athena.preprocessing.preprocess module¶

Summary¶

Functions:

`arcsinh`	Computes the arcsinh transformation of the expression values according to:
`extract_centroids`	Extract centroids from segementation masks.

extract_centroids(so, spl, mask_key='cellmasks', inplace=True)[source]¶

Extract centroids from segementation masks.

Parameters

so – SpatialOmics instance
spl – sample for which to extract centroids
mask_key – segmentation masks to use
inplace – Whether to add the metric to the current SpatialOmics instance or to return a new one.

Returns:

arcsinh(so, spl, cofactor)[source]¶

Computes the arcsinh transformation of the expression values according to:

\[X = \mathtt{arcsinh}(\frac{X}{\mathtt{cofactor}})\]

Parameters