The SWAN atlas: an open multimodal resource combining neuroimaging and high-resolution histology of the human brain in stereotactic space

Precise localization of human brain regions is critical in clinical practice and population neuroimaging, particularly in stereotactic functional neurosurgery, where small targeting errors may lead to treatment failure. Although MRI provides in vivo and postmortem brain parcellation, histology offers complementary mesoscopic and microscopic information. A major limitation of histological atlases for clinical use is accurate coregistration with in vivo imaging, since tissue processing introduces deformation. To reduce this problem, we sectioned an entire human brain using high-thickness slices, which are less prone to slice-level deformation. Histological sections were registered to the brain’s own MRI and normalized to standard stereotactic space through a multistep transform chain. Users can apply MRI-to-MRI registration to transform the atlas into patient space and vice versa, with further nonlinear refinement using SwanWarp or WarpDrive tools. Segmentations and software are being prepared for open distribution. This resource may empower both clinical neurosurgical research and the broader neuroimaging field at large.