Add/delete cell compartments by group

[ewesteinde]

Hello,

Apologies if I missed this in any of the tutorials but is there an easy way to delete compartments/sections of a cell after its been generated? For example, I'm defining a jaxley cell from a .swc file and so automatically generating its groups/branches/compartments using the jx.read_swc function. After creating the cell I then want to delete all compartments associated with the group labeled 'axon' (and actually replace it with a synthetic axon with a defined length & # compartments), which I haven't figured out how to do. Or should I edit the swc file directly before using it to generate a jaxley cell?

Thanks,
Elena

[michaeldeistler]

Hi Elena,

Thanks for bringing this up! This feature does not yet exist in Jaxley, but I agree that it would be nice to have and we should implement it.

We will keep you updated!
Michael

[michaeldeistler]

I also opened an issue here to track this.

[ewesteinde]

Got it, I'll just modify the swc file then, thanks for the quick reply!

[michaeldeistler]

Perfect!

[jnsbck]

Hey @ewesteinde,
This is now possible thanks to a flexible interface with networkX which we just added in #355. I included an example of pretty much what you were asking in this tutorial. You can either edit the graph before importing it into jaxley with from_graph, or edit a Module by exporting it to a graph (to_graph) and then re-import it (from_graph).
Lemme know in case you have any questions about. :)