Skip to main content
SpringerLink
Log in

A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics

  • Protocol
  • First Online:
Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 500))

Summary

The architecture of living cells is difficult to describe and communicate; therefore, realistic computer models may help their understanding. 3D models should correspond both to qualitative and quantitative experimental data and therefore should include specific authoring tools such as appropriate visualization and stereological measures. For this purpose we have developed a problem solving environment for stereology-based modeling (PSE-SBM), which is an automated system for quantitative modeling of cell architecture. The PSE-SBM meets the requirement to produce models that correspond in stereological and morphologic terms to real cells and their organelles. Instead of using standard interactive graphing tools, our approach relies on functional modeling. We have built a system of implicit functions and set operations, organized in a hierarchical tree structure, which describes individual cell organelles and their 3D relations. Natural variability of size, shape, and position of organelles is achieved by random variation of the specific parameters within given limits. The resulting model is materialized by evaluation of these functions and is adjusted for a given set of specific parameters defined by the user. These principles are explained in detail, and modeling of segments of a muscle cell is used as an example to demonstrate the potential of the PSE-SBM for communication of architectural concepts and testing of structural hypotheses.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Zahradník, I., Parulek, J., and Sramek, P. (2004) Geometrical modelling of the ultrastructure of muscle cells. Physiol Res 53, 44P.

    Google Scholar 

  2. Novotová, M., Pavlovičová, M., Veksler, V.I., Ventura-Clapier, R., Zahradník, I. (2006) Ultrastructural remodeling of fast skeletal muscle fibers induced by invalidation of creatine kinase. Am J Physiol Cell Physiol. 291, C1279–1285.

    Google Scholar 

  3. Parulek, J. (2007) Problem solving environment for stereology based implicit modeling of muscle cells. Ph.D. thesis, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovak Republic.

    Google Scholar 

  4. Parulek, J., Šrámek, M., and Zahradník, I. (2004) Geometrical modelling of muscle cells based on functional representation of polygons. J WSCG 12, 121–124.

    Google Scholar 

  5. Parulek, J., Zahradník, I., and Šrámek, M. (2004) A modelling tool for construction of 3d structure of muscle cells, in Analysis of Biomedical Signals and Images. Proceedings of the 17th Biennial International EURASIP Conference BIOSIGNAL 2004 (Jan, J., Kozumplik, J., and Provazník, I., eds.), Vutium Press, Brno, pp. 267–269.

    Google Scholar 

  6. Parulek, J., Zahradník, I., Novotová, M., and Šrámek, M. (2006) Geometric modeling of muscle cells. G.I.T. Imaging Microsc 8, 58–59.

    Article  Google Scholar 

  7. Parulek, J., Ciglán, M., Šimo, B., Šrámek, M., Hluchý, L., and Zahradník, I. (2007) Grid problem solving environment for stereology based modeling, in OTM Confederated International Conferences, Part II (Meersman, R., Tari, Z., eds.), Springer, Berlin, pp. 1417–1434.

    Google Scholar 

  8. Blender, http://www.blender.org, accessed on December 14, 2007.

  9. Truespace, http://www.caligari.com/, accessed on December 14, 2007.

  10. Bloomenthal, J., Bajaj, Ch., Blinn, J., Cani-Gascuel, M.-P., Rockwood, A., Wyvill, B., and Wyvill, G. (1997) Introduction to Implicit Surfaces. Morgan Kaufman, San Francisco, CA.

    Google Scholar 

  11. Velho, L., Figueiredo, L. H., and Gomes, J. A. (1998) Implicit Objects in Computer Graphics. Springer, New York.

    Google Scholar 

  12. Blinn, J. (1982) A generalization of algebraic surface drawing. ACM Trans Graph 1, 235–256.

    Article  Google Scholar 

  13. Wyvill, G., Mcpheeters, C., and Wyvill, B. (1986) Data structure for soft objects. Vis Comput 2, 227–234.

    Article  Google Scholar 

  14. Nishimura, H., Hirai, M., Kavai, T., Kawata, T., Shirakawa, I., and Omura, K. (1985) Object modeling by distribution function and a method of image generation. Trans IECE Jpn J68-D, 718–725.

    Google Scholar 

  15. Bloomenthal, J. and Wyvill, B. (1990) Interactive techniques for implicit modeling, in SI3D'90: Proceedings of the 1990 Symposium on Interactive 3D graphics, ACM, New York, pp. 109–116.

    Google Scholar 

  16. Bloomenthal, J. and Shoemaker, S. (1991) Convolution surfaces, in SIGGRAPH'91: Proceedings of the 18th Annual Conference on Computer Graphics and Interactive Techniques, ACM, New York, pp. 251–256.

