Summary
A bioRxiv preprint introduces CynoBrain, a macaque brain atlas that combines 9.4-tesla MRI, autofluorescence, cortical layers, gene-expression data and neural connectivity in one reference space. The authors also describe an online platform for exploring and integrating the data.
A team at the Institute of Neuroscience of the Chinese Academy of Sciences has presented CynoBrain, a high-resolution macaque brain atlas designed to place structural, molecular and connectivity measurements in a shared three-dimensional reference space.
The work is described in a bioRxiv preprint posted on September 13, 2026. It is a research framework rather than a clinical study: the authors' goal is to make different kinds of macaque brain-mapping data easier to align and compare.
A 75-micron reference brain
CynoBrain uses population-averaged magnetic resonance imaging data collected at 9.4 tesla to create an isotropic template with a resolution of 75 microns. An isotropic voxel has the same size along each spatial dimension, so the template uses 75-micron units in all three directions.
The authors say this represents a substantial resolution improvement over existing macaque brain-atlas resources. The atlas also includes a co-registered whole-brain autofluorescence template. Autofluorescence is a naturally occurring optical signal from tissue; in this framework, it helps reveal cytoarchitectural boundaries—boundaries based on the organisation and cellular structure of brain tissue—that are not visible in the MRI template alone.
The common reference space incorporates three existing parcellation schemes: the D99 atlas with 143 areas, the M132 atlas with 105 areas, and SARM. Brain parcellations divide the organ into named or numbered regions so that measurements from different experiments can be described using a consistent anatomical map.
Combining anatomy, gene activity and connections
A central feature of CynoBrain is its attempt to connect data collected with different methods. The authors used spatial-transcriptomic information to define cortical layers and reconstructed two-dimensional sections into a shared three-dimensional space. The resulting framework provides a six-layer cortical segmentation across the macaque cortex.
Spatial transcriptomics measures patterns of gene activity while retaining information about where in a tissue those patterns occur. In the atlas, that information is used to add a molecularly informed description of cortical lamination—the organisation of the cortex into layers—to the structural reference space.
The researchers also demonstrate the framework with two-dimensional retrograde-tracing data. Retrograde tracing is a method for studying neural connections by identifying neurons that project to a labelled location. CynoBrain maps these two-dimensional observations into its three-dimensional coordinate system, allowing connectivity data from different subjects to be compiled volumetrically.
This integration is important because MRI, tissue imaging, gene-expression measurements and tracing experiments usually differ in scale, format and anatomical coordinates. A common reference space can make it easier to relate a structure seen in one modality to molecular or connectivity information measured with another.
An online platform for the atlas
The authors say they built an interactive online platform that provides access to CynoBrain. They describe it as an open and scalable platform for cross-modal data integration in primate neuroscience.
The immediate value of the work is therefore methodological. CynoBrain brings several atlas schemes and several classes of brain data into one macaque-centred framework, rather than presenting a single anatomical image or one type of measurement. That could help researchers compare findings across experiments and subjects using shared coordinates.
The evidence currently comes from a bioRxiv preprint, so the framework is presented before formal journal publication. The supplied abstract describes the atlas, its component datasets and a demonstration using retrograde tracing, but does not provide detailed study methods, animal numbers or quantitative validation results. Those details will be important for judging registration accuracy, coverage and how reliably measurements from different experiments can be combined.
CynoBrain is also a macaque research resource. Its maps may support primate neuroscience, but the preprint itself does not report a human brain atlas, a clinical application or a medical intervention.