Vessels in tissue sections




I am new in CellProfiler and I am trying to obtain informations about the blood vessels in immunofluorescent tissue sections. I would like to know the % of area covered (per field), the number of vessels (per field), the diameter of the vessels (on this parameter I have concern mainly for the vessel with a “sling” shape as I don’t know which parameters can gave me the right result between Min Feret Diameter and Minor Axis Length), I would also try to count how many vessels have an elongated shape and how many have a “sling” shape or a hole in the middle. I am sending 2 images as example.

I wrote a pipeline but I also have issues with the pipeline as it doesn’t save the images (even if it says it does).


ValeriaVessels.cpproj (431.8 KB)



Could you please upload your images again. Images should be either 8 or 16 bit.



Valeria, did you ever solve this issue? I am trying to do something very similar!


Valeria and Ilya,
Do either or both of you also have access to Fiji/ImageJ?
If so it is very possible.


Right now I am using a processed dataset from Definiens, with defined cell centers, areas, and marker intensities. Would it be possible to use this data for the task? Otherwise, I could get ImageJ


I would have to see the data first to determine this but you should get ImageJ just to do in-between type of things.
I took the example images and got quite good results so I will send them shortly for you to inspect.


Hello again,
Due to the format of the image I had to sort of “steal” it and also split it in two so the accompanying image and data are from only the top part. I also have the bottom part is you would like.
1st Summary.csv (101 Bytes)
1st Results.csv (9.7 KB)
Adjustments can be made to suit the needs as to size/intensity etc…