    Google Scholar 

  17. Czanner, S., Durikovic, R., and Inoue, H. (2001) Growth simulation of human embryo brain, in SCCG'01: Proceedings of the 17th Spring conference on Computer graphics, IEEE Computer Society, Washington, DC, p. 139.

    Google Scholar 

  18. Durikovic, R. and Czanner, S. (2002) Implicit surfaces for dynamic growth of digestive system, in SMI'02: Proceedings of the Shape Modeling International 2002, IEEE Computer Society, Washington, DC, p. 111.

    Google Scholar 

  19. Oeltze, S. and Preim, B. (2004) Visualization of anatomic tree structures with convolution surfaces, in Joint EUROGRAPHICS–IEEE TCVG Symposium on Visualization (Deussen, O., Hansen, C., Keim, D. A., and Saupe, D., eds.), The Eurographics Association, Aire-la-Ville, Switzerland, pp. 311–320.

    Google Scholar 

  20. Barr, A. (1981) Superquadrics and angle-preserving transformations. IEEE Comput Graph Appl 1, 11–23.

    Article  Google Scholar 

  21. Pasko, A. A., Adzhiev, V., Sourin, A., and Savchenko, V. V. (1995) Function representation in geometric modeling: concepts, implementation and applications. Vis Comput 11, 429–446.

    Article  Google Scholar 

  22. Wyvill, B. and van Overveld, K. (1997) Warping as a modelling tool for csg/implicit models, in Proceedings of the International Conference on Shape Modeling and Applications, 1997, IEEE Computer Society, Aizu, Japan, pp. 205–214.

    Google Scholar 

  23. Ricci, A. (1972) A constructive geometry for computer graphics. Comput J 16, 157–160.

    Article  Google Scholar 

  24. Shapiro, V. (2007) Semi-analytic geometry with R-functions. Acta Numerica 16, 239–303.

    Article  Google Scholar 

  25. Pasko, A. A. and Savchenko, V. V. (1994) Blending operations for the functionally based constructive geometry, in Set-theoretic Solid Modeling: Techniques and Applications, CSG 94 Conference Proceedings, Information Geometers, Winchester, UK, pp. 151–161.

    Google Scholar 

  26. Dekkers, D., van Overveld, K., and Golsteijn, R. (2004) Combining CSG modeling with soft blending using Lipschitz-based implicit surfaces. Vis Comput 20, 380–391.

    Article  Google Scholar 

  27. Muraki, S. (1991) Volumetric shape description of range data using blobby model, in SIGGRAPH'91: Proceedings of the18th Annual Conference on Computer Graphics and Interactive Techniques, ACM, New York, pp. 227–235.

    Google Scholar 

  28. Duchon, J. (1977) Splines minimizing rotation-invariant seminorms in Sobolev spaces, in Lecture Notes in Mathematics, Vol. 571 (Schempp, W. and Zeller, K., eds.), Springer, Berlin, pp. 85–100.

    Google Scholar 

  29. Floater, M. S. and Iske, A. (1996) Multistep scattered data interpolation using compactly supported radial basis functions. J Comput Appl Math 73, 65–78.

    Article  Google Scholar 

  30. Savchenko, V. V., Pasko, A. A., Okunev, O. G., and Kunii, T. L. (1995) Function representation of solids reconstructed from scattered surface points and contours. Comput Graph Forum 14, 181–188.

    Article  Google Scholar 

  31. Turk, G. and O'Brien, J. F. (2002) Modelling with implicit surfaces that interpolate. ACM Trans Graph 21, 855–873.

    Article  Google Scholar 

  32. Carr, J. C., Beatson, R. K., Cherrie, J. B., Mitchell, T. J., Fright, W. R., McCallum, B. C., and Evans, T. R. (2001) Reconstruction and representation of 3d objects with radial basis functions, in SIGGRAPH'01: Proceedings of the 28th Annual Conference on Computer Graphics and Interactive Techniques, ACM, New York, pp. 67–76.

    Google Scholar 

  33. Crampin, E. J., Halstead, M., Hunter, P., Nielsen, P., Noble, D., Smith, N., and Tawhai, M. (2004) Computational physiology and the physiome project. Exp Physiol 89, 1–26.

    Article  PubMed  Google Scholar 

  34. Prusinkiewicz, P. (1993) Modeling and visualisation of biological structures, in Proceedings of Graphics Interface'93, Toronto, ON, pp. 128–137.

    Google Scholar 

  35. Wyvill, B., Guy, A., and Galin, E. (1999) Extending the csg tree (warping, blending and boolean operations in an implicit surface modeling system). Comput Graph Forum 18, 149–158.

    Article  Google Scholar 

  36. Witkin, A. P. and Heckbert, P. S. (1994) Using particles to sample and control implicit surfaces, in SIGGRAPH'94: Proceedings of the 21st Annual Conference on Computer Graphics and Interactive Techniques, ACM, New York, pp. 269–277.

