Latencies (ms) are approximate literature values for orientation. Animation pace is slowed and set by distance, not real time.
โถ fires a signal ยท ๐ฅ rides along the pathway (Space pause, โ/โ step, Esc exit). Routes are schematic splines through anatomical centroids, not tractography yet.
Switch on a condition, then fire an event and compare with the healthy brain. Conditions combine (e.g. Parkinson's + levodopa, tardive dyskinesia + antipsychotic). Signals carry an amplitude: โผ weak / dim, โฒ overactive / hot, โ fails to propagate.
Basal-ganglia effects use a didactic AlbinโDeLong firing-rate model; lesion positions and severities are illustrative, not patient data.
Structural connectome from the HCP-1065 tractography atlas. Every streamline's two endpoints are labelled with the cortical area (HCP-MMP1, 360 areas) or subcortical structure they end in. Click any region on the brain (or search) to light its real fibres and fire a wave to its partners.
Counts are streamlines in a population-average tractogram (n=1065): a measure of anatomical connection, not of synaptic strength or direction. Fibres shown are a baked subset (120โ250 per bundle).
Loaded data is kept in this page. "โค HTML" (World tab) bakes it into a new single file.
The world is generated from this text: groups, display defaults, placeholder nuclei, pathways and events. Edit it, then press Apply. Syntax is documented at the top.
A 3D brain built from MRI, with real white-matter fibres. Make something happen in the world and follow the signal, or switch on a disease and see what breaks.
Best on a desktop or tablet. Teaching model, not a clinical tool.
| Orbit mode | drag to rotate ยท right-drag to pan ยท wheel to zoom ยท double-click a structure to fly to it ยท Alt-click picks through tissue |
| Fly mode F | click to capture the mouse ยท WASD move ยท Space/E up ยท C/Q down ยท Shift fast ยท Alt slow ยท wheel changes speed ยท click picks the structure under the crosshair ยท Esc releases the mouse |
| Ride ๐ฅ | Space pause ยท โ/โ previous/next relay ยท Esc exit |
| Lessons | โ/โ previous/next step ยท Esc exit |
| Share | ๐ copies a link to exactly what you see: camera, conditions, split view, the last event, a selected structure or lesson step |
| Other | C camera follows the signal ยท V split view (healthy | condition) ยท L signal labels on/off ยท O orbit ยท R reset view ยท Tab panel ยท H help ยท X stop signals |
| Coordinates | millimetres from the model centre ยท +x right ยท +y superior ยท +z anterior |
| Signals | excitatory > radial sparks ยท inhibitory -| imploding red, dashed tube ยท modulatory ~> diffuse cloud |
Geometry: NIH 3D / HuBMAP "VH Male Allen Brain" (283 segmented structures). Items labelled [placeholder] are approximate stand-ins for structures missing from the model. Define or move them in the World tab.
Tractography: HCP-1065 population-averaged tractography atlas, CC BY-SA 4.0. Yeh F.-C., Population-based tract-to-region connectome of the human brain and its hierarchical topology, Nat Commun 13:4933 (2022). Data were provided by the Human Connectome Project, WU-Minn Consortium (PIs David Van Essen and Kamil Ugurbil; 1U54MH091657), funded by the 16 NIH Institutes and Centers that support the NIH Blueprint for Neuroscience Research, and by the McDonnell Center for Systems Neuroscience at Washington University. Registration landmarks: Harvard-Oxford atlas (FSL), plus Neudorfer and CIT168 deep structures.
Nuclei and areas: hypothalamic region atlas, Neudorfer C. et al., Sci Data 7:305 (2020), CC BY 4.0 ยท Harvard Ascending Arousal Network atlas v2.0, Edlow B.L. et al. (CC0) ยท CIT168 subcortical atlas, Pauli W.M., Nili A.N. & Tyszka J.M., Sci Data 5:180063 (2018), CC BY 4.0 ยท HCP-MMP1.0 cortical parcellation, Glasser M.F. et al., Nature 536:171 (2016), volumetric MNI version by A. Horn (figshare, CC BY 4.0). Connectome: HCP-1065 streamline endpoints ร HCP-MMP1 + Harvard-Oxford subcortical.
Data tab: drop .trk/.tck tractography, .nii/.nii.gz maps or meshes (STL/OBJ/PLY/GLB). Name a mesh like a structure (e.g. SCN_L.stl) to replace that placeholder. Standard-space data is warped in through the MNI landmarks.