3D Masked Autoencoders are Robust Learners of Volumetric and Multimodal Cellular Representations for Microscopy

arXiv:2606.23964v1 Announce Type: new Abstract: Self-supervised learning in fluorescence microscopy often relies on 2D projections, despite the inherently three-dimensional nature of cells. We present a systematic comparison of 2D and 3D masked autoencoders (MAE-2D vs. MAE-3D) on volumetric microscopy data. Under matched architectures and training protocols, MAE-3D consistently outperforms 2D max-projection and slice-based variants on downstream single-cell tasks. We further align visual represe...