Vessels in tissue sections

cellprofiler

#1

Hi

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).

thanks

ValeriaVessels.cpproj (431.8 KB)
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#2

Hi,

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

Thanks


#3

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


#4

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


#5

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


#6

Hi ILYA,
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.
Bob


#7

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.
Untitled
1st Summary.csv (101 Bytes)
1st Results.csv (9.7 KB)
Adjustments can be made to suit the needs as to size/intensity etc…
Bob