_toc.yml

format: jb-book
root: welcome
defaults:  
  caption: Default Caption
parts:
- caption: 
  chapters:
  - file: QuantitativeBioimaging
- caption: Sample Preparation
  chapters:
  - file: 01_Sample_preparation/Introduction
  - file: 01_Sample_preparation/Experimental_design 
  - file: 01_Sample_preparation/Considerations
  - file: 01_Sample_preparation/Reproducibility
  - file: 01_Sample_preparation/Resources
- caption: Sample Acquisition
  chapters:
  - file: 02_Sample_acquisition/Introduction
  - file: 02_Sample_acquisition/Picking
  - file: 02_Sample_acquisition/Practical_considerations
  - file: 02_Sample_acquisition/Resources
- caption: Image Analysis and Data Handling
  chapters:
  - file: 03_Image_analysis/Introduction
  - file: 03_Image_analysis/Common_types_of_analysis.md
    sections:
      - file: 03_Image_analysis/Shape
      - file: 03_Image_analysis/Intensity
      - file: 03_Image_analysis/Colocalization
      - file: 03_Image_analysis/Tracking
      - file: 03_Image_analysis/Classification
  - file: 03_Image_analysis/Software
    sections:
      - file: 03_Image_analysis/GeneralUseSoftware
      - file: 03_Image_analysis/SpecificUseSoftware
  - file: 03_Image_analysis/Data_management
  - file: 03_Image_analysis/Resources
- caption: Data Interpretation
  chapters:
  - file: 04_Data_presentation/Introduction
  - file: 04_Data_presentation/Presentation_images
  - file: 04_Data_presentation/Statistics
  - file: 04_Data_presentation/Resources
- caption:  Additional Resources
  chapters:
  - file: community_resources
  - file: contributors
  - file: Glossary
  - file: bibliography
  - file: genindex