Fig. 11

Quantitative spatial analysis of the substantia nigra (SN) and its subdivisions across rat brain atlases. (a) Lateral view of the WHS rat brain atlas (WHSSD) SN (SN-c, yellow; SN-l, petrol green; SN-r, light green), with magnified panel showing the spatial position and angle of three selected atlas plates (dashed lines) from rostral (a1), middle (a2) and caudal (a3) part of The Rat Brain in Stereotaxic Coordinates (RBSC) SN. The WHSSD cut to correspond with the three selected atlas plates from RBSC (a1’-a3’), showing the spatial correspondence of the SN annotations (black dashed line filled with a transparent white colour) with regions in the WHSSD. The WHSSD SN is highlighted for comparison (white dashed lines). The inset (a1”-a3”) shows the subdivisions of the SN. (b) Lateral view of the WHSSD SN, showing the spatial position and angle of the selected atlas plates (a1-a3, dashed lines) and the remaining RBSC atlas plates including SN annotations (solid lines). The boxes (b1-b3) indicate the three rostro-caudal parts used for analysis of the quantitative spatial overlap of the RBSC SN with regions in the WHSSD. The pie charts (b1’-b3’) show the proportion of the RBSC SN subdivisions situated in regions of the WHSSD. (c,d) Selected atlas plates (c1-c3,c1’-c3’,c1”-c3”), spatial position (d1-d3) and pie charts (d1’-d3’) for the Brain Maps (BM) SN annotations in relation to WHSSD regions, as described for (a,b). Note that the atlas plates from BM are registered with a mediolateral angle of 4 degrees, which in c1-c3 and d1-d3 gives an illusion of a dorsoventral angle in some atlas plates. Abbreviations: BM, Brain Maps; BS-u, brainstem, unspecified; ic-cp-lfp-py, corticofugal tract and corona radiata; ml-u, medial lemniscus, unspecified; RBSC, The Rat Brain in Stereotaxic Coordinates; SN, substantia nigra; SNc/SN-c, substantia nigra, compact part; SNCD, substantia nigra, compact part, dorsal tier; SNCM, substantia nigra, compact part, medial tier; SNCV, substantia nigra, compact part, ventral tier; SNL/ SN-l, substantia nigra, lateral part; SNR/SNr/ SN-r, substantia nigra, reticular part; STh, subthalamic nucleus; V-u, ventricular system, unspecified; VTA, ventral tegmental area; WHSSD, WHS rat brain atlas; ZI-c, zona incerta, caudal part.