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CellProfiler and KNIME: Open-Source Tools for High-Content Screening

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Target Identification and Validation in Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1953))

Abstract

High-content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tackled in academic research, HCS could experience some profound changes in the future, mainly with more imaging modalities and smart microscopes being developed. One of the limitations in the establishment of HCS in academia is flexibility and cost. Flexibility is important to be able to adapt the HCS setup to accommodate the multiple different assays typical of academia. Many cost factors cannot be avoided, but the costs of the software packages necessary to analyze large datasets can be reduced by using open-source software. We present and discuss the open-source software CellProfiler for image analysis and KNIME for data analysis and data mining that provide software solutions, which increase flexibility and keep costs low.

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Acknowledgments

This work was supported by the Max Planck Gesellschaft.

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Authors and Affiliations

  1. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

    Martin Stöter, Antje Janosch, Rico Barsacchi & Marc Bickle

Authors
  1. Martin Stöter
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  2. Antje Janosch
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  3. Rico Barsacchi
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  4. Marc Bickle
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Corresponding author

Correspondence to Marc Bickle .

Editor information

Editors and Affiliations

  1. Pharmacology and Translational Research, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria

    Jürgen Moll

  2. Department of Cancer Cell Signaling, Boehringer Ingelheim RCV GmBH & Co KG, Vienna, Austria

    Sebastian Carotta

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Stöter, M., Janosch, A., Barsacchi, R., Bickle, M. (2019). CellProfiler and KNIME: Open-Source Tools for High-Content Screening. In: Moll, J., Carotta, S. (eds) Target Identification and Validation in Drug Discovery. Methods in Molecular Biology, vol 1953. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9145-7_4

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  • DOI: https://doi.org/10.1007/978-1-4939-9145-7_4

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9144-0

  • Online ISBN: 978-1-4939-9145-7

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