Spatial proteomics

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Spatial Proteomics Analysis

Data Loading

import scimap as sm
import anndata as ad

# Load CODEX/IMC data (cell x marker matrix with spatial coordinates)
adata = ad.read_h5ad('spatial_proteomics.h5ad')

# Required: spatial coordinates in adata.obsm['spatial']
# Required: protein intensities in adata.X

Preprocessing

# Log transform intensities
sm.pp.log1p(adata)

# Rescale markers (0-1 per marker)
sm.pp.rescale(adata)

# Combat batch correction if multiple FOVs
sm.pp.combat(adata, batch_key='fov')

Phenotyping Cells

# Manual gating approach
phenotype_markers = {
    'T_cell': ['CD3', 'CD45'],
    'B_cell': ['CD20', 'CD45'],
    'Macrophage': ['CD68', 'CD163'],
    'Tumor': ['panCK', 'Ki67']
}

sm.tl.phenotype_cells(adata, phenotype=phenotype_markers,
                      gate=0.5, label='phenotype')

# Clustering-based phenotyping
sm.tl.cluster(adata, method='leiden', resolution=1.0)

Spatial Analysis

# Build spatial neighbors graph
sm.tl.spatial_distance(adata, x_coordinate='X', y_coordinate='Y')

# Neighborhood enrichment
sm.tl.spatial_interaction(adata, phenotype='phenotype',
                          method='knn', knn=10)

# Spatial clustering (communities of cells)
sm.tl.spatial_cluster(adata, phenotype='phenotype')

Visualization

# Spatial scatter plot
sm.pl.spatial_scatterPlot(adata, colorBy='phenotype',
                          x='X', y='Y', s=5)

# Heatmap of spatial interactions
sm.pl.spatial_interaction(adata)

# Marker expression overlay
sm.pl.image_viewer(adata, markers=['CD3', 'CD20', 'panCK'])

Integration with Transcriptomics

import squidpy as sq

# If matched spatial transcriptomics available
# Transfer labels or integrate modalities
sq.gr.spatial_neighbors(adata_protein)
sq.gr.spatial_neighbors(adata_rna)

# Compare spatial patterns across modalities

Platform-Specific Notes

Platform	Markers	Resolution	Notes
CODEX	40-60	Subcellular	Cyclic staining
IMC	40+	1 um	Metal-tagged antibodies
MIBI	40+	260 nm	Mass spectrometry

Related Skills

• spatial-transcriptomics/spatial-neighbors - Spatial graph construction
• spatial-transcriptomics/spatial-domains - Domain identification
• imaging-mass-cytometry/phenotyping - IMC-specific analysis

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