[Insight-users] contours extraction

[Yann GAVET]

Hi luis, thank you for your answer.

I will add some precisions: the detection of the cells , due to the bad 
quality of the images, is not perfect. So, the operators want to have 
the capability of deleting and adding borders.
To implement this, I have to group the border pixels into segments.
But before doing that, I want to close the borders that have little 
holes in it and that can easily be seen, at least with a human eye.

The really final goal is to compute statistics on cells, such as area 
and morphometry. And I want to be able to correct the drawing of the 
cells automatically done by the algorithm (cell deletion and addition).

I hope those explanations are better.

Thank you again.
Yann.

Luis Ibanez wrote:
> 
> Hi Yann,
> 
> The processing that you are attempting to implement
> is completely dependend on the discret topology
> that you define for your pixels.
> 
> The first thing that you want to avoid is to use
> 4-connectedness and 8-connectedness since both
> of them are flawed digital topologies, and for
> your application it will be hopeless to attempt
> a correct definition of what a "node" means.
> 
> The more consistent way of managing connections
> in a discrete space in 2D is to use a 6-connected
> topology.  In that context you could use the typical
> engineering approach of considering connections
> along the vertical and horizontal axis, and along
> *only one* of the diagonals. In this way you get a
> 6-connected space where the notions of neighbors
> can be properly defined.
> 
> 
> You may want to look at the classical literature
> on this area:
> 
> A. Rosenfeld, A. Kak
> Digital picture processing
> Academic Press Inc. 1982.
> 
> J. Serra
> Image Analysis and Mathematical Morphology
> Academic Press Inc. 1982
> (You will notice that most of the "formal"
> Mathematical Morphology is actually done in
> hexadecimal grids)
> 
> D. Nogly, M. Schladt
> Digital Topology on Graphs
> Computer Vision and Image Understanding,
> Vol 63, No.2; March; pp 394-396, 1996.
> 
> 
> Your description was a bit confusing regarding
> what you already have solved and what you are
> looking for.
> 
> It seems that you already have succed to detect
> the regions separating the cells, and now your
> are trying to identify the cells themselves.
> 
> It is not clear why you need to identify the
> nodes in the contours and why you plan still
> to remove borders that are "not well detected".
> 
> Maybe a description of your "real final" goal
> (not the intermediate difficulties) will be
> useful for suggesting you appropriate ways
> of taking advantage of the algorithms available
> in ITK.
> 
> 
>   Please let us know,
> 
> 
> 
>      Regards,
> 
> 
> 
>          Luis
> 
> 
> 
> 
> ------------------
> Yann GAVET wrote:
> 
>> Hi all.
>>
>> I want to perform a contour extraction from cell images.
>>
>> My program computes the skeleton of the contours, and I want to get 
>> the cells (with itkConnectedComponentImagefilter).
>> I also want to get the borders of the cells in a specific way, so that 
>> I could remove easily the borders that are not well detected. The 
>> important thing should be the detection of the "node" points, in red 
>> in the picture. Then, I could separate the borders of the cells into 
>> segments and manage segments easily.
>>
>> My question is: is there a way in itk to perform such a segmentation ? 
>> Does anyone know any method or link that could help me ?
>>
>> Thank you for your time.
>>
>> Yann
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Insight-users mailing list
>> Insight-users at itk.org
>> http://www.itk.org/mailman/listinfo/insight-users
> 
> 
> 
> 
> 
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