Extended Data Fig. 2: Cortical wide-field alignment.

a, Example wide-field images from one mouse, used to align vasculature. b, Retinotopic visual field sign maps corresponding to the sessions in a. c, Retinotopic maps averaged across all sessions for three example mice, used to align wide-field images across mice. d, Retinotopic map averaged across mice and symmetrized, used to align wide-field images to the Allen CCF atlas (used only for figure overlay purposes). e, Cortical seed pixels (left) and corresponding pixel–pixel correlation maps (right). Each pixel–pixel correlation map (right) is made by correlating a given pixel with all other pixels, which reveals clusters of pixels belonging to correlated cortical regions (for example, the central circles corresponding to limb somatomotor cortex). f, Summed edge-filtered pixel–pixel correlation maps (as in e) showing the outlines of correlated clusters of pixels. Each pixel–pixel correlation map (as in e) highlights a correlated cluster of pixels. Edge-filtering each pixel–pixel correlation map then draws a boundary around the highlighted correlated cluster. Summing these edges across all pixel–pixel correlation maps illustrates the boundaries of all correlated clusters of pixels, prominently including limb somatomotor cortex (central circles), visual cortex (posterior lateral triangular regions), retrosplenial cortex (posterior medial region) and orofacial somatomotor cortex (frontal lateral regions). The Allen CCF regions aligned using retinotopy (red) align well to correlation borders, indicating that our alignment methods based on posterior retinotopy also successfully align anterior regions.