Main description:

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.

Contents:

Preface...Table of Contents...Contributing Authors...
Part I Overview
1. Main Steps in Image Processing and Quantification: The Analysis WorkflowJose F. Pertusa and Jose M. Morante-Redolat
2. Open Source Tools for Biological Image AnalysisRomain Guiet, Olivier Burri, and Arne Seitz
Part II Methods Based on ImageJ Macro Programming
3. Proximity Ligation Assay Image Analysis Protocol: Addressing Receptor-Receptor InteractionsMarc Lopez-Cano, Victor Fernandez-Duenas, and Francisco Ciruela
4. Introduction to ImageJ Macro Language in a Particle Counting Analysis: Automation MattersManel Bosch
5. Automated Macro Approach to Quantify Synapse Density in 2D Confocal Images from Fixed Immunolabeled Neural Tissue SectionsE. Rebollo, J. Boix-Fabres, and M.L. Arbones
6. Automated Quantitative Analysis of Mitochondrial MorphologyAnna Bosch and Maria Calvo
7. Structure and Fluorescence Intensity Measurements in BiofilmsBertrand Cinquin and Filipa Lopes
8. 3D+Time Imaging and Image Reconstruction of Pectoral Fin during Zebrafish EmbryogenesisHanh Nguyen, Jaume Boix-Fabres, Nadine Peyrieras, and Elena Kardash
9. Automated Macro Approach to Remove Vitelline Membrane Autofluorescence in Drosophila Embryo 4D MoviesJ. Boix-Fabres, K. Karkali, E. Martin-Blanco, and E. Rebollo
10. Which Elements to Build Co-Localization Workflows? From Metrology to AnalysisPatrice Mascalchi and Fabrice P. Cordelieres
11. A Triple Colocalization Approach to Assess Traffic Patterns and their ModulationDaniel Sastre, Irene Estadella, Manel Bosch, and Antonio Felipe
12. Photobleaching and Sensitized Emission Based Methods for the Detection of Foerster Resonance Energy TransferTimo 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 CulturesPau Carrillo-Barbera, Jose M. Morante-Redolat, and Jose F. Pertusa
15. HCS Methodology for Helping in Lab Scale Image-Based AssaysJ. Soriano, G. Mata, and D. Megias
Part III Methods Based on ImageJ Plugin Development
16. Filopodia Quantification using FiloQuantGuillaume Jacquemet, Hellyeh Hamidi, and Johanna Ivaska
17. Coincidence Analysis of Molecular Dynamics by Raster Image CorrelationDavid F. Moreno and Marti Aldea
18. 3D Tracking of Migrating Cells from Live Microscopy Time-LapsesSebastien Tosi and Kyra Campbell
Part IV Methods Based on Machine Learning
19. A Cell Segmentation/Tracking Tool Based on Machine LearningHeather S. Deter, Marta Dies, Courtney C. Cameron, Nicholas C. Butzin, and Javier Buceta
20. 2D+Time Object Tracking using Fiji and ilastikAndrea Urru, Miguel Angel Gonzalez Ballester, and Chong Zhang
21. Machine Learning: Advanced Image Segmentation using ilastikAnna Kreshuk and Chong Zhang