swc to hoc conversion
Posted: Fri Apr 08, 2016 3:09 pm
This is perhaps an odd question, as it's less about how to make a model work in Neuron and more about how Neuron works. My apologies if this belongs in another section.
I have used the geometry of a cell from the modelDB, which was presented as a hoc file. I set up my model to record several variables from each compartment in the cell simultaneously, and ran my simulations (so far as I can tell) successfully. To manage the data I have collected, I've read the binary files Neuron wrote into python (I know this may be a suboptimal way of doing things, but it is where I'm at right now). I wanted to present the data I had collected in a similar way as the shape plot feature. There is a small python library for reading in morphometric data (swc files), so I downloaded the original swc file corresponding to the cell geometry which I got from modelDB. I want to map the data I have collected onto the proper sections of the cell, but I don't know how to do that with an swc file because I'm not sure what points correspond to which sections in the hoc code Neuron used to make this cell,
Here is where I'm stuck: I don't know how Neuron turns swc information into hoc code which assigns names to each dendritic section. I would like to be able to do a similar thing in python so that I can map the appropriate data onto the correct points in the cell. Do you have ideas for how this might be accomplished?
Thanks,
Annik
I have used the geometry of a cell from the modelDB, which was presented as a hoc file. I set up my model to record several variables from each compartment in the cell simultaneously, and ran my simulations (so far as I can tell) successfully. To manage the data I have collected, I've read the binary files Neuron wrote into python (I know this may be a suboptimal way of doing things, but it is where I'm at right now). I wanted to present the data I had collected in a similar way as the shape plot feature. There is a small python library for reading in morphometric data (swc files), so I downloaded the original swc file corresponding to the cell geometry which I got from modelDB. I want to map the data I have collected onto the proper sections of the cell, but I don't know how to do that with an swc file because I'm not sure what points correspond to which sections in the hoc code Neuron used to make this cell,
Here is where I'm stuck: I don't know how Neuron turns swc information into hoc code which assigns names to each dendritic section. I would like to be able to do a similar thing in python so that I can map the appropriate data onto the correct points in the cell. Do you have ideas for how this might be accomplished?
Thanks,
Annik