Fig. 1.

Photographs of the multiple stages of the tissue cutting. A A coronal slab of human brain tissue fixed for one day in 10% formalin and a sample cut from the coronal slab (red dashed box). The sample was embedded in a hydrogel solution and polymerized. A structural MRI scan (0.3 mm isotropic resolution) and a DTI scan (1 mm isotropic resolution) were performed on the sample. The arrows indicate the anatomical orientation, S – superior, R – right, A – anterior. B The tissue sample cut in half, with labels depicting the location of the lateral thalamus (LT), anterior thalamic nucleus (ATN), medial thalamic tract (MTT), red nucleus (RN), subthalamic nucleus (STN), and substantia nigra (SN). The rounded blue arrow denotes that the direction the sample is rotated (from S-R to S-A) for the photos shown in C and D. C The lateral part of the tissue sample was scanned on a small-bore scanner with a structural MRI scan at 0.1 mm isotropic resolution. D The superior part of the sample shown in C, which encompasses mostly gray matter and many visible vessels (black dots) that under-went the rest of the CLARITY pipeline (clearing, staining, and microscopy).