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A searchable, clickable version of the Radtke-Schuller et al. (2016) Mongolian gerbil brain atlas: 723 structures across 62 coronal plates, each with stereotaxic coordinates, and each level in all three of the ways the atlas prints it — labelled drawing, Nissl, myelin.
Plate 30 — bregma −2.35 mm — with Color regions on at a 40% wash. Eight colors over 111 regions, chosen so that no two regions that touch are alike; a color names nothing on its own. The printed plate is underneath the wash at every setting.
Nothing to install, no account, no server. Works offline if you download the file.
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Type a structure in the search box —
MSOormedial superior olive. Click a result. - Its plate opens with the structure circled, and the card under the list gives you bregma / ML / DV.
- Hover the plate to read coordinates under your pointer. Hover a printed abbreviation to see its full name; click it to jump to that structure.
- ← / → step through plates. Fit resets the zoom.
That is the whole core loop. Everything below is optional.
Start here
| Page | What it covers |
|---|---|
| Getting Started | Opening it, the three panels, the first things to click |
| Finding Structures | Search, system filters, the structure card |
| Reading a Plate | Labeled / Nissl / Myelin, zoom, hover, overlays |
| Coordinates | What AP / ML / DV mean here, and what a structure's coordinate is |
Doing things with it
| Page | What it covers |
|---|---|
| At a Coordinate | Go the other way: a point → the structures near it |
| Measuring | Grid, scale bar, distance and approach angle, landmarks, skull |
| Projection and 3D | Seeing a structure through the whole brain |
| Planning a Track | Entry point, manipulator angles, drive depth (experimental) |
| Working Frame | Read from lambda, or from your own tilted frame |
| Exporting | PNG, SVG, CSV, and shareable links |
Reference
| Page | What it covers |
|---|---|
| Keyboard Shortcuts | The whole list |
| Recipes | "How do I…" — short answers to common tasks |
| Accuracy and Caveats | Read this before you trust a number |
| Data Files | The JSON, CSVs and SVGs behind the app |
| Troubleshooting | When something doesn't load or doesn't look right |
| FAQ | Short questions, short answers |
A structure's coordinate is the median position of where its abbreviation is printed on the plates — close to, but not the same as, the structure's centre. It is a targeting aid, not a segmentation. See Accuracy and Caveats.
Development of the Gerbil Atlas Explorer was supported by NIH R01DC020742.