pyXenium.contour.generate_xenium_explorer_annotations

generate_xenium_explorer_annotations(dataset_root, *, structures, output_relpath, clusters_relpath='analysis/analysis/clustering/gene_expression_graphclust/clusters.csv', cells_parquet_relpath='cells.parquet', histoseg_root=None, barcode_col='Barcode', cluster_col='Cluster', bins_x=900, bins_y=700, gaussian_sigma=2.25, density_scale_quantile=0.98, support_quantile=0.18, tissue_quantile=0.06, min_dominance=0.34, closing_iterations=2, opening_iterations=1, fill_holes=True, min_cells=500, min_component_pixels=180, xenium_pixel_size_um=DEFAULT_XENIUM_PIXEL_SIZE_UM, save_preview_png=True)

Generate Xenium Explorer-compatible structure annotations via HistoSeg.

Parameters:

• dataset_root (str | Path)

• structures (Sequence[Mapping[str, Any]])

• output_relpath (str | Path)

• clusters_relpath (str | Path)

• cells_parquet_relpath (str | Path)

• histoseg_root (str | Path | None)

• barcode_col (str)

• cluster_col (str)

• bins_x (int)

• bins_y (int)

• gaussian_sigma (float)

• density_scale_quantile (float)

• support_quantile (float)

• tissue_quantile (float)

• min_dominance (float)

• closing_iterations (int)

• opening_iterations (int)

• fill_holes (bool)

• min_cells (int)

• min_component_pixels (int)

• xenium_pixel_size_um (float)

• save_preview_png (bool)

Return type:

dict[str, str]