Application of U-Nets for the automatic segmentation of immune cells in high-dimensional microscopy images of kidney biopsies

Lupus nephritis (LuN) is an inflammatory kidney disease characterized by the infiltration of immune cells into the kidney, including T-cells, B-cells, and dendritic cells. Here, we combine high-dimensional immunofluorescence microscopy with computer vision to identify and segment multiple populations of cells. A U-Net was trained to segment CD4+ T-cells in high-resolution LuN biopsy images and subsequently used to make CD4+ T-cell predictions on a test-set from a lower-resolution, high-dimensional LuN dataset. This produced higher precision, but lower recall and intersection over union for cells in the low-resolution dataset. Further application of U-Nets to immune cell segmentation will be discussed.