Figure 2
SADIE Analysis Identifies Rare Cell Types and Follicular Architectures. SADIE-guided workflow for cell annotation refinement, in which channels are initially screened in a quality control step. Aggregation values (Ia) are then obtained for each channel in the architecture of interest. High Ia-value channels are selected and supplemented with known canonical markers (parameter selection) for annotation refinement (A). An example 7-channel fluorescent image of a proliferating UC B-cell follicle (B). Scale bar = 300 µm. Note the honeycomb-like profile of membrane markers that results in segmentation difficulties and “bleed” into adjacent cells. Nonetheless, by directly incorporating spatial coordinates for further annotation refinement, we are able to re-annotate cells that appear to have been mis-clustered ((C), red arrow). Data space is visualized using a UMAP reduction (C). The result of SADIE-guided parameter selection and subsequent annotation refinement is displayed on the associated Voronoi image, demonstrating the successful annotation even of rare cell types (D). Associated cellular neighborhoods are displayed in their Voronoi representation (E). Pairwise interactions, in which the size of each circle represents the fraction of all cells and the width of the line represents the thresholded ratio of interactions (F).
