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Brain Monitor

The Brain Monitor is a real-time 3D visualization system that displays your genome as volumetric structures with live neural activity. It provides an immersive way to understand your neural architecture and watch your artificial brain in action.

Overview​

Brain Monitor renders cortical areas as 3D volumes positioned in space. As neurons fire, you'll see visual indicators showing the activity patterns throughout your genome. This provides intuitive insight into how information flows through your neural circuits.

Interface Components​

3D Viewport​

The main area displays:

  • Cortical Volume Meshes: 3D boxes representing cortical areas
  • Neural Activity: Colored highlights showing neuron firing
  • Connection Lines: Visual indicators of mappings between areas
  • Region Boundaries: Spatial organization of brain circuits
  • Grid Floor: Optional reference grid for spatial orientation

Camera Controls​

The camera allows free movement through 3D space:

  • Orbit: Rotate around a point of interest
  • Pan: Move laterally through space
  • Zoom: Move closer or farther from objects
  • Focus: Automatically frame specific objects

Activity Indicators​

Neural activity is visualized through:

  • Color Intensity: Brightness indicates firing strength
  • Spatial Distribution: Shows which voxels are active
  • Temporal Dynamics: Activity changes in real-time
  • Connection Flow: Lines show active pathways

Basic Navigation​

Mouse Controls​

Rotation (Orbit)

  • Left mouse drag: Rotate the camera around the focus point
  • The camera orbits while keeping the center of interest in view

Pan (Move Laterally)

  • Left mouse drag: Move left/right/up/down (Tank mode)
  • Middle mouse drag: Alternative pan
  • Shift + Left mouse drag is box selection, not pan (see Multi-Selection below)

Zoom

  • Mouse wheel scroll: Zoom in (scroll up) or out (scroll down)
  • Right mouse drag: Alternative zoom (drag up/down)
  • Get closer to see details or pull back for overview

Focus on Object

  • Click on cortical area: Click a volume to focus on it
  • Camera smoothly transitions to frame the object
  • Useful for quick navigation to specific areas

Keyboard Controls​

  • W/S: Move forward/backward
  • A/D: Move left/right
  • Q/E: Move up/down
  • Arrow Keys: Pan view
  • F: Focus on selected object
  • Home: Reset to default view
  • Shift + Click: Toggle voxel selection inside a cortical volume
  • Shift + Left Drag: Draw a rectangle to select multiple cortical areas
  • Space: Fire (stimulate) currently selected voxels once
  • Shift + Space: Continuously fire selected voxels until you press Space again
  • Delete: Clear all selected voxels (also stops continuous firing)

See Camera Controls for advanced navigation, and Navigation Basics for the full voxel-selection workflow.

Understanding Visual Elements​

Cortical Area Volumes​

Each cortical area appears as a 3D box with:

Size and Position:

  • Dimensions reflect the cortical area's voxel dimensions
  • Position reflects 3D coordinates in the genome
  • Larger areas contain more neurons

Activity Visualization:

  • Active neurons highlight within the volume
  • Color intensity shows firing rate
  • Spatial patterns show which regions are processing

Connection Lines​

When hovering over or selecting a cortical area:

  • Outgoing connections: Lines from this area to others
  • Incoming connections: Lines from other areas to this
  • Connection strength: Line thickness or opacity
  • Connection type: Color or style variations

Brain Circuits​

Regions organize cortical areas spatially:

  • Dotted or wireframe boundaries (optional)
  • Hierarchical nesting of sub-circuits
  • Helps understand organizational structure

Interacting with Objects​

Selection​

Single Selection:

  • Click on a cortical area to select it
  • Selected area highlights with an indicator
  • Properties panel updates (if visible)

Multi-Selection:

  • Ctrl + Click (Cmd + Click on macOS) to add or remove a cortical area
  • Shift + Left Drag to draw a rectangle; every cortical area whose volume intersects that rectangle is selected
  • Camera pan is paused while the box is being drawn
  • A Shift+click that does not drag still toggles voxels (see below)
  • Escape cancels an in-progress box; leaving the viewport also cancels it
  • Box select replaces the current area highlight set and opens the shared multi-edit quick menu
  • With 2 or more areas from the same circuit selected, that menu includes Arrange (Align and Distribute on X, Y, or Z)
  • Useful for comparing multiple areas and bulk operations
  • Ctrl+Z (Cmd+Z on macOS) undoes the last saved 3D move, Arrange, or area delete. Shift+Ctrl+Z (Shift+Cmd+Z) redoes it. See Navigation Basics

