Use Filterstacker to analyze within a selected area?


I am pretty new at using ImageJ and I ran into a problem that I cannot get around.

I am using the DropletFinder (more precisly Filterstacker) plugin to measure the number of lipid droplets within a specefic area of my stack. The problem is that when I select the area that I want to analyze and duplicate it I use the Clear outside function to ensure that only the slected part gets analysed. However when I get to the segment analyzer, the suroundings that I previously have cleared around the area is no longer cleared and I get a sky high number of lipid droplets because lipid droplets outside the selected area is included. I have tried several ways of selecting the area, changing all the different thresholds and nothing seems to change this.

If anyone has a suggestion to what could be the problem and how to fix it I will be very gratefull!

Thanks in advance

  • Kathrine