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Basic foilset Medical Application in CIV Project

Given by Marek Podgorny, Zeynep Ozdemir at Rome Laboratory CIV Final Review on 9 April 98. Foils prepared 9 April 98
Outside Index Summary of Material

The medical visualization work in the CIV project had 3 activities
  • 2D Visible Human
  • 3D Visible Human
  • Wavelet Compression for Images
We discussion Segmentation for 3D Visible Human Data
and collaborative 2D and 3D implementations
Medical Applications of Wavelet Compression

Table of Contents for full HTML of Medical Application in CIV Project

 Denote Foils where Image Critical
Denote Foils where HTML is sufficient
1 3D Visualization of Visible Human Data
2 The Visible Human Project
3 Data Preparation
4 Java based 2D Viewer
5 Segmentation
6 PPT Slide
7 Current Procedure
8 PPT Slide
9 PPT Slide
10 Medical Application
11 Collaborative Visible Human Applet
12 3D Visualization of VH Data
13 Wavelet Compression
14 Wavelet-based Viewer for Medical Images

Outside Index Summary of Material

HTML version of Basic Foils prepared 9 April 98

Foil 1 3D Visualization of Visible Human Data

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Marek Podgorny Rome Laboratory Final CIV Review April 8 1998 NPAC Syracuse University
HTML version of Basic Foils prepared 9 April 98

Foil 2 The Visible Human Project

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Funded by the National Library of Medicine implemented at the University of Colorado HSC.
39 - year old white male who donated his body to science after being convicted of murder and sentenced to death.
Magnetic Resonance Images(MRI- 256x256x12) - head scanned axially, the other sections scanned coronally.
Computer Tomography (CT - 512x512x12) - soft tissue and bones.
Anatomical color photographs - 1878 transverse slices, each 1 mm wide; each slice of original data is a 2048x1216 pixel 24-bit color image.
NPAC has obtained a copy of the Visible Human data set 14GB and license to use it.
Female VH not downloaded : 5,000 cross sections (40 GB). Good for 3D reconstruction (cubic voxels, 0.33 mm size)
HTML version of Basic Foils prepared 9 April 98

Foil 3 Data Preparation

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
We have cropped the original images and removed the gelation background.
We have constructed slices in two orthogonal panels (sagittal and coronal views); aligning required - linear interpolation between slices; best fit of features as a function of translations and rotations.
The resulting images were converted to PPM formats (1728x1878).
Image Clipper Application program (written in java) allows to cut the selected portion of the image and to apply the procedure to all images in the stack (head - 256x316 700 images)
Data stored in voxel representation in Illustra object-relational database (x,y,z,r,g,b).
HTML version of Basic Foils prepared 9 April 98

Foil 4 Java based 2D Viewer

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
The NPAC Visible Human Viewer is an interactive graphical interface written in Java (browsing 2D images).
Java applet allows to select and view high resolution images of 2D slices (axial, coronal, sagital) of the human body.
The lower resolution data for easier downloading (medium and low resolution) is created.
In December 1995, NPAC Visible Human Viewer was awarded two JARS (Java applet Rating Service) Awards and was featured on the February 17, 1996 episode of "Computer Chronicles" on PBS. In May, the Viewer received Java Cup International Award
http://www.npac.syr.edu/projects/vishuman/VisibleHuman.html
HTML version of Basic Foils prepared 9 April 98

Foil 5 Segmentation

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Automatic segmentation is not possible on anatomical images.
Interactive, semiautomatic segmentation is time consuming (one man-year to segment 300 anatomical objects)
Algorithms ( histogramming, thresholding, edge enhancement)
Image volume must be segmented into its anatomical constituents.
Minimum distance classifier written in C on AVS.
Segmentation was also implemented in Java.
Bone tissue cannot be separated from anatomical images.
We must come back to CT images and do aligning of CT images and anatomy images.
HTML version of Basic Foils prepared 9 April 98

Foil 6 PPT Slide

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
stack of images
(ppm formats)
ImageClipper
Segmentation
on AVS
IsoSurface
SGI-Explorer
produce AVS field
data from AVS images
save geometric object
as VRML file
HTML version of Basic Foils prepared 9 April 98

