Setting up a simple stereo system

Hardware and Drivers

  • To set up your own simple stereo system for scientific visualization,you would need the minimum system requirements to run the NVidia 3DVision Pro also described at http://www.nvidia.com/object/3d-vision-pro-requirements.html.  See  how to check : how many bits your computer has, what CPU is in your computer, how much memory your computer has and  how much disk space your computer has.
  • You will need an Nvidia Quadro graphics card that includes a 3-pin stereo connector. (Cards that have stereo controlled through USB do not support OpenGL stereo.) A list of the cards with this capability can be found at http://en.wikipedia.org/wiki/Nvidia_Quadro. We have tested the Quadro FX 4800 and Quadro 5000 in our lab. You can purchase graphics cards online from a number of vendors, for example PNY Technologies.
  • Quadro graphics cards can be connected to the computer’s motherboard via three types of connection: AGP, PCI and PCI-Express (We are using PCI Express in our lab). Your graphics card needs to be compatible with your motherboard i.e. if you are using a PCI-Express graphics card, your motherboard needs to have the PCI-Express slot.  See how to determine graphics card type compatibility.
  • To connect the graphics card  you need a  Dual-linked DVI-I cable to connect the graphics card to the display screen. These can be bought from most electronic component vendors. If you want to connect two monitors to your graphics card, the graphics card should have 2 DVI output ports.
  • You would need to check that your computer monitor has a Dual-linked DVI-I input port and is capable of refreshing the display at least 120Hz. See what a dual-linked DVI-I input looks like and how to check the refresh rate of your monitor for Windows XP and Windows 7.  The Nvidia website has a list of compatible monitors.
  • You also need the Nvidia 3D Vision Kit which contains the shutter-glasses and IR transmitter that allows the graphics card to communicate with your shutter-glasses. Most of the vendors that sell the Nvidia Quadro cards would also carry the 3D Vision Kit. This is Nvidia’s site for the 3D  Vision Kit: http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html.   Even though the site listed Geforce cards as the minimum requirement for the 3D Vision Kit, it should work with your Quadro card since the Quadro line is the more sophisticated version of the two lines of graphics cards.

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Hardware Setup and Drivers Installation

  • Once you have procured your graphics card, you need to install the graphics card into your computer. Here’s how to install the graphics card driver.
  • From the Nvidia download page, select “Option 2: Automatically find drivers for my NVIDIA products” . Click on “Graphics Driver”. Download and install the recommended driver. This is your graphics card driver.
  • From the Nvidia download page, select the 3D Vision driver for Quadro for your operating system, click Search, click Download, click Agree and Download.  Install the driver by double-clicking on the downloaded file(Quadro_3D_Vision_258.49_USB_driver).[moz-screenshot]
  • Change the refresh rate of your monitor to be at least 120Hz. (Instructions for Windows 7 and Windows XP).

Component Setup Preview

  • Here’s an overview on how to connect the 3D Vision Kit. Do not connect the components yet, you will be prompted to do so when running the 3D Vision Wizard.Just read through this section to get an idea of how components should be connected
    • In general, you would have to connect the components like this (You will not need the DVI-to-HDMI adapter and the VGA-to-DisplayPort adapter):
    • You should have only ONE monitor connected to the desktop when you are setting up the display. Once you have verified that stereo is working fine, you can add the second monitor. If you have 2 monitors already connected to the desktop, you should remove the second monitor . Your remaining connected monitor should be the one that is connected to your desktop via the dual-link DVI port.
    • The IR emitter should be in front of your monitor i.e. in an area where it could transmit signals to your 3D glasses when you are sitting in front of the monitor. The second monitor in the picture is not connected to the desktop during the 3D vision setup.
    • This is your IR-emitter. You should remove the green label when setting up the IR emitter. Ignore the fact that it asks you to insert the CD before plugging in the USB. Our setup failed when we tried that for Quadro.
    • This image shows the 3-pin stereo cable connected to the IR transmitter.
    • This image shows how you should connect your 3-pin stereo port to your computer (Click here to see what the Dual-link DVI port looks like before the cable is plugged in)
    • This image shows the USB connection. The USB cord can be connected to any USB port on your computer.
      • Be aware that you may have to wait a few seconds before the IR emitter is detected by your computer and turn from red to green.
      • This is what your IR emitter looks like if it is connected correctly.
      • This is what your IR emitter looks like when stereo is running.
      • This is what your glasses look like when they are off. You can turn on your glasses by clicking on the button highlighted in red.
      • This is what your glasses look like when they are turned on.

