Skip to content

Single Modelling with Arbor's GUI

Jump to bottom
Thorsten Hater edited this page Aug 31, 2021 · 16 revisions

Here we will show you how to re-create the first Arbor tutorial in the GUI.

Install the GUI

Download one of the binary installers found here https://github.com/thorstenhater/arbor-gui/releases/ this guide was written with https://github.com/thorstenhater/arbor-gui/releases/tag/v6.0.0alpha-2 on a MacBook.

Start the GUI and you should see a window like this

Define a Morphology

As we need a morphology that can be loaded from disk for use in the GUI, we will make a very simple SWC file

1 1     -3.0     0.0     0.0     3   -1
2 1      3.0     0.0     0.0     3    1

which sets up a cell consisting of a 3um soma extending 6um along the x-axis. If you are unfamiliar with SWC, do not worry, this is all we need to do with it. Store this data as eg soma.swc.

Now we need to load this file, in the GUI

  • click on 'File' in the top left
  • choose 'Morphology > Load'
  • navigate to your file using the dialogue
  • pick your file and click 'Load'
    • if your file is among many others, you can filter for .swc only by choosing that suffix in 'Filter'
    • SWC data has multiple interpretation, make sure the 'Flavor' selection is 'Neuron'
  • go to the cell window and take a look at your cell in 3D
    • mouse wheel and +/- zoom the view
    • pressing Shift brings up a rotation handle
    • pressing Ctrl brings up a translation handle
    • right click the cell window to
      • reset the camera
      • manipulate the axes cross
      • save a screenshot
      • tweak the model rendering resolution, might help performance in complex views
      • hover segments to learn some details about the geometry

Defining Locations

Now we are ready to continue work on the tutorial by setting up regions and locsets. On the left pane switch to the 'Locations' and expand the 'Regions' and 'Locset' All regions we need are defined, as we just have made a simple soma-only cell. However, to attach stimuli and probes we will need a locset. Click on the '+' right of 'Locsets' to add one.

Type in the following definition in the text box

(location 0 0.5)

Keep track of the status icon changing state from ❔(empty) over ⚠️ (invalid) to a ✔️(ok) as you type. You can hover your mouse over it to learn more.

The locset we just defined designates the center (0.5) of segment 0, which happens to be the soma. We can assign names to locsets to remember their use or definition. So, change the name from 'Locset 0' to 'midpoint', when done zoom in on the cell to see a marker at the locset point(s).

Note: If you have defined overlapping regions and locsets you can drag the definitions to reorder them. That will change rendering order accordingly and allow you to see hidden parts.

Assigning Bio-physical Properties

We are now done with 'Locations', switch to the 'Parameters' tab and assign -40mV under 'Cable Cell Properties' > 'Default' > 'Membrane Potential'. This set the initial value of the cell's membrane potential.

Next, expand the 'Mechanisms' > 'soma' tree and add a mechanism by clicking the '+' icon on the right and choosing 'hh' under the 'default' section from the combo box. You can expand this item further to take a look at the 'hh' mechanism's properties. With that, we have imbued the soma with Hodgekin-Huxley model behaviour and are almost ready to run the model.

Setting up the Simulation

Again switch tabs, this time to 'Simulation'. Under 'End time' enter 20ms. The expand 'Stimuli' and current clamp to the 'midpoint' locset by clicking '+' on the right.

Note: if 'midpoint' had more than one point, multiple current source would be applied, but in this case we only have one.

Expand the 'I Clamp 0' item and look for the 'Envelope' section. There, add a point at 10ms with 0.8nA and another at 12ms going back to 0nA. The result should look like this

One final step: click on 'Probes' and add a 'Voltage' probe to 'midpoint' This will allow us to record the membrane potential at the soma's center.

Running Simulations and Getting Outputs

Now click 'Run' at the top of the tab. Next switch from 'Cell' to 'Traces' on the right pane. Expand 'midpoint' on the right and select '0: Voltage'. You should now see this

Congratulations! This a complete simulation of a simple cell. Feedback welcome at https://gitter.im/arbor-sim/community.

Where to go from here

You can play with the simulation you just made, but beforehand it might help the current state (except probes). To do that choose 'File' > 'Cable' > 'Save'.

You can also attempt to expand this into the other tutorial. Good luck.

Clone this wiki locally