Optical Phase Maps: Documentation
Contents:
Image analysis pipeline
Introduction
Software installers
Scientific citations
Cube Converter
Polarised microscopy processor
Data management
Optical image processing
Multi-modal pyramid generator
Configure Z-stack
Exportation mode
Chemistry Simplifier
Image processing
Data management
Image pyramid operations
Analysis definition
Input list
Dimensionality reduction
Processed volume
Output adjustments
Montage operations
Image alignment
Phase Interpreter
Define map
Customise phase map
Image analysis
ROI annotation tool
Image Analysis Workshop
Part 1: QuPath interface
Exercise 1: Demonstration by instructor - opening a 250 GB image.
Exercise 2: QuPath multi-view canvas
Exercise 3: ‘Boxing in’ images within the multi-view canvas
Exercise 4: Multi-view with ray tracing and dimensionality reduction
Part 2A: Cube Converter and Chemistry Simplifier work
Exercise 1: Ray tracing
Exercise 2: Making a z-stack
Exercise 3: Dimensionality reduction
Part 3: Image alignment
Option A: BigWarp
Option B: Warpy
Part 4: Phase mapping and interpretation
Exercise 1: QuPath phase mapping
I. Navigation
II. Annotation
III. Generate multi-channel stack (overlay)
IV. Transfer annotations
V. Train and predict using a learning model
Exercise 2: Phase Interpreter work
Benchmarking with SEM-EDX
Optical Phase Maps: Documentation
Index
Index