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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.
Description
Spatial Transcriptomics analysis tool for processing 10x Genomics Visium or Xenium data, projecting gene expression data back onto tissue section images to draw "gene-space" distribution maps. Supports gene expression visualization, spatial clustering analysis, and morphological feature correlation.
Features
Visium Data Processing: Supports Space Ranger output (filtered_feature_bc_matrix.h5, spatial/tissue_positions_list.csv, spatial/tissue_lowres_image.png)
Xenium Data Processing: Supports Xenium Explorer output (.h5, transcripts.parquet, nucleus_boundaries.parquet)
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 spatial-transcriptomics-mapper 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:
spatial-transcriptomics-mapper 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.
