I tryed to count immunohistochemically stained (DAB not fluorescence) neurons in brain slices. The Problem is that the background within the slice is not always equal and that the staining intensity sometimes differs. Is there a module which identifies objects (e.g. neuron) relatively to it’s respective surrounding (and not a general threshold)?
E.g: A neuron has a diameter between 8 and 20 pixels and is 0.2 to 0.3 values darker (or brighter, if inverted) than it’s surrounding.

thanks for your help!


My apologies for the delayed response to your question. If you wouldn’t mind, please post a sample image on a publicly available website. It is much easier to help you if we can see an example image.

thank you,


Also, check and see whether this thread answers your question about detecting objects given a varying background:
Identify cells by analyzing its surrounding?)

Keep in mind, also, that CellProfiler is optimized for fluorescence images and we have not extensively used it on histology samples.

Keep us posted,