Initializing multiple cells using a single cell state file

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azylbertal
Posts: 4
Joined: Thu Apr 10, 2014 8:37 am

Initializing multiple cells using a single cell state file

Post by azylbertal » Wed Jun 18, 2014 9:36 pm

I have a single cell model with a combination of fast and slow processes that exhibit a very long "transient" behavior before it settles (I can't use large dt for initialization because of stability issues). I use a file generated by SaveState to start my single cell simulations with the resting state values, thus avoiding the transient behavior.
Now I want to create a small network from cells identical to this one, while initializing each one of them with the values stored in my state file. Of course I can't load the file after I create multiple cells, because I have more compartments (/cells) when loading than I had when saving.
There is probably a very simple solution that I overlooked. What would be the correct approach here?

Thanks!

hines
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Posts: 1436
Joined: Wed May 18, 2005 2:32 pm

Re: Initializing multiple cells using a single cell state fi

Post by hines » Sat Jun 21, 2014 8:31 am

Sadly, that is outside the scope of SaveState and you will have to do that under interpreter control. I can point you to
nrn/share/lib/hoc/prcellstate.hoc that visits all the states and variables of a single cell. You can copy large chunks of that (or at least use the idioms
presented that iterate over all sections, segments, mechanisms (and point processes) of a cell) and create a procedure with two cell args the copies the
state of one cell to the other. That would be a useful addition to SimToolDB.

shailesh
Posts: 104
Joined: Thu Mar 10, 2011 12:11 am

Re: Initializing multiple cells using a single cell state fi

Post by shailesh » Tue Jul 01, 2014 7:27 am

One of the advantages of the NEURON forum is to randomly go through posts and pickup tips and tricks from others experience!

Recently came across this post and my curiosity was piqued reading about SaveState. I was previously unaware of such a feature in NEURON and now realize that it has a lot of potential use with regards to our groups work. The native SaveState seems to suffice my current requirements but was interested in your suggestion of developing a procedure that copies the state of one cell to the other. I have come up with something, but think better to run it past you (for any potential issues) before posting on the forum. Shall mail you the same.

shailesh
Posts: 104
Joined: Thu Mar 10, 2011 12:11 am

Re: Initializing multiple cells using a single cell state fi

Post by shailesh » Thu Jul 03, 2014 10:03 am

azylbertal... if you still require the above functionality, you could try out this tool here:
https://senselab.med.yale.edu/simtooldb ... ool=155716
(URL updated)

Do let me know if it works out or if you face any issues. Cheers!

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