qupath-extension-sp-classify/mkdocs.yml at main · mikemcka/qupath-extension-sp-classify · GitHub

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site_name: SP Classify for QuPath
site_description: A human-in-the-loop active-learning cell classifier extension for QuPath.
site_url: https://mikemcka.github.io/qupath-extension-sp-classify/
repo_url: https://github.com/mikemcka/qupath-extension-sp-classify
repo_name: mikemcka/qupath-extension-sp-classify
edit_uri: edit/main/docs/
copyright: Copyright &copy; 2026 mikemcka — GPL-3.0-only

theme:
  name: material
  icon:
    repo: fontawesome/brands/github
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/weather-sunny
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.tracking
    - navigation.sections
    - navigation.top
    - navigation.footer
    - toc.follow
    - search.suggest
    - search.highlight
    - content.code.copy

markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - tables
  - toc:
      permalink: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

plugins:
  - search
  - glightbox

nav:
  - Home: index.md
  - Getting started:
      - Install & launch: install.md
      - Quick start — multi-class: quickstart-multiclass.md
      - Quick start — binary + composite: quickstart-binary.md
      - Setup steps: setup.md
  - Workflows:
      - Multi-class in detail: multiclass.md
      - Binary + composite in detail: binary-composite.md
      - Review mode: review-mode.md
  - Analysis:
      - Project prediction summary: prediction-summary.md
      - Intensity heatmaps: intensity-heatmaps.md
      - Distance measurements: distance-measurements.md
      - Scatter plot, clustering & gating: scatter-clustering.md
      - Cellular neighborhoods: neighborhoods.md
      - Batch normalisation (UniFORM): batch-normalisation.md
      - Image pixel prescreen: pixel-prescreen.md
  - Reference:
      - Exporting results: exporting.md
      - Utility scripts: utility-scripts.md
      - Sidebar settings: sidebar-reference.md
      - Menu items: menu-reference.md
      - Project directory layout: project-layout.md
      - Marker table format: marker-table.md
      - How to cite: how-to-cite.md
      - Tips & limitations: tips.md