Fig. 9: CCFv3 Alignment to MERFISH reads of 20 selected spatially variable genes. | Communications Biology

Fig. 9: CCFv3 Alignment to MERFISH reads of 20 selected spatially variable genes.

From: The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales

Fig. 9

a Shows initial alignment of CCFv3 to stack of 60 sections, each sampled at 200-μm resolution. d Shows final alignment of CCFv3 to stack of MERFISH sections following rigid and diffeomorphic transformation. b–f Show in-plane alignment of intersecting CCFv3 to 4 selected MERFISH sections in the anterior half of the mouse brain (spaced 500 microns apart, yellow star in (d)). Alignment between foreground-background tissue boundaries is seen particularly along the ventral and lateral edges. White arrows show matching contours of outer and inner boundaries of the CCF striatum to areas predominantly expressing Kirrel3. White arrows also illustrate alignment within the area of the lateral septal nucleus (b). g–z Show sections l–p, v–z every 0.5 mm with g–k, q–u corresponding intersection through deformed atlas following alignment, as in (d).

Back to article page