Differentiating neurons from dendrites



Hi there,

I’m trying to count fluorescent cells in various parts of the hippocampus, but I have some problems with differentiating between neurons and dendrites. I am interested in the number of fluorescent neurons that are present, but my CellProfiler pipeline also detects some dendrites (which were also a bit labeled by the fluorescent marker that I used) and I can’t seem to get rid of these.

Can anybody help me with this? Attached are both one of the images I am trying to analyse, as well as the pipeline I am currently using.

With kind regards,

TdTomato Lennart.cpproj (513.3 KB)



Can you please upload image again with bit depth either 8 or 16?



I tried it, saving it on my computer as 8 bit or 16 bit depth works fine but if I try to upload it here I get an error message saying ‘We cannot determine the size of the image, it might be compromised’…



I can’t open it either. Is it possible to share with me with Google Drive?


@Lennart, is this what you’re going for?

The increasing gradient of dendrite density from the top of sample to the bottom can be overcome by adaptive thresholding and some tuned morphological operations. The size of structuring elements used in this pipeline could be sensitive to variation across other images in your data set.

Thanks! forum6114.zip (456.9 KB)