hest.readers.pool_bins_visiumhd

hest.readers.pool_bins_visiumhd(adata: sc.AnnData, pixel_size: float, dst_bin_size_um=128, src_bin_size_um: Literal[2, 8, 16] = 16, chunk_len=50000) → sc.AnnData

Pools Visium HD bins from an initial resolution (src_bin_size_um) into larger square spots of spot_size_um. This performs a best-effort spatial downsampling (bin-to-bin aggregation).

Parameters:

  • adata (sc.AnnData) – adata containing spot center coordiniates in pxl_row_in_fullres and pxl_col_in_fullres

  • pixel_size (float) – pixel size of the WSI in um/px

  • dst_bin_size_um (int, optional) – target bin size in um. Defaults to 128.

  • src_bin_size_um (Literal[2, 8, 16], optional) – bin size of adata in um. Defaults to 16.

  • chunk_len (int, optional) – chunk size when binning a larger than RAM adata (this is for RAM optimization only). Defaults to 50000.

Returns:

AnnData object, each row in .obs represents a bin, each row in .X represents the sum of visium-hd sub-bins (of size src_bin_size_um) within that larger bin (of size dst_bin_size_um). Center coordinates of each bin (in pixel on WSI) are in adata.obsm[‘spatial’]

Return type:

sc.AnnData