Anatomical VRML
jake reid
data from MRI PET CAT scanners into vrml? Dicom is 2D any volume
rendering stuff out there? Help!!
Jake Da Rookie
P. Flavin
jake reid wrote:
>
> Hi Folks, ...
> Anybody know any tools to get data from MRI PET CAT
> scanners into vrml ?
>
> Dicom is 2D any volume rendering stuff out there ?
>
> Help!!
>
> Jake Da Rookie
>
First, think: " What's the best tool ... for the task ? "
You know the answer: It's not the old-sytle VRML plug-in.
Medical and Volumetric Imaging with Modern Tools: DICOM, MICE & Men
--------------------------------------------------------------------
|
| Medical Imaging, Volumetic Imaging: DICOM
| --------------------------------- free, open source
| Eviewbox is a java imaging suite,
| its purpose is to view and spread native DICOM
| medical images, allowing for 2D and 3 reconstructions.
| EViewbox applet will allow to see the DICOM images
| on every platform.
|
http://sourceforge.net/projects/eviewbox/
|
|
| dcm4che is an implementation of DICOM in Java.
| ----------------------------------------------
|
| The sample applications may be useful on its own.
| It also includes an IHE compliant Image Archive
| application,based on J2EE.
|
http://sourceforge.net/projects/dcm4che/
http://dcm4che.sourceforge.net/docs/guides/index.html
|
| VolumeJ, Surface and FlowJ (and ImageJ)
| -------- without downloading and installing.
| Now includes isosurface rendering algorithm,
| which is about 100 times faster than previous
| algorithms and allows real-time rendering.
| Allows opening and saving your own files.
|
http://bij.isi.uu.nl/applet.htm
|
|
| VISUALIZATION OF VISIBLE HUMAN
| ------------------------------ ...
|
| * The NPAC Visible Human Viewer is implemented in Java. ...
| ----------------------------------------------------
| * VRML1.0 and VRML2.0 are used for WorldWide Web based
| visualization of Visible Human in 3D.
|
| * 3D Visible Human Viewer is implemented in VRML2.0.
| -------------------------------------------------
|
| The slicer in the viewer is a Script node and its
| behavior in the scene is defined using JavaScript.
|
http://www.npac.syr.edu/users/zeynep/HANDOUTS/
http://www.npac.syr.edu/projects/3Dvisiblehuman/3dvisiblehuman.html
|
| Java Philosophy and Features ...
| -----------------------------
|
| * Java Features -- It's Simple and Familiar !
| * Java Features -- It's Object - oriented
| * Java Features -- It's Architecture - Neutral
| * Java Features -- It's Portable
| * Java Features -- It's Somewhat Interpreted
| * Java Features -- It's Distributed
| * Java Features -- It's Robust
| * Java Features -- It's ( Hopefully ) Secure
| * Java Features -- High Performance
| * Java Features -- It's Multithreaded
| * Java Features -- It's Dynamic
|
http://www.npac.syr.edu/projects/cps616spring96/java.html
|
|
|
Scalable Visualization "Vistools" ( NPACI )
-------------------------------------------------
| Toolkits
|
| Java
|
| The toolkits are available in 100% Java ...
|
| Mesh Viewer "User Guide" ...
| ------------------------
|
| VOL<X>REND
|
| Java
|
| VOL<X>REND is an interactive volume rendering
| ---------- platform for the Toolkits.
|
| It is designed to enable the use of data sets
| that are too large to fit in the memory and swap
| space of desktop to teraflops computer systems.
| VOL<X>REND is available in 100% Java ...
|
| VOL<X>REND Volume Renderer
|
| Contact: Joerg Meyer, University of California at Irvine
|
http://vistools.npaci.edu/Documentation/MeshViewer/UserGuide.htm#11
http://vistools.npaci.edu/Downloads/Downloads.htm
|
|
| [ & lots more info ]
|
|
http://groups.google.com/groups?threadm=41f79d6d.0305081422.35386cf4%40posting.google.com
-- Paul, Java Developer & Web Animator
--------------------------------------
Imaging the Imagined: Modeling with Math & a Keyboard
jake reid
Jake
On Fri, 09 May 2003 05:42:22 GMT, "P. Flavin"
<anim...@rochester.rr.com> wrote:
>
> First, think: " What's the best tool ... for the task ? "
>
>
> You know the answer: It's not the old-sytle VRML plug-in.
>
>
>
>Medical and Volumetric Imaging with Modern Tools: DICOM, MICE & Men
>--------------------------------------------------------------------
> -- Paul, Java Developer & Web Animator
P. Flavin
3d visualization of MRI & DECOM data sets,
-----------------------------------------
as per your request,
free for you, from the US Tax payer:
http://vistools.npaci.edu/Documentation/MeshViewer/MeshViewer.htm#Screen%20Shots
"Award winning 3D browser for the head -- University of Oregon"
---------------------------------------------------------------
|
http://www.cs.uoregon.edu/~tomc/jquest/SushiPlugin.html
|
http://www.nlm.nih.gov/research/visible/animations.html
|
| view images of 2-dimensional slices of a human body,
| using processed data from the Visible Human Project
| of the U.S. National Library of Medicine.
|
http://www.dhpc.adelaide.edu.au/projects/vishuman2/VisibleHuman.html
Figure 1.1. CT, cryosection, and segmentation volume slices.
| Visualization
|
| To visualize the 3D structure of the head,
| the Visible Human Male images are stacked to form
| data volumes.
|
| The Volume Scene Graph Toolkit composites these CT,
| cryosection, and segmentation volume data sets into
| the same volumetric scene.
