arXiv:2610.33256v1 Announce Type: new Abstract: Optical coherence tomography (OCT) and light sheet (LS) fluorescence microscopy provide complementary views of tissue morphology and molecular expression, offering a powerful approach for studying embryonic development. However, longitudinal integration of OCT+LS images is challenging because the modalities differ substantially in contrast, spatial resolution, field of view, and visible anatomical features, while embryo growth and movement introduce additional misalignment over time. These challenges stem from both the scale and multimodal nature of the OCT and LS image stacks. We present a fully automated three-dimensional rigid registration framework for aligning OCT and LS volumes of developing zebrafish embryos acquired from 21 to 48 hours post fertilization (HPF). The method does not require pre-existing segmentations or cross-modal feature correspondences, which are often unreliable because OCT and LS capture fundamentally different tissue properties. Registration performance was evaluated across developmental time points using mean target registration error (mTRE) and compared across multiple similarity metrics and optimization methods. Normalized cross-correlation combined with particle swarm optimization produced the most accurate and consistent registration, achieving the lowest mTRE at every evaluated time point compared with the alternative methods. The registration establishes spatial correspondence between OCT tissue morphology and LS fluorescence signals throughout development, enabling integrated longitudinal analysis of structural and molecular changes in living embryos.