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We introduce Multi-scale Closing Index (MCI), a new dissimilarity measure for evaluating the alignment of two 2D point sets. MCI is bounded between 0 and 1 and is based on multiscale mathematical morphology operations, with smaller values indicating greater structural agreement. The measure was motivated by the need to assess the quality of registration between point sets representing cell populations in biological images. To evaluate its behaviour under controlled conditions, we generated synthetic point clouds from Perlin-noise-based spatial structures, following established approaches for simulating biologically plausible spatial organization. We assessed MCI between those point clouds and different transformed versions, obtained by local perturbation, point removal, translation, rotation and addition of impulsive noise. Across these experiments, the dissimilarity MCI increased gradually and consistently with perturbation severity, while showing a clear discontinuity between clouds originating from the same underlying spatial structure and point clouds generated from different structures. We further compared MCI with commonly used point-set distances, including Hausdorff-based measures and Sliced Wasserstein distance. These experiments show the ability of MCI to capture structural agreement and quantify deviations between point sets, highlighting its potential as a complementary metric for evaluating two-dimensional point-set registration.