Hi Jenny. My tip would be the way you fix the lung tissue. The best way to do it is pressure-fixing - you slowly immerse PFA via trachea at certain pressure (for mouse lung it is 20 cm water), then PFA reaches all alveoli, so that no tissue is left to dry unfixed (which leads to high autofluorescence). If your experiment does not allow pressure fixing, then I would try freezing in OCT and applying PFA for 10 minutes at 4 degrees Celcius, when the lung is already cut in sections (basically, pour PFA on slides with sections). Do not let sections dry after this step. The last tip is I never tried myself, but some people apply Sudan black to reduce autofluorescence after the staining was done. https://www.ncbi.nlm.nih.gov/pubmed/20552552