A paradigm using multispectral visible and near-infrared imaging spectroscopy is presented to semi-automatically create unbiased spectral maps that guide the site selection for in situ analytical methods (e.g. fiber optic reflectance spectroscopy and X-ray fluorescence) in order to indetify and map pigments in illuminated manuscripts. This approach uses low spectral resolution imaging spectroscopy to create maps of areas having the same spectral characteristics. This paradigm is demonstrated by analysis of the illuminated manuscript leaf Christ in Majesty with Twelve Apostles (workshop of Pacino di Buonaguida, c. 1320). Using this approach the primary pigments are mapped and identified as azurite, lead-tin yellow, red lead, a red lake (likely insect-derived), a copper-containing green, brown iron oxide, and lead white. Moreover, small amounts of natural ultramarine were found to be used to enhance the blue fields around Christ, and a red lake was used to highlight different colors. These results suggest that the proposed paradigm offers an improved approach to the comprehensive study of illuminated manuscripts by comparison with site-specific analytical methods alone. The choice of broad spectral bands proves successful, given the limites palette in illuminated manuscripts, and permits operation at the low light intensity required for examination of manuscripts.