Tissue expansion of ‘cleared’ whole brains reduces contrast in ex vivo MRI

Abstract Multimodal imaging of optically-cleared brains, ex vivo, by Magnetic Resonance Imaging (MRI) and light microscopy (LM) presents unique opportunities for studying the brain at various scales and resolutions. However, CLARITY -cleared brains lack MRI contrast, implicating lipids as the major source of MRI contrast. We explored the ex vivo MRI compatibility of uDISCO, ECi and Scale -cleared brains. Surprisingly, uDISCO and ECi -cleared brains retain MRI contrast, whereas Scale-cleared brains show a severe loss of MRI contrast, as CLARITY. Determination of lipid-content in cleared samples shows that CLARITY, uDISCO and ECi are strongly delipidating, whereas Scale preserves most lipids. We conclude that MRI contrast can be associated with tissue expansion (and hyperhydration) rather than with lipid-content. Thus, we present two clearing methods compatible with ex vivo MRI.