The western honeybee Apis mellifera, with a medium-sized brain of about a million neurons, was chosen as a model to study olfactory information coding and associative memory related plasticity. We focused our attention on the primary olfactory neurophils, the antennal lobes (ALs), responsible for coding and processing the sensory information received by the olfactory receptor neurons and for delivering the encoded signals to the mushroom bodies through the projection neurons. A multiphoton microscopy set-up allowed in vivo calcium imaging recording of the antennal lobes at milliseconds resolution. Functional calcium imaging permits recording of the odour stimuli response maps of the functional units, the glomeruli. Moreover, due to the high penetration depth of the set-up, these maps, representing the spatial odour code, can now be extended to sub-surface glomeruli, so far inaccessible to functional imaging. Finally, the penetration depth of multiphoton microscopy coupled with optical clearing treatment permits high-resolution 3D reconstruction of the whole neurophil and this will allow investigating at the cellular level the morphological changes in the glomeruli associated with olfactory memory formation