BigReg: An Efficient Registration Pipeline for High-Resolution X-Ray and Light-Sheet Fluorescence Microscopy

Siyuan Mei; Fuxin Fan; Mareike Thies; Mingxuan Gu; Fabian Wagner; Oliver Aust; Ina Erceg; Zeynab Mirzaei; Georgiana Neag; Yipeng Sun; Yixing Huang; Andreas Maier

arXiv · 2404.14807

BigReg: An Efficient Registration Pipeline for High-Resolution X-Ray and Light-Sheet Fluorescence Microscopy

Siyuan Mei·Fuxin Fan·Mareike Thies·Mingxuan Gu·Fabian Wagner·Oliver Aust·Ina Erceg·Zeynab Mirzaei·Georgiana Neag·Yipeng Sun·Yixing Huang·Andreas Maier

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Abstract

Recently, X-ray microscopy (XRM) and light-sheet fluorescence microscopy (LSFM) have emerged as pivotal tools in preclinical research, particularly for studying bone remodeling diseases such as osteoporosis. These modalities offer micrometer-level resolution, and their integration allows for a complementary examination of bone microstructures which is essential for analyzing functional changes. However, registering high-resolution volumes from these independently scanned modalities poses substantial challenges, especially in real-world and reference-free scenarios. This paper presents BigReg, a fast, two-stage pipeline designed for large-volume registration of XRM and LSFM data. The first stage involves extracting surface features and applying two successive point cloud-based methods for coarse alignment. The subsequent stage refines this alignment using a modified cross-correlation technique, achieving precise volumetric registration. Evaluations using expert-annotated landmarks and augmented test data demonstrate that BigReg approaches the accuracy of landmark-based registration with a landmark distance (LMD) of 8.36\,\textmu m\,$\pm$\,0.12\,\textmu m and a landmark fitness (LM fitness) of 85.71\%\,$\pm$\,1.02\%. Moreover, BigReg can provide an optimal initialization for mutual information-based methods which otherwise fail independently, further reducing LMD to 7.24\,\textmu m\,$\pm$\,0.11\,\textmu m and increasing LM fitness to 93.90\%\,$\pm$\,0.77\%. Ultimately, key microstructures, notably lacunae in XRM and bone cells in LSFM, are accurately aligned, enabling unprecedented insights into the pathology of osteoporosis.

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Siyuan Mei, Fuxin Fan, Mareike Thies, Mingxuan Gu, Fabian Wagner, Oliver Aust, Ina Erceg, Zeynab Mirzaei, Georgiana Neag, Yipeng Sun, Yixing Huang, Andreas Maier. 2024-04-23. BigReg: An Efficient Registration Pipeline for High-Resolution X-Ray and Light-Sheet Fluorescence Microscopy. https://arxiv.org/abs/2404.14807

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