The article deals with initial research into the methods of microscopic image processing methods for the study of diverticular disease. Functional and structural changes were found in tissues of persons afflicted with diverticular disease in previous medical research. The acquired images were processed manually. The goal of research into image processing methods for automatic or semiautomatic processing followed by manual supervision is to simplify and speed-up the image processing and evaluation of object parameters. The research is focused on increasing the accuracy of and speeding up the evaluation of tissue properties. ImageJ plug-ins implementing the proposed algorithms were developed for five kinds of image processing: circular muscle layer, longitudinal muscle layer, myenteric plexus layer, interstitial cells in myenteric plexus layer and interstitial cells of cajal in smooth muscle layer.