Neuron Collections

A neuron collection is a lightweight grouping of free neurons. Collections allow neurons to be labeled, moved as a unit, connected to other layers via weight matrices or synapse groups, and coupled to other Simbrain components.

neuron collections

Collections are flexible: neurons can belong to multiple collections simultaneously, and neurons within a collection can use different update rules. Create a collection by pressing g to add a new collection from scratch, or select existing neurons and press Cmd/Ctrl+G to wrap them in a collection. Collections have a green interaction box. Deleting a collection leaves the neurons intact.

Neuron collections can be connected to other collections, neuron arrays, and subnetworks using weight matrices or synapse groups. Use the 1-2 trick for matrix-based connections or the 1-3 trick for individual synapse management.

Edit Dialog

Double-clicking the interaction box opens the collection editor:

  • Label: Display name for the collection
  • Neuron Type: The update rule applied to neurons in the collection

Additional tabs provide access to:

  • Neurons: Configure individual neuron properties
  • Layout: Arrange neurons spatially (see layouts)
  • Input Data: Set up input patterns for testing (see input tables)

Right Click Menu

  • Edit…: Opens the collection properties dialog
  • Rename Neuron Collection…: Change the display name
  • Remove Neuron Collection: Remove the collection wrapper (neurons remain)
  • Apply layout…: Rearrange neurons using layout algorithms (keyboard shortcut: Cmd/Ctrl+L)
  • Select Neurons: Select all neurons in the collection
  • Edit Neurons…: Open an editor for all neurons in the collection
  • Select Incoming Synapses: Select synapses targeting this collection
  • Select Outgoing Synapses: Select synapses originating from this collection
  • Clamp Neurons / Unclamp Neurons: Toggle clamping on all neurons
  • Connect selected objects with weight matrix: Connect to other layers using a weight matrix
  • Connect selected neuron collections with synapse group: Connect using a synapse group
  • Set Collection as Source / Clear Source Neuron Collections: Mark or clear this collection as source for connection operations
  • Create supervised model: Set up supervised learning (keyboard shortcut: Cmd/Ctrl+M)
  • Input data…: Open the input data dialog
  • Add current pattern to input data…: Add current activations to the input data table
  • Plot: Create a plot of the collection’s activations over time
  • Add coupled image world: Create an image world coupled to this collection
  • Record activations: Record activation values to a CSV file
  • Send Vector Coupling To / Receive Vector Coupling from: Create couplings to or from other Simbrain components