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Re: Analyzing adjacent ROIs

Posted by Alexander C. Taylor on Mar 24, 2011; 3:48pm
URL: http://imagej.273.s1.nabble.com/Analyzing-adjacent-ROIs-tp3685285p3685286.html

It's not our best image, just an example of the type of tissue we're looking at. I agree that the morphology shown here could pose some issues, and we're still looking at ways to remedy those or find ways of analysis that those issues won't hinder. There are some knife marks and shrinkage, and the staining is uneven on some of the early slides. This was a section we used to develop our staining procedure, but some of the final images do have similar, albeit less dramatic (fortunately), detriments.

I'm not too familiar with general problems affecting measurement of histological staining; I'll look around for posts on those to learn more. Thanks for the tip.

Fortunately we're not looking at cortical bone, just at the marrow. I probably should have mentioned that in my last post, come to think of it. I'm just trying to get a not-terribly-sophisticated measurement of whether staining intensity has some sort of gradient from the middle of the marrow to the edges or vice versa, which if it exists, will affect the direction of our study. Using ImageJ, I have been able to Set Threshold so that only areas of staining are highlighted, so there's that.

I apologize for not posting one of the higher quality images; my P.I. wouldn't condone posting those online. But as long as I can get some idea on how to work with this type of tissue section and look for a gradient, we should be able to find what we're looking for.