The wiring of the brain connects micro-architecturally diverse neuronal populations. The conventional graph model encodes macroscale brain connectivity as a network of nodes and edges, but abstracts away the rich biological detail of each regional node. Regions are different in terms of their microscale attributes, many of which are readily available through modern technological advances and data-sharing initiatives. How is macroscale connectivity related to nodal attributes? Here we investigate the systematic arrangement of white-matter connectivity with respect to multiple biological annotations. Namely, we formally study assortative mixing in annotated connectomes by quantifying the tendency for regions to be connected with each other based on the similarity of their micro-architectural attributes. We perform all experiments using four cortico-cortical connectome datasets from three different species (human, macaque and mouse), and consider a range of molecular, cellular and laminar annotations, including gene expression, neurotransmitter receptors, neuron density, laminar thickness and intracortical myelin. Importantly, we disentangle the relationship between neural wiring, regional heterogeneity and spatial embedding using spatial autocorrelation-preserving null models. We show that mixing between micro-architecturally diverse neuronal populations is supported by long-distance connections. Using meta-analytic decoding, we find that the arrangement of connectivity patterns with respect to biological annotations shape patterns of regional functional specialization. Specifically, regions that connect to biologically similar regions are associated with executive function; conversely, regions that connect with biologically dissimilar regions are associated with memory function. By bridging scales of cortical organization, from microscale attributes to macroscale connectivity, this work lays the foundation for next-generation annotated connectomics.

Assortative mixing in micro-architecturally annotated brain connectomes