dendrite order

[thats_karlo]

Hello,


To make a 3D reconstraction of cell i use import "3D model" option.

Is there any way to determine the dendrite order? for example, if i have maximum dend[500], how can find out dend[150] belongs to which order of dendrits, 6th, 7th, or...order?

I'm waiting for your suggestions!

Thank's in advance

[thats_karlo]

HI!

I am wondering that i asked stupid question, OR my question is not clear

OR there is not a simple way to do that!

??
any idea !?

[ted]

Sure there's a simple way. Use the SectionRef class. Discover the root of the tree
(use the root() method). Starting at the root of the tree, recursively descend the tree
(here, the child() and nchild() methods will be helpful) while keeping track of the level
of descent. All sections at level i are ith order. That's how to traverse the whole tree in
a single pass, finding the branch order of each section.

If you only need the branch order of a few sections, it may be simpler to start at the
section of interest and _ascend_ recursively to the root, keeping track of each level on
the way. This would use the SectionRef class's has_parent and parent methods. Example:

Code: Select all

// returns branch order of the currently accessed section
// root of tree has order 0

func branchorder() { local order  localobj sr
  order = 0
  sr = new SectionRef()
  if (sr.has_parent) {
    sr.parent order = 1 + branchorder()
  }
  return order
}

[thats_karlo]

Dear Ted

Thank you very much for your reply. i wrote the following code

Code: Select all

create soma, dend[11]
access soma
access dend 

 connect dend[0](0), soma(0.5)
  for i = 1, 2 connect dend[i](0), dend[i-1](1)
  connect dend[3](0), dend[1](1)
  connect dend[4](0), dend(1)
  for i = 5, 6 connect dend[i](0), dend[4](1)
  connect dend[7](0), soma(0.5)
  for i = 8, 9 connect dend[i](0), dend[i-1](1)
  connect dend[10](0), dend[8](1)
  //===========================
func branchorder() {local order  localobj sr
 order = 0
 sr = new SectionRef()
 if (sr.has_parent) {
    sr.parent order = 1 + branchorder()
  }
  return order
}
branchorder(dend[5])

in end of the *.hoc file i add your code. but when i use the function
"branchorder(dend[5])" i have syntax error! i don't know where is mistake.

Could you help me to find out where is mistake?


Thank's in advance,

karlo

[ted]

A section cannot be passed as an argument to a function. The instructions for
func branchorder() state

Code: Select all

// returns branch order of the currently accessed section

In other words,
sectionname branchorder()
makes branchorder() return the order of sectionname

[ted]

sectionname functionname()
calls functionname() in the context of sectionname, but doesn't do anything with the
returned value. You need to have a print or assignment statement, like this:
sectionname print branchorder()
or
sectionname foo = branchorder()
print foo

[thats_karlo]

Hi Ted

Thank you so much!

It works nicely!

Have nice day!!

Karlo