help on usage of ImageJ

[imagejuser1]

                Hello everyone. I am a mechanical engineering PhD student and
basically, I need to build domains from real structures by use of
micro-tomography images and analyze their heat transfer. I come up with
Fiji software and I started using it. Fiji should understand solid and
void areas from tomography images. I have read many articles and help
files but I am totally stuck and I need some help and advice.


I was able to construct 3D domain using 2D images. Following
building the domain, I need to create mesh on 3D domain. I have found
iso2mesh code to do that. This iso2mesh requires file type such as INR
and surface mesh for example. (http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Workflow)


My question is how can I build surface mesh using Fiji and
import it to INR file to import this mesh to iso2mesh? I tried surface
mesh command at the 3D Viewer window but I got out of memory eror: heap
space error although I allowed Fiji to use 10GB RAM and 6 cores.


I would be very happy if you can help me telling the steps needed to obtain INR file. Thank you.



       
       
       
       
   
         

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[Michael Doube-4]

Dear Hasan Celik,

Try using BoneJ's Isosurface plugin, as mentioned on the forum:

http://forum.imagej.net/t/error-with-large-models/577/2

You can write large STL meshes straight to disk, which might help you get around your out of memory error.

Michael

On 22/01/16 18:51, Hasan CELIK wrote:

>
> Hello everyone. I am a mechanical engineering PhD student and
> basically, I need to build domains from real structures by use of
> micro-tomography images and analyze their heat transfer. I come up with
> Fiji software and I started using it. Fiji should understand solid and
> void areas from tomography images. I have read many articles and help
> files but I am totally stuck and I need some help and advice.
>
>
> I was able to construct 3D domain using 2D images. Following
> building the domain, I need to create mesh on 3D domain. I have found
> iso2mesh code to do that. This iso2mesh requires file type such as INR
> and surface mesh for example. (http://iso2mesh.sourceforge.net/cgi-bin/index.cgi?Doc/Workflow)
>
>
> My question is how can I build surface mesh using Fiji and
> import it to INR file to import this mesh to iso2mesh? I tried surface
> mesh command at the 3D Viewer window but I got out of memory eror: heap
> space error although I allowed Fiji to use 10GB RAM and 6 cores.
>
>
> I would be very happy if you can help me telling the steps needed to obtain INR file. Thank you.
>

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