Computer Optimized Microscopy: Methods and Protocols

ISBN-13: 9781493996889 / Angielski / Miękka / 2020 / 467 str.

Elena Rebollo; Manel Bosch

Spis treści

Preface...

Table of Contents...

Contributing Authors...

Part I Overview

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

José F. Pertusa and Jose M. Morante-Redolat

2. Open Source Tools for Biological Image Analysis

Romain Guiet, Olivier Burri, and Arne Seitz

Part II Methods Based on ImageJ Macro Programming

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

Marc López-Cano, Víctor Fernández-Dueñas, and Francisco Ciruela

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

Manel Bosch

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

E. Rebollo, J. Boix-Fabrés, and M.L. Arbones

6. Automated Quantitative Analysis of Mitochondrial Morphology

Anna Bosch and María Calvo

7. Structure and Fluorescence Intensity Measurements in Biofilms

Bertrand Cinquin and Filipa Lopes

8. 3D+Time Imaging and Image Reconstruction of Pectoral Fin during Zebrafish Embryogenesis

Hanh Nguyen, Jaume Boix-Fabrés, Nadine Peyriéras, and Elena Kardash

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

J. Boix-Fabrés, K. Karkali, E. Martin-Blanco, and E. Rebollo

10. Which Elements to Build Co-Localization Workflows? From Metrology to Analysis

Patrice Mascalchi and Fabrice P. Cordelières

11. A Triple Colocalization Approach to Assess Traffic Patterns and their Modulation

Daniel Sastre, Irene Estadella, Manel Bosch, and Antonio Felipe

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

Timo Zimmermann

13. In Vivo Quantification of Intramolecular FRET using RacFRET Biosensors Manel Bosch and Elena Kardash

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

Pau Carrillo-Barberà, Jose M. Morante-Redolat, and José F. Pertusa

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

J. Soriano, G. Mata, and D. Megias

Part III Methods Based on ImageJ Plugin Development 

16. Filopodia Quantification using FiloQuant

Guillaume Jacquemet, Hellyeh Hamidi, and Johanna Ivaska

17. Coincidence Analysis of Molecular Dynamics by Raster Image Correlation

David F. Moreno and Martí Aldea

18. 3D Tracking of Migrating Cells from Live Microscopy Time-Lapses

Sébastien Tosi and Kyra Campbell

Part IV Methods Based on Machine Learning 

19. A Cell Segmentation/Tracking Tool Based on Machine Learning

Heather S. Deter, Marta Dies, Courtney C. Cameron, Nicholas C. Butzin, and Javier Buceta

20. 2D+Time Object Tracking using Fiji and ilastik

Andrea Urru, Miguel Angel González Ballester, and Chong Zhang

21. Machine Learning: Advanced Image Segmentation using ilastik

Anna Kreshuk and Chong Zhang

Blurb

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.