loki.align.align_tissue

loki.align.align_tissue(ad_tar_coor, ad_src_coor, pca_comb_features, src_img, alpha=0.5)

Aligns the source coordinates to the target coordinates using Coherent Point Drift (CPD) registration, and applies a homography transformation to warp the source coordinates accordingly.

Parameters:

• ad_tar_coor – Numpy array of target coordinates to which the source will be aligned.

• ad_src_coor – Numpy array of source coordinates that will be aligned to the target.

• pca_comb_features – PCA-combined feature matrix used as additional features for the alignment process.

• src_img – Source image to be warped based on the alignment.

• alpha – Regularization parameter for CPD registration, default is 0.5.

Returns:

• cpd_coor: The new source coordinates after CPD alignment.

• homo_coor: The source coordinates after applying the homography transformation.

• aligned_image: The source image warped based on the homography transformation.