Patoloji Atlası

The group’s Turkish-language pathology teaching atlas — structure, contribution flow, and publication pipeline

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patolojiatlasi.github.io | Teaching atlas |

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Content structure

  • One case, one folder. Folder name is a kebab-case organ/diagnosis slug.
  • Required files: index.qmd narrative, thumbnail, and at least one annotated WSI snapshot.
  • Case metadata: YAML frontmatter records organ, diagnosis category, ICD-O-3 code, and teaching level.
  • Language: Turkish primary; English summary optional in the same file.

Contribution workflow

  1. Fork / branch the atlas repo.
  2. Copy an existing case folder as a starting template.
  3. Replace images and text; verify frontmatter validates.
  4. Preview locally with quarto preview.
  5. Open a PR; editorial review happens before merge.

Image-handling rules

  • All images de-identified before commit.
  • Large WSI files stay on the Memorial share; the repo carries only screenshots and annotated crops.
  • Annotations exported from QuPath as PNG overlays, not raw GeoJSON — the atlas is a teaching surface, not a research dataset.

Pitfalls

  • Don’t lift images from signed-out cases without the redaction pass.
  • Don’t merge a new case without at least one second reader reviewing the teaching points.
  • The atlas is SEO-indexed; treat text as published content, not draft notes.