This study presents a novel multispectral imaging method to detect structural and biochemical alterations in paraffin-embedded embryonic mouse eye tissues caused by maternal folic acid deficiency. Using principal component analysis and endmember extraction, the technique identified changes in blood vessel regions (vitreous and choroid) linked to hemoglobin/oxyhemoglobin imbalance, as well as microstructural changes in the retina and lens. The method offers a non-invasive, label-free diagnostic tool for analyzing pathological tissues before applying molecular labeling techniques.