Finding Structures

Finding Structures

The left panel's first mode, Find a structure. Press / from anywhere to jump to the search box.

What you can type

You type	You get
MSO	The abbreviation, exactly as the atlas prints it
medial superior olive	Any part of the full name
auditory cortex, MGB, IC	Common aliases — informal names mapped to the atlas's abbreviations
auditory, thalamus	A system — same as clicking the chip
plate 30 or p30	Jumps straight to that plate
bregma -2.3	Jumps to the plate nearest that AP

Search is case-insensitive and ignores spaces in abbreviations. Partial words work: genic finds the geniculate nuclei.

genic finds ten structures across plates 29–36 — every geniculate nucleus the atlas indexes, without you having to know which of them is spelt out and which is an abbreviation.

Narrowing the list

System chips sit under the search box. Click one or more to keep only structures carrying that tag; click again to release. More systems reveals the rest.

The tags, with how many structures carry each:

Tag	n	Tag	n	Tag	n
thalamus	123	cortex	62	monoaminergic	33
fiber_tract	112	auditory	59	amygdala	32
brainstem	93	cerebellum	55	ventricular	25
midbrain	84	motor	52	vestibular	15
hypothalamus	68	visual	43	vascular	3
		somatosensory	42	claustrum	3
		hippocampal	37	landmark	2
		basal_forebrain	34
		olfactory	34

The system tags are a convenience layer added here — they are not part of the published atlas. Treat them as a way to sweep a pathway, not as an authority.

Scope — the two-button strip below the chips:

• All 723 — the whole atlas.
• On plate 30 — only structures the index lists for the plate currently showing. This follows you as you step through plates, which makes it a good way to read a level: set the scope, then walk the slider and watch the list change.

Filters combine: chips and scope and the text you typed.

The auditory chip alone: 59 of 724 structures, spanning plates 28–50. With nothing typed in the box the list opens grouped by anatomical division; type anything and it becomes a flat list of structures.

The result list

Each row is abbreviation · full name · plate range. Click a row and two things happen:

• the structure is selected — circled on the plate, highlighted in the projection and 3D views;
• the viewer jumps to the first plate the structure appears on.

The list shows up to 400 rows; past that it asks you to narrow the search. The line above it always tells you how many matched and the plate range they span.

The structure card

Selecting a structure opens a card under the list:

Row	What it is
Plates	The plate range it is indexed for, and how many plates that is
Bregma / Lambda / Interaural	The same range as an AP span, from each landmark
Label center	The stereotaxic coordinate — AP · ML · DV — the median of its printed labels
Label spread	The full ML and DV spread of those labels
Systems	The tags it carries
Divisions	The anatomical divisions it is filed under — click one to list its siblings

Under that is a row of plate-number buttons — click any one to jump straight to that level.

ML is written ± because the two hemispheres are folded together; a bilateral structure would otherwise average out to ML 0. With a working frame rotated, the symmetry breaks and the card gives a left and a right line instead, keeping the atlas figure beside each.

If a structure has no located label, the Label center and Label spread rows are simply absent rather than showing a made-up number. Twenty of the 723 structures are in that state — see Accuracy and Caveats.

Press Esc (or the × on the card) to drop the selection.

Getting the list out

CSV (top-right of the list) downloads exactly the structures currently listed, with their coordinates. See Exporting for the columns.