    Running the 3D Vision Wizard

  • Now run the 3D Vision Setup Wizard .
  • Click the Start Button. On Windows 7, the Start button is the circular button on the lower left corner of your desktop and looks like this: . Click on Enable 3D Vision.
  • Alternatively, Start up the Nvidia Control Panel and select “Set up sterescopic 3D”. Select “Enable stereoscopic 3D”. The wizard should start and guide you through the steps to set up the IR emitter and use the 3D glasses. Make sure you have read theComponent Setup Preview.
  • (Click on image to view the screenshot in full size)

3D Application Settings

  • Open the Nvidia Control Panel and edit your Nvidia graphics settings (Click on image to view the screenshot in full size):
  • Select “3D Settings”. Select “Adjust image settings with preview”. Select “Let 3D application decide”

  • Select “3D Settings”. Select “Manage 3D Settings”.
    • On this screen, under “Global Settings” tab, for the “Global presets”, select “3D App-Default Global Settings”.
    • Set the “Enable overlay” feature to “Off”

    • On the same screen, scroll down.
    • Set the “Stereo – Display mode” feature to “On-board DIN connector (with NVIDIA IR Emitter)” Note: Important part is the “(with NVIDIA IR Emitter)” as there is also a “On-board DIN connector” (without NVIDIA IR Emitter option)
    • Set the “Stereo – Enable” feature to “On”
    • Set the “Stereo – Swap eyes” feature to “Off”
    • Set the “Triple buffering” feature to “On”
    • Set the“Vertical sync” feature to “Use the 3D application setting”
    • Click Apply (the button at the lower right corner of the NVidia Control Panel).

Verifying 3D Vision Setup

  • To verify that you have stereo working correctly you can download oglplane. Double-click on the downloaded file. If stereo is working, you should see a a single-line wireframe. If it is not working, you will see a double-line wireframe.  It is normal for your monitor to flash once when switching to stereo and once when switching back from stereo.
  • Once you have verified that oglplane is running correctly, you can be assured that your stereo setup is complete.
  • Optional: Shut down the computer, plug in your second monitor via DisplayPort and Dual-link DVI to DisplayPort adapter if you have one. Start up the computer. Verify that stereo is still working. If not, check the refresh rate of your monitor. Occasionally the refresh rate switches back to 60Hz if you restart your desktop.

Troubleshooting Stereo Setup

  • If you cannot get stereo working correctly:
    • Do you have multiple monitors connected to your graphics card? Try disconnecting all of the monitors except the main monitor. Set up stereo and then connect the other monitors.
    • Have you changed the refresh rate of your monitor to be at least 120Hz ? Occasionally the refresh rate switches back to 60Hz if you unplug one of your monitors or if you restart your desktop. A symptom of this issue would be flickering monitors.
    • Try charging the 3D Vision Glasses. (Connect the glasses to the USB port of your computer via the USB cable while your computer is turned on). Make sure that your glasses are turned on before starting the stereo application.
    • Always go back to the NVidia Control Panel to check that the 3D Application Settings have not been changed if something goes wrong.

Map of symptoms to possible causes/solutions:

  1. Even NVidia 3D Vision demo is not running in stereo.
    1. Something went really wrong during your driver installation step. Please verify that there is something really wrong with your stereo setup before running the following steps.
      1. Uninstall all NVidia drivers from your computer.  To uninstall a program, Click Start. Click Control Panel. Click Uninstall a program. You will have to repeat this for all the NVidia drivers on your computer.
      2. Follow the driver installation instructions,  and all the setup instructions after that.
  2. Monitor is flickering all the time:
    1. The refresh rate is less than 120Hz. Change the refresh rate to  at least 120Hz.  (Instructions for Windows 7 and Windows XP).
    2. Another user is logged onto the computer and has left stereo running. Ask the other user to exit their stereo applications.
    3. If and only if all else fails, restart the computer.
  3. Oglplane does not start at all.
    1. Check that your 3D Application Settings are correct.
  4. Oglplane is not running in stereo (you see a double-line wireframe instead of a single-line wireframe )
    1. The refresh rate is less than 120Hz. Change the refresh rate to  at least 120Hz.  (Instructions for Windows 7 and Windows XP).
    2. The 3D glasses are not charged. Connect the glasses to the USB port of your computer via the USB cable while your computer is turned on.
    3. The 3D glasses are not turned on before the application is started. Turn on the glasses before starting oglplane.  This is what your glasses look like when they are off. You can turn on your glasses by clicking on the button highlighted in red. This is what your glasses look like when they are turned on.
    4. Your IR emitter is blocked so your 3D glasses could not receive signals from the IR emitter. Make sure that the IR emitter is not blocked from your 3D glasses.

