Figure 1

Preprocessing of resources by Allen Institute for Brain Science. (a) Online public resources at AIBS for anatomical template (AT, left), annotation volume (AV, middle), and anatomical ontology (AO, right) of the mouse brain. AT is shown with its left hemisphere cropped to display its subcortical structures. AV is shown in NIH color scheme, with each voxel assigned an integer value for an ID of a brain structure. This original AV is single-sided: homotopic brain structures on the left and right sides of the brain have the same ID and constitute a single node. The same brain structure (ID) is shown in the same color, e.g. arrows indicate a single node in green color, caudoputamen (CP). L denotes the left side of the brain. AO is a JSON-formatted text file shown here as a rooted tree with each brain structure regarded as a node in a graph theoretical term, demonstrating its anatomical hierarchy. A double line rectangle shows a root node of a rooted tree graph. A parent node is one-level higher than its child nodes in the anatomical hierarchy. For example, a node “root” is a parent node of its child nodes “grey” and “fiber tracts”. Similarly, a node “FRP” is a parent node of its child nodes “FRP1” and “FRP2/3”. Nodes “grey and fiber tracts” and “FRP1 and FRP2/3” respectively occupy the same level of the hierarchy. Ellipses and rectangles respectively denote leaf nodes, which do not have a child node, and inner nodes, which have at least one child node, with its acronym for a brain structure: grey, grey matter; FRP, Frontal pole in the cerebral cortex; FRP1 and 2/3, Layer 1 and 2/3 of FRP. (b) Preprocessing of the original AO (left) for eliminating destructive nodes to obtain a modified AO (designated as AObase; right). The original AV was updated to AVbase by reflecting AObase. A pair of AObase and AVbase was designated collectively as a flexible annotation atlas base (FAAbase). Filled and open nodes: nodes with and without corresponding voxels in AV. CNU, cerebral nuclei; STR, striatum; STRd and STRv, dorsal and ventral region of STR; OT, olfactory tubercle; isl, islands of Calleja; OT1, molecular layer of OT. (c) Distribution of size (voxel count in AVbase) of leaf nodes in FAAbase (blue plots). Too small or too large nodes for fMRI analysis are evident in FAAbase. Specifically, 6.7% of all leaf nodes in FAAbase were smaller than a single voxel in fMRI (30 nL, dashed line). Four nodes were extremely large (> 10,000 nL, dotted line). Red and green plots are for FAAcoarse and FAAdetailed (see Figs. 2 and 3). (d) This icicle plot presents the anatomical hierarchy of brain structures in FAAbase. Each node is shown with its acronym and size in units of nL. For example, “CH: 275611” stands for a brain structure “Cerebrum” with a volume size of 275,611 nL. Note that 1 nL corresponds to a single voxel (100 × 100 × 100 μm³) of a volume data (AT and AV). The width of each node represents its size. Hence, the plot clearly shows the relationship between volumes of child and parent nodes. Root nodes are at the top; leaf nodes (shown in bold face) are at the bottom such as CP in blue (indicated by the arrow at the middle). Inner nodes are between a root node and leaf nodes, such as cerebral cortex (CTX) in pale green (indicated by the arrowhead at the left). Nodes for fiber traces and ventricular systems (VS) are included in FAAbase (indicated by the dashed arrow at the upper right). FAAbase is also single-sided. For nodes with collapsed letters, see the zoomable HTML version of this plot at https://github.com/ntakata/flexible-annotation-atlas/tree/master/FAAs. The color code for the brain structure follows that of AIBS, and is applicable to Figs. 2b,d, 3e, 4a,b,d, and Supplementary Fig. 1a. CH cerebrum, BS brain stem, CB cerebellum. For other acronyms, see the original AO file.