how to calculate section area

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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fabien tell
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how to calculate section area

Post by fabien tell » Mon Aug 27, 2018 5:29 am

Hello,
I'd like to calculate areas of different sections. I've read the documentation and searched through the forum but it remains unclear to me.

How do I use the the area () command ?

I loaded a hoc file with full morphology then

I tried this :

Code: Select all

soma { 
surface= area(0.5)
print surface } 

axon  { 
surface2= area(0.5)
print surface2 } 
It doesn't work

Thanks a lot

ted
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Re: how to calculate section area

Post by ted » Mon Aug 27, 2018 10:54 am

Works for me. After starting NEURON I entered two lines of text and got the expected result.

Code: Select all

oc>create soma
oc>soma { surface = area(0.5)
>	oc>print surface }
157079.63 
oc>
Try it.

What might be happening in your case? Try this:
1. start NEURON
2. load your "hoc file with full morphology"
3. at the oc> prompt execute the command
forall print secname()
just to make sure that the sections exist.

fabien tell
Posts: 43
Joined: Mon Mar 25, 2013 1:36 pm
Location: france
Contact:

Re: how to calculate section area

Post by fabien tell » Mon Aug 27, 2018 11:25 am

Hello Ted,

Actually you're right; it works as it should. I mixed up with section names. Sorry for bothering....

Acting fast is sometimes the enemy of thinking !!!!

Thanks a lot

fabien tell
Posts: 43
Joined: Mon Mar 25, 2013 1:36 pm
Location: france
Contact:

Re: how to calculate section area

Post by fabien tell » Tue Aug 28, 2018 10:51 am

Hello again,

I have a soma : L= 31 diam = 10
So according to I learned at school, the surface of a cylinder S= PI*diam*L (if we neglect the disk surfaces).

With neuron I got :

Code: Select all

oc>soma {print L}
31 
oc>soma {print diam}
10 
oc>soma {print area(0.5)}
324.63124 
By hand I got 3.14*10*31 = 31.4*31= 973.4

What's the problem ?

I have three nseg for the soma, so I guess that the problem since 973.4/324.63 = 3 . How do I get the full area ? I tought I could mutilply by nseg :

Code: Select all

oc>soma {sur= area(0.5)*nseg}
oc>print sur
973.89372 
It works but what about dendrites with tapering , it would overestimate the area ?

Thanks a lot

ted
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Re: how to calculate section area

Post by ted » Tue Aug 28, 2018 11:35 am

totalarea = 0
soma for (x,0) totalarea += area(x)

fabien tell
Posts: 43
Joined: Mon Mar 25, 2013 1:36 pm
Location: france
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Re: how to calculate section area [SOLVED]

Post by fabien tell » Tue Aug 28, 2018 11:44 am

Thanks a lot

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