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Brain Circuits

Brain circuits are organizational containers that help you structure and manage complex genomes. They group related cortical areas and sub-circuits into logical hierarchies, making large neural architectures easier to understand and navigate.

What is a Brain Circuit?​

A brain circuit is a named container that can hold:

  • Cortical Areas: The actual neural processing units
  • Sub-Circuits: Other brain circuits, creating hierarchical organization
  • Metadata: Name, description, and organizational properties

Think of brain circuits as folders in a file system - they help organize and categorize without affecting the actual neural processing.

Purpose and Benefits​

Organization​

  • Group functionally related cortical areas
  • Create logical divisions (vision, motor, memory, etc.)
  • Build hierarchical structures that reflect your architecture
  • Jump directly to specific circuits
  • View circuits in isolation
  • Focus on subsystems independently

Scalability​

  • Manage genomes with hundreds or thousands of cortical areas
  • Hide complexity in sub-circuits
  • Work on one part without seeing everything

Collaboration​

  • Clear structure helps teams understand the genome
  • Named regions document the architecture
  • Regions can be worked on independently

The Main Circuit​

Every genome has a root circuit called Main Circuit:

  • Created automatically by FEAGI
  • Contains all top-level cortical areas and regions
  • Cannot be deleted
  • The starting point for navigation

Creating Brain Circuits​

Method 1: From Selection​

Create a circuit and automatically add selected areas:

  1. In Circuit Builder, select cortical areas you want to group
  2. Right-click on selection or empty space
  3. Select Create Circuit
  4. Enter region name and properties:
    • Name: Descriptive name (e.g., "Visual Processing")
    • Description: Optional notes
    • Parent Circuit: Where to create it (default: current region)
  5. Click Create

Selected areas move into the new region automatically.

Method 2: Empty Region​

Create an empty region and add areas later:

  1. Right-click empty space in Circuit Builder
  2. Select Create Circuit
  3. Don't select any cortical areas beforehand
  4. Configure name and properties
  5. Click Create

Add areas later using "Add to Region" operation.

Method 3: From Top Toolbar​

Quick access from anywhere:

  1. Click Circuits in top toolbar
  2. Click + button
  3. Configure region properties
  4. Choose parent circuit
  5. Click Create

Opening Regions​

Method 1: Double-Click

  • In Circuit Builder, double-click a circuit node
  • The view switches to show that region's contents

Method 2: Dropdown Menu

  • Click Circuits in top toolbar
  • Select region from the list
  • Opens in new Circuit Builder tab

Method 3: Quick Menu

  • Right-click region node
  • Select Open or Open 3D Tab

To return to parent circuit:

  • Use the navigation breadcrumbs (if visible)
  • Click Circuits dropdown and select parent circuit
  • Close the current region tab

Viewing Hierarchy​

The Circuits dropdown shows:

  • All regions in hierarchical tree structure
  • Current region highlighted
  • Quick navigation to any region

Region Structure​

Visual Representation​

In Circuit Builder (2D):

  • Appears as larger rectangular node
  • Contains smaller cortical area and region nodes
  • Double-click to "enter" and view contents
  • Shows name and brief metadata

In Brain Monitor (3D):

  • Spatial grouping of contained areas
  • Optional boundary visualization
  • Dedicated 3D tabs for focused viewing

Contents​

Regions can contain:

  • Cortical Areas: Any number of IPU, OPU, Memory, Custom areas
  • Sub-Circuits: Nested regions for deeper hierarchy
  • Mixed: Both cortical areas and sub-circuits together

Hierarchy Depth​

Regions can nest arbitrarily deep:

Main Circuit
├── Visual System
│   ├── Left Eye Processing
│   │   ├── Edge Detection
│   │   └── Color Processing
│   └── Right Eye Processing
├── Motor Control
│   ├── Left Motors
│   └── Right Motors
└── Memory Systems
    ├── Short Term Memory
    └── Long Term Memory

Managing Region Contents​

Adding Areas to Region​

Method 1: At Creation

  • Select areas first
  • Create region
  • Areas automatically added

Method 2: Move Existing Area

  1. Right-click cortical area
  2. Select Add to Region
  3. Choose destination region
  4. Confirm move

Method 3: Drag and Drop (if enabled)

  • Drag cortical area onto region node
  • Area moves into that region

Moving Areas Between Regions​

  1. Right-click cortical area
  2. Select Add to Region
  3. Choose new parent circuit
  4. Click Move

The area moves, maintaining all connections.

