time series threshold

[smh73]

Hi,

I am trying to use multi-measure to measure all pixels above a certain threshold in a time series stack. The problem is that the threshold slider only allows you to set the maximum to the maximum pixel in the current slice. If there are brighter pixels in other stacks, they are excluded.  Even if I manually enter a larger treshold, it immediately reverts to the max for that slice.

I cannot use analyze particles (this could work with the "include holes" setting) because the pixels are not always contiguous.

Anyone know how to get around this?

Thanks!
Michael

[ved sharma-2]

Hi Michael,

I had a similar problem, and the way I resolved it, was as follows:

1. Find the slice which has the global max pixel value (I wrote a little macro to do that quickly for me).

2. while on that slice, click threshold. Now you would be able to set the upper threshold value to the global max value, if it is not already set.

3. Instead of multi-measure, run the following code in a macro. Make sure that "Limit to threshold" is checked under "Set Measurements...".

-----------------------------------
       for (i=1; i<=nSlices; i++) {
          setSlice(i);
          run("Measure");
      {
-----------------------------------

Hope it helps.

Ved

-------------------------------------------
Ved Sharma, Ph.D.
Dept. of Anatomy and Structural Biology
Albert Einstein College of Medicine
Bronx, NY 10461