Vision Transformers (ViTs) have demonstrated strong performance in many computer vision tasks but do not naturally extend beyond the natural image domain. One important example is Fourier-space data, which is used to represent a rich and diverse set of modalities, including medical imaging and microscopy. Standard ViT tokenization partitions an image into square patches on a Cartesian grid, which poorly fit the frequency and phase structure of Fourier-space data. We introduce Non-Uniform ViT, a simple, general-purpose vision transformer that redesigns image tokenization, data representation, and positional encoding to respect this structure. Experiments on Fourier-domain image classification, 2D crystal lattice identification, MRI annotation, and cryo-EM protein heterogeneity analysis show that NUViT consistently captures the structure of Fourier data better than standard architectures.

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