COSIE.data_preprocessing.clr_normalize_each_cell

clr_normalize_each_cell(adata, inplace=True)[source]

Normalize each cell’s protein counts using Centered Log-Ratio (CLR) normalization, following the approach used in Seurat and SpatialGLUE.

Parameters

adataAnnData: Input AnnData object where .X stores raw count data (e.g., protein abundance).
inplacebool, optional: Whether to modify the input adata in place. If True, the normalization will overwrite adata.X. If False, a normalized copy of adata is returned. Default is True.

Returns

adataAnnData: The AnnData object with CLR-normalized .X. If inplace=True, returns the modified input object; if inplace=False, returns a new normalized copy.