Find Maxima ... segmentation (macro issue)

Posted by Christian R.-2 on
URL: http://imagej.273.s1.nabble.com/Find-Maxima-segmentation-macro-issue-tp5023746.html

Hi all,

I've run into an issue when running the "Find Maxima..." segmentation algorithm by Michael Schmid:
Basically, running the segmentation from a macro produces different results than a manual run -
from the same image, with the same parameters provided.

Parameters: "prominence=32767 strict above output=[Segmented Particles]"

The image is a 500x500 px overlay of nuclei (values: 0, 65535) and cytosol markers (values: 0-32767),
which, in principle, works as a marker-based segmentation - when run manually.
But it looks like a marco run produces additional particles, which are lines with a width of single pixels.
I've tried to exclude those additional particles with the Analyze Particles... with size or circularity limits,
but unfortunately that also excludes valid results (particles derived from maxima).

Could I run the "Find Maxima..." segmentation from the macro in Java or JS as a workaround / for testing?
(I've consulted the ImageJ documentation, but unfortunately my understanding of ImageJ is still too limited.)

I'd like to troubleshoot this issue, since it's currently a roadblock in my image processing pipeline.


Thanks in advance,
Christian R.

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