CynoBrain: A unified high-resolution framework for cross-modal data integration for macaque brain mapping

Abstract

The cynomolgus macaque is a widely used primate model in neuroscience, yet existing brain atlas resources remain limited in resolution and lack a standardized framework for integrating structural, molecular, and connectivity data within a common reference space. Here we present CynoBrain, a high-resolution multi-modal brain atlas constructed from population-averaged MRI data at 9.4 Tesla, yielding a 75 micron isotropic template with significant improvement in resolution. A co-registered whole-brain autofluorescence template resolves cytoarchitectural boundaries not visible in MRI template. Three major parcellation schemes, D99 143-area, M132 105-area, and SARM are incorporated in CynoBrain space. Spatial transcriptomic based laminar definition, reconstructed from 2D sections into volumetric common space, provides a six-layer cortical segmentation spanning the whole cortex. As a demonstration of the integrative capability of this framework, 2D retrograde tracing data is reconstructed and mapped to the Cynobrain space, enabling volumetric compilation of 2D macaque brain mapping data across subjects. An online interactive platform was constructed to allow full access to Cynobrain, establishing it as a scalable, open platform for cross-modal data integration for primate neuroscience. Overall, CynoBrain is a unified framework for cross-modal data integration for macaque brain mapping with high-resolution, multiple atlases and transcriptomic based laminar definition.