paste3.visualization.stack_slices_center

paste3.visualization.stack_slices_center(center_slice, slices, pis)[source]

Align spatial coordinates of a list of slices to a center_slice.

In other words, align:

slices[0] --> center_slice

slices[1] --> center_slice

slices[2] --> center_slice

...

Parameters:

  • center_slice (AnnData) -- Inferred center slice.

  • slices (list[AnnData]) -- List of original slices to be aligned.

  • pis (list[ndarray]) -- List of pi (center_align() output) between center_slice and slices.

  • output_params -- If True, additionally return angles of rotation (theta) and translations for each slice.

  • matrix -- If True and output_params is also True, the rotation is return as a matrix instead of an angle for each slice.

Return type:

tuple[AnnData, list[AnnData], list[float] | None, list[ndarray] | None]

Returns:

  • Center slice with aligned spatial coordinates.

  • List of other slices with aligned spatial coordinates.

If output_params = True, additionally return:

  • List of angles of rotation (theta) for each slice.

  • List of translations [x_translation, y_translation] for each slice.