| name | pathology-roi-selector |
| description | Use pathology roi selector for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries. |
| license | MIT |
| author | AIPOCH |
Source: https://github.com/aipoch/medical-research-skills
Pathology ROI Selector
WSI region detection for AI training.
When to Use
- Use this skill when the task needs Use pathology roi selector for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
- Use this skill for data analysis tasks that require explicit assumptions, bounded scope, and a reproducible output format.
- Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.
Key Features
- Scope-focused workflow aligned to: Use pathology roi selector for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
- Packaged executable path(s):
scripts/main.py.
- Structured execution path designed to keep outputs consistent and reviewable.
Dependencies
See ## Prerequisites above for related details.
Python: 3.10+. Repository baseline for current packaged skills.Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.
Example Usage
cd "20260318/scientific-skills/Data Analytics/pathology-roi-selector"
python -m py_compile scripts/main.py
python scripts/main.py --help
Example run plan:
- Confirm the user input, output path, and any required config values.
- Edit the in-file
CONFIG block or documented parameters if the script uses fixed settings.
- Run
python scripts/main.py with the validated inputs.
- Review the generated output and return the final artifact with any assumptions called out.
Implementation Details
See ## Workflow above for related details.
- Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
- Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
- Primary implementation surface:
scripts/main.py.
- Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
- Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.
Quick Check
Use this command to verify that the packaged script entry point can be parsed before deeper execution.
python -m py_compile scripts/main.py
Audit-Ready Commands
Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.
python -m py_compile scripts/main.py
python scripts/main.py --help
Workflow
- Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
- Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
- Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
- Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
- If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.
Use Cases
- Tissue microarray creation
- AI model training data
- Pathology education
- Research sampling
Parameters
wsi_file: Whole slide imagetissue_type: Tumor/normalmagnification: 20x/40x
Returns
- ROI coordinates
- Tissue percentage
- Quality metrics
- Export ready crops
Example
Identify tumor-rich regions from 100K x 100K image
Risk Assessment
| Risk Indicator | Assessment | Level |
|---|
| Code Execution | Python/R scripts executed locally | Medium |
| Network Access | No external API calls | Low |
| File System Access | Read input files, write output files | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Output files saved to workspace | Low |
Security Checklist
Prerequisites
No additional Python packages required.
Evaluation Criteria
Success Metrics
Test Cases
- Basic Functionality: Standard input → Expected output
- Edge Case: Invalid input → Graceful error handling
- Performance: Large dataset → Acceptable processing time
Lifecycle Status
- Current Stage: Draft
- Next Review Date: 2026-03-06
- Known Issues: None
- Planned Improvements:
- Performance optimization
- Additional feature support
Output Requirements
Every final response should make these items explicit when they are relevant:
- Objective or requested deliverable
- Inputs used and assumptions introduced
- Workflow or decision path
- Core result, recommendation, or artifact
- Constraints, risks, caveats, or validation needs
- Unresolved items and next-step checks
Error Handling
- If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
- If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
- If
scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
- Do not fabricate files, citations, data, search results, or execution outcomes.
Input Validation
This skill accepts requests that match the documented purpose of pathology-roi-selector and include enough context to complete the workflow safely.
Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
pathology-roi-selector only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
Response Template
Use the following fixed structure for non-trivial requests:
- Objective
- Inputs Received
- Assumptions
- Workflow
- Deliverable
- Risks and Limits
- Next Checks
If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.
