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Automated Macro Approach to Quantify Synapse Density in 2D Confocal Images from Fixed Immunolabeled Neural Tissue Sections

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Computer Optimized Microscopy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2040))

Abstract

This chapter describes an ImageJ/Fiji automated macro approach to estimate synapse densities in 2D fluorescence confocal microscopy images. The main step-by-step imaging workflow is explained, including example macro language scripts that perform all steps automatically for multiple images. Such tool provides a straightforward method for exploratory synapse screenings where hundreds to thousands of images need to be analyzed in order to render significant statistical information. The method can be adapted to any particular set of images where fixed brain slices have been immunolabeled against validated presynaptic and postsynaptic markers.

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Acknowledgments

We are grateful to Juan Arranz for immunofluorescence experiments and Manel Bosch for useful advice on macro programming. MLA provided samples and biological input. JBF contributed the chromatic shift calculation macro. ER performed the imaging, designed and programmed the macro analysis pipeline, and wrote the paper. Images were acquired at the Molecular Imaging Platform IBMB (CSIC) with the support from the Spanish Ministry of Economy and Competitiveness and the European Regional Development Fund CSIC13-4E-2065.

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Authors and Affiliations

  1. Molecular Imaging Platform, Molecular Biology Institute of Barcelona, Spanish Research Council (CSIC), Barcelona, Spain

    Jaume Boix-Fabrés

  2. Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain

    Maria L. Arbones

  3. Molecular Imaging Platform, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Spain

    Elena Rebollo

Authors
  1. Elena Rebollo
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  2. Jaume Boix-Fabrés
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  3. Maria L. Arbones
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Corresponding author

Correspondence to Elena Rebollo .

Editor information

Editors and Affiliations

  1. Molecular Imaging Platform, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Spain

    Elena Rebollo

  2. Scientific and Technological Centers (CCiTUB), Universitat de Barcelona, Barcelona, Spain

    Manel Bosch

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Rebollo, E., Boix-Fabrés, J., Arbones, M.L. (2019). Automated Macro Approach to Quantify Synapse Density in 2D Confocal Images from Fixed Immunolabeled Neural Tissue Sections. In: Rebollo, E., Bosch, M. (eds) Computer Optimized Microscopy. Methods in Molecular Biology, vol 2040. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9686-5_5

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  • DOI: https://doi.org/10.1007/978-1-4939-9686-5_5

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9685-8

  • Online ISBN: 978-1-4939-9686-5

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