Less is More: AMBER-AFNO -- a New Benchmark for Lightweight 3D Medical Image Segmentation

Abstract: This work presents the results of a methodological transfer from remote sensing to healthcare, adapting AMBER -- a transformer-based model originally designed for multiband images, such as hyperspectral data -- to the task of 3D medical datacube segmentation. In this study, we use the AMBER architecture with Adaptive Fourier Neural Operators (AFNO) in place of the multi-head self-attention mechanism. While existing models rely on various forms of attention to capture global context, AMBER-AFNO achieves this through frequency-domain mixing, enabling a drastic reduction in model complexity. This design reduces the number of trainable parameters by over 80% compared to UNETR++, while maintaining a FLOPs count comparable to other state-of-the-art architectures. Model performance is evaluated on two benchmark 3D medical datasets -- ACDC and Synapse -- using standard metrics such as Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD), demonstrating that AMBER-AFNO achieves competitive or superior accuracy with significant gains in training efficiency, inference speed, and memory usage.