The kidney continuously filters blood in the human body. The functional unit of the kidney, the glomerulus and its filtering cells, the podocytes, play an important role in this filtration process. Therefore, we particularly study the morphological changes to podocytes and glomeruli in various chronic kidney diseases from immunofluorescence and histopathology images of kidney biopsies by using deep learning-based segmentation networks. We are interested in classifying the different diseases, evaluating their stage and predicting disease progression for individual patients, as well as advancing the understanding of disease mechanisms.