nucleus counter

[Shilpashree Balakrishnan]

Hi,
thanks for the replies regarding the montages, am a new user, and want to do nucleus counting in imageJ. I tried the thresholding and analyze particle method, but it detects even a speckle that would arise by thresholding so the error is unacceptable. So i wish to use the Nucleus Counter but am unable to find the plugin. Could someone suggest a solution....
 
shilpa

[markou]

Hi, you mean ITCN detector?

here is a URL
http://rsb.info.nih.gov/ij/plugins/itcn.html

where can you download .jar file in your pluin directory.

I hope i will help
Bye
Marko


Navajanje Shilpashree Balakrishnan <[hidden email]>:

> Hi,
> thanks for the replies regarding the montages, am a new user, and want to
> do nucleus counting in imageJ. I tried the thresholding and analyze
> particle method, but it detects even a speckle that would arise by
> thresholding so the error is unacceptable. So i wish to use the Nucleus
> Counter but am unable to find the plugin. Could someone suggest a
> solution....
>  
> shilpa
>

-------------------------------------------------
Najdi.si Mail  http://mail.najdi.si/

[Tony Collins-4]

Hi Shilpa,

It's included in the bundle here:
http://www.macbiophotonics.ca/downloads.htm 

This bundle includes a bunch of plugins you'll find useful - especially
if you're using the imagej for microscopy online manual.

Email me off list if you'd like me to send you just the Nucleus counter
plugin.

Regards,
Tony

Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca


> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Shilpashree Balakrishnan
> Sent: Friday, February 09, 2007 7:23 AM
> To: [hidden email]
> Subject: nucleus counter
>
> Hi,
> thanks for the replies regarding the montages, am a new user, and want
to
> do nucleus counting in imageJ. I tried the thresholding and analyze
> particle method, but it detects even a speckle that would arise by
> thresholding so the error is unacceptable. So i wish to use the
Nucleus
> Counter but am unable to find the plugin. Could someone suggest a
> solution....
>
> shilpa

[Perry, Griffin M]

If you only have a few isolated pixels that made it past the threshold,
they can be disregarded in the actual particle analysis by setting a
minimum size range (default range is 0-infinity) above 0 pixels^2...  I
hope this helps.  To test to see if it your new range works, you can use
the Show Outlines to see if some of the noise was included in the
particle analysis.

-Griffin
SA, TX
Res. Asst.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Shilpashree Balakrishnan
Sent: Friday, February 09, 2007 6:23 AM
To: [hidden email]
Subject: nucleus counter

Hi,
thanks for the replies regarding the montages, am a new user, and want
to do nucleus counting in imageJ. I tried the thresholding and analyze
particle method, but it detects even a speckle that would arise by
thresholding so the error is unacceptable. So i wish to use the Nucleus
Counter but am unable to find the plugin. Could someone suggest a
solution....
 
shilpa

[Corentin Cras-Méneur-2]

On Feb 9, 2007, at 08:07 , Tony Collins wrote:

> Hi Shilpa,
>
> It's included in the bundle here:
> http://www.macbiophotonics.ca/downloads.htm
>
> This bundle includes a bunch of plugins you'll find useful -  
> especially
> if you're using the imagej for microscopy online manual.


The same page offers a "cell segmentation example script" that looks  
very interesting. Unfortunately the script comes with a .scipt  
extension and despite looking all over the place on how to use it in  
ImageJ, I couldn't figure out how to :-\
So it might be a trivial question, but could anybody let me know how  
to use a .script in ImageJ???
Thanks a million,


        Corentin

[Tony Collins-4]

Hi Corentin,

That script's for Acapella which is the acquisition and processing software for Evotec's high content screening platform.

Tony

Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Corentin Cras-Méneur
> Sent: Friday, February 09, 2007 12:42 PM
> To: [hidden email]
> Subject: Re: nucleus counter
>
> On Feb 9, 2007, at 08:07 , Tony Collins wrote:
>
> > Hi Shilpa,
> >
> > It's included in the bundle here:
> > http://www.macbiophotonics.ca/downloads.htm
> >
> > This bundle includes a bunch of plugins you'll find useful -
> > especially
> > if you're using the imagej for microscopy online manual.
>
>
> The same page offers a "cell segmentation example script" that looks
> very interesting. Unfortunately the script comes with a .scipt
> extension and despite looking all over the place on how to use it in
> ImageJ, I couldn't figure out how to :-\
> So it might be a trivial question, but could anybody let me know how
> to use a .script in ImageJ???
> Thanks a million,
>
>
> Corentin

[Corentin Cras-Méneur-2]

On Feb 9, 2007, at 12:22 , Tony Collins wrote:

> Hi Corentin,
>
> That script's for Acapella which is the acquisition and processing  
> software for Evotec's high content screening platform.
>
> Tony


OK, thanks a lot for the clarification. It certainly explains why I  
couldn't figure out how to get it to work with ImageJ…

COrentin