Point coordinate data showing spatial distribution of corticostriatal, corticothalamic, corticocollicular, and corticopontine projections in transgenic mice

The data set comprises three-dimensional point coordinate data representing the spatial distribution of subcortical projections from 11 locations in the cerebral cortex to the striatum, thalamus, superior colliculus, and pontine nuclei in transgenic mice (Scnn1a-Tg3-Cre, Trib2-F2A-CreERT2, Rbp4-Cre_KL100, Sim1-Cre_KJ18 Tlx3-Cre_PL56). The point data are derived from public high-resolution images of anterogradely labeled axonal projections from different cerebro-cortical locations to four subcortical brain regions. Serial two-photon tomography images and derived segmented images series were programmatically downloaded via API from the Allen Brain Atlas Data Portal. The spatial registrations of the images with the Allen mouse brain atlas Common Coordinate Framework 3 were slightly adjusted to improve anatomical correspondence in regions of interest. The segmented images were binarized, and pixels representing tracer labelling within the caudate-putamen, thalamus, superior colliculus, and pontine nuclei were converted to 3-D point coordinates. The data points are suitable for co-visualization of different combinations of data sets, for comparison the topographic arrangement of visual corticostriatal, corticothalamic, corticocollicular, and corticopontine projections.