Removing Areas from Region​

To move an area to the parent circuit:

  1. Right-click area
  2. Select Add to Region
  3. Choose the parent circuit
  4. Confirm

Nesting Regions​

Regions can contain other regions:

  1. Right-click a circuit node
  2. Select Add to Region
  3. Choose a destination region
  4. The region moves with all its contents

Editing Region Properties​

Basic Properties​

Right-click region → Details to edit:

General:

  • Name: The display name
  • Description: Optional notes
  • Parent Circuit: Where it's located in hierarchy
  • Region ID: Unique identifier (read-only)

Statistics:

  • Total Cortical Areas: Count of areas in region (recursive)
  • Direct Children: Immediate child areas and sub-circuits
  • Neuron Count: Total neurons in region
  • Synapse Count: Total synapses

Contents:

  • List of contained cortical areas
  • List of contained sub-circuits
  • Quick navigation links

Renaming Regions​

  1. Right-click region
  2. Select Details
  3. Edit name field
  4. Press Enter or click Apply

Good names describe the function or purpose.

Moving Regions​

Change Parent:

  1. Right-click region
  2. Select Add to Region
  3. Choose new parent
  4. Confirm

2D Position (in Circuit Builder):

  • Drag the region node to new position
  • Position is relative to parent circuit view

Cloning Regions​

Clone Icon

Duplicate an entire region with all contents:

  1. Right-click region
  2. Select Clone
  3. Configure:
    • New Name: Must be unique
    • Clone Contents: Include all cortical areas and sub-circuits
    • Clone Connections: Include internal connections
    • Clone External Connections: Include connections to outside areas
  4. Click Clone

Note: Cloning large regions creates many new neurons. Check capacity first.

Deleting Regions​

Delete Icon

Remove a circuit and optionally its contents:

  1. Right-click region
  2. Select Delete
  3. Choose deletion mode:
    • Delete Region Only: Move contents to parent circuit
    • Delete Region and Contents: Remove everything
  4. Confirm deletion

Warning: Deleting region and contents removes all cortical areas inside (recursive). This cannot be undone.

Working with Region Tabs​

Circuit Builder Tabs​

Each region can open in its own Circuit Builder tab:

Benefits:

  • View multiple regions side-by-side
  • Compare structures
  • Work on different parts independently
  • Maintain context while navigating

Opening Tabs:

  • Use Circuits dropdown
  • Each selection opens new tab
  • Switch tabs using tab bar

Closing Tabs:

  • Click X on tab
  • Right-click tab → Close

3D Brain Monitor Tabs​

View region contents in isolated 3D view:

  1. Right-click region in Circuit Builder
  2. Select Open 3D Tab
  3. Split view opens with:
    • Circuit Builder for that region (left/top)
    • Brain Monitor showing region in 3D (right/bottom)

Benefits:

  • Focus on specific subsystem
  • Less visual clutter
  • Better performance with large genomes
  • Synchronized 2D/3D view of region

See Split View for more details.

