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. Author manuscript; available in PMC: 2014 Jul 10.
Published in final edited form as: Nature. 2013 Apr 10;497(7449):332–337. doi: 10.1038/nature12107

Figure 2. Intact adult mouse brain imaging.

Figure 2

Imaging was performed in adult mouse brains (3 months old). a, Cajal quote before CLARITY. b, Cajal quote after CLARITY: Thy1–eYFP line-H mouse brain after hydrogel–tissue hybridization, ETC and refractive-index matching (Methods). c, Fluorescence image of brain depicted in b. d, Dorsal aspect is imaged (single-photon (1p) microscopy), then brain is inverted and ventral aspect imaged. e, Three-dimensional rendering of clarified brain imaged (×10 water-immersion objective; numerical aperture, 0.3; working distance, 3.6 mm). Left, dorsal half (stack size, 3,100 µm; step size, 20 µm). Right, ventral half (stack size, 3,400 µm; step size, 20 µm). Scale bar, 1 mm (Supplementary Videos 3–5). f, Non-sectioned mouse brain tissue showing cortex, hippocampus and thalamus (×10 objective; stack size, 3,400 µm; step size, 2 µm). Scale bar, 400 µm (Supplementary Video 2). g–l, Optical sections from f showing negligible resolution loss even at ~3,400-µm deep: z=446 µm (g, h), z=1,683 µm (i, j) and z=3,384 µm (k, l). h, j and l, boxed regions in g, i and k, respectively. Scale bars, 100 µm.m, Cross-section of axons in clarified Thy1–channelrhodopsin2 (ChR2)–eYFP striatum: membrane-localized ChR2–eYFP (1-mm-thick coronal block; ×63 glycerol-immersion objective; numerical aperture, 1.3; working distance, 280 µm). Scale bar, 5 µm. n, Dendrites and spines of neurons in clarified Thy1–eYFP line-H cortex (1-mm-thick coronal block; ×63 glycerol objective). Scale bar, 5 µm.