Abstract
Holotomography (HT) provides label-free, quantitative three-dimensional (3D) imaging of live cells and organoids by mapping their intrinsic refractive index (RI) distributions [1,2]. In analogy to X-ray computed tomography, HT records multiple holograms of a sample under varied illumination angles and reconstructs the 3D RI distribution by inverting the wave equation [1,6]. The resulting data are inherently quantitative and free of exogenous labels, yet they are also physically abstract - RI is not a molecular identity - and each measurement yields gigabyte-scale volumes. Both properties make HT an unusually good substrate for machine learning: the physics fixes the units, and the learning supplies the interpretation.
In this presentation, I will discuss what the combination of HT and artificial intelligence (AI) has delivered so far and where it still breaks down, across three tasks: segmentation of unlabeled subcellular structures, classification of cell types and states [4], and inference of molecular contrast - including virtual staining of fluorescence-like or histology-like images from RI volumes [5,7,8]. For each, I will address the limitations that matter in practice: the scarcity of paired ground-truth data, the difficulty of validating an inference that has no label to compare against, generalization across instruments and sample-preparation protocols, and the interpretability required for clinical adoption. I will close with the directions I consider most consequential - physics-informed reconstruction [3,9], standardized RI measurement across platforms [6], and prospective clinical validation - and with what would be needed for label-free 3D imaging with AI to become a routine tool in biology and diagnostics.
References:
1. Y. Park, C. Depeursinge and G. Popescu, Nature Photonics 12 (10), 578-589 (2018)
2. Y. Baek and Y. Park, Nature Photonics 15 (5), 354-360 (2021)
3. S. Shin and Y. Park, Nature Materials 21, 317-324 (2022)
4. Y. Jo et al., Nature Cell Biology 23, 1329-1337 (2021)
5. J. Park et al., Nature Methods 20, 1645-1660 (2023)
6. G. Kim et al., Nature Reviews Methods Primers 4, 51 (2024)
7. C. Oh et al., Nature Communications 16, 1685 (2025)
8. J. Park et al., Nature Communications 16, 4781 (2025)
9. J. Lee et al., Nature Photonics 21, 1 (2026)