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Single-cell sequencing and proteomics have been critical for the study of human disease. However, highly multiplexed microscopy has revolutionized spatial biology by measuring cell expression from ~50 proteins while maintaining spatial locations of cells. This presents unique computational challenges; acquiring manual annotations across so many image channels is challenging, therefore supervised learning methods for classification are undesirable. To overcome this limitation we have developed a decision-tree classifier for the multiclass annotation of renal cells that is analogous to well-established flow cytometry-based cell analyses. We demonstrate this method of cell annotation in a dataset of 54 kidney biopsies from patients with three different pathologies: 25 with lupus nephritis, 23 with renal allograft rejection, and six with non-autoimmune conditions. Biopsies were iteratively stained and imaged using the PhenoCycler protocol to acquire high-resolution, full-section images with a 43-marker panel. Nucleus segmentation was performed using Cellpose2.0 and whole cell segmentation was approximated by dilating the nucleus masks. In our decision tree, cells are sequentially sorted into marker-negative and marker-positive populations using their mean fluorescence intensity (MFI). A multi-Otsu threshold, in conjunction with manual spot checking, is used for determining the optimal MFI threshold for each branching of the decision tree. Marker order is based upon well-established, hierarchical expression of immunological cell markers created in consultation with expert immunologists. We have further developed another algorithm to probe microtubule organizing center polarization, an important immunologic behavior. Ultimately, we were able to assign biologically-defined cell classes to 1.59 million of 2.19 million cells captured in tissue.
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