Google Groups no longer supports new Usenet posts or subscriptions. Historical content remains viewable.

Dismiss

Medical and Volumetic Imaging with Modern Tools: DICOM, MICE & Men

7 views

Skip to first unread message

P. Flavin

unread,

May 8, 2003, 11:21:08 AM5/8/03

Free open source portable medical apps including DICOM visualization
--------------------------------------- tools are available ( below ):

Rendering 3d data: Sharing Standarardized Portable Scientific Data
-----------------

across the web and across our community is enbabled
by standards such as the DICOM medical imaging format
and standard internet protocols and Java which allow
life saving information, data, and programs to be
safely and quickly transported across to web to whereever
we need it, and onto whatever device we need it.

Yes. Certainly.

Yes, of course, most standard formats including DICOM
--------------- are read & rendered by Java.

| Medical Image Format FAQ ... DICOM Information Sources
| ------------------------------------------------------
| DICOM File Convertors and Viewers:
| ---------------------------------
|
| DICOM software - EViewBox DICOM Viewer (Java)
| DICOM software - RAIM Java DICOM image viewer
| DICOM software - JDicom Java DICOM tools from Tiani:
| DICOM software - Imread Java DICOM Viewer
|
http://www.dclunie.com/medical-image-faq/html/part8.html
http://www.dclunie.com/medical-image-faq/html/part8.html#DICOMSoftwareEViewBox
http://www.dclunie.com/medical-image-faq/html/part8.html#DICOMSoftwareJDicom
http://www.dclunie.com/medical-image-faq/html/part8.html#DICOMSoftwareImread
http://www.tiani.com/JDicom/
http://www.uchsc.edu/sm/neuroimaging/download/imread/imread1.htm

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

DICOM Imaging -- Eviewbox java homepage
---------------------------------------
http://eviewbox.sourceforge.net/
http://eviewbox.sourceforge.net/EVBApplet/eViewBox.html
^--- applet, data ---v
http://eviewbox.sourceforge.net/EVBApplet/rm3_DICM

http://wwwusers.imaginet.fr/~sderhy/DicomApplet.html
http://sourceforge.net/project/showfiles.php?group_id=3339

Medical Imaging with NIH "ImageJ": DICOM extension
-----------------------------------------------
| This package contains a set of plugins for the
| ImageJ framework (http://rsb.info.nih.gov/ij/)
| to import and export DICOM images.
|
| Dcm_Import:
|
| This plugin imports DICOM compatible images to ImageJ.
|
| Dcm_Export:
|
| This plugin exports all ImagesJ images (besides 32-bit float)
| as DICOM Secondary Capture images.
|
http://www.iftm.de/produkte/dicomie/dcmie.htm

http://sourceforge.net/projects/dcm4che/

National Institue of Health (NIH) Imaging App : 2d, free
------------------------------------------( opens source )
http://rsb.info.nih.gov/ij/docs/concepts.html
http://rsb.info.nih.gov/ij/plugins/index.html
| "ImageJ" Features
|
| Runs Everywhere:
|
| ImageJ runs on Linux, Mac OS 9, Mac OS X and Windows.
|
| Data Types:
| 8-bit grayscale or indexed color,
| 16-bit unsigned integer,
| 32-bit floating-point and
| 32-bit RGB color.
|
| File Formats:
|
| Open and save all supported data types as
| TIFF (uncompressed) or as raw data.
| Open and save GIF, JPEG and ASCII.
| Open BMP, DICOM and FITS.
| Open GIFs, JPEGs and raw data using a URL.
|
| Speed:
| ImageJ is the world's fastest pure Java
| image processing program.
|
| It can filter a 2048x2048 image in 0.5 seconds.
| That's over 8 million pixels per second!
|
http://rsb.info.nih.gov/ij/features.html
http://rsb.info.nih.gov/ij/applet/
http://rsb.info.nih.gov/ij/docs/pdfs/examples.pdf

