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
>
>