QUINT workflow

Introduction

• What is QUINT?
  • Supported atlases
  • The QUINT workflow
  • FAQ
  • Examples of use
• Cite us
  • Cite the atlases
• Contact us
  • Acknowledgements

Preparing your images

• File naming and size
  • Naming convention

Atlas-registration

• QuickNII
• VisuAlign
• DeepSlice

Quality Control

• QCAlign

Feature extraction

• Ilastik
  • Preparing images for ilastik
  • Segmentation with ilastik
    • 1. Pixel Classification Workflow
    • 2. Object Classification Workflow
    • 3. Applying the Glasbey Lookup table
  • FAQ and troubleshooting
    • 1. Which pixel classification features should I select?
    • 2. Which images should I upload in the Input Data applet?
    • 3. What are training images?
    • 4. How many classes should I use?
    • 5. Which part of the image, and how much, should I label?
    • 6. How do I test the trained classifier on the other images in the series?
    • 7. Which export settings should I select?
    • 8. Help! ilastik keeps crashing. I have very large images. What do I do?
• Alternative tools

Analyse

• Nutil
• MeshView Atlas Viewer