Visualizing Using the GUI¶
For all of these tasks, make sure you have done the following:
- Load your model in NEURON
- Load BlenderNEURON in NEURON (by either opening the BlenderNEURON.hoc file or running
from blenderneuron.quick import bn)
- Load Blender with the BlenderNEURON add-on (NEURON tab should be visible in Blender left panel)
- Test the connectivity between NEURON and Blender (Should say “Ready”)
See Installation for how to perform steps 2-4.
Visualizing Morphology¶
Follow these steps to visualize the cell morphology of a NEURON model:
- Once your model is loaded, click “Send to Blender” button
- A moment later, your model should appear in Blender
- Navigate around the Blender scene to inspect the model. If you’re not familiar with Blender, these tutorials will give an overview of basic scene navigation.
By default, BlenderNEURON will export the morphology of all cells (sections) in the model. It will use NEURON’s x/y/z3d() and diam3d() values to build the 3D meshes in Blender.
In BlenderNEURON, 1 cm corresponds to 1 micron in NEURON.
If you add or make changes to your model’s sections/cells, click the “Re-Gather Sections” before clicking “Send to Blender” to ensure that they are included in the export.
Visualizing Activity¶
Follow these steps to visualize the morphology and simulated activity of a NEURON model:
- Once your model is loaded, click “Prepare For Simulation” button. This will add a handler to gather section voltage values during the simulation.
- Run your simulation
- Once the simulation is finished, click the “Send to Blender” button
- A moment later, your model should appear in Blender
- Use the buttons under the bottom timeline in Blender to re-play the simulation. If your cells emit action potentials (Vm > -20mV), you should be able to see them as glowing compartments. By default, 1 frame in Blender corresponds to 0.5ms in NEURON.
- You can scrub the timeline to re-play any part of the simulation and use the left/right arrow keys to step through the frames.