| 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
- Select center cells/spots by
adata.obs label.
- Keep all observations within a user-defined radius of those centers.
- Optionally restrict neighbors to a second label filter.
- Export a subset h5ad that preserves original coordinates and annotations.
- 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.h5adtables/selected_observations.csvtables/center_observations.csvtables/label_composition.csvtables/selection_summary.csvfigures/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
