Various diseases including laminopathies and certain types of cancer are associated with abnormal nuclear mechanical properties that influence cellular and nuclear deformations in complex environments. Recently, microgroove substrates designed to mimic the anisotropic topography of the basement membrane have been shown to induce 3D nuclear deformations in various adherent cell types. Importantly, these deformations are different in myoblasts derived from laminopathy patients from those in cells derived from normal individuals. Here we assess the ability of a Variational Autoencoder (VAE) and a Gaussian Mixture Model (GMM) to cluster patches of nuclei of both wildtype myoblasts and myoblasts with laminopathy-associated mutations cultured on microgroove substrates, and we explore the impact of image processing parameters on clustering performance. We show that a standard VAE with GMM is able to cluster nuclei based on their morphologies and degrees of deformations and that these clusters correspond to either wildtype myoblasts or myoblasts with LMNA mutations. The current results suggest that combining deep learning techniques with microgroove substrates enables automatic classification of nuclear deformations and thus provides a promising approach for easy and rapid diagnosis of pathologies that involve abnormalities in nuclear deformation.