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Navigating the interface

BrainDeer is built around four zones. Learn where everything lives, then dig into each panel — and how Sims Mode lets you act on structures without hunting through menus.

The layout at a glance

Center Synchronized multiplanar 2D views and the live VTK 3D scene

Left View Adjustments: appearance, colormap, contrast, opacity

Right Plugin Studio: Atlas Browser, Warpdrive, ROI Studio, …

Bottom Data Organization: loaded volumes, tracts, layers, visibility

The three surrounding panels, and how they frame the views.

Center: synchronized views

Every 2D tile (sagittal, coronal, axial) and the 3D scene share one crosshair. Click a voxel in any view and the others follow. Volumes, overlays and tractography all live in the same space, so you never lose context.

Scroll or scrub: the crosshair stays locked across every view.

  • Click in a 2D tile to move the crosshair everywhere
  • Orbit the 3D scene; the slice planes stay put on the same voxel
  • More detail: 2D ↔ 3D linking

Left: View Adjustments

Appearance, colormap, contrast, brightness, opacity and resampling for the active volume. This is where the view becomes readable.

View Adjustments panel

Typical moves

  • Switch colormap and tweak contrast / brightness
  • Dial opacity for overlays
  • Toggle the colorbar beside the views

Right: Plugin Studio

Plugins dock here as tabs: Atlas Browser, Warpdrive, ROI Studio, Blender bridge, VR, AI, and anything you write yourself. The studio is how BrainDeer grows with you.

Plugin Studio panel

Typical moves

  • Open the Atlas Browser and toggle structures
  • Jump into Warpdrive to nudge a normalization
  • Browse the Plugin catalog

Bottom: Data Organization

Everything you have loaded: volumes, overlays, tracts and their layer order. Show, hide, reorder and inspect from here.

Data Organization panel

Typical moves

  • Drag layers to change draw order
  • Toggle visibility without unloading data
  • Inspect which space a volume lives in

Sims Mode

Sims Mode turns structures into something you can point at and act on. Enable it in View Adjustments (Appearance → Sims Mode) or press Shift+S. Hover a structure for the edge glow, then short-click: a radial pie opens around the green plumbob with quick actions for that layer.

Enable Sims Mode, hover a structure, short-click — the pie appears.

Sims Mode pie menu over a selected structure

Typical moves from the pie

  • Change color, see-through, hide / show
  • Style the layer, or “Look At Me” to frame it
  • Drag the plumbob to reposition when the action allows
  • Shift+S toggles Sims Mode (same as the left-panel checkbox)
  • Short-click on a 2D slice or a 3D structure — long-drag keeps normal navigation
  • The center of the pie names the active layer so you always know what you are editing

Full screen a view

Any tile in the 2×2 layout can go full screen. Right-click the view (including the 3D scene), choose Full Screen, and work in that pane alone. Right-click again and pick Exit Full Screen to restore the grid. The same menu also switches layouts (2x2, 1x3, 3x1).

Right-click → Full Screen → explore → Exit Full Screen.

Gestures & view controls

No media here yet — the essentials:

2D slices (sagittal / coronal / axial)

  • Scroll (or trackpad swipe) to change the slice
  • Click to move the shared crosshair; the other views follow
  • Drag the crosshair when you want to scrub continuously

3D scene

  • Left-drag to orbit
  • Pan with the middle button / trackpad pan gesture (or the scene’s pan control)
  • Scroll to zoom
  • Right-click → Full Screen for an uncluttered orbit (see above)

With Sims Mode on

  • Short-click a structure for the pie; a longer drag keeps normal navigation

Shortcuts (navigation)

A short list for moving around. The full table lives under Keyboard shortcuts once it is filled out.

Shortcut Action
Shift+S Toggle Sims Mode
Right-click on a view Layout / Full Screen menu
Click in a 2D tile Jump the crosshair (all views sync)

Next steps