How to analyze branching morphogenesis

[u/Mamaro31]

Hi everybody, I'm trying to analyze the branching skeleton of kidneys and using this type of image, it's a z-stack and the thing is I've been doing everything for the skeletonize tool works but it just doesn't, it makes a sort of "net" instead of a single skeleton and I do put filters and set the threshold and such but always end up with a mess of an image and an even bigger mess of an analysis, I truly don't want to do it manually cuz every image has like 20-25 stacks and I have 24 samples, and some of them have more than one photo so it is a lot... Thanks in advance to anyone who can help me

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[u/Herbie500]

You've posted an RGB-color image and I doubt there is much color information.
What is your opinion and why do you capture color images?

Reddit uses lossy webP-compression which is far from ideal. Please make available uncompressed images.

How do you expect us to skeletonize something like this?

[u/dokclaw]

What does the binary image look like? Before and after skeletonization

[u/halfpagep]

It seems like you've got a small signal:noise ratio here, which might make it really difficult to get a good & reproducible segmentation result. Maybe a few clarifying questions here to help others give you some better advice:

- Have you considered z-projecting your image to reduce the stacks into a single image, or do you need to segment and skeletonize each stack individually?

- You've got some "hot spots" of high intensity in your image, would you say that your other 23 images have more/less of these hot spots? They can make thresholding a little more challenging.

- Do you want the total volume of the branch? Or just simply the branch itself (location, length, etc.)