Skip to content

Geometric Shapes

The BrainGenix-Client library provides three fundamental geometric shapes: spheres, cylinders, and boxes, which can be used in various neural simulations and visualizations. This page offers a brief overview of each shape followed by examples of how they can be created and configured within your simulation environment.

Overview of Geometric Shapes

  • Sphere: Represents a three-dimensional ball with a given radius and center position. It can be used to model cellular structures or other round objects in your neural network simulation.
  • Cylinder: Models a three-dimensional object that extends infinitely in two directions along two parallel lines (the cylinder's axis) but is bounded by two parallel planes (the cylinder's bases). It's useful for simulating axon-like structures or other elongated entities.
  • Box: Represents a three-dimensional rectangular prism with specified dimensions and positioning. It's ideal for simulating cuboidal compartments or regions within your neural model.

Sphere Setup Example

# Create Sphere Configuration
SphereCfg = NES.Shapes.Sphere.Configuration()
SphereCfg.Name = "My Sphere"
SphereCfg.Radius_um = 10.0  # Radius in micrometers
SphereCfg.Center_um = [2, 11, 11]  # Center position in micrometers

# Create Sphere instance in the simulation
MySphere = MySim.AddSphere(SphereCfg)
In this example, we define a sphere named My Sphere with a radius of 10 micrometers (um) centered at [2, 11, 11]. This sphere can then be used to create compartments or other elements in your simulation.

Cylinder Setup Example

# Create Cylinder Configuration
CylinderCfg = NES.Shapes.Cylinder.Configuration()
CylinderCfg.Name = "My Cylinder"
CylinderCfg.Point1Position_um = [0, 7.5, 0]  # First base position in micrometers
CylinderCfg.Point2Position_um = [0, 7.5, 3]  # Second base position in micrometers
CylinderCfg.Point1Radius_um = 0.7  # Radius of the first base in micrometers
CylinderCfg.Point2Radius_um = 2    # Radius of the second base in micrometers (the radius can be different)

# Create Cylinder instance in the simulation
MyCylinder = MySim.AddCylinder(CylinderCfg)
This example shows how to set up a cylinder named My Cylinder that extends along the z-axis from [0, 7.5, 0] to [0, 7.5, 3]. It has different radii at its bases: 0.7 micrometers at [0, 7.5, 0] and 2 micrometers at [0, 7.5, 3].

Box Setup Example

# Create Box Configuration
BoxCfg = NES.Shapes.Box.Configuration()
BoxCfg.Name = "My Box"
BoxCfg.CenterPosition_um = [13, 11, -1]  # Center position in micrometers
BoxCfg.Dimensions_um = [20, 20, 8]       # Length, width, height in micrometers
BoxCfg.Rotation_rad = [0, 0, 0.785398]   # Rotation angles in radians around x, y, z axes

# Create Box instance in the simulation
MyBox = MySim.AddBox(BoxCfg)
Here, we define a box named My Box that is centered at [13, 11, -1]. It has dimensions of [20, 20, 8] micrometers and a rotation of 0.785398 radians around the z-axis.

Using Geometric Shapes in Compartments

Once you've created your geometric shapes, you can use them as the basis for defining compartments in your neural simulation using the NES.Models.Compartments module. Below are examples of how to create compartments using each shape:

Sphere Compartment Example

# Create BS Compartment Configuration
Cfg = NES.Models.Compartments.BS.Configuration()
Cfg.Name = "My Compartment 1"
Cfg.SpikeThreshold_mV = 0.0  # Threshold voltage in millivolts for firing spikes (optional)
Cfg.DecayTime_ms = 0.0       # Decay time in milliseconds (optional)
Cfg.MembranePotential_mV = 0.0  # Membrane potential in millivolts (optional)
Cfg.RestingPotential_mV = 0.0  # Resting potential in millivolts (optional)
Cfg.AfterHyperpolarizationAmplitude_mV = 0.0  # After-hyperpolarization amplitude in millivolts (optional)
Cfg.Shape = MySphere          # The shape of the compartment (either MySphere or MyBox)

# Create Sphere Compartment instance in the simulation
MySphereCompartment = MySim.AddBSCompartment(Cfg)
In this example, we create a Ball-and-Stick (BS) compartment named My Compartment 1 that uses MySphere as its shape. You can customize spike threshold, decay time, membrane potential, resting potential, and after-hyperpolarization amplitude according to your model requirements.

This documentation is provided by BrainGenix, a division of Carboncopies Foundation R&D. BrainGenix is a platform focused on advancing the field of whole-brain-emulation and computational neuroscience. BrainGenix is part of the CarbonCopies Foundation, a 501(c)3 non-profit organization dedicated to researching and promoting whole brain emulation. Learn more about CarbonCopies at https://carboncopies.org. For any queries or feedback regarding BrainGenix projects or documentation, please write to us at braingenix@carboncopies.org.