12A limitation of current methods for examining neural activity over long periods of time in the 13 fly, Drosophila melanogaster, is the need to remove the head cuticle and the underlying tissue 14 to gain optical access to the brain, a process that damages circulation and restricts the length 15 of imaging time. Here, we developed a non-invasive preparation for structural and functional 16 imaging of the fly brain through the intact head cuticle. We first showed that the head cuticle 17 transmits long-wavelength laser light with surprisingly high efficiencies. In fact, the tissue 18 that interferes with laser light during multiphoton imaging is the air sacs underneath the 19 head cuticle. We developed a non-invasive imaging preparation that compresses the air sacs, 20 and used it to image the mushroom body Kenyon cells and central complex ring neurons 21 through the cuticle at cellular resolution using both 2-and 3-photon microscopy. We also 22 performed non-invasive short-term and long-term functional imaging (for the first time for 23 12 consecutive hours) of odour-evoked calcium responses from the mushroom body Kenyon 24 cells. Our results demonstrate that the non-invasive imaging preparation developed here 25 extends the time limits of current in vivo imaging methods used in flies that require an 26 invasive surgery, and opens up new ways to capture neural activity from the intact fly brain.27