Find Maxima ... segmentation (macro issue)

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Find Maxima ... segmentation (macro issue)

Christian R.-2
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 (value: 65535) and cytosol
markers (values: 0-32767),
which, in principle, works as a marker-based segmentation - when run
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

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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