Unsupervised Variational-Autoencoder-Based Analysis of Morphological Representations in Magnetic-Nanoparticle-Treated Macrophages

Magnetic nanoparticles (MNPs) are widely applied in biomedicine, including bioimaging, drug delivery, and cell tracking. As central mediators of immune surveillance, macrophages phagocytize foreign substances, rendering their interactions with MNPs particularly consequential. During MNP uptake, macrophages undergo cytoplasmic remodeling that can lead to morphological alterations. Although prior studies have predominantly focused on MNP uptake efficiency and cytotoxicity, systematic quantitative assessments of macrophage morphological alterations following MNP treatment remain scarce. In this study, phase-contrast microscopy images of macrophages before and after MNP treatment were analyzed using unsupervised variational autoencoder (VAE)-based frameworks. Specifically, the β-VAE, β-total correlation VAE, and multi-encoder VAE frameworks were employed to extract latent representations of cellular morphology. The analysis revealed that MNP-treated macrophages exhibited pronounced structural alterations, including membrane expansion, central density shifts, and shape distortions. These findings were further substantiated through quantitative evaluations, including effect size analysis, kernel density estimation, latent traversal, and difference mapping. Collectively, these results demonstrate that VAE-based unsupervised learning provides a robust framework for detecting subtle morphological responses of macrophages to nanoparticle exposure and highlights its broader applicability across varied cell types, treatment conditions, and imaging platforms.