Using the app

Drag rotates, right-drag or the wheel zooms, middle- or shift-drag pans, a click selects.

Key	Action
H	Hide the selection (a group hides everything inside it)
I	Isolate the selection
U	Show all
T	Show or hide all tracts
R	Reset the view
C	Centre the slice on the selection
F1	About, data sources and licences
Q	Start a quiz (Study menu)
Left / Right	Previous or next step of a pathway (Pathways panel)
Esc	Leave the pathway, or end a quiz
Space	Play or pause the current pathway (Pathways or Activity panel)
Ctrl+F	Filter the structure tree (names, abbreviations, synonyms, atlas labels)

Tree checkboxes show and hide structures; unticking a group hides its whole subtree. The info panel shows the description with numbered references, the geometry source and its licence. Entries marked Draft have not been reviewed yet. The Activity chart shows placeholder data until a real model exists.

The Slices panel shows axial, coronal or sagittal cross-sections: coloured labels over the Colin27 MRI template, in neurological convention (the patient's left on the screen's left, with L/R, A/P and S/I letters on the edges). The slider moves the plane, which also appears as a translucent sheet in the 3D view; the second slider sets label opacity. Hovering shows the structure under the cursor, clicking selects it, and C (Centre slice) moves the plane through the selected structure.

The Study menu starts a quiz (Q) or shows your progress. Name it highlights a structure on both sides and asks for its name: type it (synonyms, abbreviations, any word order and small typos count) or pick one of four. Find it names a structure and you click it in 3D or in a slice. Flashcards show reviewed descriptions only. Choose single structures or bigger groups, the whole atlas or one part of it, and either what is due now or a practice round that leaves your schedule alone. Scheduling uses FSRS, the spaced repetition method Anki uses, with at most 20 new items a day per mode. Progress is saved after every answer in ~/.local/share/mnemosyn/progress.sqlite. During a quiz the tree, the info panel and hover names are hidden; Esc ends the quiz and restores the window.

Tracts (43 white-matter pathways: 41 from the HCP-1065 atlas, among them the corticospinal tract, the lemnisci, the cerebellar peduncles and seven cranial nerves, and the mammillothalamic tract and inferior thalamic peduncle from the hypothalamus atlas) are hidden when the app opens. T shows or hides them all, the tree shows single tracts, and selecting a tract shows it. In slices, visible tracts are outlined in their colour, and hovering or clicking where tracts overlap picks the smallest. Quizzes have a Tracts level of their own; while a tract is named, the grey matter around it is dimmed.

The Pathways panel, a tab next to Structures, follows routes station by station in two groups. Sensory and motor: the visual and auditory pathways, the Papez circuit, voluntary movement, touch and position, pain and temperature, and the basal ganglia and cerebellar motor loops. Behaviour: the dopamine, serotonin, noradrenaline and acetylcholine systems, the fear circuit, the stress axis, the body clock, hunger, memory, and decision and self-control. For a sensory or motor route, choose a pathway and a start side (Left or Right): everything off the route fades and cannot be clicked, the route's tracts are shown, and the current station is highlighted with its role and the effect of a lesion there, with references. Back and Next in the Activity panel (or the arrow keys) move along the route and the slice follows; crossings and relays the atlas has no shape for are steps of their own. Leaving (Esc or the Leave button) restores the view as it was. Behaviour routes light both sides and show, for each step, its role, the disorders linked to it and the drugs that act there.

While a pathway is open, the Activity panel holds the playback controls: Back, Play / Pause, Next, a speed choice (½×, 1×, 2×) and the current step. Play (Space) steps through a route on its own; the stress axis, body clock and hunger routes also play a schematic hormone timeline in the chart, where a cursor follows the steps, the time is shown next to the controls, and a click in the plot jumps to that moment. All pathway texts and timelines are drafts awaiting review.