Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space
(A) A schematic illustrated using a model material. Two types of data, material shape images (drawn with green lines) and gene expression densities (shown in red) of fractions (indicated with asterisks), are obtained with sectioning, conjugated with block-face imaging and expression density measurement, along three body axes (shown in parentheses). The three series of sectioning are named after orthogonal planes (C, S and H). The densities are assigned to the voxels (pixels on a regular grid in a 3D space) in the images (as shown with +) and subjected to tomographic reconstruction (indicated in purple). A series of the process from one direction needs one material; therefore, at least three genetically identical materials were required. (B) An outline of the technique and the first dataset creation. Two types of data, fraction templates, which are the material shape image (in green) and fraction data, which are gene expression densities measured with microarray (in dotted red), were acquired from the same fractions prepared with a sectioning machine 3D-ISM . The fractions were named “image fractions” for the former data and “material fractions” for the latter (the preparation process seen in Video S1). Six fraction templates for the first dataset, two groups of three series sectioned in each of orthogonal and slightly oblique to the orthogonal planes: S/C/H and So/Co/Ho, composed of 9/13/6 and 10/16/7 fractions, respectively, (61 fractions in total as seen in Figure S1B), are shown with fraction numbers in Template C: 13 fractions of 1 mm (5 µm×200 sections)-thickness. The pseudo-tomography technique of mapping in a single coordinate space (named ViBrism) including image registration, pseudo-back projection and tomographic reconstruction is shown in the flowchart (see details in Figure S1A and Text S1). After volume rendering, 3D expression maps for genes (a sample: Slitrk6) are visualized as pseudo-colored expression densities and anatomical images with an 80% cutoff filter (also seen in Video S2). Slitrk6 is known to be expressed mostly in the thalamus as shown in the Allen Brain Atlas and BrainStars databases: 2Dand 3D views displayed here are compatible to those data shown below in Figure 4A and B and VideoS2.