qupath-guidelisted

Guides QuPath users in digital pathology with troubleshooting, interface navigation, image analysis workflows, and Groovy scripting. Use when the user mentions QuPath, or uses QuPath-specific signals such as .qpproj/.qpdata files, "Run for Project", "stain vectors", "TMA dearrayer", "detection objects", or "Brightfield (H-DAB)". Also use for QuPath cell detection, tissue/tumor annotation, IHC scoring (Ki-67, HER2, PD-L1), stain separation/deconvolution, pixel or object classification, TMA analysis, multiplex/mIF analysis, Groovy scripts for pathology slides, measurement export, batch processing, QuPath extensions, or QuPath errors. Provides menu paths, workflows, ready-to-run Groovy snippets, and fetches official QuPath docs for version-specific details. Do NOT use for general non-QuPath image processing, ImageJ/Fiji-only questions, or standalone deep-learning pipelines (e.g. StarDist/Cellpose in plain Python) outside QuPath.
patolojiAI/pathology-skills-collection · ★ 0 · Code & Development · score 66

Install: claude install-skill patolojiAI/pathology-skills-collection

# QuPath Guide Help users get the most out of QuPath — the open-source platform for bioimage analysis widely used in digital pathology research. This skill covers troubleshooting, interface navigation, image analysis workflows, and Groovy scripting. ## Approach When a user asks a QuPath question, follow this decision flow: 1. **Assess the user's level** from context cues (terminology, question complexity, error messages). Adapt language accordingly — a pathologist new to QuPath needs different guidance than a developer building extensions. 2. **Identify the category** of the question: - **Troubleshooting** → Read `references/troubleshooting.md` first. Most users come with a problem. - **UI / Navigation** → Read `references/ui-guide.md` for interface guidance. - **Analysis workflows** → Read `references/analysis-workflows.md` for step-by-step workflows. - **Scripting** → Read `references/scripting-guide.md` for Groovy patterns and examples. - **Multiple categories** → Read the relevant reference files in combination. 3. **Fetch official docs when needed.** For version-specific details, API questions, or anything where the reference files don't have enough detail, search or fetch from QuPath's official documentation: - Main docs: `https://qupath.readthedocs.io/en/stable/` - Javadoc API: `https://qupath.github.io/javadoc/docs/` - Community forum: `https://forum.image.sc/tag/qupath` - GitHub: `https://github.com/qupath/qupath` 4. **Pr