Fig. 3 Analysis of macrophage distribution using the CUBIC Body Atlas (IMAGE)
Caption
(A) Workflow for macrophage analysis using the neonatal whole-body atlas. First, nuclear staining images visualizing all cells and immunostained images labeling macrophages were acquired. Next, nuclear images were computationally aligned to the reference atlas by estimating the transformations required to match the sample’s shape and orientation. The resulting registration parameters were applied to the detected cells (macrophage), allowing automatic assignment of each cell to its anatomical location within the body. This enabled mapping of macrophages onto the 3D atlas and detailed analysis of their organ-specific distribution.
(B) Distribution of all detected macrophages (left) and atlas-annotated whole-body macrophage distribution (right), with color-coding by organ.
(C) Quantitative analysis of macrophage distribution across organs. For each tissue, the distance between each macrophage and its nearest neighboring macrophage was calculated and visualized as a histogram. A left-shifted distribution indicates local clustering. The analysis revealed strong leftward shifts in specific organs such as the spleen, indicating localized aggregation of macrophages. These findings suggest that macrophages may have organ-specific functional roles.
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