Renal multimodal workflows#

pyXenium ships two renal-focused multimodal workflows under pyXenium.multimodal.workflows.

1. Validated renal FFPE smoke workflow#

Use run_validated_renal_ffpe_smoke(...) or:

pyxenium multimodal validate-renal-ffpe-protein \
  "Y:/long/10X_datasets/Xenium/Xenium_Renal/Xenium_V1_Human_Kidney_FFPE_Protein"

This workflow verifies that the canonical Xenium RNA + protein loading path reproduces the validated public renal dataset dimensions and artifact availability.

2. Renal immune-resistance pilot#

Use run_renal_immune_resistance_pilot(...) or:

pyxenium multimodal renal-immune-resistance-pilot \
  "Y:/long/10X_datasets/Xenium/Xenium_Renal/Xenium_V1_Human_Kidney_FFPE_Protein" \
  --output-dir ./renal_immune_resistance_outputs

The pilot workflow packages:

  • joint cell classes and cell states

  • RNA/protein discordance summaries

  • spatial niche construction

  • ranked ROI patches

  • report-ready tables, markdown, JSON, and figures

Python example#

from pyXenium.multimodal import run_renal_immune_resistance_pilot

study = run_renal_immune_resistance_pilot(
    base_path="/path/to/xenium_export",
    output_dir="./renal_immune_resistance_outputs",
)