This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Reconstruction of Cellular Biological Structures from Optical Microscopy Data
July/August 2008 (vol. 14 no. 4)
pp. 863-876
ASCII Text
x 
 
Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang, Joel Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," IEEE Transactions on Visualization and Computer Graphics, vol. 14, no. 4, pp. 863-876, July/August, 2008.
 
 
BibTex
x
 
@article{ 10.1109/TVCG.2008.30,
author = {Kishore Mosaliganti and Lee Cooper and Richard Sharp and Raghu Machiraju and Gustavo Leone and Kun Huang and Joel Saltz},
title = {Reconstruction of Cellular Biological Structures from Optical Microscopy Data},
journal ={IEEE Transactions on Visualization and Computer Graphics},
volume = {14},
number = {4},
issn = {1077-2626},
year = {2008},
pages = {863-876},
doi = {http://doi.ieeecomputersociety.org/10.1109/TVCG.2008.30},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE Transactions on Visualization and Computer Graphics
TI - Reconstruction of Cellular Biological Structures from Optical Microscopy Data
IS - 4
SN - 1077-2626
SP863
EP876
EPD - 863-876
A1 - Kishore Mosaliganti,
A1 - Lee Cooper,
A1 - Richard Sharp,
A1 - Raghu Machiraju,
A1 - Gustavo Leone,
A1 - Kun Huang,
A1 - Joel Saltz,
PY - 2008
KW - Segmentation
KW - Region growing
KW - partitioning
KW - Size and shape
KW - Image Representation
KW - Image Processing and Computer Vision
KW - Image-based rendering
VL - 14
JA - IEEE Transactions on Visualization and Computer Graphics
ER -
 
Early efforts in the visualization of microscopic biological structures have been impeded by the lack of a rigorous cellular segmentation approach, insufficient slicing resolution and slicing deformations associated with serial-section histology volumes. We develop algorithms that address these challenges. In this paper, geodesic active contours using shape priors is employed to obtain initial segmentations of salient cellular structures. Overlapping cells are resolved by imposing a Voronoi-like tessellation of the image space optimized by a Bayesian probability framework. Intermediate slices are introduced between images to account for the insufficient slicing resolution. Results of the cellular segmentation step are used in conjunction with a cell shape model to interpolate the 3D cellular locations and shapes onto the adjacent slices thereby enhancing the expressivity and utility of the resulting visualizations. Our methods are applied in a case-study involving the 3D visualization of the epithelial cell lining and lobules in mouse mammary ducts.

