Patoloji Atlası
The group’s Turkish-language pathology teaching atlas — a public, SEO-indexed case collection with a defined contribution and image-handling pipeline.
Purpose
Publish teaching cases with images in Turkish, as the teaching surface of the group’s public content estate (distinct from research outputs).
Data used
De-identified teaching cases. Large WSI files stay on the Memorial share; the repo carries only screenshots and annotated crops.
Methods
One case per folder, named as a kebab-case organ/diagnosis slug. Required files: an index.qmd narrative, a thumbnail, and at least one annotated WSI snapshot. Case metadata in YAML frontmatter records organ, diagnosis category, ICD-O-3 code, and teaching level. Turkish primary with optional English summary in the same file. Annotations are exported from QuPath as PNG overlays rather than raw GeoJSON, because the atlas is a teaching surface and not a research dataset.
Current state / open questions
Active. Contribution flow: branch, copy an existing case folder, replace images and text, validate frontmatter, preview with quarto preview, open a PR for editorial review. Documented pitfalls: no images from signed-out cases without the redaction pass; no merge without a second reader reviewing the teaching points; the atlas is SEO-indexed so text is published content, not draft notes.
Sibling content repos: patoloji-hakkinda (longer explainers), patoloji-ve-bilisim (informatics essays), rutinde-dijital-patoloji (digital pathology in routine practice), and ParaPathology.
Two corrections to that list, from reading the ParaPathology tree on 2026-07-26. This page previously described ParaPathology as “pathology-adjacent topics: workload, education, communication, policy”, which materially understates it: of 360 source markdown files the largest section is statistics and bioinformatics (64 files), ahead of systemic pathology (43) and medical school lectures (35), with roughly 100 files across statistics, bioinformatics, computational pathology and bibliometrics. Workload and policy are a small part of it. And patoloji-hakkinda is not only a separate sibling repository — its rendered output, 1,662 HTML files, is vendored inside ParaPathology with its own GitHub Action, which accounts for most of that repository’s size.