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Measuring
Four overlays above the plate turn it from a picture into something you can take numbers off: Grid, Scale, Measure, and the reference overlays Landmarks and Skull.
- Grid — a 1 mm stereotaxic grid over the section, aligned to the coordinate space the whole app uses.
- Scale — a scale bar under the plate, which relabels itself as you zoom (mm, then µm).
Both survive a source switch, so a Nissl section gets the same grid as the drawing.
Tick Measure, then click two points on the plate. The readout under the image gives:
2.94 mm in plane · ΔML +1.20 · ΔDV −2.68 · 24.1° from vertical
- in plane — the straight-line distance within this coronal section. Both points are on the same plate, so there is no AP component.
- ΔML / ΔDV — the two components, signed.
- from vertical — the angle of the line off vertical. This is the approach angle a straight electrode track between those two points would need in this plane.
Two clicks on plate 30, from the dorsal surface down toward lateral entorhinal cortex: 6.04 mm in plane, ΔML +2.46, ΔDV −5.51, 24.0° from vertical.
Clear resets it, as does Esc. Drag the second point around before you click to see the numbers update live.
With a rotated working frame on, the millimetres still hold — a rotation preserves length — but the angle does not, so the tool stays in atlas coordinates and says so. Moving the origin changes neither reading, since both are differences.
Landmarks marks bregma, lambda and the occipital crest on whichever plate their plane falls in, and draws the interaural line — solid where it lies in the plane, dashed elsewhere as the ear-bar height.
Plate 23 is where bregma's plane falls, so bregma is marked on the section itself; the interaural line is dashed because its plane is elsewhere, and the height is what is being drawn. The olive outline is the CT skull's cut through this plane.
The AP of each is the atlas's own printed figure and is exact. Only the heights — and the ear canals the interaural line runs between — come off the skull fit, so those inherit its approximation.
On the projection views all four become reference rules across the plot.
Skull traces a CT skull's cut through the current coronal plane. The same surface appears as an outline around either projection and as a translucent shell in 3D.
The atlas prints no skull, so this fit is computed here, not published. The scan is a different animal, aligned first on the paper's own landmarks (the coronal suture for bregma, the ear canals for the interaural line), with the tilt, height and three axis scales then set by the drawn sections of all 62 plates. Because the two animals are not the same shape, the skull is stretched about 3% along AP and 4% across, and shortened 4% in depth, to seat the vault on the cortex.
Good to a few tenths of a millimetre. Context around the sections, not a surface to measure against. The * button beside the checkbox opens this note in the app.
A measurement is included in the PNG and SVG exports (its own measure group in
the SVG) and in the track planner's Copy notes text. See Exporting.