Plane Focus Shortcuts:

  • Ctrl + 1 + Click: Focus clicked cortical area on XY plane
  • Ctrl + 2 + Click: Focus clicked cortical area on XZ plane
  • Ctrl + 3 + Click: Focus clicked cortical area on YZ plane

Selecting and Stimulating Voxels​

Hold Shift and click voxels inside a cortical volume to toggle them on or off. Selected voxels stay highlighted across one or more cortical areas. Shift + Left Drag is different: it box-selects whole cortical areas, not voxels.

One-shot fire: Release Shift, then press Space. FEAGI stimulates the current selection once.

Continuous fire: Press Shift + Space. FEAGI stimulates the same selection once per burst until you press Space again (with or without Shift). A notification confirms start and stop.

Stop continuous fire:

  • Press Space (or Shift + Space)
  • Press Delete to clear the voxel selection
  • Clear the last selected voxel so nothing remains selected

If you still hold Shift from voxel picking, Space is Shift + Space and starts continuous fire. Release Shift first when you want a single pulse.

See Navigation Basics and Navigation Action Reference.

Quick Menu​

Right-click on a cortical area to access context menu:

  • Details - View/edit properties
  • Quick Connect - Create connections
  • Clone - Duplicate area
  • Move 3D - Activate 3D gizmo for positioning
  • Resize 3D - Activate 3D gizmo for resizing
  • Add to Region - Move to different region
  • Reset - Clear neural state
  • Delete - Remove area (Ctrl+Z restores custom, memory, and input/output areas)

See Quick Menu for complete details.

Hovering​

Hover over a cortical area to:

  • See all connections highlighted
  • View tooltip with area information
  • Temporarily highlight connected areas
  • Understand data flow at a glance

Viewing Neural Activity​

Activity Display Modes​

Neural activity can be visualized in different ways:

Voxel-Level Activity

  • Individual voxels light up when neurons fire
  • Spatial patterns emerge showing processing
  • Color intensity indicates firing strength

Area-Level Activity

  • Entire cortical area glows based on average activity
  • Quickly see which areas are active
  • Useful for high-level understanding

Connection Activity

  • Connection lines pulse or glow when data flows
  • Shows information pathways
  • Helps debug connectivity issues

Global Neural Connections Toggle​

Hover Inspectors on the main top bar or the Brain Monitor tab bar, then choose the connection inspector:

  • Enable: Show all connections globally
  • Disable: Show connections only on hover
  • Useful for understanding overall architecture
  • Can be visually overwhelming with many connections

Camera Features​

Camera Animations​

Record and play camera paths for:

  • Demonstrations and presentations
  • Consistent viewpoints for comparisons
  • Documentation and screenshots
  • Guided tours of complex genomes

See Camera Animations for detailed instructions.

Saved Viewpoints​

Quickly return to important views:

  1. Position camera at desired viewpoint
  2. Save camera animation with single frame
  3. Play animation to instantly return

Focus Operations​

Focus on Cortical Area:

  1. Select area in Circuit Builder OR Brain Monitor
  2. Press F, or hover a top bar title and select the area
  3. Camera smoothly frames the object

Focus on Brain Circuit:

  1. Hover Circuits on the top bar
  2. Select a circuit
  3. The camera focuses on that circuit. This does not open a new tab.

Advanced Features​

3D Gizmos​

Manipulate objects directly in 3D space:

Move Gizmo:

Relocate Icon

  1. Right-click cortical area → Move 3D
  2. Colored arrows appear (X=Red, Y=Green, Z=Blue)
  3. Click and drag arrows to move along that axis
  4. Click central sphere to move freely

Resize Gizmo:

Scale Icon

  1. Right-click cortical area → Resize 3D
  2. Colored handles appear on box corners and edges
  3. Drag to resize along specific dimensions
  4. Only available for areas that allow dimension editing

Indicator Flashing​

When navigating from a top bar list:

  • Selected object flashes briefly
  • Helps locate object in busy scenes
  • Visual confirmation of focus target

Region Visualization​

3D Brain Monitor Tabs for Regions:

  1. Right-click region in Circuit Builder
  2. Select Open 3D Tab
  3. Opens dedicated 3D view for that region
  4. Isolates region for focused work

Split View Workflow​

Best practice: Use Brain Monitor alongside Circuit Builder

Setting Up Split View:

  1. Right-click brain circuit
  2. Select Open 3D Tab
  3. Circuit Builder and Brain Monitor appear side-by-side

Benefits:

  • See 2D topology and 3D spatial layout simultaneously
  • Selection syncs between views
  • Edit in one, visualize in the other
  • Different perspective aids understanding

See Split View for more details.

