Background subtraction


I need to analyze the microvessels in this image but imagej keeps picking up the background. I tried to adjust the contrast and using the subtract background settings but it still isnt working. I was wondering what else I could try. Thanks!

Hi @Pat_Jas

Welcome to the Forum!

Let’s start getting you some help… but first can you answer these questions for us? A little more information is needed to better assist you…

  1. What is a microvessel in this image? Can you tell us what they should look like? (Not all of us on here are biologists or if we are, we aren’t necessarily looking the same types of samples, etc. - so be as specific as you can.)
  2. Adjusting Brightness & Contrast is only for rendering purposes, so this will not change your analysis results/calculations. What is the exact procedure you are currently applying?
  3. When you say “the subtract background isn’t working…”, what exactly do you mean? You are getting a ‘bug’ in the software or the results just are not what you want?

Also - if you can post the raw image/dataset (as opposed to this .png file) - that would be ideal. :slight_smile:

To get more familiar with Segmentation in ImageJ/Fiji, here are some helpful links:

Hope this helps!

eta :slight_smile:



I am also curious to see if you could circle or show what the microvessel is.


The standard way of counting blood vessels is to label them properly with some immunohistochemical marker like e.g. anti-factor VIII antibodies. If you do not do that you do not know what you are counting. Presence of red blood cells in them is not guaranteed as they might have been washed away during preparation. There is a lot of literature on this.