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Setting up Stereo on Multiple Displays

I have only tried two graphics cards, each with a DVI dual-linked output port.

  1. In the Nvidia Control Panel, select “Set up SLI Mosaic mode”.
  2. Select “Use SLI Mosaic Mode”
  3. Choose the “Display setup” that fits your monitor positions.
  4. Change “Refresh rate” to 120 Hertz.

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Setting up Stereo Displays on a Linux Workstation

We tested with:

  1. Red Hat Enterprise Linux (6.x)
  2. Two NVidia Quadro 5000 video cards
  3. Two ASUS VG236H – 23″ 1920×1080 screens
  4. NVidia video driver versions 270.41.19 or 275.43
  5. NVidia 3D Vision IR emitter and shutter glasses

Steps:

  1. Install the NVidia driver. Make sure it works.
  2. Turn off fancy window manager effects if they are on.
  3. Attach the 3D Vision Emitter to the computer with the included USB cable. You can verify if the kernel sees the device with
    $ dmesg | grep 'NVIDIA stereo'
  4. Attach the 3-pin mini-din to 1/8″ stereo cable to the Quadro graphics board and the 3D Vision Emitter. Check that the pins are clean and straight that and you have a good solid connection.
  5. Configure the stereo settings: See the “Stereo” X configuration documentation in the README for the specific options.
    /usr/share/doc/NVIDIA_GLX-1.0/README.txt

    Edit the file /etc/X11/xorg.conf. “[...]” represents snipped parts of the file.

    [...]
    Section "Screen"
        [...]
        Option "Stereo" "10"
    EndSection
    [...]
    Section "Device"
        [...]
        Option "FlatPanelProperties" "Scaling = Native"
    EndSection
    [...]
    Section "Extensions"
        Option "Composite" "off"
    EndSection
  6. Run “sudo /usr/bin/nvidia-settings”. Verify that the refresh rate on your monitor is set to 120 Hz.
  7. Try rebooting the computer (or at least log out to restart X11. At this point, if everything is going right, you should see the light on the emitter turn green. Test a stereo-enabled application with:
    $ glxgears -stereo

References:

  1. NVIDIA 3D Vision for Quadro – Linux
  2. NVIDIA Linux Graphics Driver README
  3. NV Forum / 3D Vision Linux Question
  4. NVNews Forum / Disabling Composite Mode Question

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Troubleshooting Linux Stereo

Q) My monitor keeps showing that my resolution isn’t 120 Hz any more. When I load nvidia-settings, it fixes itself. What’s going on?

A) Add the line
Option "FlatPanelProperties" "Scaling = Native"

to the -Device- section in /etc/X11/xorg.conf. This will permanently uncheck -Force Fill GPU scaling- and let you set a refresh rate.

Q) Everything is plugged in, but the emitter is always blinking red. What could be going on?

A) It may be that the stereo driver has failed to load during X11 startup. Look at the /var/log/Xorg.0.log and search for -stereo- I may report that stereo failed to load becasue it confliced with the compositing extension. In that case,
Section "Extensions"
    Option "Composite" "off"
EndSection

in your xorg.conf will fix it.

Q) How do I enable the driver for the stereo emitter?

A) The “Stereo” option under the screen section of your xorg.conf will set it. Look at …/NVIDIA_GLX-1.0/README.txt for details. “10″ means NVIDIA 3D Vision (infrared emitter and glasses). “11″ means NVIDIA 3D VisionPro (the (presumably more expensive) radio emitter and glasses).

Q) It still doesn’t work! I run a stereo application, I see double on my monitor, but the emitter doesn’t turn bright green. What could be happening?

A) The emitter may not be getting a good timing signal from the video card. It may be that one of the three pins in the 3-pin cable is bent or broken. Inspect the cable and then be sure that it is snugly plugged in.

Q) I’m having trouble installing the NVidia driver in RHEL6. How do I completely disable the Nouveau driver?

A) Check two things. First, a file in the directory /etc/modprobe.d/ should contain the lines
blacklist nouveau
options nouveau modeset=0

Normally, this file is called disable-nouveau.conf.

