Question on using the 3D tool

[Meena]

I read an article on the NEURON webpage ( news section) that now you can convert files from Neurolucida to NEURON using the Main Menu>Tools>Misc>Import 3D

So I have this simple Neuron trace...which is a .dat file, but however, a message prompt came up saying format not recognized.

Please note that I just installed the NEURON package today.
Please do feedback.....

[ted]

Import3D handles NeuroLucida v. 1 and 3 files (as well as swc and Eutectic files)
but they must be ASCII, not binary. Is your dat file binary?

--Ted

[Meena]

Ted, thanks for your earlier reply.

My file initially was a binary file...so that was the problem.

I am still learning to use Neuron. I made the conversion , with one problem. My simple neuron had 5 spines...and during the translation...
all 5 spines were ignored ?

I was wondering why this happened and how to fix it ?

[ted]

The Import3D tool translates all x,y,z,diam measurements. It also preserves "subset"
information (i..e. which branches are axonal, somatic, apical, basilar etc.). As far as I
know, it does not preserve "point of interest" marks (equivalent to "here I saw a spine').
So if you measured the dimensions of your spines, the hoc code will create corresponding
sections. If you merely marked the locations at which you saw spines, they won't show up
in the hoc code.

--Ted

[ted]

You asked how to fix the problem, not what caused it.

If it is critically important that your model have a spine that is located at a particular
point, the spine must be attached to the 0 or 1 end of a section (otherwise its actual
location will be at an internal node, which depends on nseg and probably will not be
at the location you want--you can read more about spatial discretization in NEURON
in chapter 5 of The NEURON Book). So if your spines are located anywhere except
at the ends of neurites, you will want to go back to NeuroLucida and edit your data
files so that

Code: Select all

    S
    |
AAAAAAAAA

(spine S is attached somewhere along the length of neurite A)
becomes

Code: Select all

     S
     |
AAAAA+BBBB

(neurite B and spine S are attached to one end of neurite A).
Or, if you don't have any measurements of diameter or length for spine S,
then at least break it into two neurites at the point where the spine is supposed
to be attached. You can then import the data with the Import3D tool. Once you
have a model cell, it will be straightforward* to identify which sections
correspond to A and B, and then you can attach a model spine to the end of A.

*--NEURON Main Menu / Tools / Distributed Mechanisms / Viewers / Shape Name
Then zoom in and translate the shape plot until you find the sections. Click on one
and it will turn red, and its name will be highlighted in the list of section names (right
hand panel of that tool).

--Ted

[Meena]

Thanks for that info.

I was looking at the .asc file for this particular neuron. I want to try and fix the code per your suggestion.....
A section of the code I have looks like this :

( (Color Yellow)
(Dendrite)
( -0.50 -2.37 53.38 1.33) ; Root
( 5.65 -11.37 53.38 1.33) ; R, 1
( 10.31 -17.98 48.06 1.16) ; R, 2
( 14.80 -23.58 47.14 1.16) ; R, 3
( 23.12 -30.20 70.80 1.16) ; R, 4
( 29.60 -38.17 70.80 1.16) ; R, 5
( 33.38 -40.79 108.46 1.16) ; R, 6
( 39.20 -45.04 109.76 1.16) ; R, 7
( 46.69 -56.40 109.76 1.16) ; R, 8
( 51.84 -62.17 109.76 1.16) ; R, 9
( 57.50 -66.24 109.76 1.16) ; R, 10
( 60.49 -70.48 109.74 1.16) ; R, 11
<( 59.49 -71.33 109.74 0.33)> ; Spine
( 62.99 -74.04 109.74 1.16) ; R, 12
( 67.64 -77.44 109.74 1.16) ; R, 13
<( 66.48 -79.47 152.30 0.50)> ; Spine
( 70.47 -79.64 152.30 1.16) ; R, 14
( 75.96 -83.88 152.30 1.16) ; R, 15
( 79.75 -86.96 144.28 1.16) ; R, 16
( 82.41 -88.83 144.28 1.16) ; R, 17
( 82.41 -91.20 144.28 1.16) ; R, 18
( 92.55 -99.86 144.28 1.16) ; R, 19
( 100.20 -104.61 155.70 1.16) ; R, 20
( 106.86 -108.85 273.22 1.16) ; R, 21
( 111.01 -112.92 326.06 1.16) ; R, 22
( 121.32 -115.46 334.30 1.16) ; R, 23
( 132.97 -118.52 334.30 1.16) ; R, 24
( 135.13 -117.33 334.30 1.16) ; R, 25
Normal

Please correct me in these assumptions if I am wrong
1 ) The first three 2 decimal points represent coordinates
2 ) The 4th number represents the diameter

But what is the root ? ie R,1 and R,2 and R,24 etc represent?

and what <( 66.48 -79.47 152.30 0.50)> ; Spine
does this mean?

I would really appreciate your feedback.

Thanks again....

[ted]

The root of a tree is the branch that has no parent.

If those spines are attached to the soma, and the soma has a "reasonable" shape,
then it doesn't matter exactly where on the soma they are located--they'll have
exactly the same effect on electrical signals. So you don't have to change the
file at all. Just attach your own model spines to the middle of the soma. If the
spines aren't located on the soma, you'll have to take the action I suggested
in the previous email.

Doesn't NeuroLucida come with a file viewer/editor that would allow you to make
the necessary changes without having to wrestle with the data file itself? Or at
least documentation of the basic syntax of the file format? Maybe that information
is somewhere on MicroBrightField's WWW site, or maybe they'll send it to you if
you ask.

--Ted

[ted]

Another approach is to edit the model that you produced by importing the morphometric
data. This is less direct than using whatever tools MicroBrightField provides, but properly
done it should achieve the goal. If you want help with this, send me the morphometric data
file by email and I'll see what can be done.

--Ted
ted (dot) carnevale (at) yale (dot) edu

[Meena]

Hi there again,

I had downloaded the cvapp from the compneuro.org website...
This seems like a fairly straighforward tool....yet...when I try opening the .asc file....nothing seems to happen ?

Can you please advice ? I am doing something wrong here ?

Thanks,
Meena