2d Imaging App with multiple effects & filters: Free ( NIH )
-----------------------------------------------------------
| ImageJ is an Open/Free imaging tool implemented in Java
| by Wayne Rasband. This tool is extensible via a simple
| plugin model, and several dozen plugins already exist.
| This project provides a home for ImageJ plugins and plug
|
http://rsb.info.nih.gov/ij/
|
http://sourceforge.net/projects/imagejplugins/

| Bio-medical Imaging in Java
| ---------------------------
|
| VolumeJ - volume rendering in Java,
| -------- with sources and extensive API
| documentation of the VJ library.
|
| SurfaceJ (NEW) - three-dimensional rendering
| -------- of images and image sequences.
|
| FlowJ - optical flow estimation and visualization
| ----- software with several popular
| (2-D) optical flow algorithms in Java, with sources
| and API documentation.
|
| Flow3J - a new three-dimensional optical flow algorithm,
| based in part on the VJ API. Running as an applet:
| you can use 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/

| 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

| High-Performance Object-Oriented Distributed Medical Imaging
| ------------------------------------------------------------
| My research group at Washington University is developing various
| OO tools and design techniques (including ACE) to develop
| OO architectures for a high-performance medical imaging system
| for transporting X-ray images across high-speed ATM LANs and WANs.
|
| The following papers discuss various aspects of our work on
| distributed electronic medical imaging systems.
|
| * The Design and Performance of MedJava --
| a Distributed Electronic Medical Imaging System Developed
| with Java Applets and Web Tools (updated January 7th)
| appeared in the USENIX Conference on Object-Oriented Technologies
| and Systems (with Prashant Jain and Seth Widoff).
| This received the best student paper award at the conference.
|
| The Java programming language has gained substantial
| popularity in the past two years. Java's networking features,
| along with the growing number of Web browsers that execute
| Java applets, facilitates Internet programming. ...
|
| This paper makes three contributions to the study of Java
| for performance-sensitive distributed applications. First,
| we describe an architecture using Java and the Web to develop
| MedJava, which is a distributed electronic medical imaging
| system with stringent networking and computation requirements.
| Second, we present benchmarks of MedJava image processing
| and compare the results to the performance of xv, which is
| an equivalent image processing application written in C.
| Finally, we present performance benchmarks using Java as a
| transport interface to exchange large medical images over\
| high-speed ATM networks.
|
| For computationally intensive algorithms, such as
| image filters, hand-optimized Java code, coupled with
| use of a JIT compiler, can sometimes compensate for
| the lack of compile-time optimization and yield
| performance commensurate with identical compiled C code.
|
| With rigorous compile-time optimizations employed,
| C compilers still tend to generate more efficient code.
|
| However, with the advent of highly optimizing Java compilers,
| it should be feasible to use Java for the performance-sensitive
| distributed applications where C and C++ are currently us
|
http://www.cs.wustl.edu/~schmidt/imaging.html
http://www.cs.wustl.edu/~schmidt/PDF/MedJava.pdf

IN LIVING COLOR Java Technology Brings Medical Imaging to Life
--------------------------------------------------------------
| Constructing Medical Imaging Libraries ...
|
| The long-term goal of the Visible Human Project and
| AnatLine is to act as a test bed for the construction
| of medical imaging libraries that can be accessed through
| high-bandwidth computer networks. But with the wild
| proliferation of new technologies ever around the corner,
| such a goal is a perpetual work-in-progress.
| "Future incarnations of the project, utilizing the
| Next Generation Internet, will include such facilities
| as real-time 2D and 3D visualizations under haptic
| (touch-sensitive) control, as well as virtual reality
| applications," reports Henderson.
|
http://java.sun.com/features/2001/01/visible.html

