Supplementary Figure 1: Atlas-based mechanical or laser dissection of tissue

(a) An open-source brain block designed from our 3D atlas printed which can be directly ordered from (http://www.shapeways.com/shops/wholebrain) with all profit going to further development of the atlas. Alternatively, the brain block can be downloaded (https://github.com/tractatus/brain-blocks) modified for any needs and 3D printed by the user itself. (b) The brain block is designed to be used with a standard and can cut coronal sections anchored in the atlas with 1 mm apart, ranging from stereotactic anterior-posterior coordinates +5 mm to −11 mm relative to bregma (white arrow). (c) Top view. (d) Close-up, the small circular bevel marks bregma 0 mm (black and red arrow). (e) Specimen holder for the Leica LMD system scanning stage accommodating 3 slides, with only the middle one loaded with one membrane slide mounted with a single brains section. (f) Entire membrane microscope slide imaged with bright-field at 10× optical magnification and stitched by Leica LMD, this overview image is exported as raw TIF and used as input to WholeBrain registration. (g) Close up on brain section after registration to matched coordinate (+0.2 mm from bregma) (h). The user can select any region desired to laser capture with the get.region() command, in this case selecting SSp (left hemisphere), MOp2/3 (right hemisphere), SSp-bfd5 (right hemisphere), ADP, SI, MS i.e. get.regions(acronym=c("SSp","MOs2/3","SSp-bfd5","ADP","SI","MS"), right.hemisphere=c(0,1,1,2,2,2) registration=regi), where regi is the registration output. (i) Registration result superimposed on the microscope slide. (j) with regions to be laser captured.