Diffraction tomography and angle recovery algorithms for 3D refractive index reconstruction of microorganisms

Monitoring aquatic microorganisms is essential for assessing water security, yet conventional microscopy suffers from a limited depth of field and invasive labeling. We report a label-free 3D platform combining microfluidics and off-axis digital holographic diffraction tomography for aquatic microorganism monitoring. By utilizing spontaneous Paramecium rolling, multi-angle holograms are acquired at 55 fps. An SSIM-based algorithm retrieves rolling angles for mechanical stage-free tomography. A GPU-accelerated framework based on the Fourier diffraction theorem, incorporating trilinear interpolation and positivity constraints, reconstructs 3D refractive index (RI) distributions. Results resolve subcellular organelles, including oral grooves (RI≈1.32) and vacuoles (RI≈1.35), with a 40-fold computational speedup. This system enables high-throughput, high-speed sensing of pristine biological specimens.