National Library of Medicine, the Visible Human Project
--------------------------------------------------------
|
| # The NPAC 3D Visible Human Viewer, under development ...
|
| a VRML application that allows one to extract axial views
| of the Visible Human male dataset
|
| ( requires a VRML enabled Web client ).
|
| # Visible Human Explorer, produced by a collaboration
| between NLM and the University of Maryland (a fast X-Windows
| data viewer that requires a Sun workstation with at least
| 30MB of disk space).
|
| # The Cross Sectional Anatomy viewer from Loyola University
| (Chicago) Stritch School of Medicine.
|
| # The Digital Anatomy Lab, 2D and 3D browsing of
| CT and anatomical sections using a graphical browser
| or forms based input - from the Queensland University
| of Technology (Australia).
|
| # Visible Human Female Head and Pelvis Browsers
| from the University of Michigan's Digital Microscopy
| and Scientific Visualization Laboratory
| (requires a Java enabled Web client).
|
| # Workshop Anatomy for the Internet (WAI) from
| the Johannes Gutenberg University, Mainz, Germany.
| Labeled and unlabeled cryosections, correlated
| CT - MR images, animations, and a vocabulary of gross anatomy.
|
http://www.nlm.nih.gov/research/visible/visible_gallery.html
http://www.nlm.nih.gov/research/visible/applications.html

| VISUALIZATION OF VISIBLE HUMAN
| ------------------------------
|
| Technology Used in this project
| -------------------------------
| * Manual Segmentation is implemented in C under AVS system.
| * The 3D surfaces are generated using SGI explorer isosurface module.
|
| * 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

| One of the most fascinating enterprises of the
| National Library of Medicine, the Visible Human Project
| has produced computer-generated images of two cadavers,
| one male and one female.
|
| These datasets are being used (without charge)
| by 1,400 licensees in 41 countries, and at four mirror
| sites in Asia and Europe.
|
http://www.nlm.nih.gov/news/press_releases/visible_humanspr00.html

Dicom Java Viewer Project
---------------------------
|
| Java language is simple yet powerful for
| imaging applications. One of its major feature
| is its multiplatform ability that makes it possible
| to run in almost every multimedia computer
| ( PC's, Macs and unix workstations ) .
|
| Dicom (Digital Imaging Communication in Medicine )
| is getting to be a standard for digital image storage
| in medicine, the idea is to replace the old physician
| lightbox by a simple DicomViewer which uses few room
| in your doctor's computer's memory and let him
| read the images like the radiologist :
|
| on a computer screen
|
http://wwwusers.imaginet.fr/~sderhy/dicJava.html
http://wwwusers.imaginet.fr/~sderhy/DicomApplet.html

| SDSC'S MPIRE Renders Entire Visible Female Data Set
| ------------------------------------ -------------
| on CRAY T3E
|
| Volume renderer driven by Java interface produces
| image from nine-gigabyte data set in just over nine seconds
|
| The rendering engines are controlled via a graphical
| user interface in the form of either an Application
| Visualization System (AVS) module or a Java applet.
|
| Using either interface, the user can select the
| rendering engine, control the rendering parameters,
| and with a "virtual trackball," the user can change
| the angle and distance of the view.
|
http://mpire.sdsc.edu/intro/intro.html

Scalable Visualization "Vistools" ( NPACI )
-------------------------------------------------
| Toolkits
|
| Java
|
| The toolkits are available in ___ 100% Java ___
| for all platforms supporting JDK 1.3 or later.
| TAR and ZIP archives include Java source, class,
| JAR, and documentation files.
|
| File: npaci_vis_mesh_v1.0a1_java.tar ...
|
| Contents Java source code, class files, JAR files,
| and documentation for the Mesh toolkit and
| sample command-line applications.
|
|
| 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 __
| for all platforms supporting JDK 1.3 or later
| and Java3D 1.2.1 or later.
|
| The compressed (gzip) TAR archive includes
| Java JAR and documentation files.
|
| File: volxrend_java_2.0.tar.gz
|
|
| Contents Java JAR and documentation files for the
|
| 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

