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Exporting
Four ways to take something out of the app. Everything happens in your browser — no upload.
PNG, under Controls → Notes and export. Saves the plate exactly as shown: the current source (Labeled / Nissl / Myelin), the grey and contrast settings, every overlay that is on, and a coordinate caption.
Use it when you want the histology in the figure.
SVG, beside it. Saves the same sheet, but the plate is regional outlines as vector paths instead of a photograph — traced off the printed plate — with whatever overlays were showing and the same caption. About 10–80 kB.
The SVG for plate 30 with DLG selected, the grid and the landmarks on, opened in a browser. The section image is not in it — every line is a vector path.
The section image is not in the file. This is the drawing, not the histology.
Every part is its own named group, so a figure can be restyled or cut down without redrawing anything:
outlines-solid · outlines-dashed · grid · skull · landmarks · highlight ·
measure · track · query · caption
Opens in Illustrator, Inkscape, or a browser.
How the outlines are registered
The tracing was done on the published pages at 3296 × 2481 px and is kept in that frame; each plate carries the matrix that puts it on the 1100 × 703 crop everything else here measures in. That matrix is fitted to each plate's own printed ink, not assumed from the page layout — which is what catches the pages the journal set sideways or off-centre. Plate 20 is printed at a quarter turn, and plate 31 comes out 47 px low. Every plate lands within 1.8 px of its own drawn lines, about 0.03 mm.
CSV, at the top-right of the result list. Downloads exactly the structures currently listed — so filter first, then export.
Columns:
| Column | |
|---|---|
abbr, name
|
Identity |
first_plate, last_plate, n_plates, plates
|
Plate coverage |
bregma_anterior_mm, bregma_posterior_mm
|
AP span from bregma |
lambda_anterior_mm, lambda_posterior_mm
|
…from lambda |
interaural_anterior_mm, interaural_posterior_mm
|
…from the interaural line |
label_AP_bregma_mm, label_ML_abs_mm, label_DV_mm
|
The label-centre coordinate |
n_labels |
How many printed labels it came from |
systems |
The tags, space-separated |
With a working frame on, extra columns are added beside the atlas
ones, never in place of them — plus a frame_spec column recording the exact frame
(angles, origin, pivot, offset, rotation order, sign conventions). A CSV outlives the
session that made it, so the file carries both readings and says which frame produced the
second.
UTF-8 with a BOM, CRLF line endings — opens cleanly in Excel.
Copy link, at the right of the toolbar. Puts a URL on your clipboard that restores what you are looking at. Paste it into a lab notebook, a message, or a paper's methods.
The link looks like:
…/gerbil_atlas_explorer.html#p30/MGV&v=rg&ps=nissl&t=plate
It carries, when they differ from the default:
- the plate and the selected structure (
#p30/MGV) - zoom and pan
- which overlays are on
- the source (Nissl / Myelin), the contrast, and grey
- which view you are in, and the projection orientation
- the 3D settings — rendering mode, plate slab, half, ortho, skull opacity
- the planned track — target, side and all three angles
- the working frame
The URL in the address bar updates as you work — it is rewritten in place rather than pushed as history — so you can copy it from there at any time, or bookmark a view.
A link is just text — it works offline too, against your own downloaded copy of the file.
In the track planner: Copy notes puts the plan on the clipboard as plain text, and Download writes it to a file. Both record the frame it was planned in and any measurement you had on the plate. See Planning a Track.