title: How to align two scans in Python (meshes, point clouds, CT and MRI volumes) description: Align two meshes, two point clouds or two volumes in Python with one call that picks the right method for the object type: RANSAC + ICP for geometry, mutual-information rigid registration for volumes, Coherent Point Drift for non-rigid cases; the transform and how to apply it.

How to align two scans in Python¶

align(moving) is defined on every object type and picks the method that fits it:

You have	Call	Method underneath
two point clouds	`target.align(moving)`	FPFH + RANSAC, then point-to-plane ICP (`registration.ransac_icp_pipeline`)
two meshes	`target.to_points().align(moving.to_points())`	same, on sampled points
two volumes (CT, MR, any modality)	`fixed.align(moving)`	SimpleITK rigid, Mattes mutual information (`simpleitk_registration.rigid`)
a scan and an atlas with labels	`scan.align(atlas)` then transfer labels	see Label a scan from an atlas
organ motion, breathing	rigid first, then `deformable_registration.cpd_deformable` (points) or `simpleitk_registration.bspline` (volumes)	non-rigid

import pardesline as pl

a = pl.load("scan_a.stl")  # Mesh
b = pl.load("scan_b.stl")
pa, pb = a.to_points(num_points=50000, seed=1), b.to_points(num_points=50000, seed=1)
moved = pa.align(pb)  # pb moved onto pa
T = moved.transform["transformation_matrix"]  # 4x4, apply it to b's vertices to move the mesh

Applying the transform to the original mesh¶

import numpy as np

T = np.asarray(T)
verts = b.to_numpy()
moved_verts = (T[:3, :3] @ verts.T).T + T[:3, 3]

Or let PyVista do it: b.to_pyvista().transform(T, inplace=False).

Units first¶

Both inputs must be in the same units and the frame must be known: a.frame, a.units; with_frame("sensor", "mm") to declare them. A millimetre scan against a metre scan "aligns" to nonsense with a plausible-looking fitness.

Verify¶

Fitness caps at the overlap and lies when the threshold is wide; inlier RMSE should approach the noise level; landmarks not used by the algorithm are the real test. Why our defaults work has the numbers for each method.