Region Organization Strategies​

Functional Grouping​

Group by purpose:

├── Sensory Input
│   ├── Vision
│   ├── Audio
│   └── Touch
├── Processing
│   ├── Feature Extraction
│   ├── Pattern Recognition
│   └── Decision Making
├── Memory
│   ├── Working Memory
│   └── Long Term Storage
└── Motor Output
    ├── Movement
    └── Speech

Hierarchical Decomposition​

Break complex systems into layers:

├── Navigation System
│   ├── Perception Layer
│   │   ├── Obstacle Detection
│   │   └── Path Recognition
│   ├── Planning Layer
│   │   ├── Route Planning
│   │   └── Collision Avoidance
│   └── Execution Layer
│       ├── Motor Commands
│       └── Steering Control

Modular Architecture​

Create reusable modules:

├── Shared Modules
│   ├── Edge Detection (reusable)
│   ├── Pattern Matching (reusable)
│   └── Memory Buffer (reusable)
├── Application A
│   └── (uses shared modules)
└── Application B
    └── (uses shared modules)

Common Patterns​

Sensory Processing Pipeline​

Vision System
├── Raw Input (IPU)
├── Preprocessing
│   ├── Normalization
│   └── Noise Reduction
├── Feature Extraction
│   ├── Edge Detection
│   ├── Color Analysis
│   └── Motion Detection
└── Pattern Recognition
    └── Object Identification

Motor Control Hierarchy​

Motor System
├── High-Level Planning
├── Trajectory Generation
├── Motor Commands (OPU)
└── Feedback Processing

Memory System​

Memory
├── Sensory Buffers
├── Short-Term Memory
├── Long-Term Storage
└── Retrieval Mechanisms

Best Practices​

Naming Conventions​

Good Names:

  • Descriptive: "Visual Processing System"
  • Functional: "Object Recognition"
  • Hierarchical: "Vision → Left Eye → Edge Detection"

Avoid:

  • Generic: "Region 1", "New Region"
  • Ambiguous: "Stuff", "Misc"
  • Technical: "r_0034_v2"

Depth Guidelines​

  • 2-4 levels: Ideal for most genomes
  • 5+ levels: May be over-organized
  • Flat structure: Hard to navigate with many areas

Balance organization with simplicity.

Size Guidelines​

  • 10-30 areas per region: Comfortable to view
  • 50+ areas: Consider subdividing
  • 1-5 areas: Might be over-organized

Find the right granularity for your needs.

Documentation​

Use region descriptions to document:

  • Purpose of the region
  • How it connects to other regions
  • Design decisions
  • References to papers or algorithms

Inter-Region Connections​

Cortical areas can connect across region boundaries:

Connection Rules:

  • Any area can connect to any other area
  • Connections are NOT limited to same region
  • Region boundaries are organizational only

Viewing Cross-Region Connections:

  • In Circuit Builder, lines may cross region boundaries
  • In Brain Monitor, hover areas to see all connections
  • Use Mapping Editor to view connection details

Managing Complex Connections:

  • Minimize unnecessary cross-region connections
  • Document major inter-region pathways
  • Use regions to represent information flow stages

Performance and Scalability​

Large Genomes​

For genomes with 100+ cortical areas:

  1. Use Regions Heavily: Group into 10-20 regions
  2. Work in Tabs: Focus on one region at a time
  3. Use 3D Tabs: Isolate regions for better performance
  4. Close Unused Tabs: Free up resources
  • Dropdowns: Fastest way to jump between regions
  • Double-Click: Fast for nearby regions
  • 3D Tabs: Good for frequently-accessed regions

Organization Maintenance​

  • Reorganize as genome grows
  • Create sub-circuits when regions get large
  • Rename regions to reflect current purpose
  • Delete empty or obsolete regions

Troubleshooting​

"Can't find my cortical area"

  • Check which region it's in
  • Use global search (if available)
  • Navigate through region hierarchy
  • Use Circuits dropdown to view all regions

"Region appears empty"

  • Ensure you've navigated into it (double-click or open)
  • Check that areas weren't accidentally moved
  • Verify in FEAGI that region exists

"Can't delete region"

  • Main Circuit cannot be deleted
  • Check if region contains areas (delete or move them first)
  • Ensure no references elsewhere

"Lost in hierarchy"

  • Use Circuits dropdown to see structure
  • Click on parent circuits to go up
  • Open Main Circuit to start over

"Performance is slow"

  • Close unnecessary region tabs
  • Use 3D tabs for large regions
  • Simplify region hierarchy
  • Reduce visible cortical areas

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