Immuno-oncology and transplantation medicine share the medical need for robust, immune cell-based biomarkers extracted from tissue biopsies. In an interdisciplinary approach, the Tissue Phenomics methodology is applied to mine clinically annotated image data. We provide proof-of-concept that spatial distribution of immune cells can provide valuable hints towards novel transplantation biomarkers. Correlating spatial immune cell patterns in protocol biopsies with the yearly loss of Glomerular Filtration Rate (GFR), we show that features, previously not considered to be of prognostic value, can be discovered. The potential of Tissue Phenomics technology to exploit the full predictive power of image based-information is currently investigated in the disease-overarching SYSIMIT consortium.