Performance Considerations​

Optimizing Display​

For large genomes:

  • Hide connections when not needed (toggle off global connections)
  • Focus on sub-circuits instead of viewing entire genome
  • Reduce activity rendering if performance suffers
  • Close unused tabs to free resources

Activity Update Rate​

Neural activity updates at the burst rate frequency:

  • Higher burst rates = more frequent updates
  • Lower rates reduce visual updates but save performance
  • Adjust burst rate in top toolbar if needed

Visual Customization​

Camera Settings​

Adjust camera behavior in Options:

  • Movement speed
  • Rotation sensitivity
  • Zoom speed
  • Inertia and smoothing

Display Options​

Configure what's visible:

  • Grid floor on/off
  • Connection lines always/hover/never
  • Activity rendering quality
  • Transparency effects

Access via Options menu in top toolbar.

Common Workflows​

Monitoring Neural Activity​

  1. Open Brain Monitor (use Split View)
  2. Ensure burst rate > 0 Hz
  3. Watch cortical areas light up as they process
  4. Hover areas to see their connections
  5. Look for unexpected patterns or dead zones

Probing Voxels With Manual Stimulation​

  1. Hold Shift and click the voxels you want to test
  2. Press Space for a single stimulation, or Shift + Space to keep stimulating every burst
  3. Watch downstream areas for evoked activity
  4. Press Space again to stop continuous stimulation
  5. Press Delete when you are done with the selection

Exploring Genome Structure​

  1. Start with overview (zoom out to see all)
  2. Identify major regions and their spatial layout
  3. Focus on specific circuits of interest
  4. Examine connections between areas
  5. Navigate through regional hierarchy

Debugging Connections​

  1. Select source cortical area
  2. Note outgoing connections (lines)
  3. Verify expected targets are connected
  4. Check for unexpected connections
  5. Edit mappings if needed

Creating Documentation​

  1. Position camera for best view
  2. Use camera animations to save position
  3. Take screenshots (system screenshot tool)
  4. Record camera animations for demos
  5. Share viewpoints with team

Troubleshooting​

"No activity showing"

  • Check burst rate is above 0 Hz
  • Verify FEAGI is processing data
  • Ensure cortical areas have input connections
  • Check activity rendering is enabled

"Can't see my cortical areas"

  • Zoom out to get overview
  • Hover Circuits and select a circuit to focus it
  • Check you're in correct region tab
  • Verify areas exist in FEAGI

"Camera movement is too fast/slow"

  • Adjust camera speed in Options
  • Use different navigation methods (keyboard vs mouse)
  • Reset camera settings to defaults

"Performance is poor"

  • Disable global neural connections
  • Focus on smaller regions
  • Close unnecessary tabs
  • Reduce activity rendering quality

"Lost my position"

  • Use camera animations to save important views
  • Use Focus (F key) to return to selected object
  • Hover Circuits and select a circuit for quick navigation

Tips for Effective Monitoring​

  1. Use Split View: See structure and activity simultaneously
  2. Name Areas Clearly: Helps identify volumes in 3D space
  3. Organize Spatially: Position related areas near each other
  4. Save Camera Positions: Record important viewpoints
  5. Watch for Patterns: Look for expected vs unexpected activity
  6. Check Connections: Hover to verify data flow paths
  7. Explore Regions: Navigate hierarchically for large genomes
  8. Monitor Performance: Adjust settings if visualization slows

Integration with Circuit Builder​

Brain Monitor and Circuit Builder work together:

  • Synchronized Selection: Click in one, highlights in both
  • Synchronized Focus: Focus operations affect both views
  • Complementary Perspectives: 2D graph + 3D spatial
  • Cross-Navigation: Jump between views seamlessly

Use both views to fully understand your genome's structure and behavior.

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