    Google Scholar 

  37. Adzhiev, V., Cartwright, R., Fausett, E., Ossipov, A., Pasko, A., and Savchenko, V. (1999) Hyperfun project: A framework for collaborative multidimensional f-rep modeling, in Proceedings of the Implicit Surfaces'99 EUROGRAPHICS/ACM SIGGRAPH Workshop, New York, pp. 59–69.

    Google Scholar 

  38. Schroeder, W. J., Martin, K. M., and Lorensen, W. E. (1996) The design and implementation of an object-oriented toolkit for 3D graphics and visualization, in VIS'96: Proceedings of the Seventh conference on Visualization'96, IEEE Computer Society, Los Alamitos, CA, pp. 93–100.

    Google Scholar 

  39. Lorensen, W. E. and Cline, H. E. (1987) Marching cubes: a high resolution 3D surface construction algorithm. Comput Graph 21, 163–169.

    Article  Google Scholar 

  40. Bloomenthal, J. (1988) Polygonization of implicit surfaces. Comput Aided Geom Des 5, 341–355.

    Article  Google Scholar 

  41. Povray. Povray — the persistence of vision ray tracer. http://www.povray.org/, accessed on October 17, 2007.

  42. Parulek, J., Novotný, P., and Šrámek, M. (2006) XISL – a development tool for construction of implicit surfaces, in SCCG'06: Proceedings of the 22nd Spring Conference on Computer Graphics, Comenius University, Bratislava, pp. 128–135.

    Google Scholar 

  43. Pasko, A., Savchenko, A., and Savchenko, V. (1996) Polygon-to-function conversion for sweeping, in The Eurographics/SIGGRAPH Workshop on Implicit Surfaces (Hart, J. and van Overveld, K., eds.), Eurographics, Eindhoven, The Netherlands, pp. 163–171.

    Google Scholar 

  44. Sourin, A. I. and Pasko, A. A. (1996) Function representation for sweeping by a moving solid. IEEE Transactions on Visualization and Computer Graphics 2, 11–18.

    Article  Google Scholar 

  45. Schmidt, R. and Wyvill, B. (2005) Generalized sweep templates for implicit modeling, in GRAPHITE'05: Proceedings of the 3rd International Conference on Computer Graphics and Iinteractive Techniques, ACM, New York, pp. 187–196.

    Google Scholar 

  46. Parulek, J. and Šrámek, M. (2007) Implicit modeling by metamorphosis of 2D shapes, in SCCG'07: Proceedings of the 23rd Spring Conference on Computer Graphics, Comenius University, Bratislava, pp. 227–234.

    Google Scholar 

  47. GeomCell http://cvs.ui.sav.sk/twiki/bin/view/EGEE/UserGuide, accessed on December 13, 2008.

    Google Scholar 

  48. PLY format. http://www.cc.gatech.edu/projects/large_models/ply.html, accessed on December 14, 2007.

  49. Sramek, M., Dimitrov, L. I., Straka, M., and Cervenansky, M. (2004) The f3d tools for processing and visualization of volumetric data. J Med Inform Technol 7, MIP-71—MIP-79

    Google Scholar 

  50. Elias, H., Henning, A. and Schwarz, D. E. (1971) Stereology: application to biomedical research. Physiol Rev 51, 158–196.

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was made possible due to the support of APVT 51-31104, APVV-20-056105, and VEGA 2/6079/26. The authors are thankful to M. Ciglan for collaboration on grid application, and to A. Zahradníková for comments on the manuscript.

Author information

Authors and Affiliations

  1. Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlárska 5, 833 34, Bratislava, Slovak Republic

    Ivan Zahradník*

Authors
  1. Július Parulek
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Miloš Šrámek
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michal Červęanský
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marta Novotová
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ivan Zahradník*
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ivan Zahradník* .

Editor information

Editors and Affiliations

    Rights and permissions

    Reprints and permissions

    Copyright information

    © 2009 Humana Press

    About this protocol

    Cite this protocol

    Parulek, J., Šrámek, M., Červęanský, M., Novotová, M., Zahradník*, I. (2009). A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics. In: Maly, I. (eds) Systems Biology. Methods in Molecular Biology, vol 500. Humana Press. https://doi.org/10.1007/978-1-59745-525-1_10

    Download citation

    • DOI: https://doi.org/10.1007/978-1-59745-525-1_10

    • Published:

    • Publisher Name: Humana Press

    • Print ISBN: 978-1-934115-64-0

    • Online ISBN: 978-1-59745-525-1

    • eBook Packages: Springer Protocols

    Publish with us

    Policies and ethics

    Search

    Navigation