Multimodal 3D imaging has emerged as a powerful approach for investigating complex tissue architecture in pathological specimens. Techniques such as propagation-based phase-contrast computed tomography (PCT), light-sheet microscopy (LSM), and three-photon microscopy (3PM) provide complementary information on unlabeled tissue morphology based on distinct intrinsic contrast mechanisms. However, integrating these heterogeneous datasets into a unified spatial framework remains challenging due to differences in imaging geometry, spatial resolution, and modality-specific distortions. In this study, we present a registration pipeline for spatially aligning volumetric datasets acquired with PCT, LSM, and 3PM from formalin-fixed paraffin-embedded (FFPE) human colon cancer specimens. Biopsies from theses specimens were optically cleared and imaged sequentially using the three high-resolution modalities. To compensate for large positional differences between acquisitions, a three-stage cascade registration strategy was developed, consisting of coarse global alignment on down-sampled data, followed by rigid refinement at intermediate resolution. Mutual information was used as the similarity metric to ensure robust multimodal registration. The resulting framework enables the generation of spatially aligned multi-channel 3D datasets that combine structural information from X-ray phase-contrast imaging with complementary optical contrast signals. Beyond registration, we demonstrate that the fused six-dimensional feature space can be further exploited for unsupervised tissue characterization using a Gaussian Mixture Model (GMM), enabling data-driven identification of spatially coherent tissue regions without manual annotation. Qualitative evaluation confirms consistent alignment of major anatomical structures across modalities, while the unsupervised clustering reveals biologically meaningful patterns despite modality-specific noise and resolution differences. While further optimization and validation across larger datasets will enhance its computational efficiency and breadth of application, the approach already demonstrates strong potential for comprehensive tissue analysis and enables scalable, label-free 3D characterization of colon cancer tissue architecture.
Dullin, C., Schroeter, M., Pinkert-Leetsch, D., Ramos-Gomes, F., Markus, A., Missbach-Guentner, J., Bohnenberger, H., Stroebel, P., Alves, F.
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