|
| The approach used here is fairly simple and is
| provided as an example of the style of use of the
| Volume Scene Graph Toolkit.
|
| The Visible Human Male project, administered by the
| ------------------------------
|
| National Library of Medicine, used CT, MRI,
| ------------------------------------------
| and cryosection technologies to create a full-body
| data set.
|
| CT data of the head alone contains 230 grayscale
| images at a 512 x 512 resolution.
|
| Cryosection data of the head contains 672 color images
| at 547 x 710. In addition to this publically available
| data, we have added a commercially available data set
| that segments the head, marking the brain, eyes, skull,
| etc, with unique colors in a new color data set with
| 672 images at 547 x 710. Figure 1.1 shows sample images
| from each of the CT, cryosection, and segementation volumes.
|
http://vistools.npaci.edu/examples/VisibleMale.htm#Data
http://vistools.npaci.edu/Documentation/MeshViewer/MeshViewer.htm#Screen%20Shots
Visible Human Server : Slice, surface and animation server
----------------------------------------------------------
| three forms of control for navigating within the
| Visible Human. By clicking on the buttons
|
| (1), you can select a standard slice orientation
| (axial, sagittal, coronal). By clicking and
| dragging either on the small 3D model
|
| (2) or on the currently displayed slice
|
| (3), you can move as illustrated on the figure below.
|
| When using the left mouse button on the miniature
| 3D model, the slice follows the mouse cursor position.
|
| When interacting on the displayed slice, translations
| and rotations are carried out relatively to the current
| slice position and orientation.
|
http://visiblehuman.epfl.ch/intapplet.php
http://visiblehuman.epfl.ch/stdappletv2.php
http://visiblehuman.epfl.ch/applet3D/help/EditingModels.htm#Editing%20the%20structure%20of%20the%20scene
http://visiblehuman.epfl.ch/applet3D.php
The "Windows Only" Gang doesn't like portable solutions ?
The Prentice-Hall, Yumetech.com & NIST fraudsters are evil.
Create & Play Games with Java & VRML : Be happy & smart
--------------------------------------------------------
http://www.javagaming.org/cgi-bin/JGOForums/YaBB.cgi?board=3D
http://www.frontiernet.net/~imaging/java_games.html
http://www.frontiernet.net/~imaging/games_with_java3d.html
http://www.frontiernet.net/~imaging/avatar_builder.html
Let your 3d animations be portable: Use VRML & Java.
Joerg Scheurich aka MUFTI
>> scanners into vrml ?
>>
>> Dicom is 2D any volume rendering stuff out there ?
> First, think: " What's the best tool ... for the task ? "
> You know the answer: It's not the old-sytle VRML plug-in.
Of course not. VRML is not a Volume/Voxelspace renderer.
It is about 3D surface rendering
And the support of Volume/Voxelspace renderering is not very
widespread in 3D surface based graphics API's like OpenGL, java3D
etc.
You can either try to see Volume data as 3D textures (available
in furture X3D ?) or use advanced API's like SGI's Volumizer
http://www.sgi.com/software/volumizer/
For open source tools you should search sourceforge for a possible
starting point to build a Volume/Voxelspace data to VRML converter 8-(
Maybe http://gts.sourceforge.net/ would be a good choice for the API
"in the middle" of the convertion ?
so long
MUFTI
--
Persönlicher Benutzer - für den einzelnen Benutzer hing der
Wunsch des kompakten, hohen Klarheit Kopfes SVGA-Bildschirmanzeigen
(aus einer Webseite fuer einen 3D Datenhelm)
P. Flavin
We agree, as you wrote:
"VRML is not Volume/Voxelspace render."
Thus my answer was to choose the "best tool"
and please note the SuperComputer Centers
at some of my country's top schools ( as you know )
use Java3d as the tool for this task ( as you know )
as was documented in my previous post ( as you know ).
Please note your link to a sourceforge project
may be "sub-optimal" in many respects perhaps
most noticably in that your link was to program
optimized for __ surface rendering __ and not
__ Volumetic / Voxelspace __ rendering.
Brain surgeons preparing for brain surgery do NOT
want a computer graphics model displaying an
approximation of the surface of the patients skin
~~~~~~ THEY CAN SEE THAT ~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
what they want is a "gods view" of
the interior soft tissues ...
so they don't put the knife
where the knife shouldn't be put
killing the patient, creating a lawsuit,
and doing no good.
It's ironic, the US government workers paid
to address this, can't, because of their fraud.
-
Joerg Scheurich aka MUFTI wrote:
>>> Anybody know any tools to get data from MRI PET CAT
>>> scanners into vrml ?
>>>
>>> Dicom is 2D any volume rendering stuff out there ?
>>
>
>> First, think: " What's the best tool ... for the task ? "
>
>
>> You know the answer: It's not the old-sytle VRML plug-in.
>
>
> Of course not. VRML is not a Volume/Voxelspace renderer.
> It is about 3D surface rendering
>
> And the support of Volume/Voxelspace renderering is not very
> widespread in 3D surface based graphics API's like OpenGL, java3D
> etc.
>
> You can either try to see Volume data as 3D textures (available
> in furture X3D ?) or use advanced API's like SGI's Volumizer
>
> http://www.sgi.com/software/volumizer/
>
> For open source tools you should search sourceforge for a possible
> starting point to build a Volume/Voxelspace data to VRML converter 8-(
>
> Maybe http://gts.sourceforge.net/ would be a good choice for the API
> "in the middle" of the convertion ?
>
> so long
> MUFTI
-- Paul, Java Developer & Web Animator