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Designing Image Analysis Pipelines in Light Microscopy: A Rational Approach

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Light Microscopy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1563))

Abstract

With the progress of microscopy techniques and the rapidly growing amounts of acquired imaging data, there is an increased need for automated image processing and analysis solutions in biological studies. Each new application requires the design of a specific image analysis pipeline, by assembling a series of image processing operations. Many commercial or free bioimage analysis software are now available and several textbooks and reviews have presented the mathematical and computational fundamentals of image processing and analysis. Tens, if not hundreds, of algorithms and methods have been developed and integrated into image analysis software, resulting in a combinatorial explosion of possible image processing sequences. This paper presents a general guideline methodology to rationally address the design of image processing and analysis pipelines. The originality of the proposed approach is to follow an iterative, backwards procedure from the target objectives of analysis. The proposed goal-oriented strategy should help biologists to better apprehend image analysis in the context of their research and should allow them to efficiently interact with image processing specialists.

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Author information

Authors and Affiliations

  1. Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain

    Ignacio Arganda-Carreras

  2. Computer Science and Artificial Intelligence Department, Basque Country University (UPV/EHU), 20018, Donostia-San Sebastian, Spain

    Ignacio Arganda-Carreras

  3. Donostia International Physics Center (DIPC), 20018, Donostia-San Sebastian, Spain

    Ignacio Arganda-Carreras

  4. Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78000, Versailles, France

    Philippe Andrey

  5. Sorbonne Universités, UPMC Univ Paris 06, UFR 927, Paris, France

    Philippe Andrey

Authors
  1. Ignacio Arganda-Carreras
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  2. Philippe Andrey
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Correspondence to Philippe Andrey .

Editor information

Editors and Affiliations

  1. Department of Biological Chemistry, UCLA School of Medicine, Los Angeles, California, USA

    Yolanda Markaki

  2. Biozentrum der LMU Munchen, Planegg-Martinsried, Germany

    Hartmann Harz

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Arganda-Carreras, I., Andrey, P. (2017). Designing Image Analysis Pipelines in Light Microscopy: A Rational Approach. In: Markaki, Y., Harz, H. (eds) Light Microscopy. Methods in Molecular Biology, vol 1563. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6810-7_13

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  • DOI: https://doi.org/10.1007/978-1-4939-6810-7_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6808-4

  • Online ISBN: 978-1-4939-6810-7

  • eBook Packages: Springer Protocols

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