**6. Conclusions**

There are only a handful of studies on pancreatic exocrine and endocrine ultrastructure in mice under diabetogenic conditions. One of the reasons for this relative underrepresentation of such a translationally relevant topic in the literature *Application of Transmission Electron Microscopy to Detect Changes in Pancreas Physiology DOI: http://dx.doi.org/10.5772/intechopen.104807*

may be the rather complex study design typically accompanying work with genetic or dietary mouse models and electron microscopy. An even more important reason may often be a lack of a toolbox to easily, objectively, and reproducibly analyze ultrastructural changes in exocrine and endocrine cells in a quantitative manner. In this chapter, we tried to specifically address this problem by providing the readers with a robust step-by-step approach and detailed instructions on how to quantify changes in the ultrastructure of mitochondria, rough endoplasmic reticulum, and secretory vesicles, as well as the presence of vacuoles, by means of shape descriptors, thresholding, manual selection, and machine-learning supported image segmentation, followed by different quantification steps employed in the opensource Fiji software. With some field-specific modifications, our analyses shall also be useful for many other life scientists.
