Re: brown staining

Posted by Toby Cornish on Sep 24, 2007; 1:54am
URL: http://imagej.273.s1.nabble.com/Brown-staining-tp3698345p3698346.html

Zhengyu,

I have considerable experience using ImageJ to quantitate brown (DAB) IHC staining on TMAs.

If you aren't familiar with the HSV colorspace, please refer to wikipedia. There is an excellent article on colorspaces.  Brown, unfortunately has a broad absorbance spectrum and therefore the hue value stretches across the hue range.  I can recommend colorspace inspector and color segmentation plugins to help understand how brown pixels can be segmented using HSV colorspace segmentation (G. Landini's threshold color). links here:

  http://rsb.info.nih.gov/ij/plugins/color-inspector.html 

  http://www.dentistry.bham.ac.uk/landinig/software/software.html 

At JHU we have produced an application (using ImageJ libraries) for HSV-based quantitation of IHC staining, FrIDA.  You can test it here:

  http://bui2.win.ad.jhu.edu/frida/ 

and source is available from sourceforge (the project name is fridajhu).

I have used both color deconvolution and HSV colorspace segmentation for IHC quantitation, and I have ImageJ macros for performing color deconvolution as well.  There are caveats with both methods, the discussion of which would be off topic in this forum.

Please contact me if you need additional assistance.

toby


Toby C. Cornish, M.D., Ph.D.
Pathology Resident
Johns Hopkins Medical Institutions
[hidden email]