I can see this thread is currently about Windows, but here is another J3D/Stereo data 
point: we have stereo viewing basically working on

RedHat 7.2
kernel 2.4.9-34smp
NVidia Quadro4 750 (vendor: PNY)
NuVision 60GX glasses with VGA sync pick-off (direct DIN connection does not work)
NVidia 4191 drivers (must follow instructions exactly)
Java3D 1.3
J2SDK 1.4.0
XFree86 4.1.0

I say "basically working" because we have some minor visual artifacts and some other 
ugliness to deal with (but no time to deal with it unfortunately).

I have also seen J3D stereo working with a Wildcat II 4110 on Windows 2000 using the 
same glasses, but this was some time ago.

Unfortuantely I can't share our code but I can tell you that we are not doing anything 
unusual to enable stereo.

We will be making a free public binary release of our system in a few months, I will 
be sure to post to this list when it is out.

Karsten (I think), commenting on your issues with the quality of the stereo effect, 
eye separation, viewing frusta, etc.  In my short experience with stereo, addressing 
those kinds of issue is hard, and cannot be done fully by the hw/driver/API alone, but 
must also include very careful design of the model and application.  I have found that 
I am not yet expert enough to know how to do this properly & without a lot of trial 
and error.  And I have not had the time to invest in that trial and error.

It doesn't help that I seem to be one of the people that has a hard time seeing the 
stereo effect.  Remember that people like me are out there.  FWIW, I don't think this 
perceptual issue is a binary function.  Sometimes with an expertly prepared stereo 
display I can really see the effect. An NVidia driver demo on Windows I saw once was 
awesome for example.  But for a lot of things I just see a flickering image and get a 
headache while others see 3D.

Anyone working with stereo who hasn't read this handbook should do so:

http://www.stereographics.com/x_downloads/developers/handbook.pdf

Oops, I guess that includes me, I've only skimmed it...

You may also find additional interesting information here:

http://www.stereographics.com/support/developers/
http://www.stereographics.com/support/body_whtpaprs.html

Marty Vona
NASA/JPL
Science Activity Planner for MER

Opinions expressed herein are my own and do not reflect those of my employer.

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