A Procedure for the 3D
Reconstruction of Biological Organs from 2D Image
Sequences
Authors:
Kirana Kumara P, Ashitava Ghosal
Centre for Product Design and Manufacturing Indian Institute of Science, Bangalore
International Conference on Biomedical Engineering and Assistive Technologies (BEATS 2010)
17-19 December 2010
Dr. B R Ambedkar National Institute of Technology Jalandhar
Motivation
• Simulating biological organs - Surgery planning
- Surgery simulation
• Need for 3D models of biological organs
• Patient specific models
• Organ simulations need numerical
techniques like FEM
Difficulties
• 3D models of biological organs NOT readily downloadable from the internet!
• Cost a few hundred dollars (approximate)
• Also, not patient specific
Get 3D models from 2D images obtained through CT-scan (patient specific, or archived)
2D images for the entire human body FREELY available for download (requires license)
Popular software for extracting 3D models from 2D image sequences (FOR THE PRESENT PROBLEM) are NOT free!
Downloadable (Demo) versions cannot Save
Present Work
Use multiple FREE software packages
Utilize useful features from different software
Different stages of reconstruction can use different software
Necessary software packages: ImageJ, ITK-SNAP,
MeshLab
Example: Using ImageJ
Original Image After Processing with ImageJ Porcine liver (from [14])
ITK-SNAP
Segmentation I Segmentation II Segmentation III Segmentation IV
(Images from ITK-SNAP documentation available from [8])
Control the Level of Detail in the Model:
Use MeshLab
Liver: 576376 Faces
Liver: 2000 Faces
Liver: 200 Faces
Liver: 200 Faces (Well Shaped Triangles)
FE Analysis
The Liver (Undeformed + Deformed)
Advantages
• All software used are free
• Can control the level of detail of the 3D model constructed
• Surface meshes which describe the model
are of good quality (model can be used for
FE Analysis)
Limitations
• Multiple software need to be used
• Maybe easier & more efficient to use a
commercial software
Possible Future Work
• Source codes for all software are freely available; the codes may be used to build a free software comparable to a typical
commercial software
• Adding new useful features to the free software
• Modify free software to make them more
easy and more efficient to use
References
[1] http://www.3d-doctor.com [2] http://www2.amira.com [3] http://www.rhino3d.com [4] http://www.ansys.com/
[5] http://rsbweb.nih.gov/ij/
[6] Rasband, W.S., ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA,
http://rsb.info.nih.gov/ij/, 1997-2009.
[7] Abramoff, M.D., Magelhaes, P.J., Ram, S.J., "Image Processing with ImageJ", Biophotonics International, Volume 11, issue 7, pp. 36-42, 2004.
[8] http://www.itksnap.org
[9] Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee, and Guido Gerig, “User-guided 3D active contour segmentation of
anatomical structures: Significantly improved efficiency and reliability”, Neuroimage, 2006 Jul 1;31(3):1116-28.
[10] http://www.gnu.org/licenses/gpl.html [11] http://meshlab.sourceforge.net/
[12] MeshLab, Visual Computing Lab - ISTI – CNR
[13] Oztireli, Guennebaud and Gross, “Feature Preserving Point Set Surfaces based on Non-Linear Kernel
Regression”, Eurographics 2009 [14] http://biorobotics.harvard.edu
[15] Amy Elizabeth Kerdok, Characterizing the Nonlinear
Mechanical Response of Liver to Surgical Manipulation, Ph.D Thesis, The Division of Engineering and Applied Sciences, Harvard University, 2006.