Secondly, /boot/grub/grub.conf should contain the phrase

rdblacklist=nouveau

appended to the kernel parameters.

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Software

ImageSurfer

ImageSurfer is a 3D imaging software for visualizing and analyzing multi-channel volumes in microscopy. You can download the latest version of ImageSurfer from the download page

Starting ImageSurfer in stereo mode

  1. In Windows 7, click the Start Button. On Windows 7, the Start button is the circular button on the lower left corner of your desktop and looks like this:
  2. In the “Search programs and files” input box, type Run ImageSurfer with Stereo Support. Click on the link that says “Run ImageSurfer with Stereo Support”

    or
  3. Click  Start.  Click All Programs.  Click CISMM.  Click ImageSurfer 1.27 . Click  Run ImageSurfer with Stereo Support

Here are some tutorials to get you started:

Video of Dendritic Spines tutorial in 3D stereo Part I
Video of Dendritic Spines tutorial in 3D stereo Part II

Starting ImageSurfer in stereo and tracker mode

  1. Plug in your SpaceNavigator into any USB port in your computer.
  2. Start ImageSurfer
    1. In Windows 7, click Start. In the “Search programs and files” input box, type Run ImageSurfer with Stereo and Tracker Support. Click on the link that says “Run ImageSurfer with Stereo and Tracker Support”
      or
    2. Click  Start.  Click All Programs.  Click CISMM.  Click ImageSurfer 1.27 . Click  Run ImageSurfer with Stereo and Tracker Support
  3. Start the Magellan server. In Windows 7, click Start. In the “Search programs and files” input box, type Run Magellan server. Click on the link that says “Run Magellan server”.
  4. Load the files as described in ImageSurfer Tutorial: Dendritic Spines.
  5. This is how you use the tracker:

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Stereo Spin

StereoSpin a program that displays stereo images from a spinning-loop video, making it easy to display stereo content from scientific visualizations or animations that were not originally rendered in stereo. You can download the latest version of StereoSpin from here.

Here’s a video of how to install StereoSpin.

How to run StereoSpin:

  1. Drag a video file or image file onto the desktop icon that was created when the program was installed. To select a stack of image files that are numbered consecutively, drag any one of the files onto the icon. video
    or
  2. Click  Start.  Click All Programs.  Click CISMM. Click StereoSpin.  A file-chooser window will open.  Select a video or image file (AVI, TIF, or BMP, PPM, raw). see this page.

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ParaView

ParaView is a general-purpose visualization program developed at Sandia National Laboratories and Kitware. It is more complicated than the CISMM-supported ImageSurfer and Stereo Spin programs described above. It provides the ability to load additional file formats and do more flexible data conversion and display.

Installation

  1. From the ParaView download site select either Windows, 32 bit or Windows, 64 bit, depending on your operating system.
  2. Run the executable.
  3. To start ParaView, click Start.  Click All Programs. Click ParaView 3.8.1. Click ParaView.

ParaView tutorials

Here are some Paraview tutorials:

Starting ParaView in stereo mode

You can start ParaView in stereo using 1 of the the 2 methods:

  • Create and use a stereo ParaView shortcut (You can still use ParaView in non-stereo mode by directly clicking on paraview.exe)
    • Go to the directory where you installed your ParaView. Click on the bin directory.
    • Right click on paraview.exe,select “Create Shortcut” . It will usually be automatically named “Paraview -shortcut”
    • Right click on the shortcut, select “Properties”
    • Append --stereo --stereo-type="Crystal Eyes" at the end of the Target field. Do not replace the original path, just add --stereo --stereo-type="Crystal Eyes". Click “Ok”. 
      • (The dashes before stereo and stereo-type are double-dashes, not single dashes: refer to screenshot)
      • If the commands do not work (if ParaView starts and disappears in a second), try typing the commands instead of copying and pasting it from the browser.

  • Start Paraview using command-line input (Not recommended if you are not familiar with the command-line).
    • In Windows Vista & 7, from the Start button, type “cmd” and enter into the Search button. In Windows XP, click “Run” and type in “cmd”
    • Navigate to the ParaView folder.  For example, cd "C:\Program Files\ParaView 3.8.1\bin"
      • You should type the full names of the folders. The previous command could also be cd "C:\Program Files (x86)\ParaView 3.8.1\bin"
      • Make sure you get all the space and character cases correct.
    • Start ParaView by typing paraview.exe --stereo --stereo-type="Crystal Eyes"

You can view any ParaView data files in stereo. Here are some example files: blow.vtk , and disk_out_ref.ex2

Here’s an video of ParaView in stereo mode (because this is a video replay, it is not rendered in stereo).

