FishFeats/mkdocs.yml at main · gletort/FishFeats · GitHub

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site_name: FishFeats Documentation
site_url: https://gletort.github.io/FishFeats/
repo_url: https://github.com/gletort/FishFeats/

nav:
    - Home: index.md
    - Installation: Installation.md
    - Starting:
        - Open image: Open-image.md
        - Image Scalings: Image-scalings.md
        - Separate stainings: Separate-junctions-and-nuclei.md
    - Cells:
        - Segment Cells: Get-cells.md
        - 3D cell positions: 3d-cell-positions.md
    - Nuclei:
        - Segment Nuclei: Get-nuclei.md
        - Associate to cell: Associate.md
        - Preprocess nuclei: Preprocess-nuclei.md
    - RNAs:
        - Segment&assign RNAs: Get-RNAs.md
    - Measures:
        - Measures: Measures.md
        - Classify cells: Classify-cells.md
        - Measure cytoplasmic intensity: Measure-cytoplasmic-staining.md
        - Measure nuclear intensity: Measure-nuclear-staining.md
    - Additionnal options:
        - Touching labels: Touching-labels.md
        - Hierarchical clustering: Hierarchical-clustering.md
        - Add grid: Add-grid.md
        - Threshold channel: Threshold-channel.md
    - Step by step example: Step-by-step.md
    - Troubleshooting: Known-errors-and-solutions.md

theme:
    logo: imgs/snap.png
    name: material
    features:
        - navigation.footer
        - navigation.tabs
        - navigation.tabs.sticky
        - navigation.path
        - navigation.top
        - navigation.expand
        - toc.integrate
    color_mode: dark
    palette:
        # Palette toggle for dark mode
        - media: "(prefers-color-scheme: dark)"
          scheme: slate
          primary: white
          accent: teal
          toggle:
            icon: material/lightbulb
            name: Switch to light mode
        # Palette toggle for light mode
        - media: "(prefers-color-scheme: light)"
          scheme: default
          primary: white
          accent: dark blue
          toggle:
            icon: material/lightbulb-outline
            name: Switch to dark mode

    icon:
        annotation: material/plus-circle-outline
        admonition:
            note: fontawesome/solid/note-sticky
            example: fontawesome/solid/sliders
            abstract: fontawesome/solid/puzzle-piece
            bug: fontawesome/solid/bug
            tip: fontawesome/solid/keyboard
            warning: fontawesome/solid/triangle-exclamation

extra_css:
    - stylesheets/extra.css

## display code options
markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - admonition
  - tables
  - pymdownx.details
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - attr_list
  - md_in_html
  - pymdownx.keys
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg