Table 1.

Summary of experiments before, during and after tissue clearing.

	Longitudinal MRI	Longitudinal NMR	Quantitative MRI	ICP-OES	protein analysis (BCA)	pH	Staining
Before clearing	T1w, T2w, MD, FA of 2 mouse brain samples embedded in hydrogel	1H and 31P measurements of 2 uncleared mouse brains	T1-map, T2-map, T2*w, PDw, MD and FA of mouse brain fixed with PFA and mouse brain fixed in hydrogel	Fe, Ca and P measurement of the olfactory bulb of 4 uncleared mouse brains	Five regions (cortex, corpus callosum, cerebellum, hypocap us, brain stem) were dissected from three hydrogel-embedded but uncleared samples and three cleared brain samples and analyzed for their protein content	pH of uncleared mouse brain
During clearing	Each week T1w, T2w, MD and FA for 4 week clearing period	Each week 1H and 31P spectrum for 4 week clearing period
After clearing	T1w, T2w, MD, FA of 2 cleared mouse brain samples	1H and 31P spectrum of 2 cleared mouse brain samples	T1-map, T2-map, T2*w, PDw, MD and FA of cleared mouse brain and a pure hydrogel and PBS sample	Fe, Ca and P measure ment of the olfactory bulb of 4 cleared mouse brains	The same regions as above of three cleared brains were analyzed for their protein content	pH of cleared mouse brain	Staining of cleared mouse brain for cells using PI and neurofilaments using NF

ICPOES - Element analysis using Inductively coupled plasma optical emission spectrometry, BCA - Protein analysis using bicinchoninic acid assay, T1w - T1-weighted, T2w - T2-weighted, MD - Mean diffusivity, FA - fractional anisotropy, PDw - Proton density weighted, PFA - 4 % Paraformaldehyde, PI - Propidium Iodide, NF -Neurofilament