Neurolucida text morphology changes when using import3D

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jhlee
Posts: 2
Joined: Thu Sep 10, 2020 12:06 am

Neurolucida text morphology changes when using import3D

Post by jhlee »

Dear all,

What I'm struggling with is to bring a Neurolucida text file from the original blue brain project "L1_DAC_bNAC219_1" source files into my customized project.
The below is my custom code for testing the import of text file.

Code: Select all

load_file("nrngui.hoc")
load_file("import3d.hoc")
objref this
objref nl,import
objref s
nl = new Import3d_Neurolucida3()
nl.quiet = 1
nl.input("C:/L1_DAC_bNAC219_1/morphology/sm090918b1-3_idA_-_Scale_x1.000_y1.025_z1.000.asc")
import = new Import3d_GUI(nl, 0)
import.instantiate(this)
s = new Shape()
The code runs well without errors.

However, the generated morphology is quite different from the original morphology that can be shown from running the original source files.
The below link shows the original morphology. (*Sorry for hyperlinking the image. I'm not really good at bbcode.)
https://drive.google.com/file/d/1CkhGAX ... sp=sharing

And the following link shows the image generated from the above code.
https://drive.google.com/file/d/1PcVng_ ... sp=sharing

As you can see, my imported morphology has so many unnecessary branches.

Even, I also tried to use import3D through "nrngui" itself, and the result was the same as my custom code.
(the process was nrngui -> Tool -> Miscellaneous -> Import3D)
https://drive.google.com/file/d/1U8wR8R ... sp=sharing


Is there any idea which point I'm missing for the proper morphology import?

Thanks for all your interests and wish your healthy days!
ted
Site Admin
Posts: 5819
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: Neurolucida text morphology changes when using import3D

Post by ted »

I'll have to reproduce this for myself. Please send the necessary morphometric data file(s) to ted dot carnevale at yale dot edu
jhlee
Posts: 2
Joined: Thu Sep 10, 2020 12:06 am

Re: Neurolucida text morphology changes when using import3D

Post by jhlee »

ted wrote: Thu Oct 22, 2020 11:00 am I'll have to reproduce this for myself. Please send the necessary morphometric data file(s) to ted dot carnevale at yale dot edu
Ted,

Thanks for your interest in my question!
Then, I've found that the original hoc files actually include the additional codes for re-shaping the unnecessary axons in the morphology data such as ones with diameter zero. This code was in the part of biophys() procedure instead of morphology procedures.
This is why I couldn't catch it at first.
Even though I spent some days and the trick mad me a little bit feel ridiculous, I could learn many things from the example.
I appreciate again you for paying attention!

Best,
Jiho Lee.
ted
Site Admin
Posts: 5819
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: Neurolucida text morphology changes when using import3D

Post by ted »

Yes, there are many lessons to learn from this, like how to write code that is difficult for anyone else to use.
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