Hi Carl,

I am not totally familiar with ImageJ but i do know that what you are
asking can be done in MetaMorph. With MetaMorph you can manually set a
range of RGB, HSL or HSI values to threshold your colour image.
Alternatively you can click on the parts of the image you want
thresholded and MetaMorph will build up the range based on the examples
you give it.

In the past i have had great success thresholding brown BAD, red AEC
etc. I have not tried it on H and E but i can't see why it wouldn't
work.

So the question is i guess is there a plugin for ImageJ that can do the
same function?

I should note that i have no commercial tie to MetaMorph (or Molecular
Devices) but have been a satisfied user for the last 4 years.


Cheers



Cam



Cameron J. Nowell
Microscopy Manager 
Centre for Advanced Microscopy 
Ludwig Institute for Cancer Research 
PO Box 2008 
Royal Melbourne Hospital 
Victoria, 3050 
AUSTRALIA 
Office: +61 3 9341 3155 
Mobile: +61422882700 
Fax: +61 3 9341 3104 
Facility Website



-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]]
On Behalf Of Carl Boswell
Sent: Wednesday, 15 April 2009 7:49 AM
To: [log in to unmask]
Subject: Re: imagej plugin

HI All,

It's clear that I should have been more obvious about "color" in my
query. 
I'm working with H&E stained slides, so color is really color, not 
pseudocolor, and there are subtleties to the shading and density of the 
colors.
Sorry for the confusion.
carl

Carl A. Boswell, Ph.D.
Molecular and Cellular Biology
University of Arizona
520-954-7053
FAX 520-621-3709
----- Original Message ----- 
From: "Joel Sheffield" <[log in to unmask]>
To: "Carl Boswell" <[log in to unmask]>
Sent: Tuesday, April 14, 2009 12:45 PM
Subject: Re: imagej plugin


> Assuming that you have labeled your nuclei with either DAPI or
> Propidium Iodide, you can convert the color image into its three
> components and threshold the one that isolates the nuclei.  For DAPI,
> depending on your filter set, the nuclei will appear in the blue
> channel.  We have a broad band emission filter on our UV cube, so we
> also pick up a nice signal in the green channel.
>
> In a sense, you are using the color system of the camera to do a
> color separation for you (assuming, of course, that you work in
> primary colors).
>
>> Does anyone know if there is a plugin for ImageJ that will threshold
an
>> image by color?  If not, how does one segment a color image to
identify
>> particular structures, in this case nuclei?
>> Thanks,
>> carl
>>
>> Carl A. Boswell, Ph.D.
>> Molecular and Cellular Biology
>> University of Arizona
>> 520-954-7053
>> FAX 520-621-3709
>
>
> --
> Joel B. Sheffield, Ph.D.
> Biology Department, Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
> [log in to unmask]
> (215) 204 8839, fax (215) 204 0486
> http://astro.temple.edu/~jbs
>
> 

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