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This work presents the implementation of Visible Hyperspectral Imaging for the in-situ analysis of glass chromophores in two glass windows from the Casa-Museu Dr. Anastácio Gonçalves (Lisbon, Portugal). The measurements were taken inside the building using natural sunlight as the illumination source. In addition, advantages and disadvantages of the followed methodology are discussed.The Dining Room glass window presents glasses colored in bulk with iron, manganese, cobalt, copper, and chromium; silver staining was also detected and was used to create the yellow and orange colors. The Atelier panel was produced with uncolored glasses painted with grisaille and enamels; the chromophores identified are similar to the species identified in the Dining Room panel.