Foil 7 Current Procedure

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Segmentation done using modules written C on AVS.
  • minimum distance strategy
  • time consuming
  • human assistance necessary (training stage, inspection and correction of misclassified pixels on each slide).
Surfaces are extracted from AVS field data by using SGI-Explorer isosurface algorithms.
  • aliasing problem (steps) - geometric smoothing
  • holes on surface
  • data reduction 2 mm x 2 mm x 2 mm (downsampling)
  • transmission time - surface/polygon simplification
Conversion to VRML
HTML version of Basic Foils prepared 9 April 98

Foil 8 PPT Slide

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Head
  • Volume Dimensions: 104 x 144 x 119
  • Pixel Dimensions: 2 mm x 2 mm x 2 mm
  • Pixel Depth: 24-bit (8-bits x RGB)
  • Volume Size: 5.4 MByte (as AVS field data)
  • # of Points in vrml file : 85216
  • # of polygons : 23739
  • the size of vrml file : 8014534 Byte (ascii)
Brain
  • Volume Dimensions: 104 x 144 x 119
  • Pixel Dimensions: 2 mm x 2 mm x 2 mm
  • Pixel Depth: 24-bit (8-bits x RGB)
  • Volume Size: 5.4 MByte (as AVS field data)
  • # of Points in vrml file : 32656
  • # of polygons : 8667
  • the size of vrml file : 3035864 Byte (ascii)
HTML version of Basic Foils prepared 9 April 98

Foil 9 PPT Slide

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Leg
  • Volume Dimensions: 112 x 184 x 112
  • Pixel Dimensions: 2 mm x 2 mm x 2 mm
  • Pixel Depth: 24-bit (8-bits x RGB)
  • # of Points in vrml file : 216146
  • # of polygons : 56626
  • the size of vrml file : ~18M Byte (ascii)
HTML version of Basic Foils prepared 9 April 98

Foil 10 Medical Application

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
3D Visible Human (stereographic mode)
  • continuation of the main 3D visualization effort
Collaborative Visible Human Applet
  • integrates all elements of the telemedical application and provides collaboratory support
Wavelet-based viewer for medical images
  • capitalizes on and promotes to the application level our earlier wavelet compression research work
HTML version of Basic Foils prepared 9 April 98

Foil 11 Collaborative Visible Human Applet

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
http://www.npac.syr.edu/projects/vishuman/
http://www.npac.syr.edu/projects/3Dvisiblehuman
  • Visible Human Project, Format of data (MRI, CT, anatomical), data preparation
  • Java-based 2D applet - axial, coronal and sagital slices
  • Segmentation procedure - brain, skin, leg muscles
  • VRML files and MPEG movies
Segmented Data for Visible Human is now available commercially from Gold Standard Multimedia
  • price tag: $250K per body part, $1M for the entire body
Demo: 2D and 3D Viewer of Visible Human Data Integrated with Tango
HTML version of Basic Foils prepared 9 April 98

Foil 12 3D Visualization of VH Data

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Image Clipper --> Segmentation --> SGI Explorer -->OpenInventor/VRML
  • head : #points 85,216 #polygons 23,739 size 8MB
  • brain: #points 32,656 #polygons 8,667 size 3MB
  • leg: #points 216,146 #polygons 56,626 size 18 MB
  • other organs (heart, stomach, etc.) converted from AutoCAD to Open Inventor
Stereo Visualization
  • quad stereo approach
  • divided-screen stereo approach
HTML version of Basic Foils prepared 9 April 98

Foil 13 Wavelet Compression

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Wavelet technology suitable for compression of natural scenes with high compression ratios
Lossy compression- selectively disregards "less important" information
Controversy: what is important and what is not (legal issues)
Wavelet-based compression is superior to all other compression technologies (keeps details, high compression ratios)
  • wavelet transformation, quantization, coding
HTML version of Basic Foils prepared 9 April 98

Foil 14 Wavelet-based Viewer for Medical Images

From Medical Application in CIV Project Rome Laboratory CIV Final Review -- 9 April 98. *
Full HTML Index
Implementation
  • standalone codec (wv3e, wv3d, wvr3e, wvr3d)
  • applet viewer (decompression and display)
  • application integrated with Tango (whiteboard)
Comparison with Accupress, Aware, Inc.
  • source code available
  • file formats: raw, rgb, ppm, yuv, raf (any 2 var func)
  • functionality: codec for color and black&white images
  • better encoding/decoding time, better quality represented by PSNR [db]
Demo: Integration with Tango
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