Not finding a axonal section in the imported 3D structure

Using the graphical user interface to build and exercise models. Includes customizing the GUI by writing a little bit of hoc.
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divyeshsah_89
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Joined: Tue Aug 11, 2009 12:54 pm

Not finding a axonal section in the imported 3D structure

Post by divyeshsah_89 »

I downloaded the 3D structure from the site neuromorpho.org in the swc format & tried to import it in the cell builder.
But a problem came that when i saw the subsets part of cell builder i was not able to identify the axon.the parts were " all, somatic, basal & apical. So please help me how can i make a axonal section.
ted
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Re: Not finding a axonal section in the imported 3D structure

Post by ted »

Most reconstructions don't include axons, for a variety of reasons (axons are hard to fill, hard to see, and often ignored maybe because of all the attention that has been focussed on dendrites). Some labs have generated data that includes axons--you might look in NeuroMorpho.org for cells from Ascoli's lab--this one
http://neuromorpho.org/neuroMorpho/neur ... _name=ca1c
has a monster axon.

Your alternative is to "invent" an axon by writing hoc code that contains "plausible" assumptions about anatomy and biophysics. This is what Mainen and Sejnowski did for
Mainen ZF, Sejnowski TJ (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382:363-6
and I think also for
Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995) A model of spike initiation in neocortical pyramidal neurons. Neuron 15:1427-39
The source code for these models is in ModelDB
http://senselab.med.yale.edu/modeldb/
divyeshsah_89
Posts: 11
Joined: Tue Aug 11, 2009 12:54 pm

Re: Not finding a axonal section in the imported 3D structure

Post by divyeshsah_89 »

Thank you for your reply.
But then structure which u gave now does not have apical dendrities.
I am working on BAP & memory retention in CA1.I am only concentrating on one type of channel i.e. Atype-Transient K+ channel so do u think its ok if i dont have a subset with name axon.
ted
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Re: Not finding a axonal section in the imported 3D structure

Post by ted »

divyeshsah_89 wrote:structure which u gave now does not have apical dendrities.
There may not be a subset labeled "apicals" or any neurite with the name "apical" but I bet you dollars to donuts that it has an apical tree. Show it to an anatomist.
I am working on BAP & memory retention in CA1.
So all the action will be in the dendrites and the synapses attached to them. All you need is a spike trigger zone. Experimental evidence in many classes of cells (please don't merely take my word for it; check the literature yourself so you can quote it with authority) suggests that, under ordinary conditions, the site of spike initiation is in the axon hillock, or at the first axonal branch point, or (for cells with myelinated axons) at the first node of Ranvier. In principle, then, there is no need for the entire axon with all of its manifold ramifications--you just need the very proximal part of the axon, maybe out to the first branch point or node of Ranvier. If you have an anatomical reconstruction that lacks these structures, you only need to create them yourself in hoc code and attach them to the soma.
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