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Strategies and Solutions to Maintain and Retain Data from High Content Imaging, Analysis, and Screening Assays

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High Content Screening

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1683))

Abstract

Data analysis and management in high content screening (HCS) has progressed significantly in the past 10 years. The analysis of the large volume of data generated in HCS experiments represents a significant challenge and is currently a bottleneck in many screening projects. In most screening laboratories, HCS has become a standard technology applied routinely to various applications from target identification to hit identification to lead optimization. An HCS data management and analysis infrastructure shared by several research groups can allow efficient use of existing IT resources and ensures company-wide standards for data quality and result generation. This chapter outlines typical HCS workflows and presents IT infrastructure requirements for multi-well plate-based HCS.

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References

  1. Liu B, Li S, Hu J (2004) Technological advances in high-throughput screening. Am J Pharmacogenomics 4(4):263–276

    Article  CAS  Google Scholar 

  2. Kozak K (2010) Large scale data handling in biology. Ventus Publishing ApS, Frederiksberg. ISBN: 978-87-7681-555-4

    Google Scholar 

  3. Michel P, Antony A, Trefois C, Stojanovic A, Baumuratov AS, Kozak K (2013) Light microscopy applications in systems biology: opportunities and challenges. Cell Commun Signal 11:24. doi:10.1186/1478-811X-11-24

    Article  Google Scholar 

  4. Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, Ohl P, Thiel K, Wiswedel B (2009) KNIME - the Konstanz information miner. ACM SIGKDD Explor Newsl 11:26

    Article  Google Scholar 

  5. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 2012(9):676–682

    Article  Google Scholar 

  6. Zwolinski L, Kozak M, Kozak K (2013) 1Click1View: interactive visualization methodology for RNAi cell-based microscopic screening. Biomed Res Int 2013:1–11

    Article  Google Scholar 

  7. Linkert M et al (2010) Metadata matters: access to image data in the real world. J Cell Biol 189:777–782

    Article  CAS  Google Scholar 

  8. Millard BL et al (2011) Adaptive informatics for multifactorial and high-content biological data. Nat Methods 8:487–493

    Article  CAS  Google Scholar 

  9. Nichols A (2007) High content screening as a screening tool in drug discovery. Methods Mol Biol 356:379–387

    CAS  Google Scholar 

  10. Myers G (2012) Why bioimage informatics matters. Nat Methods 9:659–660

    Article  CAS  Google Scholar 

  11. Swedlow JR, Eliceiri KW (2009) Open source bioimage informatics for cell biology. Trends Cell Biol 19:656–660

    Article  CAS  Google Scholar 

  12. Peng H (2008) Bioimage informatics: a new area of engineering biology. Bioinformatics 24:1827–1836

    Article  CAS  Google Scholar 

  13. Eliceiri KW, Berthold MR, Goldberg IG, Ibánez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE (2012) Biological imaging software tools. Nat Methods 9:697–710

    Article  CAS  Google Scholar 

  14. Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan M, Schneider JE, Tomancak P, Hériché JK (2010) Visualization of image data from cells to organisms. Nat Methods 7:S26–S41

    Article  CAS  Google Scholar 

  15. Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmstrom L, Aebersold R, Rinn B (2011) openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics 12:468. doi:10.1186/1471-2105-12-468

    Article  Google Scholar 

  16. Jackson D, Lenard M, Zelensky A, Shaikh M, Scharpf JV, Shaginaw R, Nawade M, Agler M, Cloutier NJ, Fennell M, Guo Q, Wardwell-Swanson J, Zhao D, Zhu Y, Miller C, Gill J (2010) HCS road: an enterprise system for integrated HCS data management and analysis. J Biomol Screen 15(7):882–891

    Article  Google Scholar 

  17. Columbus Platform. http://www.perkinelmer.com/pages/020/cellularimaging/products/columbus.xhtml

  18. Berthold MR et al (2009) KNIME - the Konstanz information miner: version 2.0 and beyond. SIGKDD Explor. Newsletter 11:26–31

    Google Scholar 

  19. Peter A (2007) Blume: The LabVIEW Style Book Part of the National Instruments Virtual Instrumentation Series. Prentice Hall, Upper Saddle River

    Google Scholar 

  20. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7:R100. PMID: 17076895

    Article  Google Scholar 

  21. Rouilly V, Pujadas E, Hullár B, Balázs C, Kunszt P, Podvinec M (2012) iBRAIN2: automated analysis and data handling for RNAi screens. Stud Health Technol Inform 175:205–213

    Google Scholar 

  22. Snijder B et al (2012) Single-cell analysis of population context advances RNAi screening at multiple levels. Mol Syst Biol 8:579

    Article  Google Scholar 

  23. Datta SSR (2006) "Spotfire's predictive technology helps companies mine data". CNNMoney.com. Spotfire, a Business-intelligence software company based in Somerville

  24. Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4(2):67–73

    Article  CAS  Google Scholar 

  25. Screener Platform: https://www.genedata.com/products/screener/

  26. Konig R et al (2007) A probability-based approach for the analysis of large-scale RNAi screens. Nat Methods 4:847–849

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Carl Gustav Carus University Hospital, Clinic for Neurology, Medical Faculty, Technical University Dresden, Fetscherstraße 74, 01307, Dresden, Germany

    K. Kozak

  2. Fraunhofer IWS, Winterbergstraße 28, Dresden, 01277, Germany

    K. Kozak

  3. Scientific IT Services, ETH Zürich, Zurich, Switzerland

    B. Rinn

  4. Screener Business Unit, Genedata AG, Basel, Switzerland

    O. Leven

  5. University of Basel and SyBIT, Basel, Switzerland

    M. Emmenlauer

  6. Wroclaw University of Economics, Wrocław, Poland

    K. Kozak

Authors
  1. K. Kozak
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  2. B. Rinn
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  3. O. Leven
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  4. M. Emmenlauer
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Corresponding author

Correspondence to K. Kozak .

Editor information

Editors and Affiliations

  1. Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

    Paul A. Johnston

  2. Bahama Bio, LLC, Bahama, North Carolina, USA

    Oscar J. Trask

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Kozak, K., Rinn, B., Leven, O., Emmenlauer, M. (2018). Strategies and Solutions to Maintain and Retain Data from High Content Imaging, Analysis, and Screening Assays. In: Johnston, P., Trask, O. (eds) High Content Screening. Methods in Molecular Biology, vol 1683. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7357-6_9

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  • DOI: https://doi.org/10.1007/978-1-4939-7357-6_9

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7355-2

  • Online ISBN: 978-1-4939-7357-6

  • eBook Packages: Springer Protocols

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