(A) Examples of fixed (left) and cleared/decolorized (right) sternums and femurs from HIV-1-infected BLT hu-mice. Squares are 5 mm by 5 mm. Images of tissues before and after clearing were captured on an iPhone 5 (Apple). (B) Representative confocal Z-slice of cleared sternum from an HIV-1–infected hu-mouse 63 days post-infection immunostained for hCD4 (magenta), hCD68 (red), HIV-1 p24 (green), and nuclei (blue). (C) Gallery of zoomed confocal Z-slices showing characteristic sizes and morphologies of hCD4+ cells (magenta), hCD68+ cells (red), and p24+ cells (green). Arrows indicate p24+ cells. (D) Volume of autofluorescence from cleared femur of an HIV-1 infected hu-mouse 10 days post-infection captured with light sheet microscope (left). Segmented model of bone from the same volume (center left). Dashed red box shows region of interest for subsequent panels. Light sheet volume of a region of BM immunostained for hCD4 (magenta), hCD68 (red), and HIV-1 p24 (green) (center right). Segmented model from the same dataset showing individual cell distributions within BM (right). (E) Quantification of individual cell population densities over time. (F) Percent of total p24+ cells co-localizing with hCD68+ cells (red), hCD4+ cells (magenta), or not co-localized with hCD68+ or hCD4+ cells (green) at specific times post-infection. Error bars represent standard deviations from the mean of 3 measurements from separate volumes of tissue greater than 0.5 mm3 each. Scale bars: (B = 20 μm; C = 5 μm; D = 4 mm, left panels; 500 μm, right panels).