Extended Data Fig. 8: Whole-mount imaging and data analysis.

a, Whole-mount imaging data of a Cxcl12–GFP bone section stained for Alpl and Emcn was segmented in 3D using the imaris software. Large Alpl⁺ surfaces (red, corresponding to endosteum and arteries) were identified and any GFP+ spots with <20µm proximity to these structures were excluded from further analysis (yellow spots). The strong Alpl signal in these regions prevents a quantitative assessment. Remaining GFP⁺ spots were classified as within 15µm of sinusoidal vessels (purple dots), of away from sinusoidal vessels (cyan dots). GFP⁺ spots were further classified as Alpl⁺ (right panels, red spots) or Alpl^- (right panels, green spots). Scale bar left panel: 200µm; right panels: 50µm. b, Additional whole-mount imaging data of a femur from a Cxcl12–GFP mouse, stained for Alpl and the arteriolar marker Sca1. Arrowheads point to Alpl⁺Cxcl12⁺ cells near, but not overlapping with, Sca1⁺ arteriolar endothelial cells. See also Fig. 4f. In ROI 3, asterisk correspond to GFP⁺Alpl⁺ protrusions on, but clearly distinct from, Sca1⁺ arteriolar endothelial cells. In ROI 4, various z-sections of a highly reticulate Cxcl12–GFP⁺Alpl⁺ cell are shown. Scale bars in ROIs: 20µm; scale bar in main panel: 300µm.