[Insight-users] Centerline length of a "pipe"

[Luis Ibanez]

Hi Ramu,

The applications can be found in a separate CVS checkout

     cvs -d :pserver....   co InsightApplications

You can also download tar.gz  and .zip files with
the applications code.

Instruction are available in the itk download page
http://www.itk.org/HTML/Download.php

---

The two applications in question are

1)
InsightApplications/Curve2DExtractor
http://www.itk.org/HTML/Curve2DExtraction.htm
which is in CVS under
http://www.itk.org/cgi-bin/cvsweb.cgi/InsightApplications/Curves2DExtractor/?cvsroot=Insight

2)
InsightApplication/Morphogenesis
http://www.itk.org/HTML/Morphogenesis.htm
which is in CVS under
http://www.itk.org/cgi-bin/cvsweb.cgi/InsightApplications/Morphogenesis/?cvsroot=Insight




In (2) you may want to take a look at the
species  named:

    "Gradient Eating Bacteria".

These bacteria reproduce under a condition of
the extracellular matrix.
(Which in this case is your image  :-)   )

Here is an animation of this species segmenting
a ventricle from an MRI image
http://www.itk.org/Art/MorphogenesisSegmentation.mpg

The bacteria is colored using three pigment
genes conveniently named R, G and B. Color
changes made evident cellular differentiation.

This species is pressure-sensitive and stop
replicating when pressure from neighbor cells
is higher than a threshold. This mechanism
will ensure that cellular division only
happens in the direction of the ends of the
pipe.

You can basically put an egg-cell in the
middle of the pipe, set the maximum cell
raidus to half of the pipe radius,
and...let them reproduce...

The U-shape or L-shape will not be a problem
as long as the pipe diameter everywhere is larger
than the maximum cellular radius. A factor of
2 should be a safe range.

BTW, You will have to think in a condition
for stopping the cells when they get out
of the pipe-ends...

You certainly don't want this little guys
replicating all over the image.


---

Let us know if you find any problem with
the applications.


Thanks


Luis



--------------------------------
ramu chandran wrote:
> Hello Luis,
>              Thanks for your time. The pipe is a hollow tube with some 
> thickness. The radius of the pipe may not be uniform as it might have 
> different inlet and exit diameters. Also the pipe may be curved like U- 
> shape or L - shape. I could not find the code for the applications you 
> mentioned. It would be of great help if you can send me some more 
> details. Hope I am not troubling you.
> 
> Thanks
> Ramu
> 
> 
> On Thu, 10 Apr 2003 Luis Ibanez wrote :
> 
>>
>> Hi Ramu,
>>
>> Is the pipe like a hollow tube ?
>> or is it like a solid bar ?
>>
>> You may want to take a look at the
>> Curve2DExtractor application in
>>
>> InsightApplications/Curve2DExtractor
>> http://www.itk.org/HTML/Curve2DExtraction.htm
>>
>> The process in this application can be
>> generalized to 3D. The only extra piece
>> of code to write is a filter that compute
>> eigevalues of 3x3 matrices.
>>
>> You can also take a look at the Blox
>> objects which extract core atoms from
>> figures in the image.
>>
>>
>> If the only objective is to measure the
>> tube lenght, you could also program
>>  a cellular aggregate for reproducing
>> cells with radii ~= to the pipe radius.
>> By restricting the cells to reproduce
>> only inside the pipe, the final number
>> of cells will be proportional to the
>> pipelength. Take a look at the Morphogenesis
>> example in
>>
>>
>>   InsightApplications/Morphogenesis
>>
>> This example uses bacteria with a
>> genome of less than ten genes.
>>
>>
>>
>>    Regards,
>>
>>
>>
>>      Luis
>>
>>
>>
>> -------------------------------
>>
>>
>> ramu chandran wrote:
>>
>>> Hello,
>>>           I have a "pipe" visual object which may be cylindrical
>>> conical or bent pipe. I want to calculate the center line length
>>> of the pipe. Is there any algorithm available in VTK for this?. I 
>>> posted this question to user list couple of times, but there was no 
>>> answer. please help me with this, I am stuck with the problem.
>>>
>>> Thanks
>>> Ramu
>>>
>>>
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>>
>>
>>
> 
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