FAQ

FAQ

Do I need to install anything? No. It is one HTML file that runs in any modern browser.

Does it work offline? Yes. Download gerbil_atlas_explorer.html and open it. The whole atlas is inside the file. Deep links work too.

Is any of my data sent anywhere? No. There is no server. Searches, exports and links are all handled in your browser.

Which atlas is this? Radtke-Schuller et al. (2016), Brain Struct Funct 221(Suppl 1):1–272 — doi:10.1007/s00429-016-1259-0, open access. Cite the atlas, not this tool.

Is this the atlas itself, or a reinterpretation? The structure-to-plate assignments are the authors' published Index of structures, verbatim. The plate images are the published plates. What is added here is the search, the coordinate readout, the label positions, the system tags, the outlines, the skull fit and the views.

What exactly is a structure's coordinate? The median position of where its abbreviation is printed across the plates — near, but not identical to, its centroid. See Coordinates.

Why is ML written with a ±? The two hemispheres are folded together, because a bilateral structure would otherwise average out to ML 0.

Where is DV zero? The plane through the most dorsal points of cerebrum and cerebellum — the brain surface, not skull bregma. The two differ by roughly the skull thickness.

Can I read coordinates from lambda? Yes. Frame → Origin → lambda → Turn on. Exact, no caveats. See Working Frame.

How far apart are the plates? 350 µm. Plate 1 is bregma +7.80 mm, plate 62 is bregma −13.55 mm.

Are the Nissl and myelin sections aligned with the drawing? Yes, by construction — each of the 186 pages was cropped to its own printed coordinate box. Everything on the plate stays in place when you switch. The myelin section is an adjacent section, though, not the same slice.

Is there a segmentation / a volumetric label map? No. The contours are the atlas's drawn boundaries and the labels are printed positions. Nothing here is a segmentation.

Can I use the figures in a paper? The plate images are the published atlas's — the atlas is open access; follow its licence and cite it. The SVG export gives you editable outlines rather than the printed image.

Which parts are experimental? The skull overlays, the track planner, and frame rotation (pitch / roll / yaw). Each is labelled in the app. Moving the origin is not experimental.

Can I get the underlying data? Yes — JSON, two CSVs and per-plate SVGs. See Data Files.

Who made this? Daniel Stolzberg and the Caras Lab, Department of Biology, University of Maryland.

I found an error / want a feature. Raise an issue.