Single Modelling with Arbor's GUI

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.

When done zoom in 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'.