cell & nuclear boundary detection

[shibsankar]

Hi, I am new to imagej and  I am working on microscopic cell image analysis. I need help regarding cell & nuclear boundary detection plugins.Can anybody please suggest me about how to approach for this microscopic image cell & nuclear boundary detection and what are the plugins to use for this purpose. Tell me from where  can I get Sobel filter plugins. I needed the best solution for this problem .

Thanks

Shib Sankar

[Thomas Boudier]

Hi,

That's depend on your labelling, DAPI-like labellings are best to
segment nuclei using automatic thresholding. For cells if you have a
cytoplasmic marker you can use the same method, if you have nice
membrane labelling you can do the same, threshold then fill inside with
fill holes. hope this helps.

Thomas


Le 23/01/2013 20:46, shibsankar a écrit :

> Hi, I am new to imagej and  I am working on microscopic cell image analysis.
> I need help regarding cell&  nuclear boundary detection plugins.Can anybody
> please suggest me about how to approach for this microscopic image cell&
> nuclear boundary detection and what are the plugins to use for this purpose.
> Tell me from where  can I get Sobel filter plugins. I needed the best
> solution for this problem .
>
> Thanks
>
> Shib Sankar
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/cell-nuclear-boundary-detection-tp5001510.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

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[shibsankar]

Thanks, Thomas for your valuable reply.

Hi, I need automatic gland and nuclear segmentation tool and as a part of that segmentation I want to detect cell &  nuclear boundary. As Thomas has suggested to use cytoplasmic marker , membrane labelling, I will try that also. But the main objective is to automatic gland and nuclear segmentation, anybody please tell me how to approach to this problem. What are the plugins available for this work and where to get directions for this work.

Thanks
Shib Sankar.

[carlo bianco]

hi
if you are working

on   E&H stained slides you can try with color deconvlolution
or color segmentation (plugin available), it could be a first step to

highlight theforegroud from the background.
Hope this useful
bes regards
carlo-bologna italy



________________________________
 Da: shibsankar <[hidden email]>
A: [hidden email]
Inviato: Giovedì 24 Gennaio 2013 20:24
Oggetto: Re: cell & nuclear boundary detection
 
Thanks, Thomas for your valuable reply.

Hi, I need automatic gland and nuclear segmentation tool and as a part of
that segmentation I want to detect cell &  nuclear boundary. As Thomas has
suggested to use cytoplasmic marker , membrane labelling, I will try that
also. But the main objective is to automatic gland and nuclear segmentation,
anybody please tell me how to approach to this problem. What are the plugins
available for this work and where to get directions for this work.

Thanks
Shib Sankar.



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Sent from the ImageJ mailing list archive at Nabble.com.

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[carlo bianco]

some example are immuno ratio http://153.1.200.58:8080/immunoratio/
or immunomembrane, try it. these are quantitative approach.
for evaluation of structural complexity the best approach is fractal, in my opinion
cheers
carlo




________________________________
 Da: shibsankar <[hidden email]>
A: [hidden email]
Inviato: Giovedì 24 Gennaio 2013 20:24
Oggetto: Re: cell & nuclear boundary detection
 
Thanks, Thomas for your valuable reply.

Hi, I need automatic gland and nuclear segmentation tool and as a part of
that segmentation I want to detect cell &  nuclear boundary. As Thomas has
suggested to use cytoplasmic marker , membrane labelling, I will try that
also. But the main objective is to automatic gland and nuclear segmentation,
anybody please tell me how to approach to this problem. What are the plugins
available for this work and where to get directions for this work.

Thanks
Shib Sankar.



--
View this message in context: http://imagej.1557.n6.nabble.com/cell-nuclear-boundary-detection-tp5001510p5001522.html
Sent from the ImageJ mailing list archive at Nabble.com.

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[shibsankar]

Thanks, carlo-bologna for your valuable reply.

hi
I am working on H&E stained slides and as fer your saying I have used color deconvolution
or color segmentation,
now to get segmentation boundary what should I do, is there any sequential steps. I want to get the nuclear boundary at first. if any body having any source code or information regarding this, then kindly help me by forwarding that or give me a  suggestion because I am still in a learning stage of imagej.

best regards
Shib Sankar