Volume Scene Graph API Overview
-------------------------------
| Volume Scene Graphs
|
| Generically, a scene graph is a hierarchical
| organization of shapes, groups of shapes, and
| groups of groups that collectively define the
| content of a scene. Shapes and subtrees may be
| shared among multiple groups, creating a directed
| acyclic graph. Scene graphs are widely used to
| define complex 3D scenes with hundreds or
| thousands of separate shapes.
|
| APIs and file formats, such as
|
| PHIGS, Open Inventor, IRIS Performer, Java 3D, and VRML,
|
| all support the creation and rendering of scene graphs.
|
http://vistools.npaci.edu/Documentation/Overview/ArchitectureSceneGraph.htm#MoreVolumeSceneGraphNodes

| # Introduction to VRML 97, ...
| # 3D Graphics Programming with Java 3D
| # An Introduction to Programming VR Applications with Java 3D
| Introduction to Programming with Java 3D
|
http://www.sdsc.edu/~nadeau/nadeau_courses.html
http://www.sdsc.edu/~nadeau/PhD/VolumeSceneGraphs.pdf
|
|
| Introduction to Programming with Java 3D
|
| San Diego Supercomputer Center
|
http://www.sdsc.edu/~nadeau/Courses/SDSCjava3d/

| Java Explorer: Enables __ Web Deployment __
| -------------------------------------------
| of Data Explorer Visualization Solutions
|
http://www.sdsc.edu/dx/JavaExplorer.htm

| Molecular Interactive Collaborative Environment ( MICE )
| -------------------------------- 3d molecular modeling
|
| Molecular Interactive Collaborative Environment (MICE)
| project is developing new methods of collaborative,
| interactive visualization of complex scientific data.
|
| While most existing methods of representing scientific
| data are static and two-dimensional, the technologies
| being used and developed for MICE provide interactive,
| three-dimensional environments within which multiple
| users can examine complex datasets in real-time.
|
| The MICE application provides high quality,
| interactive visualization of molecular scenes.
|
| Written in Java and Java3D, MICE is designed
| according to the Java philosophy of
|
| 'write once, run anywhere.'
|
| Portable and web-deliverable, the MICE application
| enables users to not only view molecular scenes on
| their own computer, but to distribute these scenes
| and interact with other users anywhere on the internet.
|
|
| Funding for the MICE project is provided by NSF grant DBI 9723475.
|
http://mice.sdsc.edu/site/index.html
http://mice.sdsc.edu/
http://www.sdsc.edu/~agramada/PDB_Help.html

| Publications
|
| A Prototype Molecular Interactive Collaborative Environment
| -----------------------------------------------------------
http://www.smi.stanford.edu/projects/helix/psb98/bourne.pdf
|
| Contributors ( SDSC MICE )
|
| * Phil Bourne (SDSC/UCSD) Principle Investigator
| * Mike Gribskov (SDSC/UCSD) Co-principle Investigator
| * John Moreland (SDSC) Senior Programmer
| * Steve Wavra (Southwest High School) Evaluator
| * Helge Weissig (SDSC/UCSD) Project Manager, RCSB ...
| * John Tate (SDSC/UCSD) Post Doctoral Fellow
|
http://mice.sdsc.edu/site/people.html

| ChemAxon releases JChem 2.0 and New Tools
| for Pharmacophore Screening, ... Reaction Modeling and
| Metabolite Prediction.
|
| JChemAxon, a software solutions provider for
| biotechnology, today announced the release of JChem 2.0,
| the latest version of the Java database engine enabling
| chemical communication across networks.
|
| The release also sees the addition of five powerful
| tool sets for pharmacophore screening, structure
| standardization, RECAP fragmentation, reaction modeling
| and metabolite prediction.
|
| As the first commercially available Java chemical
| database manager, JChem opened the door to powerful
| web based chemical storage and network communication.
| By supporting chemical structure storage and retrieval,
| substructure and similarity searching in various relational
| databases, such as Oracle and MySQL, JChem deployment
| has been extensive and rapid.
|
http://industry.java.sun.com/javanews/stories/story2/0,1072,52072,00.html
http://www.chemaxon.com/marvin/view/demo-table3d.html?jvm=builtin&gui=awt10
http://www.chemaxon.com/marvin/demos.html
http://www.jchem.com/mediverse/index.jsp
http://www.jchem.com/example/index.jsp

| Mississippi State developed applications for
| hierarchical data transformation and quantization
| based on wavelets, compression algorithms,
| hierarchical data structures and storage schemes
| for volume data, a communication layer for
| client-server communication, and a texture-based
| 3-D volume rendering application in __ Java3D. ___
|
| SDSC is hardening the VisTools implementation on
| multiple platforms, porting them to scalable graphics
| clusters, integrating the functional scene graph toolkit,
| and integrating the Storage Resource Broker.
|
http://www.npaci.edu/Alpha/visualization.html

