In many cases, identifying objects needs to be controlled by adjusting not only the threshold (which you can also set manually), but also by the size. You could try processing the image with filters first to eliminate artefacts, or you could subject your “objects” to further selection based on other criteria after identification.
This is a very simple pipeline that you could build on. I like using manual thresholds whenever I can, but make sure your images all have similar background! Using higher resolution images (if you can get them) would help too.
Zenk_BrdU_test.cpproj (527.4 KB)
The next to last module will classify the objects, I use it just to see if the pipeline actually works (I prefer working with the original intensity values, but if you set your bins to classify the cells the way you want, the exported Nuclei.csv will contain the classification info)