This is also the approach we have taken.
Use a macro to activate/grab an ROI from the ROI manager, duplicate it, and threshold it. If your ROI is not a square (ie., it's a polygon), do the same thing, but you can clear the outside of the ROI and then perform your threshold analysis.
Best,
Dave
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Ed Simmons
Sent: Monday, October 28, 2013 4:43 AM
To:
[hidden email]
Subject: Re: Thresholding in an area of interest
On 27/10/13 22:21, davidzhuodavid wrote:
> Hi guys,
>
> I've got a problem working with my ImageJ. Generally the problem is
> with non-uniform illumination so the result is bad if I threshold the
> image as a whole. I tried to select an area and threshold in this
> small area but I failed. Is there a way for me to threshold in a
> specific area that I selected rather than threshold in the image as whole? Thank you!
>
>
I have a similar situation where I needed to make a binary image to analyse, the source image contained three regions that required different settings to obtain a good result - in the end, I duplicated the image once per region and thresholded at different settings to ensure I was successful in getting all the features of interest. This is easiest as a macro/plugin...
To correct for illumination irregularity, you should probably be making use of flat-field correction to obtain an easier image to work with.
You could threshold the image as needed for your region of interest, then run whatever analysis you need only inside the ROI, but this doesn't seem as neat as correcting for the uneven illumination.
I hope that helps...
Best regards,
Ed
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Ed Simmons
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