Skip to main content

A Web2.0 Strategy for the Collaborative Analysis of Complex Bioimages

  • Conference paper
Advances in Intelligent Data Analysis X (IDA 2011)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 7014))

Included in the following conference series:

Abstract

Life science research aims at understanding the relationships in genomics, proteomics and metabolomics on all levels of biological self organization, dealing with data of increasing dimension and complexity. Bioimages represent a new data domain in this context, gaining growing attention since it closes important gaps left by the established molecular techniques. We present a new, web-based strategy that allows a new way of collaborative bioimage interpretaion through knowledge integration. We show, how this can be supported by combining data mining algorithms running on powerful compute servers and a next generation rich internet application (RIA) front-end offering database/project management and high-level tools for exploratory data analysis and annotation. We demonstrate our system BioIMAX using a bioimage dataset from High-Content Screening experiments to study bacterial infection in cell cultures.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Megason, S.G., Fraser, S.E.: Imaging in Systems Biology. Cell 130(5), 784–795 (2007)

    Article  Google Scholar 

  2. Shneiderman, B.: Science 2.0. Science 319, 1349–1350 (2008)

    Article  Google Scholar 

  3. Waldrop, M.M.: Science 2.0 - Great new tool, or great risk? Scientific American (January 9, 2008)

    Google Scholar 

  4. Loyek, C., et al.: BioIMAX: A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data. BMC Bioinformatics 12, 297 (2011)

    Article  Google Scholar 

  5. Image Processing and Analysis in Java, http://rsbweb.nih.gov/ij/

  6. Abramoff, M.D., Magelhaes, P.J., Ram, S.J.: Image Processing with Image. J. Biophoto. Int. 11(7), 36–42 (2004)

    Google Scholar 

  7. Insight Segmentation and Registration Toolkit (ITK), http://www.itk.org

  8. Yoo, T.S., et al.: Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK - the Insight Toolkit. In: Westwood, J. (ed.) Proceedings of Medicine Meets Virtual Reality, pp. 586–592. IOS Press, Amsterdam (2002)

    Google Scholar 

  9. Carpenter, A.E., et al.: CellProfiler: image analysis software fpr identifying and quantifying cell phenotypes. Genome Biol. 7(10), R100 (2006)

    Article  Google Scholar 

  10. Lamprecht, M.R., Sabatini, D.M., Carpenter, A.E.: CellProfiler: free, versatile software for automated biological image analysis. Biotechniques 42, 71–75 (2007)

    Article  Google Scholar 

  11. Swedlow, J.R., et al.: Informatics and Quantitative Analysis in Biological Imaging. Science 300, 100–102 (2003)

    Article  Google Scholar 

  12. Kvilekval, K., et al.: Bisque: a platform for bioimage analysis and management. Bioinformatics 26(4), 544–552 (2010)

    Article  Google Scholar 

  13. Ramaswamy, V., et al.: Listeria - review of epidemiology and pathogenesis. J. Microbiol. Immunol. Infect. 40(1), 4–13 (2007)

    Google Scholar 

  14. Ireton, K.: Entry of the bacterial pathogen Listeria monocytogenes into mammalian cells. Cell Microbioll. 9(6), 1365–1375 (2007)

    Article  Google Scholar 

  15. Adobe Flex, http://www.adobe.com/products/flex/

  16. MySQL, http://www.mysql.com/

  17. AMFPHP - Action Message Format PHP, http://amfphp.sourceforge.net/

  18. Manders, E., et al.: Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy. J. Cell Science 103, 857–862 (1992)

    Google Scholar 

  19. Ware, C.: Information Visualization - Perception for Design. Morgan Kaufmann Publishers Inc., San Francisco (2004)

    Google Scholar 

  20. Keim, D.A.: Information Visualization and Visual Data Mining. IEEE Transactions on Visualization and Computer Graphics 7(1), 100–107 (2002)

    MathSciNet  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Loyek, C., Kölling, J., Langenkämper, D., Niehaus, K., Nattkemper, T.W. (2011). A Web2.0 Strategy for the Collaborative Analysis of Complex Bioimages. In: Gama, J., Bradley, E., Hollmén, J. (eds) Advances in Intelligent Data Analysis X. IDA 2011. Lecture Notes in Computer Science, vol 7014. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24800-9_25

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-24800-9_25

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-24799-6

  • Online ISBN: 978-3-642-24800-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics