cyto7: an open, surface-native cytoarchitectural type atlas of the human cortex with multimodal validation and a per-vertex confidence map

A vertex-resolution map of human cortical cell-layer types, validated against imaging, genetics, and brain dynamics — and shipped with per-vertex uncertainty estimates.

The cerebral cortex isn't uniform. It varies systematically in how many distinct layers it has, and especially in how developed its fourth layer (the "granular" layer) is. This gradient — from the nearly layerless allocortex near the hippocampus, through transitional limbic cortex, up to the hyper-granular primary sensory areas — is called the cortical-type axis. It predicts how areas connect, how plastic they are, and which diseases hit them hardest. The problem is that existing digital maps of this axis assign one type per classical brain area, like painting a country a single color. A type boundary that runs through an area is invisible. cyto7 fixes this by painting types vertex-by-vertex on the standard fsaverage surface — roughly 164,000 points — following an established expert protocol, then having the protocol's own authors revise the result.

The map enforces four spatial rules the theory predicts: types must change gradually between neighbors (no skipping a level), the least-differentiated limbic cortex must form a continuous belt around the medial wall, and the most differentiated types must appear as isolated islands. Satisfying these rules required relabeling only 0.78% of vertices, and removing those relabeled vertices barely moves any correlation. The map is then benchmarked against the older area-level map: they agree at 52.5% of vertices, with disagreement almost always just one ordinal step and concentrated inside the large heterogeneous areas that a single areal label can't resolve. Where they disagree, cyto7's label better matches independent MRI features (myelin, thickness, functional connectivity gradient) at 60% of disagreement vertices versus a chance rate of ~46–54% under conservative null tests.

The multimodal validation is the external, independent leg. Intracortical myelin rises along the type axis, cortical thickness falls, and the principal functional-connectivity gradient reverses — all surviving a spatial-autocorrelation null with FDR control. Resting-state MEG dynamics also track the axis: neural timescales shorten toward more granular cortex (ρ ≈ −0.46), and the spectral centroid rises, consistent with faster dynamics in more differentiated areas. Notably, the aperiodic 1/f exponent — often interpreted as an excitation-inhibition proxy — does not track type, a reliable null given good spectral fits and high reproducibility. The clearest separation from simply quantizing a continuous MRI map comes from laminar marker genes: cyto7 tracks the layer-IV marker RORB (ρ = +0.78) and the layer-V marker FEZF2 (ρ = −0.59) more closely than seven-level bins of myelin or the functional gradient, because those continuous maps have no way to represent a marker that runs against myelin.

Each vertex also gets an anatomical support score — a number between 0 and 1 built purely from anatomy (atlas concordance, topological consistency, geometry, and a per-type provenance prior), deliberately excluding the imaging data used for validation. Eulaminate and koniocortex vertices score highest; the developmentally-defined allocortex scores lowest, flagging exactly the tissue where the typing rests on embryological reasoning rather than surface atlases. The honest limitations are stated plainly: single rater, no independent second painting, and the one direct histological check (BigBrain) is inconclusive at single-specimen scale. The map is released open, with the full change log, per-vertex support components, and a crossed parcellation for region-based models.