1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J....
-
Upload
andrew-lee -
Category
Documents
-
view
212 -
download
0
Transcript of 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J....
![Page 1: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/1.jpg)
1
CAVASS: Computer Assisted Visualization and Analysis Software System
Jayaram K. Udupa, George J. Grevera* Dewey Odhner, Ying Zhuge, Andre Souza, Tad Iwanaga, Shipra Mishra
Medical Image Processing GroupDepartment of Radiology - University of Pennsylvania
Philadelphia, PA
*Department of Mathematics and Computer ScienceSaint Joseph’s University
Philadelphia, PA
http://www.mipg.upenn.edu/~cavass
![Page 2: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/2.jpg)
2
CAVA
CAVA: Computer-Aided Visualization and Analysis
The science underlying computerized methods of image processing, analysis, and visualization to facilitate new therapeutic strategies, basic clinical research, education, and training.
![Page 3: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/3.jpg)
3
CAD vs CAVA
CAD: Computer-Aided Diagnosis
The science underlying computerized methods of image processing, visualization, and analysis for the diagnosis of diseases via images
![Page 4: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/4.jpg)
4
Purpose of CAVA
In: Multiple multimodality multidimensional images of an object system.
Out: Qualitative/quantitative information about objects in the object system.
Object system – a collection of rigid, deformable, static, or dynamic, physical or conceptual objects.
![Page 5: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/5.jpg)
5
CAVA Operations
Image processing: for enhancing information about and defining object system.
Visualization: for viewing and comprehending object system.
Manipulation: for altering object system (virtual surgery).
Analysis: for quantifying information about object system.
![Page 6: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/6.jpg)
6
3D CAVA Software Systems (MIPG)
DISPLAY mini computer + frame buffer 1980
DISPLAY82 mini computer + frame buffer 1982 3D83 GE CT/T 8800 1983 3D98 GE CT/T 9800 1986 3DPC PC-based 1989 3DVIEWNIX Unix, X-Windows 1993 CAVASS platform independent, wxWidgets 2007
![Page 7: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/7.jpg)
7
CAVA User Groups
UG1 – CAVA basic researchers/technology developers
UG2 – CAVA application developers
UG3 – Users of CAVA methods in clinical research
UG4 – Clinical end users in patient care
CAVASS is aimed at UG1-UG3.
![Page 8: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/8.jpg)
8
Key Features of CAVASS
• Open source, C/C++, wxWidgets
• Inherits most CAVA functions of 3DVIEWNIX
• Incorporates most commonly used CAVA operations
• Optimized implementations for efficiency
• Time intensive operations parallelized and implemented using Open MPI on a cluster of workstations (COWs)
• Interfaces to popular toolkits (ITK, VTK), CAD/CAM formats, DICOM support, other popular formats
• Stereo interface for visualization
![Page 9: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/9.jpg)
9
CAVA Operations in CAVASS
Image Processing: VOI, Filtering, Interpolation, Segmentation, Registration, Morphological, Algebraic
Visualization: Slice, Montage, Reslice, Roam through, Color overlay, MIP, GMIP, Surface rendering, Volume rendering
Manipulation: Cut, Separate, Move, Reflect, Reposition,hard and fuzzy objects
Analysis: Intensity profile/statistics, Linear, Angular, Area,Volume, Architecture /shape of objects, Kinematics
![Page 10: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/10.jpg)
10
Parallelization of CAVA Operations
Approach: Chunking
Chunk – data contained in a contiguous set of slices
Type-1: Operation chunk-by-chunk, each chunk accessed only once. Ex: slice interpolation
Type-2: As in Type-1, but significant further operation needed to combine results. Ex: 3D rendering
Type-3: Operation chunk-by-chunk, but each chunk may have to be accessed more than once. Ex: graph traversal
![Page 11: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/11.jpg)
11
Results
Regular: 25625646, MR brain image (6 MB)
Large: 512512459, CT of thorax (241 MB)
Super: 10231023417, CT of head (873 MB)
(visible woman)
Sequential and parallel implementations of several Type-1,
Type-2, Type-3 operations in CAVASS, ITK, VTK compared.
![Page 12: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/12.jpg)
12
Results
Operation SystemRegular Large Super
seq parallel seq parallel seq parallel
InterpolationITK 2.9 1.7 [2] 87.7 62.8 [2] Failed Failed [2]
CAVASS 0.6 1 [2] 54.9 14.9 [2] 139.1 49.2 [2]
AnisotropicDiffusive Filtering
ITK 57 2206.6
CAVASS 52.7 1664.2
Gaussian
Filtering
ITK 1.5 65.2 Failed
CAVASS 0.4 18.3 83
Distance
Transform
ITK 10.5 473.7 Failed
CAVASS 18.7 916.5 3382.4
![Page 13: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/13.jpg)
13
Results
Operation SystemRegular Large Super
seq parallel seq parallel seq parallel
ThresholdingITK 0.3 11.4 340.6
CAVASS 0.1 2.7 20.2
Fuzzy ConnectedSegmentation
ITK 108.4 Failed Failed
CAVASS 49.5 17.8 [5] 843.7 298.6 [5] Failed 1312.6 [5]
Registration
(rigid)
ITK 57.2 Failed Failed
CAVASS 56.1 8.6 [5] 1860.6 301.6 [5] 3863.4 1089.1 [5]
Registration (affine - 12 parameters)
ITK 208.3 Failed Failed
CAVASS 155.3 25.1 [5] 3602.4 1018.6 [5]
13,111 3662.2 [5]
![Page 14: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/14.jpg)
14
Results
Surface Rendering:
Data Set CAVASS seq
/no aaCAVASS seq/aa
VTK
Regular 0.03 0.06 0.29
Large 0.11 0.19 0.41
Super 0.16 0.26 1.38
![Page 15: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/15.jpg)
15
Results
Volume Rendering:
Data Set CAVASS VTK
sequential parallel Ray Casting 2D Texture
Regular 0.56 0.06 [6] 1.09 1.20
Large 3.53 1.36 [6] 5.03 18.32
Super 9.77 3.66 [6] 6.94 > 240.00
![Page 16: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/16.jpg)
16
Conclusions
(1) COWs are more cost/speed effective than multi-processing systems and are expandable.
(2) Most CAVA operations can be accomplished in reasonable time on COWs in portable software.
(3) COWs can be built quite inexpensively with publicly available hardware / software and standards.
(4) CAVASS can handle very large data sets; considerably faster than ITK.
![Page 17: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/17.jpg)
17
Further Information
www.mipg.upenn.edu/~cavass
Release date: July/August 2007
Other papers: 6509-03 – Visualization
6509-66 – Visualization
6519-07 – PACS
![Page 18: 1 CAVASS: Computer Assisted Visualization and Analysis Software System Jayaram K. Udupa, George J. Grevera * Dewey Odhner, Ying Zhuge, Andre Souza, Tad.](https://reader035.fdocuments.net/reader035/viewer/2022072006/56649d215503460f949f6227/html5/thumbnails/18.jpg)
18
Issues
(1) How to evaluate open source systems.
(2) Quality assurance in open source software (correctness, accuracy, efficiency,….).