VRML is a standard for 3d geometric shapes and
Java is can read & render VRML objects and animation
in a browser with Java3d using the __ Sun VRML Loaders __
including the animation of NSF Funded Finger Spelling
for the Deaf Animations using Web3d.org's VRML based
H-Anim Avatar standard ( desipite the criminal false
and fraudulent claims of the Yumetech.com fraudsters
and the false and fraudulent claims of Aaron Walsh
and the unreiable Prentice-Hall / Pearson Education books
with their known, uncorrected errors, omissions, and
self-serving lies of the Web3d.org insiders with the
criminal complicity of NIST staffers including Sandy Resller ).

Nasa, NSF, NIST, Navy PGS VRML animated with Java3d
---------------------------------------------------
* and the Sun VRML Loaders (NSF Chem Lab, Nasa Robot, Nist & NPGS VR)
--------------------------
http://www.frontiernet.net/~imaging/virtual_chemistry_lab.html
http://www.frontiernet.net/~imaging/terrain_rendering.html#Nasa_using_Sun_VRML_Loaders
http://www.frontiernet.net/~imaging/terrain_rendering.html
http://www.frontiernet.net/~imaging/vrml_loaders_working.html

The defacto NIST, NSF, & US Navy PGS policy of

"you can lie and commit fraud if you help us"

is counterproductive, illegal, harmful, and must stop.

-- Paul, Java Developer & Web Animator
--------------------------------------
Imaging the Imagined: Modeling with Math & a Keyboard

Hoppy Thing

unread,

May 8, 2003, 6:22:30 PM5/8/03

"P. Flavin" <anim...@rochester.rr.com> wrote in message news:<3EBA7677...@rochester.rr.com>...

>
> VRML is a standard for 3d geometric shapes and
> Java is can read & render VRML objects and animation

> in a browser with Java3d using the Sun VRML Loaders

Most people use VRML plugins such as Cosmo Player, Cortona, blaxxun,
FreeWRL, OpenVRML, and others to view VRML files.

> including the animation of NSF Funded Finger Spelling
> for the Deaf Animations using Web3d.org's VRML based
> H-Anim Avatar standard ( desipite the criminal false
> and fraudulent claims of the Yumetech.com fraudsters
> and the false and fraudulent claims of Aaron Walsh
> and the unreiable Prentice-Hall / Pearson Education books
> with their known, uncorrected errors, omissions, and
> self-serving lies of the Web3d.org insiders with the
> criminal complicity of NIST staffers including Sandy Resller ).
>
>
>
> Nasa, NSF, NIST, Navy PGS VRML animated with Java3d
> ---------------------------------------------------
> * and the Sun VRML Loaders (NSF Chem Lab, Nasa Robot, Nist & NPGS VR)
> --------------------------

> http://www.frontiernet.net/~imaging/virtual chemistry lab.html
> http://www.frontiernet.net/~imaging/terrain rendering.html#Nasa using Sun
> VRML Loaders
> http://www.frontiernet.net/~imaging/terrain rendering.html
> http://www.frontiernet.net/~imaging/vrml loaders working.html

>
>
> The defacto NIST, NSF, & US Navy PGS policy of
>
> "you can lie and commit fraud if you help us"
>
> is counterproductive, illegal, harmful, and must stop.

I couldn't find this policy on any of their web pages. Do you have
some inside information that we don't? This policy sounds more like
Enron or Arthur Anderson.

>
>
> -- Paul, Java Developer & Web Animator
> --------------------------------------
> Imaging the Imagined: Modeling with Math & a Keyboard

Imagining your Image: ???

0 new messages