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
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Documentation Hub

Welcome to the mineralogy analysis documentation.

Dr. Marco Andres Acevedo Zamora – School of Earth and Atmospheric Sciences, Queensland University of Technology (QUT) – marco.acevedozamora@qut.edu.au

Contents:

  • Image analysis pipeline
    • Introduction
    • Software installers
    • Scientific citations
  • Cube Converter
    • Polarised microscopy processor
    • Multi-modal pyramid generator
  • Chemistry Simplifier
    • Image processing
    • Analysis definition
    • Output adjustments
  • Phase Interpreter
    • Define map
    • Customise phase map
    • Image analysis
  • Image Analysis Workshop
    • Part 1: QuPath interface
    • Part 2A: Cube Converter and Chemistry Simplifier work
    • Part 3: Image alignment
    • Part 4: Phase mapping and interpretation
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© Copyright 2026, Marco Acevedo.

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