Improved instance segmentation of immune cells in human lupus nephritis biopsies with Mask R-CNN

Madeleine S. Durkee; Adam Sibley; Junting Ai; Rebecca Abraham; Vladimir M. Liarski; Marcus R. Clark; Maryellen L. Giger

doi:10.1117/12.2549751

16 March 2020 Improved instance segmentation of immune cells in human lupus nephritis biopsies with Mask R-CNN

Madeleine S. Durkee, Adam Sibley, Junting Ai, Rebecca Abraham, Vladimir M. Liarski, Marcus R. Clark, Maryellen L. Giger

Proceedings Volume 11320, Medical Imaging 2020: Digital Pathology; 1132019 (2020) https://doi.org/10.1117/12.2549751
Event: SPIE Medical Imaging, 2020, Houston, Texas, United States

Abstract

We demonstrate an instance segmentation method with Mask R-CNN using a ResNet-101 plus Feature Pyramid Network convolutional backbone to segment and classify T cells and antigen presenting cells (APCs) in multi-channel fluorescence confocal images. This network improves on our previous cell distance mapping (CDM) pipeline, which used a custom 10- layer convolutional neural network for cell segmentation. We have validated Mask R-CNN on two independent datasets of fluorescence confocal images: 1) mouse lymph node tissue, and 2) human lupus nephritis (LuN) biopsies. For dataset 1, mice were injected with fluorescent dendritic cells and two populations of fluorescent T cells. Mask R-CNN improved sensitivity averaged across all cell types from 0.88 to 0.94. Specificity improved from 0.92 to 0.95 across all cell types, and intersection over union score (IOU) improved significantly from 0.82 to 0.86 (p < 0.0001). Human LuN biopsies in dataset 2 were stained with two T cell markers and two APC markers, with separate staining panels to identify different populations of APCs. Mask R-CNN again improved segmentation and classification averaged across all cell types, increasing overall sensitivity from 0.72 to 0.76, specificity from 0.86 to 0.93, and significantly increasing IOU from 0.71 to 0.81 (p < 0.0001). Improved IOU scores are particularly important in CDM to be able to quantify cell shape for identification of functional interactions of immune cells. Mask R-CNN is therefore a superior method for instance segmentation of immune cells in microscopy images for image analysis of cellular function in pathological immune states.

Citation Download Citation

Madeleine S. Durkee, Adam Sibley, Junting Ai, Rebecca Abraham, Vladimir M. Liarski, Marcus R. Clark, and Maryellen L. Giger "Improved instance segmentation of immune cells in human lupus nephritis biopsies with Mask R-CNN", Proc. SPIE 11320, Medical Imaging 2020: Digital Pathology, 1132019 (16 March 2020); https://doi.org/10.1117/12.2549751

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