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

Rebecca Abraham; Madeleine S. Durkee; Margaret Veselits; Junting Ai; Jordan D. Fuhrman; Marcus R. Clark; Maryellen L. Giger

doi:10.1117/12.2577788

5 March 2021 Application of U-Nets for the automatic segmentation of immune cells in high-dimensional microscopy images of kidney biopsies

Rebecca Abraham, Madeleine S. Durkee, Margaret Veselits, Junting Ai, Jordan D. Fuhrman, Marcus R. Clark, Maryellen L. Giger

Author Affiliations +

Proceedings Volume 11647, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XIX; 116470N (2021) https://doi.org/10.1117/12.2577788
Event: SPIE BiOS, 2021, Online Only

Abstract

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.

Conference Presentation

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Rebecca Abraham, Madeleine S. Durkee, Margaret Veselits, Junting Ai, Jordan D. Fuhrman, Marcus R. Clark, and Maryellen L. Giger "Application of U-Nets for the automatic segmentation of immune cells in high-dimensional microscopy images of kidney biopsies", Proc. SPIE 11647, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XIX, 116470N (5 March 2021); https://doi.org/10.1117/12.2577788

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