CellBuilder changes

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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chels

CellBuilder changes

Post by chels » Mon Jun 09, 2008 4:15 pm

Hi,

I have a hoc file of a rat dorsal lateral geniculate nucleus interneuron from ModelDB. I imported this file into CellBuilder and, under geometry, clicked on dend[214] and saw the location highlighted in red. However, when I exported this file to a new hoc file and reloaded the new hoc file into CellBuilder, the location of dend[214] had changed. I tried this a couple of times and the location kept changing. I was wondering why this happens?

Also, I know how to measure the distance between the soma and a particular dendrite using hoc code, but is there any way to measure distances using CellBuilder? I'm trying to determine which is the most distal dendrite.

Thanks so much in advance.

ted
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Re: CellBuilder changes

Post by ted » Mon Jun 09, 2008 7:47 pm

chels wrote:I know how to measure the distance between the soma and a particular dendrite using hoc code, but is there any way to measure distances using CellBuilder?
No.
I'm trying to determine which is the most distal dendrite.
Best done algorithmically.
Please give a precise definition of what you mean by "most distal dendrite".
First, what is your definition of distance: radial distance from a reference point, path distance
along neurites from a reference point, or electrotonic distance from a reference point? What
reference point? If electrotonic distance, do you mean for Vin or Vout?
Second, by "most distal" do you mean the neurite that has the most distal 0 end, the most
distal 1 end, the "most distal length" (the one with max INTEGRAL over length of distance *
dlength) or the "most distal area" (the one with max INTEGRAL over length of area *
distance)?
Last edited by ted on Tue Jun 10, 2008 9:18 am, edited 1 time in total.

hines
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Post by hines » Tue Jun 10, 2008 8:22 am

new hoc file into CellBuilder, the location of dend[214] had changed.
The existing cell sections are imported in root to leaf order defined by
SectionList.wholetree() and the index of a repeated basename is
incremented as each is imported. I'm slightly surprised that a cycle
of continuous create, import into new CellBuild does not settle to a
stable set of indices. CellBuild ought only to care that for any path
from a section to the root of the tree it does not encounter an index
(for the name) which is greater than that of the section.

chels

Post by chels » Tue Jun 10, 2008 2:20 pm

Hi,

Thanks so much for the responses!

When I say most distal dendrite, I mean path distance along dendrites from a reference point, which is the 0 end of the soma. By distal I mean the most distal 1 end. The code I wrote to do this is:

Code: Select all

 proc distal() { 
	access soma
	distance(0,0) // set origin
	for i = 0, ndend-1 dend[i] {
		print "ndend[", i, "] is at distance ", distance(1)
	}
}
Is this ok, or is there a better way to do this? Thanks!

ted
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Location: Yale University School of Medicine
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Post by ted » Tue Jun 10, 2008 5:20 pm

If the soma is alreay the default section, there is no need for another
access soma
statement.

If you only want to know which dendrite has the most distal 1 end, this will do:

Code: Select all

proc mostdistal() { local i, imax, maxdist
  distance(0,0) // set origin
  imax = -1
  maxdist = 0
  for i = 0, ndend-1 dend[i] {
    if (distance(1) > maxdist) {
      imax = i
      maxdist = distance(1)
    }
    printf("most distal 1 end is at %g and belongs to dend[%d]\n", maxdist, imax)
  }
}

hjunji21
Posts: 2
Joined: Fri Apr 20, 2018 7:30 pm

Re: CellBuilder changes

Post by hjunji21 » Tue Apr 24, 2018 11:19 am

Hello all!

I am just a beginner here. So, I have had some difficulties to deal with some commands...

I included the following code into mine:

Code: Select all

proc mostdistal() { local i, imax, maxdist
  distance(0,0) // set origin
  imax = -1
  maxdist = 0
  for i = 0, ndend-1 dend[i] {
    if (distance(1) > maxdist) {
      imax = i
      maxdist = distance(1)
    }
    printf("most distal 1 end is at %g and belongs to dend[%d]\n", maxdist, imax)
  }
}


However, the following error message appears:

Code: Select all

proc mostdistal() { local i, imax, maxdist
              ^
SyntaxError: invalid syntax
I really have no idea about what could be the cause of this error. Please, If someone has any idea, could you share it here?

I have already installed the latest version of proc package (proc 0.14). But the error still remains.

Thank you very much! m(_ _)m

ted
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Posts: 5376
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: CellBuilder changes

Post by ted » Tue Apr 24, 2018 3:38 pm

The problem has absolutely nothing to do with Python's proc package. I'll have to see your program before I can tell you why the error message happened. If you email it to me
ted dot carnevale at yale dot edu
I'll let you know what I find out.

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