finding appropriate anatomical and biophysical parameters

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pnainar
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Joined: Fri Jun 03, 2016 11:36 am

finding appropriate anatomical and biophysical parameters

Post by pnainar »

Hi,
I am trying to create a network as a combination of real-neurons (species specific - mammals, rodents & humans) from data available in NeuroMorpho.org of the thalamic reticular & thalamocortical neurons. I am stuck on the following:
a. In a number of situations I found that just parts of the neuron included: dendrites, no soma, no axon. I would like to have whole real or at least as close to as possible neurons in my model.
b. obtaining species specific gmax for sodium, potassium, calcium, chloride and H ions. I have not been successful in getting the electrophysiological properties for the neurons in question.
Could anyone please advise me on how to overcome the issues? Many thanks.

Padma
ted
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Re: finding appropriate anatomical and biophysical parameter

Post by ted »

Finding the anatomical and biophysical parameters that match one's needs is a recurring problem.
pnainar wrote:In a number of situations I found that just parts of the neuron included: dendrites, no soma, no axon. I would like to have whole real or at least as close to as possible neurons in my model.
That's the way it goes. Your options are:
(1) try to find suitable morphometric data. Fortunately, NeuroMorpho.org contains lots of data. Have you really exhausted it, or has it exhausted you (I know the feeling)? It seems unlikely that ModelDB will contain anything useful that is not already in NeuroMorpho.
(2) get some experimentalist to generate such data for you
(3) do it yourself--spend time in a lab that has the required equipment and expertise, learn the techniques, and collect your own data
(4) ask yourself whether it is necessary for your model to include explicit representations of axons, or whether it is sufficient to use NetCons to detect the occurrence of a spike in the presynaptic cell and then convey events to event-driven synaptic mechanisms on that cell's targets.
obtaining species specific gmax for sodium, potassium, calcium, chloride and H ions. I have not been successful in getting the electrophysiological properties for the neurons in question.
Here you are not only at the mercy of what has been published, but also confronted by the challenge of finding relevant observations. A lot has been published, but some species, cell classes, and ion channels are more popular than others, so gaps are common. That said, difficulty finding X does not mean that X doesn't exist. If you are not intimately familiar with the experimental literature, find an experimentalist who can help you with your search strategies. You might also find it helpful to look at the Allen Institute's models for relevant channel descriptions (a lot of them are in ModelDB, but be sure to read the associated publication, and maybe also poke around the Institute's own web site). Another useful resource is Channelpedia. Last but not least, examine related models in ModelDB to see what practicing modelers have done. If none of these actions works to your satisfaction, your options are
(1) get some experimentalist to generate such data for you
(2) do it yourself--spend time in a lab that has the required equipment and expertise, learn the techniques, and collect your own data
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