How to measure cell area?

I am trying to measure cell area for endothelial cells (red marks the cell outlines, but some are empty cavities while green marks the inside of endothelial cells). I attached a jpg of one slice. My files are czi’s with the whole z-stack and so far I’ve experimented with taking one slice and using color threshold on it, but I can’t get just the red outlines…
Another option is to just manually trace all the cells and measuring that way, but I have a lot of data, so I’m in search of a more efficient method.
Someone suggested I try CellProfiler, but I think it would be extremely difficult for me to come up with a pipeline…
I’m still a beginner so any help or advice would be appreciated.

1 Like


the image quality is really bad. The .jpg you provided does not help. Please avoid .jpgs due to their compression for image analysis:

At the moment it is very hard to say if this is possible to be analyzed automatically. I would guess that is too blurry at the moment. Try to improve optical sectioning in your images.

One can in principle detect the green cells and use the cell outline for a segmentation for example marker controlled watershed part of for example the MorphoLibJ plugin:

Hello jchan,
Use Image > Color > Split channels. And then just work with the red channel.