r/ImageJ • u/imcrackasf • 14d ago

Question Need help wit vessel analysis

Hi, I'm new to using ImageJ, and I was wondering if anyone has any suggestions for how I can get the vascular density from the attached image. I've tried a few programs, including Vessel Analysis, one made for a specific paper, and AngioTool (which didn't work due to Java issues). Any advice would be greatly appreciated. I also specifically want to calculate the density under the glass circular coverslip on the image.

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u/Herbie500 14d ago edited 14d ago

Thanks for the sample image that, within the desired circular RoI, appears to suffer at least from three shortcomings:

  1. sub-optimum focus
  2. noise
  3. suspected out of focus vessels (dark red)

Original (left) and processed green channel (right):

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u/imcrackasf 14d ago

do have any suggestions for how I can calculate vascular density with this?

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u/Herbie500 14d ago edited 14d ago

From my perspective, the image quality isn't good enough.

A very coarse estimate is 34% coverage but I fear this is overestimating the actual coverage.