Spot-Based Global Registration for Subpixel Stitching of Single-Molecule Resolution Images for Tissue-Scale Spatial Transcriptomics.

Single-molecule imaging at the tissue scale has revolutionized our understanding of biology by providing unprecedented insight into the molecular expression of individual cells and their spatial organization within tissues. However, achieving precise image stitching at the single-molecule level remains a challenge, primarily due to heterogeneous background signals and dim labeling signals in single-molecule images. This paper introduces Spot-Based Global Registration (SBGR), a novel strategy that shifts the focus from raw images to identified molecular spots for high-resolution image alignment. The use of spot-based data enables straightforward and robust evaluation of the credibility of estimated translations and stitching performance. The method outperforms existing image-based stitching methods, achieving subpixel accuracy (83 ± 36 nm) with exceptional consistency. Furthermore, SBGR incorporates a mechanism to surgically remove duplicate spots in overlapping regions, maximizing information recovery from duplicate measurements. In conclusion, SBGR emerges as a robust and accurate solution for stitching single-molecule resolution images in tissue-scale spatial transcriptomics, offering versatility and potential for high-resolution spatial analysis.

Rapid calculation of static magnetic field perturbation generated by magnetized objects in arbitrary orientations.

PURPOSE: Most previous work on the calculation of susceptibility-induced static magnetic field (B0 ) inhomogeneity has considered strictly unidirectional magnetic fields. Here, we present the theory and implementation of a computational method to rapidly calculate static magnetic field vectors produced by an arbitrary distribution of voxelated magnetization vectors. THEORY AND METHODS: Two existing B0 calculation methods were systematically extended to include arbitrary orientations of the magnetization and the magnetic field; they are (1) Fourier-domain convolution with k-space-discretized (KD) dipolar field, and (2) generalized susceptibility voxel convolution (gSVC). The methods were tested on an analytical ellipsoid model and a tilted human head model, as well as against experimentally measured B0 fields induced by a stainless-steel implant located in an inhomogeneous region of a clinical 3T MRI magnet. RESULTS: Both methods were capable of correctly calculating B0 fields inside a magnetized ellipsoid in all tested orientations. The KD method generally required a larger grid and longer computation time to achieve accuracy comparable to gSVC. Measured B0 fields due to the implant showed a good match with the gSVC-calculated fields that accounted for the spatial variation of the applied magnetic field including the radial components. CONCLUSION: Our method can provide a reliable and efficient computational tool to calculate B0 perturbation by magnetized objects under a variety of circumstances, including those with inhomogeneous magnetizing fields, anisotropic susceptibility, and a rotated coordinate system.

Rapid, theoretically artifact-free calculation of static magnetic field induced by voxelated susceptibility distribution in an arbitrary volume of interest.

PURPOSE: To demonstrate a computationally efficient and theoretically artifact-free method to calculate static field (B0 ) inhomogeneity in a volume of interest induced by an arbitrary voxelated susceptibility distribution. METHODS: Our method computes B0 by circular convolution between a zero-filled susceptibility matrix and a shifted, voxel-integrated dipolar field kernel on a grid of size NS +NT - 1 in each dimension, where NS and NT are the sizes of the susceptibility source and B0 target grids, respectively. The computational resource requirement is independent of source-target separation. The method, called generalized susceptibility voxel convolution, is demonstrated on three susceptibility models: an ellipsoid, MR-compatible screws, and a dynamic human heartbeat model. RESULTS: B0 in an ellipsoid calculated by generalized susceptibility voxel convolution matched an analytical solution nearly exactly. The method also calculated screw-induced B0 in agreement with experimental data. Dynamic simulation demonstrated its computational efficiency for repeated B0 calculations on time-varying susceptibility. On the contrary, conventional and alias-subtracted k-space-discretized Fourier convolution methods showed nonnegligible aliasing and Gibbs ringing artifacts in the tested models. CONCLUSION: Generalized susceptibility voxel convolution can be a fast and reliable way to compute susceptibility-induced B0 when the susceptibility source is not colocated with the B0 target volume of interest, as in modeling B0 variations from motion and foreign objects.