Pseudo-image generation

Add_Pseudo_Image creates a spatial image from any categorical or continuous column in adata.obs and registers it in the SpatialData object.

Categorical columns

sdata = gp.Add_Pseudo_Image(sdata, "GPCA_clusters")

Each unique category gets a randomly assigned colour. To use a specific matplotlib colourmap:

sdata = gp.Add_Pseudo_Image(sdata, "GPCA_clusters", cmap="tab20")

Continuous columns

Set is_continuous=True to automatically bin the values and apply a sequential colourmap:

sdata = gp.Add_Pseudo_Image(sdata, "MPI", is_continuous=True, cmap="viridis")

Parameters

Parameter	Default	Description
image_ident	required	Column name in adata.obs to visualise
tables	"maldi_adata"	Table name in sdata.tables
library_id	"Spatial"	Key in adata.uns["spatial"]
cmap	None	Matplotlib colourmap name or dict mapping categories to RGB
is_continuous	False	Bin continuous values before colouring
img_upscaling	1	Additional upscaling for the pseudo-image

Output

The pseudo-image is stored in sdata.images["optical_image"] as a multiscale Image2DModel, compatible with napari and spatialdata-plot.