Fig. 3: Cell type classification model successfully identifies important cell types in inflammatory arthritis.

A Uniform Manifold Approximation and Projection (UMAP) plot after principal component analysis dimensional reduction on 856 cell features of the annotated cells (colored by cell type, n = 4,712). B A gradient boosted decision tree was trained using a parameter grid search with a nested, stratified, 5-fold cross-validation training strategy. The F1 scores (M ± SD) of the five folds for each cell class are presented with the overall weighted F1 of 0.88 ± 0.03 (M ± SD). C–E On the remaining (not-annotated) cells (~300,000) on the 9 training slides, the cell class was predicted using the most performant model. Tissue class was also predicted using the Original segmentation model. C Predicted cell class is plotted as a percent of total cells within the Fat tissue (Top) and Cartilage and Meniscus tissue (Bottom). D Representative images of Synovial tissue cell class predictions within an inflamed synovium. E Cell counts from the synovial tissue on the Healthy, Mild disease and Severe disease training slides of lymphocytes (Left), Synovial Lining Cells (Middle) and Fibroblast (Right). Each dot represents one slide, M ± SD.