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ParaView on 3DTV

Hardware

You need

  1. A 3DTV that implements “Checkerboard stereo”*.   We used the Samsung PNC8000.
  2. If you are using a Nvidia  Geforce graphics card, a HDMI cable.
  3. If you are using a Nvidia  Quadro graphics card, a HDMI cable and a DisplayPort-to-HDMI adapter.

*Due to the plethora of 3DTVs in the market, we are not able to test everyone of them to determine what type of stereo display is available on each model.  We tested the Lg LX6500 and found the checkerboard to be less than satisfactory. The Panasonic Viera does not have Checkerboard stereo.

Setting up Hardware

  1. Install the graphics card on your computer.
  2. Connect the TV to the graphics card on your computer using
    1. a HDMI cable if your graphics card is Nvidia Geforce.
    2. a HDMI cable via a DisplayPort-to-HDMI adapter if your graphics card is Nvidia Quadro
  3. Turn on the TV and the computer.
  4. Click on the 3D TV button. Select the option that looks like a checkerboard.

How to start ParaView in 3D stereo for 3DTVs:

Create and use a stereo ParaView shortcut (You can still use ParaView in non-stereo mode by directly clicking on paraview.exe)

  • Go to the directory where you installed your ParaView. Click on the bin directory.
  • Right click on paraview.exe,select “Create Shortcut” . It will usually be automatically named “Paraview -shortcut”
  • Right click on the shortcut, select “Properties”
  • Append --stereo --stereo-type="Checkerboard" at the end of the Target field. Do not replace the original path, just add --stereo --stereo-type="Checkerboard". Click “Ok”. 
    • (The dashes before stereo and stereo-type are double-dashes, not single dashes)
    • If the commands do not work (if ParaView starts and disappears in a second), try typing the commands instead of copying and pasting it from the browser.

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FAQ

  1. Could there be a conflict between the installation of the NVidia driver files and ParaView/ImageSurfer/StereoSpin ?
    1. No, there should not be any conflict between the NVidia driver files and the scientific visualization applications.
  2. Can I use other graphics cards?
    1. To the best of our knowledge, at this point in time, there are no other graphics cards that support quad-buffered stereo with OpenGL. Please contact us if you have newer information.
  3. I have a 120Hz 3DTv with HDMI ports. Can I use the NVidia 3D Vision Kit with the 3DTv?
    1. The short answer is no, based on #3 (The 3D Vision Kit does not work on HDMI).
    2. The long answer is: You will not need a 3D Vision Kit to run the applications on your 3DTV (because the 3D Vision Kit does not work on your 3DTv). You will need to use the 3D glasses that are compatible with your 3DTv. You will not be able to run quad-buffered stereo on your 3DTv.
      1. If the application that you are running (e.g. ParaView/ImageSurfer/Stereo Spin) can produce a 3D format (side-by-side/checkerboard/top-bottom/interleaved) that is compatible with your 3DTv (this depends on the cable input port of your Tv, the latest cable format is HDMI 1.4), then  you can run the application in 3D.
      2. The caveat is you have to accept lower resolution and half the frequency:
        1. The graphics card will be sending 60Hz to the LCD 3DTv  (60Hz for the left eye and 60Hz for the right eye but at half the resolution i.e. 720p instead of 1080p).
        2. In comparison, the graphics card sends 120Hz at full resolution (1080p) to the stereo-capable LCD monitor at 60Hz for the left eye and 60Hz for the right eye.
  4. I have a 120Hz HDTv with HDMI ports. Can I use it to run ParaView in 3D?
    1. If your HDTv is not specified as 3D-Ready by its manufacturer, it means that it does not have its own IR emitter and 3D glasses, so it is incapable of displaying 3D stereo unless if you tamper with the hardware.
  5. I see severe ghosting (double images) at the top part of my screen, but the 3D stereo looks fine on other parts of the monitor. What is wrong?
    1. This is a known issue caused by the lag between the IR emitter and the rendering of the screen. Track this forum: http://forums.nvidia.com/index.php?s=91c2fa0a30210c7603f0d4e30bff0067&showtopic=89261&hl=alienware&st=360
  6. Other questions:
    1. You can check out this website http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options and  contact us for more information
  • try restarting computer if monitors are flickering.