This paper reveals for the first time that the nonuniformity in spatial light modulator (SLM)-based multi-beam modulation and the coupling effect between phase aberrations and modulation depth are the key factors causing spectral aliasing in structured illumination digital holographic microscopy (SI-DHM). We propose an intensity-compensated spectral separation method: downsampling principal component analysis (PCA) selectively extracts the SI low-frequency aberrations to decouple the spectral aliasing between the modulation phase and system aberrations; the separation matrix is reconstructed by directly extracting the complex amplitudes of the high- and low-frequency peaks from three-step phase-shifted SI spectra to eliminate the intensity discrepancies. Experimental results show that the proposed method enables SI-DHM to achieve an isotropic resolution enhancement of 1.98×, which approaches the theoretical maximum (2×) for linear structured illumination microscopy. The quantitative phase measurements exhibit good agreement with white light interferometry (WLI) reference (0.04% relative deviation, 0.71 nm uncertainty). By combining the intensity compensation, the enhanced conventional methods achieve 5.16× improvement in structural similarity index (SSIM) and 93.14% reduction in root-mean-square error (RMSE). This work provides an innovative solution for SI-DHM that combines super-resolution imaging capability and a scalable computational framework.
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