Extended Data Fig. 5: Aligning units with the Common Coordinate Framework (CCFv3).

a, After each experiment, the brain is removed and cleared using a variant of the iDISCO method. b, The cleared brain is imaged at 400 rotational angles using a custom-built optical projection tomography microscope. c, We generated an isotropic 3D volume from rotational images using a computational tomography algorithm. d, Key points from the CCFv3 template brain are manually identified in each individual brain. e, Points along each fluorescently labelled probe track are manually identified in the volume. Using the key points from d, we define a warping function to translate points along the probe axis into the Common Coordinate Framework. f, We then align the regional boundaries to boundaries in the physiological data, primarily the decrease in unit density at the border between the cortex and hippocampus, and between the hippocampus and thalamus. The shaded area represents unit density on each recording site, and pink dots represent low-frequency LFP power (<10 Hz) along the probe axis. g, Finally, units in the database are mapped to a 3D location in the CCFv3 and are assigned a structure label. Units in cortex are also assigned a relative depth (0, surface; 1, white matter) and a layer label (L1, L2/3, L4, L5 or L6), on the basis of the annotation of the CCFv3 template volume (10-μm resolution).