How to count positive cells on cellprofiler

I try to identify nuclei by hematoxylin staining.But cellprofiler seems to recognize a weird area other than nuclei.
This is the original photo

This is the result:

counter-1.pipeline.cppipe (6.3 KB)

Could someone help me figure out this?
Thankyou so much!



I seems to ask a silly question.I figure it out now…

How did you solve the problem? I’m having problems using the Align module as well, would be great to hear how you got it to work.

I just try to identify nuclei.As to alignment,I think cellprofiler takes a long time.So I haven’t figure it out.