It might be possible to come by to the office, but first I'd like to see what you already have. What are your images, what is the segmentation (it can be saved in the IQO file, measurement options).
"embeddeness" measurement maybe measured after dilating of the objects and measuring co-localization, though it might be tricky.
If you export to Excel only the last data, then you export a wrong table. You should collect data from every image to Data Collector, and then in the end you export Data Collector table to Excel.
You can send me the images, screenshots and options files to firstname.lastname@example.org