3D parameterization of barrels and barrel columns in rat vibrissal cortex.

<p>(A) Tangential view of the left hemisphere of a rat brain. The barrel field is located in the primary somatosensory cortex (S1), adjacent to the secondary somatosensory cortex (S2). (B) The barrels are arranged in a somatotopic layout of rows (A–E) and arcs (1–6). The four barrels in front of the first arc are given greek labels (α-δ). The barrel center (BC) is the centroid of a barrel and is used to describe the 3D location of individual barrels. The coordinate system used to describe the 3D layout of the barrel field based on the position of the BCs is centered on the C2 barrel (red), which is centrally located within the barrel field. The z axis points vertically along the C2 barrel column axis, the x axis is chosen to point towards the C3 barrel center (approximately along the row) and the y axis is perpendicular to the x and z axes and points approximately along the arc. (C) View of a coronal section of the left hemisphere (see dashed line in a). Barrels can be visualized by preparing cortical sections tangential to the barrel cortex. (D) The barrel cortex is organized into vertical barrel columns. These are obtained by cylindrical extrapolation of the barrel outlines along their respective BC axis to the pia and subcortical White matter (WM), respectively. The location of a barrel along the BC axis is described by the barrel top (BT) and barrel bottom (BB) points. (E) Tangential sections through rat cortex, indicating the relative depth below the pia, with automatically detected anatomical landmarks: red – pia, blue – WM, orange – blood vessels. The inset in section S13 shows an example of a high-resolution optical section of the barrel field.