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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.
List of contents
Main Steps in Image Processing and Quantification: The Analysis Workflow.- Open Source Tools for Biological Image Analysis.- Proximity Ligation Assay Image Analysis Protocol: Addressing Receptor-Receptor Interactions.- Introduction to ImageJ Macro Language in a Particle Counting Analysis: Automation Matters.- Automated Macro Approach to Quantify Synapse Density in 2D Confocal Images from Fixed Immunolabeled Neural Tissue Sections.- Automated Quantitative Analysis of Mitochondrial Morphology.- Structure and Fluorescence Intensity Measurements in Biofilms.- 3D+Time Imaging and Image Reconstruction of Pectoral Fin during Zebrafish Embryogenesis.- Automated Macro Approach to Remove Vitelline Membrane Autofluorescence in Drosophila Embryo 4D Movies.- Which Elements to Build Co-Localization Workflows? From Metrology to Analysis.- A Triple Colocalization Approach to Assess Traffic Patterns and their Modulation.- Photobleaching and Sensitized Emission Based Methods for the Detection of Förster Resonance Energy Transfer.- In Vivo Quantification of Intramolecular FRET using RacFRET Biosensors Manel.- Cell Proliferation High-Content Screening on Adherent Cell Cultures.- HCS Methodology for Helping in Lab Scale Image-Based Assays.- Filopodia Quantification using FiloQuant.- Coincidence Analysis of Molecular Dynamics by Raster Image Correlation.- 3D Tracking of Migrating Cells from Live Microscopy Time-Lapses.- A Cell Segmentation/Tracking Tool Based on Machine Learning.- 2D+Time Object Tracking using Fiji and ilastik.- Machine Learning: Advanced Image Segmentation using ilastik.
Summary
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.
