This chapter presents several case studies, each based on a published journal article. The case studies include questions on the article itself and activities using ImageJ, in which image processing related to the subject of the article is performed. The case study article concentrated on manual segmentation of two brain structures, the hippocampus and the amygdala. Fully automatic segmentation would be very challenging because of the complexities of the anatomy, small size and low image contrast. The definition of the anatomical structure may vary from laboratory to laboratory. In practical studies, it is necessary to compare results of segmentation with a reference segmentation. In a few cases, for example, with synthetic data and phantoms, this is the ground truth. To investigate intraobserver reproducibility repeat the segmentation of PDw.tif and the comparison with the binary reference image.