spatial-microenvironment-subset

name	spatial-microenvironment-subset
description	Extract a local spatial microenvironment by selecting cells or spots within a physical radius of a center population, preserving coordinates and labels in a downstream-ready h5ad subset for tumor microenvironment, neighborhood, spatial communication, and related downstream analyses.
version	0.1.0
author	OmicsClaw Team
license	MIT
tags	["spatial","microenvironment","neighborhood","radius","subset","communication","xenium","visium"]
metadata	{"omicsclaw":{"domain":"spatial","script":"spatial_microenvironment_subset.py","allowed_extra_flags":["--center-key","--center-values","--target-key","--target-values","--exclude-centers","--radius-microns","--radius-native","--microns-per-coordinate-unit"],"legacy_aliases":["spatial-neighborhood-subset","spatial-proximity-subset","microenvironment","microenvironment subset","tumor microenvironment","neighborhood subset"],"saves_h5ad":true,"requires_preprocessed":false,"trigger_keywords":["microenvironment","neighborhood subset","spatial radius","neighboring cells","nearby cells","tumor microenvironment","extract cells within 50 microns"]}}

Spatial Microenvironment Subset

Use this skill when the user wants to keep only the local neighborhood around a center population before running downstream spatial analyses.

Core Capabilities

1. Select center cells/spots by adata.obs label.
2. Keep all observations within a user-defined radius of those centers.
3. Optionally restrict neighbors to a second label filter.
4. Export a subset h5ad that preserves original coordinates and annotations.
5. Annotate selected observations with center/neighbor role and nearest-center distance.

Expected Inputs

• AnnData with spatial coordinates in obsm["spatial"] or obsm["X_spatial"]
• At least one annotation column in adata.obs describing cell or spot identity
• Radius provided in either:
  • microns via --radius-microns
  • native coordinate units via --radius-native

Practical Guidance

• Prefer --radius-microns when coordinate scaling is known or can be inferred.
• For Xenium-like inputs, coordinates are often already in microns.
• For custom or partially processed h5ad files, pass --microns-per-coordinate-unit if radius in microns cannot be inferred safely.
• Keep centers included by default when the subset will feed directly into spatial-cell-communication.

Outputs

• spatial_microenvironment_subset.h5ad
• tables/selected_observations.csv
• tables/center_observations.csv
• tables/label_composition.csv
• tables/selection_summary.csv
• figures/microenvironment_selection.png

Example

python skills/spatial/spatial-microenvironment-subset/spatial_microenvironment_subset.py \
  --input data/sample.h5ad \
  --output output/microenv \
  --center-key cell_type \
  --center-values tumor \
  --radius-microns 50