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Reading a Plate
The Plate view is the default, and the one you will spend most time in.
Everything the plate is steered by sits in one strip: the view, the source, the zoom, the two overlays you reach for most — and Controls, which opens the rest.
- The ← anterior / posterior → buttons and the slider at the bottom.
- The ← and → keys.
- Typing
plate 30,p30orbregma -2.3into the search box. - Clicking a plate number on a selected structure's card.
Plate 1 is the most anterior (bregma +7.80 mm); plate 62 the most posterior (bregma −13.55 mm). Sections are 350 µm apart. The strip above the image always shows the plate number and its AP.
The atlas prints every level three times, and all three are here:
| Button | What it shows |
|---|---|
| Labeled | The atlas's own drawing — contours and printed abbreviations |
| Nissl | The unlabelled Nissl-stained section at that level |
| Myelin | The unlabelled Gallyas myelin-stained section printed beside it |
The same corner of plate 30 — hippocampus, thalamus and auditory cortex — at the same zoom and pan in all three sources. Switching source moves nothing.
They are registered to each other, because each of the 186 pages carries the atlas's own printed ML/DV coordinate box and each was cropped to its own box. So switching source moves nothing: the grid, the scale bar, the measure tool, the circled structure and the hover readout are all still in the right place on a section with nothing printed on it — and hovering where the drawing prints an abbreviation still names it, even on the Nissl.
Two extras, under Controls → Advanced:
- Gray — drops the drawing's colour so all three read alike. The histology was published in grey already.
- Contrast — stretches whichever source is showing, 0.6× to 2.6×.
Both carry into the PNG and SVG exports.
The myelin plate is an adjacent section, not the same slice as the Nissl — the two stains cannot both be applied to one section. It is aligned as the authors published it.
| Action | How |
|---|---|
| Zoom in / out | + / − buttons, or the + / − keys |
| Zoom to a point | Double-click the plate there |
| Pan | Drag |
| Back to fit | Fit button, or the 0 key |
The current zoom level shows between the buttons.
Two things happen under the pointer, independently:
- Any point — with Coords ticked, the readout under the plate gives bregma / ML / DV for that point, continuously.
- A printed abbreviation, or the region it names (Labeled source, or the same spot on Nissl/Myelin) — a tooltip gives the full name, the plates it runs over, and how much area the region has on this plate. Click it to select that structure.
Hovering the dorsal lateral geniculate nucleus: the region is outlined in both hemispheres, the tooltip names it, and with Coords on the readout under the plate follows the pointer.
Coords and Grid are on the toolbar. Everything else is behind Controls — the button at the right of the toolbar, which opens a panel beside the plate. C opens it, Esc closes it, and a badge on the button counts what is on.
| Toggle | What it draws |
|---|---|
| Coords (toolbar) | The bregma / ML / DV readout under the pointer |
| Grid (toolbar) | A 1 mm stereotaxic grid over the section |
| Color regions | Fills every region so that no two that touch are the same colour, at a wash you set. The colours name nothing — they only tell neighbours apart |
| Scale | A scale bar |
| Measure | Click two points for distance and approach angle — see Measuring |
| Skull * | The CT skull's cut through this coronal plane (experimental) |
| Landmarks | Bregma, lambda and the occipital crest where they fall, plus the interaural line |
| Compare | A second plate beside this one, sharing zoom, pan and crosshair: the other histology of this level, the drawing, or the plate before or after |
| Notes | Your own markers on the plates, kept in this browser |
The * beside Skull opens the note on why its alignment is approximate. Advanced, at the foot of the panel, holds Gray and Contrast.
Every toggle is carried in Copy link, so a link restores the view you were looking at.
PNG and SVG sit under Controls → Notes and export. PNG saves the plate as shown, with the overlays and a coordinate caption; SVG saves the same sheet as editable vector paths instead of an image. See Exporting.