Objective. The objective of this research is to unify the molecular representations of spatial transcriptomics and cellular scale histology with the tissue scales of computational anatomy for brain mapping.Impact Statement. We present a unified representation theory for brain mapping based on geometric varifold measures of the microscale deterministic structure and function with the statistical ensembles of the spatially aggregated tissue scales.Introduction. Mapping across coordinate systems in computational anatomy allows us to understand structural and functional properties of the brain at the millimeter scale. New measurement technologies in digital pathology and spatial transcriptomics allow us to measure the brain molecule by molecule and cell by cell based on protein and transcriptomic functional identity. We currently have no mathematical representations for integrating consistently the tissue limits with the molecular particle descriptions. The formalism derived here demonstrates the methodology for transitioning consistently from the molecular scale of quantized particles—using mathematical structures as first introduced by Dirac as the class of generalized functions—to the tissue scales with methods originally introduced by Euler for fluids.Methods. We introduce two mathematical methods based on notions of generalized functions and statistical mechanics. We use geometric varifolds, a product measure on space and function, to represent functional states at the micro-scales—electrophysiology, molecular histology—integrated with a Boltzmann-like program to pass from deterministic particle descriptions to empirical probabilities on the functional states at the tissue scales.Results. Our space-function varifold representation provides a recipe for traversing from molecular to tissue scales in terms of a cascade of linear space scaling composed with nonlinear functional feature mapping. Following the cascade implies every scale is a geometric measure so that a universal family of measure norms can be introduced which quantifies the geodesic connection between brains in the orbit independent of the probing technology, whether it be RNA identities, Tau or amyloid histology, spike trains, or dense MR imagery.Conclusions. We demonstrate a unified brain mapping theory for molecular and tissue scales based on geometric measure representations. We call the consistent aggregation of tissue scales from particle and cellular scales, molecular computational anatomy.