Hey,

Select the wand tool and adjust the threshold; in the dense core region, select low tolerance and analyze; this worked for my cancer IHC images, and I hope it will work for you.

You can try to use the Analyze Particles to build a binary mask based on threshold and size (assuming your dense-core plaques have higher intensities), it should create a binary image only with your dense-core plaques selected and after that you probably want to use the ROI manager to add regions of interest based on that mask to your original image so that you can measure each plaque intensity individually. To analyse the diffuse plaques you will need a mask similar to what you did above, but with a different threshold and maybe a different size range, and the rest of the procedure is similar. You can always subtract masks on imageJ, so creating a binary image that selects all your plaques and subtract the mask for the dense-core can also work fine to have the mask for the diffuse plaques only. Finally, there's a relatively new segmentation plugin called labkit (https://imagej.net/plugins/labkit/ ) maybe it could help you make the process more automated 😊