Core Functions Reference

register_stack(image_stack, bbox, reference_slice=0, config=None):

Aligns a stack of images using template matching.

Arguments

• image_stack (np.ndarray): 3D numpy array (slices, height, width)
• bbox (Tuple[int, int, int, int]): (x, y, w, h) tuple defining the template region
• reference_slice (int, default 0): Index of the reference slice
• config (AlignmentConfig, optional): Alignment configuration

Returns

• aligned_stack (np.ndarray): 3D numpy array of aligned images
• displacements (List[Tuple[float, float]]): List of (dx, dy) tuples for each slice

Raises

• ValueError: If image_stack is not 3D or bbox is invalid
• IndexError: If reference_slice is out of bounds

Example

aligned, displacements = register_stack(stack, bbox)

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See also: StackAligner, AlignmentConfig