi.uio.no
windemut@lisboa.tmc.edu (Andreas Windemuth) (11/08/90)
andyrose@batcomputer.tn.cornell.edu (Andy Rose) writes: > <Pardon the rambling nature of this note, consider this some free think> Likewise ... > If a seemingly strong commitment to graphics, if judged by the size of > Tek's booth at SIGGRAPH, can vanish, where do graphics people put their > "beans"? IBM (RS6000), Silicon Graphics, Stardent,souped up apples? One possible solution to advanced scientific visualization that comes to my mind is the NeXTdimension board from NeXT computer Corp. We are definitely considering this machine for the visualization of macromolecules here. A list of the features of such a system ($20k educational with 16M RAM and 2.8Gb Disk) includes full 24 bit colour plus 8 bit alpha, 60-80 MFlops graphics performance (an i860), 30,000 Polygons per second (Gouraud shaded) and actual live video capture, storage and playback. The latter would make all the expensive video equipment that is usually associated with scientific visualization obsolete, as the NeXTdimension board is supposed to be able to digitize live video, store it on disk, do any editing in software using an application with a friendly user interface and output the result as a high quality video signal. Generating animations with rendering software such as Renderman would also be possible. All that is needed in the way of video equipment is a VCR to put final edited videos (of which up to 60min can be stored on 2.8 Gbytes of disk) on tape. The VCR can supposedly be connected to the board with a standard video cable (both RGBS and Composite). Given that the NeXT is a full-blown workstation and has the most progressive software development environment on the market (especially compared with that of Silicon Graphics, Stardent or Sun), it would seem to me that the NeXTdimension machine is superior to any other configuration that I can think of costing three times as much, not even considering the video feature. One problem with this setup might be the (as yet) unavailability of ready-to-go software packages. Having tried my hand at Wavefront, though, I must say that I would prefer custom coding in NeXTstep to using this awfully kludgy package. On the other hand, maybe I just don't know it well enough. AVS is more in the spirit of NeXTstep, and I suppose that NeXT (or some third-party developer) are planning to implement something like that in the future. IMHO, if there is any machine/philosophy for doing Visualisation and Animation already evident at this time that could be "sailing into the 21st century", chances are it's the NeXTdimension system. Even though I might not sound like that, I have no connection to NeXT other than as a very satisfied customer. Andreas Windemuth Theoretical Biophysics Group University of Illinois at Urbana-Champaign 3121 Beckman Institute 405 N. Mathews, Urbana Illinois 61801
andyrose@batcomputer.tn.cornell.edu (Andy Rose) (11/09/90)
It would be interesting to know how fast the Next machine (or whatever
comes next from Next) will display 3D vectors and shaded polygons.
> desperately need back propogation of data in AVS
Why? Scientist writes groovy simulation and wants to visualize.
I stuff the science into an AVS DATA module so it produces a FIELD.
This module is asynchronous and spews data when it can. I then
build a network which passes the field data to, say, 'bubble viz' and
then to render and then display and finally 'write Wavefront'. All thse
modules are synchronous (they execute only when input or parameters
change). It takes the Stardent longer to write the image to disk than
to generate a new data set so I record every third frame or something like
that. Woah...
Now I want to let the science module know when I am done writing the frame
so it will wait. I try to output an integer from the bottom of the network
(the write wavefront module) for input into the science module at the top,which
I have now made synchronous (so it will be activated when it sees the integer
input from the write module)..
AVS bugs out. Call support. No cyclic nets.
Woah...
Solution: Create TAP module which uses unix sleep call to wait 20 seconds and
output an integer asynchronously. This becomes the impetus for the data
module to fire. tap->science->geometry->render->write. Kind o' Kludgy.
BIG NOTE: apE can apparently handle cyclic nets...
Has anyone had experience with apE doing this?
OTHER BIG NOTE: avs 3 (demonstrated at SIGGRAPH three months ago) had this
worked out.
--
Andrew Newkirk Rose '91 Department of Visualization CNSF/Theory Center
632 E & T Building, Hoy Road Ithaca, NY 14583
607 254 8686 andy@cornellf.tn.cornell.edu