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Forget About Electron Micrographs: A Novel Guide for Using 3D Models for Quantitative Analysis of Dense Reconstructions

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Book cover Volume Microscopy

Part of the book series: Neuromethods ((NM,volume 155))

Abstract

With the rapid evolvement in the automation of serial micrographs, acquiring fast and reliably giga- to terabytes of data is becoming increasingly common. Optical, or physical sectioning, and subsequent imaging of biological tissue at high resolution, offers the chance to postprocess, segment, and reconstruct micro- and nanoscopical structures, and then reveal spatial arrangements previously inaccessible or hardly imaginable with simple, single section, two-dimensional images. In some cases, three-dimensional models highlighted peculiar morphologies in a way that two-dimensional representations cannot be considered representative of that particular object morphology anymore, like mitochondria for instance. Observations like these are taking scientists toward a more common use of 3D models to formulate functional hypothesis, based on morphology. Because such models are so rich in details, we developed tools allowing for performing qualitative, visual assessments, as well as quantification directly in 3D. In this chapter we will revise our working pipeline and show a step-by-step guide to analyze our dataset.

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Author information

Authors and Affiliations

  1. BESE Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Daniya J. Boges, Pierre Julius Magistretti & Corrado Calì

  2. Visual Computing Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

    Marco Agus

  3. Department of Neuroscience “Rita Levi Montalcini”, Neuroscience Institute Cavalieri Ottolenghi, Università degli studi di Torino, Torino, Italy

    Corrado Calì

Authors
  1. Daniya J. Boges
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  2. Marco Agus
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  3. Pierre Julius Magistretti
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  4. Corrado Calì
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Corresponding author

Correspondence to Corrado Calì .

Editor information

Editors and Affiliations

  1. Cryo EM, Centre for Advanced Materials (CAM), Universität Heidelberg, Heidelberg, Germany

    Irene Wacker

  2. Sector Life Science, Carl Zeiss Microscopy GmbH, Oberkochen, Germany, Carl Zeiss, Oberkochen, Germany

    Eric Hummel

  3. BioQuant, Universität Heidelberg, Heidelberg, Germany, Cryo EM, BioQuant, Universitätsklinikum Heidelberg, Heidelberg, Germany

    Steffen Burgold

  4. Cryo EM, Centre for Advanced Materials (CAM), Universität Heidelberg, Heidelberg, Germany, Cryo EM, BioQuant, Universitätsklinikum Heidelberg, Heidelberg, Germany

    Rasmus Schröder

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Boges, D.J., Agus, M., Magistretti, P.J., Calì, C. (2020). Forget About Electron Micrographs: A Novel Guide for Using 3D Models for Quantitative Analysis of Dense Reconstructions. In: Wacker, I., Hummel, E., Burgold, S., Schröder, R. (eds) Volume Microscopy . Neuromethods, vol 155. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0691-9_14

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  • DOI: https://doi.org/10.1007/978-1-0716-0691-9_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0690-2

  • Online ISBN: 978-1-0716-0691-9

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