Visualization and Analysis of Large Data Collections: a Case Study Applied to Confocal Microscopy Data
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In this paper we propose an approach in which interactive visualization and analysis are combined with batch tools for the processing of large data collections. Large and heterogeneous data collections are difficult to analyze and pose specific problems to interactive visualization. Application of the traditional interactive processing and visualization approaches as well as batch processing encounter considerable drawbacks for such large and heterogeneous data collections due to the amount and type of data. Computing resources are not sufficient for interactive exploration of the data and automated analysis has the disadvantage that the user has only limited control and feedback on the analysis process. In our approach, an analysis procedure with features and attributes of interest for the analysis is defined interactively. This procedure is used for off-line processing of large collections of data sets. The results of the batch process along with ``visual summaries'' are used for further analysis. Visualization is not only used for the presentation of the result, but also as a tool to monitor the validity and quality of the operations performed during the batch process. Operations such as feature extraction and attribute calculation of the collected data sets are validated by visual inspection. This approach is illustrated by an extensive case study, in which a collection of confocal microscopy data sets is analyzed.
[1] 1251 L. Bavoil, S. P. Callahan, P. J. Crossno, J. Freire, C. E. Scheidegger, C. T. Silva, and H. T. Vo, VisTrails: Enabling interactive multiple-view visualizations. In C. Silva, E. Gröller, and H. Rushmeier, editors, Proceedings IEEE Visualization 2005, pages 135–142, Los Alamitos (CA), 2005. IEEE Computer Society Press.
[2] T. Biddlecomei, S. Fang, K. Dunn, and M. Tuceryan, Image guided interactive volume visualization for confocal microscopy data exploration. In Proceedings 1998 SPIE International Symposium on Medical Imaging, pages 130–140, 1998.
[3] Bitplane. http://www.bitplane.com.
[4] M. Brink, Y. der Velden, W. de Leeuw, J. Mateos-Langerak, A. Belmont, R. V. Driel, and V. P.J., Truncated hp-1 lacking a functional chromodomain induces heterochromatinization upon in vivo targeting. Histochemistry and Cell Biology, 125: 53–61, 2006.
[5] D. Cmarko, P. Verschure, T. Martin, S. Krause, X. Fu, R. van Driel, and S. Fakan, Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-utp microinjection. Molecular Biology of the Cell, 10: 211–223, 1999.
[6] D. Cmarko, P. Verschure, A. Otte, R. van Driel, and S. Fakan, Polycomb group gene silencing proteins are concentrated in the perichromatin compartment of the mammalian nucleus. Journal of Cell Science, 116: 335–343, 2003.
[7] T. Cox and M. Cox, Multidimensional Scaling. Chapman & Hall, London, 1994.
[8] W. de Leeuw, R. van Liere, P. Verschure, A. Visser, E. Manders, and R. van Driel, Visualization of time dependent confocal microscopy data. In T. Ertl, B. Hamann, and A. Varshney, editors, Proceedings IEEE Visualization 2000, pages 473–476, Los Alamitos (CA), 2000. IEEE Computer Society Press.
[9] H.-C. D. Stalling, M. Westerhoff, Amira — a highly interactive system for visual data analysis. In C. Johnson and C. Hansen, editors, The Visualization Handbook, pages 749–767. Elsevier, 2005.
[10] S. Fang, T. Biddlecome, and M. Tuceryan, Image-based transfer function design for data exploration in volume visualization. In D. Ebert, H. Hagen, and H. Rushmeier, editors, Proceedings IEEE Visualization '98, pages 319–326. IEEE Computer Society Press, 1998.
[11] R. Fernandez-Gonzalez, A. Jones, E. Garcia-Rodriguez, P. Chen, A. Idica, M. Barcellos-Hoff, and C. O. de Solorzano, A system for combined three-dimensional morphological and molecular analysis of thick tissue samples. Microscopy Research and Technique, 6 (59): 522–530, 2002.
[12] W. Gu, J. Vetter, and K. Schwan, An annotated bibliography of interactive program steering. SIGPLAN Notices, 29 (9): 140–148, 1994.
[13] P. Horn and C. Peterson, Molecular biology: Chromatin higher order folding: Wrapping up transcription. Science, 297: 1824–1827, 2002.
[14] A. Inselberg, The plane with parallel coordinates. The Visual Computer, 1: 69–91, 1985.
[15] ITK. http:/www.itk.org.
[16] R. Jaenisch and A. Bird, Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet, 33: 245–254, 2003.
[17] T. Jankun-Kelly and K.-L. Ma, Visualization exploration and encapsulation via a spreadsheet-like interface. IEEE Transactions on Visualization and Computer Graphics, 7 (3): 275–287, July/September 2001.
[18] T. J. Jankun-Kelly and K.-L. Ma, A spreadsheet interface for visualization exploration. In T. Ertl, B. Hamann, and A. Varshney, editors, Proceedings IEEE Visualization 2000, pages 69–76. IEEE Computer Society, October 2000.
[19] A. Kaufman, R. Yagel, R. Bakalash, and I. Spector, Volume visualization in cell biology. In A. Kaufman, editor, Proceedings IEEE Visualization'90, pages 160–167. IEEE Computer Society Press, October 1990.
[20] D. Knowles, C. O. de Solorzano, and S. Lockett, Analysis of the 3d spatial organization of cells and sub cellular structures in tissue. In D. Farkas and R. Leif, editors, Proceedings of SPIE Vol. 3921, pages 66–73, 2000.
[21] K. Luger, A. Mader, R. Richmond, D. Sargent, and T. Richmond, Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature, 389: 251–260, 1997.
[22] G. Sakas, M. Vicker, and P. Plath, Visualization of laser confocal microscopy datasets. In R. Yagel and G. Nielson, editors, Proceedings IEEE Visualization '96, pages 375–380. IEEE Computer Society Press, 1996.
[23] R. van Driel, P. Fransz, and P. Verschure, The eukaryotic genome: a system regulated at different hierarchical levels. Journal of Cell Science, 116: 4067–4075, 2003.
[24] P. Verschure, Positioning the genome within the nucleus. Biol. Cell, 96: 569–577, 2004.
[25] P. Verschure, I. van der Kraan, W. de Leeuw, J. van der Vlag, A. Carpenter, A. Belmont, and R. van Driel, In vivo hp1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. Molecular and Cellular Biology, 25: 4552–4564, 2005.
[26] P. Verschure, I. van der Kraan, J. Enserink, M. Mone, E. Manders, and R. van Driel, Large-scale chromatin organization and the localization of proteins involved in gene expression in human cells. J.Histochem. Cytochem, 50: 1303–1312, 2002.
[27] P. Verschure, I. van der Kraan, E. Manders, and R. van Driel, Spatial relationship between transcription sites and chromosome territories. J. Cell Biology, 147: 13–24, 1999.
[28] VolView. http://www.kitware.com/productsvolview.html.
[29] Voxblast. http://www.vaytek.comvoxblast.html.
[30] R. Whitaker, D. Breen, K. Museth, and N. Soni, Segmentation of biological volume datasets using a level set framework. In A. Kaufman, editor, Volume Graphics, pages 249–263, Vienna, 2001. Springer.
Index Terms:
Biomedical visualization, features in volume data sets, large data set visualization. Author 1:
Citation:
Wim de Leeuw, Pernette Verschure, Robert van Liere, "Visualization and Analysis of Large Data Collections: a Case Study Applied to Confocal Microscopy Data," IEEE Transactions on Visualization and Computer Graphics, vol. 12, no. 5, pp. 1251-1258, Sept. 2006, doi:10.1109/TVCG.2006.195
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