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Computer Optimized Microscopy

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Elena Rebollo

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Manel Bosch

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

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

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Overview

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Main Steps in Image Processing and Quantification: The Analysis Workflow

      • José F. Pertusa, Jose M. Morante-Redolat
      Pages 3-21

    3. Open Source Tools for Biological Image Analysis

      • Romain Guiet, Olivier Burri, Arne Seitz
      Pages 23-37

  3. Methods Based on ImageJ Macro Programming

    1. Front Matter

      Pages 39-39
      Download chapter PDF

    2. Proximity Ligation Assay Image Analysis Protocol: Addressing Receptor-Receptor Interactions

      • Marc López-Cano, Víctor Fernández-Dueñas, Francisco Ciruela
      Pages 41-50

    3. Introduction to ImageJ Macro Language in a Particle Counting Analysis: Automation Matters

      • Manel Bosch
      Pages 51-70

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

      • Elena Rebollo, Jaume Boix-Fabrés, Maria L. Arbones
      Pages 71-97

    5. Automated Quantitative Analysis of Mitochondrial Morphology

      • Anna Bosch, Maria Calvo
      Pages 99-115

    6. Structure and Fluorescence Intensity Measurements in Biofilms

      • Bertrand Cinquin, Filipa Lopes
      Pages 117-133

    7. 3D + Time Imaging and Image Reconstruction of Pectoral Fin During Zebrafish Embryogenesis

      • Hanh Nguyen, Jaume Boix-Fabrés, Nadine Peyriéras, Elena Kardash
      Pages 135-153

    8. Automated Macro Approach to Remove Vitelline Membrane Autofluorescence in Drosophila Embryo 4D Movies

      • Jaume Boix-Fabrés, Katerina Karkali, Enrique Martín-Blanco, Elena Rebollo
      Pages 155-175

    9. Which Elements to Build Co-localization Workflows? From Metrology to Analysis

      • Patrice Mascalchi, Fabrice P. Cordelières
      Pages 177-213

    10. Triple-Colocalization Approach to Assess Traffic Patterns and Their Modulation

      • Daniel Sastre, Irene Estadella, Manel Bosch, Antonio Felipe
      Pages 215-233

    11. Photobleaching and Sensitized Emission-Based Methods for the Detection of Förster Resonance Energy Transfer

      • Timo Zimmermann
      Pages 235-274

    12. In Vivo Quantification of Intramolecular FRET Using RacFRET Biosensors

      • Manel Bosch, Elena Kardash
      Pages 275-297

    13. Cell Proliferation High-Content Screening on Adherent Cell Cultures

      • Pau Carrillo-Barberà, Jose M. Morante-Redolat, José F. Pertusa
      Pages 299-329

    14. HCS Methodology for Helping in Lab Scale Image-Based Assays

      • Joaquim Soriano, Gadea Mata, Diego Megias
      Pages 331-356

  4. Methods Based on ImageJ Plugin Development

    1. Front Matter

      Pages 357-357
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    2. Filopodia Quantification Using FiloQuant

      • Guillaume Jacquemet, Hellyeh Hamidi, Johanna Ivaska
      Pages 359-373
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Keywords

About this book

This volume explores open-source based image analysis techniques to provide a state-of-the-art collection of workflows covering current bioimage analysis problematics, including colocalization, particle counting, 3D structural analysis, ratio imaging and FRET quantification, particle tracking, high-content screening or machine learning. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and scripts, step-by-step, readily reproducible image analysis protocols, and tips on troubleshooting and avoiding known pitfalls.

Comprehensive and cutting-edge, Computer Optimized Microscopy: Methods and Protocols is a valuable resource for both novice and experienced researchers who are interested in learning more about this developing field. 



Editors and Affiliations

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

    Elena Rebollo

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

    Manel Bosch

Bibliographic Information

  • Book Title: Computer Optimized Microscopy

  • Book Subtitle: Methods and Protocols

  • Editors: Elena Rebollo, Manel Bosch

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9685-8Published: 21 August 2019

  • Softcover ISBN: 978-1-4939-9688-9Published: 21 August 2020

  • eBook ISBN: 978-1-4939-9686-5Published: 20 August 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 467

  • Number of Illustrations: 8 b/w illustrations, 181 illustrations in colour

  • Topics: Imaging / Radiology, Biological Microscopy

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