Fwd: Counting osteoclasts in culture

[Juanjo Vega]

(Rejected because of the attached image size...)

Hello,

It's difficult to isolate your cells so you can count them accurate. Anyway, I tried to threshold your image with a plugin that I developed some months ago, which allows you to select areas (multiple areas as well, by pressing SHIFT) and then to threshold those pixels which match a tolerance criteria based in the selection mean and standard deviation.

This plugin calculates the area matching the criteria, so it might help you to solve that part of your problem.

The bad new is that I can't find a good result, as you can see in the attached picture.

If you want to try it by yourself (maybe the results are better after applying some other preprocessing algorithms), let me know and I can send you the plugin, as it's not published.

Sincerely,

Juanjo.


http://imageshack.us/photo/my-images/820/screenshot20110921at414.png/

>
> On Sep 21, 2011, at 3:45 PM, Hanna Artsi wrote:
>
>> sorry the image...
>>
>>> Hi all,
>>> 1)I'm trying to use imagej to count osteoclasts in culture, picture
>>> attached (low resolution) each purple stain is a cell. I need to count the
>>> area% occupied and number. I'm new to this but i thought it was possible (in
>>> the high resolution image the boundaries are better visible). I tried color
>>> segmentation but I did not manage to separate the cells, I tried converting
>>> to gray and use various options suggested to others, I tried the fiji
>>> trainable segmentation but it simply got stuck.
>>> 2)A different matter entirely, how can i save the masks from the roi
>>> manager.
>>> Please help me...
>>> Hanna
>>>
>>> --
>>> *Curiosity Killed The Cat Satisfaction Brought It Back*
>>>
>>>
>>
>>
>> --
>> *Curiosity Killed The Cat Satisfaction Brought It Back*
>> <b4.jpg>
>
> ------------------------------------------------------------
> Juanjo Vega ([hidden email])
>
> Unidad de Biocomputación. Laboratorio B-13.
> Centro Nacional de Biotecnología. CNB-CSIC.
> C\ Darwin, 3. Campus de Cantoblanco.
> Universidad Autónoma de Madrid.
> 28049, Madrid, Spain.
>
> http://www.cnb.csic.es
> http://www.biocomp.cnb.csic.es
>
> [phone]
>
> "Las mejores almas son capaces de los mayores vicios como de las mayores
> virtudes, y aquellos que caminan despacio por el camino recto pueden
> llegar más lejos que los que corren pero se apartan de él." - Discurso
> del Método, René Descartes.
>

------------------------------------------------------------
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.csic.es

[phone]

"Las mejores almas son capaces de los mayores vicios como de las mayores
virtudes, y aquellos que caminan despacio por el camino recto pueden
llegar más lejos que los que corren pero se apartan de él." - Discurso
del Método, René Descartes.

[s c narula]

kindly send your plugin
I am working on medical images
Dr S C Narula
Prof.&HOD

On Wed, Sep 21, 2011 at 8:14 PM, Juanjo Vega <[hidden email]> wrote:

> (Rejected because of the attached image size...)
>
> Hello,
>
> It's difficult to isolate your cells so you can count them accurate.
> Anyway, I tried to threshold your image with a plugin that I developed some
> months ago, which allows you to select areas (multiple areas as well, by
> pressing SHIFT) and then to threshold those pixels which match a tolerance
> criteria based in the selection mean and standard deviation.
>
> This plugin calculates the area matching the criteria, so it might help you
> to solve that part of your problem.
>
> The bad new is that I can't find a good result, as you can see in the
> attached picture.
>
> If you want to try it by yourself (maybe the results are better after
> applying some other preprocessing algorithms), let me know and I can send
> you the plugin, as it's not published.
>
> Sincerely,
>
> Juanjo.
>
>
> http://imageshack.us/photo/my-images/820/screenshot20110921at414.png/
>
>
> >
> > On Sep 21, 2011, at 3:45 PM, Hanna Artsi wrote:
> >
> >> sorry the image...
> >>
> >>> Hi all,
> >>> 1)I'm trying to use imagej to count osteoclasts in culture, picture
> >>> attached (low resolution) each purple stain is a cell. I need to count
> the
> >>> area% occupied and number. I'm new to this but i thought it was
> possible (in
> >>> the high resolution image the boundaries are better visible). I tried
> color
> >>> segmentation but I did not manage to separate the cells, I tried
> converting
> >>> to gray and use various options suggested to others, I tried the fiji
> >>> trainable segmentation but it simply got stuck.
> >>> 2)A different matter entirely, how can i save the masks from the roi
> >>> manager.
> >>> Please help me...
> >>> Hanna
> >>>
> >>> --
> >>> *Curiosity Killed The Cat Satisfaction Brought It Back*
> >>>
> >>>
> >>
> >>
> >> --
> >> *Curiosity Killed The Cat Satisfaction Brought It Back*
> >> <b4.jpg>
> >
> > ------------------------------------------------------------
> > Juanjo Vega ([hidden email])
> >
> > Unidad de Biocomputación. Laboratorio B-13.
> > Centro Nacional de Biotecnología. CNB-CSIC.
> > C\ Darwin, 3. Campus de Cantoblanco.
> > Universidad Autónoma de Madrid.
> > 28049, Madrid, Spain.
> >
> > http://www.cnb.csic.es
> > http://www.biocomp.cnb.csic.es
> >
> > [phone]
> >
> > "Las mejores almas son capaces de los mayores vicios como de las mayores
> > virtudes, y aquellos que caminan despacio por el camino recto pueden
> > llegar más lejos que los que corren pero se apartan de él." - Discurso
> > del Método, René Descartes.
> >
>
> ------------------------------------------------------------
> Juanjo Vega ([hidden email])
>
> Unidad de Biocomputación. Laboratorio B-13.
> Centro Nacional de Biotecnología. CNB-CSIC.
> C\ Darwin, 3. Campus de Cantoblanco.
> Universidad Autónoma de Madrid.
> 28049, Madrid, Spain.
>
> http://www.cnb.csic.es
> http://www.biocomp.cnb.csic.es
>
> [phone]
>
> "Las mejores almas son capaces de los mayores vicios como de las mayores
> virtudes, y aquellos que caminan despacio por el camino recto pueden
> llegar más lejos que los que corren pero se apartan de él." - Discurso
> del Método, René Descartes.
>