www.neuron.yale.edu

Posted: **Sun Oct 15, 2006 6:13 pm**

Hi,

Suppose you have a complex morphology data of a cell, and you have successfully convert it to neuron.

in "sh" windowes, when i type oc> topology() i will see my sections that consists of :
soma , dend1[0], dend1[1],.........
dend2[0], dend2[1],.........
.......................................
.......................................
dend10[0], dend10[1],.........

i want to write a code that contain a for loop,which in this loop i like to have access to every section. Assume, we can show dendrtic segment with symbol dendj[0:end], that "j" showes barnch , [0:end] shows number for barnch segmant( i hope it is clear).

my for loop is like:

for j=1,end{
for i=1,end{
accecc dendj

dendj.dima=2*j // for example!
}
}

so, is there any command to find how many barnch we have? j=1,?
is there any command to find how many segment are attributed to a barnch? i=1,?

or, maybe you have other way, to have access to every segment?

Thanks in advance!

Karlo

Posted: **Mon Oct 16, 2006 5:09 am**

Have a look at the statements forall and forsec in the quick index:
http://www.neuron.yale.edu/neuron/stati ... tml#forall
http://www.neuron.yale.edu/neuron/stati ... tml#forsec

Posted: **Mon Oct 16, 2006 3:24 pm**

Hi,
thanks Raj,

I look at "forall" and "forsec" , but i doesn't help me.

consider you have soma, and 10 barnch of dendrits, and ever brach contanis defferent number of section. so, in NEURON section names are consiste of:

soma

dend1[0],dend1[1],......dend1[n1]
dend2[0],dend2[1],......dend2[n2]
....
.....
dend10[0], dend10[1],......dend10[n10]

1-do you know any way to determine, how many barnches we have?

here, 10 barnch

2- for every barnch, how many sub-section we have?

here, what 's n1,n2,....n10?

3-Can i change the name of section from

(dend1[0],..dend1[n1],dend2[0],...dend2[n2],.....dend10[n10])

to

(dend[0],dend[1],dend[2],.......,dend[100],.........dend[500])

4- Or, can i make a section list, with some command to access every emembre of list,e.g,

mylist=[dend1[0] dend1[1]........dend5[18]........dend10[11]]

for i=1, size(list){
access mylist
mylist.diam=2*i // for example!
}

await for any suggestion!

thanks,

Karlo

Posted: **Tue Oct 17, 2006 3:22 am**

Code: Select all

forall {
	print secname()
}

gives you all section names.

Alternatively you can use the topology function:http://www.neuron.yale.edu/neuron/stati ... l#topology
The output of this function also gives you how they are connected and you can read of the information you need. In this is case it might not be worth it to try to automate the process further.

With for example

Code: Select all

forsec "dend11" {
// do my thing
}

You can now operate on most of the individual branches, but be in for a surprise when you use dend1, you will get dend11 and dend10 for free! If you only use dend you will get them all, which you can use to make the SectionList you like to use:

Running

Code: Select all

objref dendriticSections
dendriticSections=new SectionList()
forsec "dend" {
dendriticSections.append()
}

adds all section which have dend in their name to the section list.
With:

Code: Select all

forsec dendriticSections {
// do my thing
}

you can now iterate over all sections in your sectionList.

Posted: **Tue Oct 17, 2006 3:12 pm**

Thanks,

Just could you tell more one more point! in the code

Code: Select all

objref dendriticSections
dendriticSections=new SectionList()
forsec "dend" {
                    dendriticSections.append()
}

forsec dendriticSections {
                                 // do my thing
}

i like to insert my function in part "// do my thing". Actually i use my function like

Code: Select all

sectionname   result=myfunc()
print result

or

access sectionname
result= myfunc()
print result

Could you tell me how can i use, my function in
forsec dendriticSections {
// do my thing
}

to do calculation for every member of section list!

thanks again,

Karlo

Posted: **Tue Oct 17, 2006 4:40 pm**

Just define a function, example:

Code: Select all

func myfunc(){
  return diam
}

and call it:

Code: Select all

forsec dendriticSections {
  print myfunc()
}

Posted: **Tue Oct 17, 2006 11:32 pm**

Thanks Raj!

Your comments were very usefull. I have learned alot from this post.

www.neuron.yale.edu

access to section!

access to section!