Visualizer - Filtering Shown Neurons

It's possible to select which neurons are shown when visualizations are rendered using an optional parameter.

This section discusses how to do that.

Parameter	Description
Optional_VisibleNeuronIDs	Optional list of neuron IDs that if present will only be shown

Note

The soma for other neurons will also be shown, but not the compartments or synapses.

---

Let's say we are building a large scale network and have the following output without any filtering.

That output could be generated from something like this:

# NOTE: This example assumes you already have a simulation and client setup 
VisualizerJob = BrainGenix.NES.Visualizer.Configuration()
VisualizerJob.ImageWidth_px = 8192
VisualizerJob.ImageHeight_px = 4096

# Render In Circle Around Sim
Radius = 500
Steps = 10
ZHeight = -550

for Point in PointsInCircum(Radius, Steps):
    VisualizerJob.CameraFOVList_deg.append(110)
    VisualizerJob.CameraPositionList_um.append([Point[0], Point[1], ZHeight])
    VisualizerJob.CameraLookAtPositionList_um.append([0, 0, -1000])

Visualizer = Simulation.SetupVisualizer()
Visualizer.GenerateVisualization(VisualizerJob)

Visualizer.SaveImages(f"{YOUR_SAVE_DIRECTORY_HERE}/Visualizations/0", 2) # Save images two at a time

Info

By adding the filter configuration line, you can select which neuron(s) to show:

Single Neuron By IDMultiple Neurons By IDSingle Neuron By ObjectMultiple Neurons By Object

If you want to select for a single neuron and you know it's ID, do this:

VisualizerJob.Optional_VisibleNeuronIDs = [1] # Show neuron with ID 1

If you want to select for a multiple neurons and you know their IDs, do this:

VisualizerJob.Optional_VisibleNeuronIDs = [0, 1] # Show neuron with IDs 0,1

Alternatively, if you want to select for a neuron by the object, ExampleNeuron, do this:

VisualizerJob.Optional_VisibleNeuronIDs = [ExampleNeuron.ID] # Show example neuron only

Alternatively, if you want to select for multiple neurons by the objects, ExampleNeuron1 and ExampleNeuron2, do this:

VisualizerJob.Optional_VisibleNeuronIDs = [ExampleNeuron1.ID, ExampleNeuron2.ID] # Show example neurons

So for our example, updating our visualizer job configuration to include the new filter (as follows) results in the following image.

# NOTE: This example assumes you already have a simulation and client setup 
VisualizerJob = BrainGenix.NES.Visualizer.Configuration()
VisualizerJob.ImageWidth_px = 8192
VisualizerJob.ImageHeight_px = 4096

## ONLY SHOW NEURON 1, DISABLE OTHERS (EXCEPT FOR THEIR SOMA) ##
VisualizerJob.Optional_VisibleNeuronIDs = [1] 

# Render In Circle Around Sim
Radius = 500
Steps = 10
ZHeight = -550

for Point in PointsInCircum(Radius, Steps):
    VisualizerJob.CameraFOVList_deg.append(110)
    VisualizerJob.CameraPositionList_um.append([Point[0], Point[1], ZHeight])
    VisualizerJob.CameraLookAtPositionList_um.append([0, 0, -1000])

Visualizer = Simulation.SetupVisualizer()
Visualizer.GenerateVisualization(VisualizerJob)

Visualizer.SaveImages(f"{YOUR_SAVE_DIRECTORY_HERE}/Visualizations/0", 2) # Save images two at a time

---

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 contact@carboncopies.org.