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The results were compared with conventional light microscopy after staining with hematoxylin eosin, and elastica van Gieson. The spectral unmixing algorithm vertex component analysis was applied for data analysis and image reconstruction. IR microscopy allowed for differentiation between lipids and proteins in plaques of full aortic cross sections. Raman microscopy further discriminated cholesterol esters, cholesterol and triglycerides. FTIR and Raman images were recorded at a resolution near 20 micrometer per pixel for a large field of view. High resolution Raman images at 1 micrometer per pixel revealed structural details at selected regions of interest. The intima\u2010media and the lipid\u2010protein ratio were determined in five specimens for quantitation. These results correlate well with histopathology. The described method is a promising tool for easy and fast molecular imaging of atherosclerosis. (\u00a9 2013 WILEY\u2010VCH Verlag GmbH &amp; Co. 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