Re: stack threshold

Posted by Michael Schmid on Jul 09, 2007; 2:09pm
URL: http://imagej.273.s1.nabble.com/stack-threshold-tp3698921p3698922.html

Hi Cosmin,

what about converting the threshold of the first slice into a
selection
   run("Create Selection");
and then either replacing these pixels (or the non-selected ones,
using "Make Inverse", depending on your needs) by some value
that does not interfere with the analysis?
E.g. "Clear", "Fill", run("Min...", "value=255 stack"); etc.

Even without modifying the image, the selection will restrict
the area for future measurements of other slices, so just creating
the selection might be enough (e.g. if you use the histogram or
getStatistics for analysis of the stack slices).

Michael
________________________________________________________________

On 6 Jul 2007, at 21:55, Cosmin Mihai wrote:

> Hi,
>
> I have a question regarding thresholding of ImageJ stacks.
> When using the threshold comand on the first slice, the rest of the  
> stack
> is thresholded in the same limits. I am studying bleaching  
> processes and I
> am interested in eliminating from my analysis pixels above a certain
> value. The problem in the standard threshold is that the pixels  
> eliminated
> from the first slice might be reintroduced in the later slices when  
> their
> intensity falls in the threshold interval.
> Is there any way to permanently eliminate those pixels from the whole
> stack ?
>
> Thank you,
> Cosmin