This Dataset consists of TIFF 100 images, split in 20 test and 80 training images, of axons with their synapses (boutons) labelled. The labels are in form of ground-truth binary images of the same size, in which the corresponding synapses have been labelled as boxes. This data was collected in the live mouse cortex, using a two-photon microscope, with a 40x objective, at zoom 4, with a resolution of 512 x 512 x 0.147 microns per pixel, and a Point Spread Function characterised by a Full Width at Half Maximum (FWHM) values of 0.45 x 0.45 x 2.5 microns (x, y, z). Please cite the following paper when using this dataset: Bass C, Helkkula P, De Paola V, Clopath C, Bharath AA. Detection of axonal synapses in 3D two-photon images. Giniger E, ed. PLoS ONE. 2017;12(9):e0183309. doi:10.1371/journal.pone.0183309.