I am relatively new to image analysis in ImageJ, but I am trying to analyze images with structures that contain a lumen. I’m interested in obtaining the area of all of the structures including the lumen.
However, I’m having troubles setting thresholds because the lumen is difficult to discriminate from the background for example by brightness.
I realize I could threshold the borders than -Close and Fill Holes, but this way I will also include the space between different structures that are close together.
Any suggestions on what would be a good way to start?
The image I will upload in second post is a Tiff, where I already subtracted background and improved brightness/contrast (auto).