[1] U. Adiga and B. Chaudhuri, “An Efficient Method Based on Watershed and Rule-Based Merging for Segmentation of 3-DHisto-Pathological Images,” Pattern Recognition, vol. 34, no. 7, pp. 1449-1458, 2001.
[2] A. Almsherqi, S. Kohlwein, and Y. Deng, “Cubic Membranes: A Legend Beyond the Flatland of Cell Membrane Organization,” CellBiology, vol. 173, pp. 839-844, 2006.
[3] U. Braumann, J. Kuska, J. Einenkel, L. Horn, M. Löffler, and M. Höckel, “Three-Dimensional Reconstruction and Quantificationof Cervical Carcinoma Invasion Fronts from Histological Serial Sections,” IEEE Trans. Medical Imaging, vol. 24, no. 10, pp. 5-7, 2005.
[4] A. Carpenter, T. Jones, M. Lamprecht, C. Clarke, T. Kang, O. Friman, D. Guertin, J. Chang, R. Lindquist, J. Moffat, P. Golland, and D. Sabatini, “Cellprofiler: Image Analysis Software for Identifying and Quantifying Cell Phenotypes,” Cell Biology, vol. 7, no. R100, 2006.
[5] K. Conor, H. Voorheis, and C. Ó Sullivan, “3D Visualisation of Confocal Fluorescence Microscopy Data,” Proc. Fifth Irish WorkshopComputer Graphics, pp. 49-54, 2004.
[6] L. Cooper, K. Huang, A. Sharma, K. Mosaliganti, and T. Pan, “Registration versus Reconstruction: Building 3-D Models from 2-DMicroscopy Images,” Proc. Workshop Multiscale Biological Imaging, Data Mining and Informatics, pp. 57-58, 2006.
[7] Q. Du and X. Wang, “Centroidal Voronoi Tessellation Based Algorithms for Vector Field Segmentation and Visualization,” Proc. IEEE Visualization, pp. 43-50, 2004.
[8] R. Fernandez-Gonzalez, T. Deschamps, A. Idica, R. Malladi, and C. de Solorzano, “Automatic Segmentation of Histological Structures in Mammary Gland Tissue Sections,” Biomedical Optics, vol. 9, no. 3, pp. 444-453, 2004.
[9] J. Fiala and K. Harris, “Computer-Based Alignment and Reconstructionof Serial Sections,” Microscopy and Analysis, vol. 52, pp. 5-7, 2002.
[10] P. Fialkow, “Clonal Origin of Human Tumors,” Ann. Rev. of Medicine, vol. 30, pp. 135-143, 1979.
[11] D. Gendzwill and M. Stauffer, Analysis of Triaxial Ellipsoids: Their Shapes, Plane Sections, and Plane Projections. Springer, 1981.
[12] R. Halir and J. Flusser, “Numerically Stable Direct Least Squares Fitting of Ellipses,” Proc. Int'l Conf. Central Europe on Computer Graphics, Visualization and Interactive Digital Media, pp. 125-132, 1998.
[13] A. Kaufman, R. Yagel, R. Bakalash, and I. Spector, “Volume Visualization in Cell Biology,” Proc. IEEE Visualization, pp.160-167, 1990.
[14] K. Kurose, K. Gilley, S. Matsumoto, P. Watson, X. Zhou, and C. Eng, “Frequent Somatic Mutations in PTEN and TP53 Are Mutually Exclusive in the Stroma of Breast Carcinomas,” Nature Genetics, vol. 32, no. 3, pp. 355-357, 2002.
[15] M. Leventon, W. Grimson, and O. Faugeras, “Statistical Shape Influences in Geodesic Active Contours,” Proc. IEEE Conf. Computer Vision and Pattern Recognition, pp. 232-316, 2000.
[16] N. Malpica, C. Solorzano, J. Vaquero, A. Santos, I. Vallcorba, J. Garcia-Sagredo, and F. Poze, “Applying Watershed Algorithmsto the Segmentation of Clustered Nuclei,” J.Cytometry, vol. 28, pp.289-297, 1997.
[17] K. Mosaliganti, R. Machiraju, J. Heverhagen, J. Saltz, and M. Knopp, “Exploratory Segmentation Using Geometric Tessellations,” Proc. 10th Int'l Fall Workshop Vision, Modeling and Visualization, pp. 1-8, 2005.
[18] K. Mosaliganti, T. Pan, R. Sharp, R. Ridgway, A. Gulacy, S. Iyengar, P. Wenzel, A. deBruin, R. Machiraju, K. Huang, G. Leone, and J. Saltz, “Registration and 3D Visualization of Large Microscopy Images,” Proc. SPIE Conf. Medical Imaging, pp.923-934, 2006.
[19] T. Ohtake, I. Kimijima, T. Fukushima, H. Yasuda, M. Sekikawa, S. Takenoshita, and R. Abe, “Computer-Assisted Complete Three-Dimensional Reconstruction of the Mammary Ductal/Lobular Systems,” Cancer, vol. 91, no. 12, pp. 2263-2314, 2001.
[20] S. Raman, B. Parvin, C. Maxwell, and M. Barcellos-Hoff, “3D Segmentation of Mammospheres for Localization Studies,” Proc. Int'l Symp. Visual Computing, pp. 427-436, 2005.
[21] R. Ridgway, O. Irfanoglu, R. Machiraju, and K. Huang, “Image Segmentation with Tensor-Based Classification of N-Point CorrelationFunctions,” Proc. MICCAI Workshop Medical Image Analysis with Applications in Biology, 2006.
[22] G. Sakas, M. Vicker, and P. Plath, “Visualization of Laser Confocal Microscopy Datasets,” Proc. IEEE Visualization, pp. 375-379, 1996.
[23] R. Sharp, R. Ridgway, K. Mosaliganti, P. Wenzel, T. Pan, A. Bruin, R. Machiraju, K. Huang, G. Leone, and J. Saltz, “Volume Rendering Phenotype Differences in Mouse Placenta Microscopy Data,” Computing in Science and Eng., special issue on anatomic rendering and visualization, vol. 9, no. 1, pp. 38-47, 2007.
[24] C. Tang and B. Ewert, “Automatic Tracking of Neural Stem Cells,” Proc. Workshop Digital Image Computing (WDIC '05), pp. 61-66, 2005.
[25] M. Tscherepanow, F. Zöllner, and F. Kummert, “Automatic Segmentation of Unstained Living Cells in Bright-Field MicroscopeImages,” Proc. Workshop Mass-Data Analysis of Images and Signals in Medicine, Biotechnology and Chemistry (MDA '06), pp.86-95, 2006.
[26] Q. Wang, Y. Sun, B. Rajwa, and J. Robinson, “Interactive Volume Visualization of Cellular Structures,” Proc. SPIE, vol. 6065, pp.424-435, 2006.
[27] Q. Wang, Y. Sun, and J. Robinson, “GPU-Based Visualization Techniques for 3D Microscopic Imaging Data,” Proc. SPIE, vol. 6498, p. 6498H, 2007.

Index Terms:
Segmentation, Region growing, partitioning, Size and shape, Image Representation, Image Processing and Computer Vision, Image-based rendering
Citation:
Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang, Joel Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," IEEE Transactions on Visualization and Computer Graphics, vol. 14, no. 4, pp. 863-876, July-Aug. 2008, doi:10.1109/TVCG.2008.30
Usage of this product signifies your acceptance of the Terms of Use.