Anne was so kind directing me to this forum. Thank you!
Here is my problem:
I have two stacks of histological aligned images. One stack includes a structure protein witch is a marker for blood vessels. The other one witch is colocalized to the first one is a protein that is found embedded by the blood vessels. I allready thresholded my images and did some particle area measurements with ImageJ.
But now I want to do the following:
I want to measure the area of every vessel cross-section and put this in a relation to the total area of the embedded protein in every single cross-section. I thought of your software because of the chance of interpreting the vessel cross-sections as cells that contain structures like a nucleus, in my case the embedded protein. And then calculating a nucleus-cytoplasm-relationship and absolute values. Unfortunately in some vessel cross-sections there is more than one embedded protein particle and a the total amount has to be calculated.
Anne recommended me to illustrate my problem with some images:
stack with vessel cross-sections:
stack with corresponding embedded proteins:
Thank you very much for your advice !