Fig. 1: Spatial analysis pipeline and histopathology categorisation of samples.

a Overview of the workflow and SpOOx pipeline. The steps of the analysis are presented in Supplementary Fig. 1 in more detail. n = 677,623 single cells refer to segmented cells, without filtering for cells with no antibody staining, and ‘undefined’ clusters. IMC – imaging mass cytometry. b H&E section from COVID-19 tissue section showing formal histopathology features of alveolitis (ALV), diffuse alveolar damage (DAD) and organizing pneumonia with their corresponding MCD file image showing staining for 5 of 35 antibodies (α-SMA, EpCAM, PanCK, Col 1a and CD31). ‘a–‘c’ in figure refer to characteristic features of ALV, DAD and OP. ‘a’ - thickened alveolar epithelial wall and septae with immune cell infiltrate and congestion of alveolar walls ‘b’ widespread presence of hyaline membrane, and regenerating/proliferating Type II alveolar epithelium and ‘c’ -fibroblasts and collagen presence around bronchial epithelium. See also Supplementary Fig. 2. Representative H&E and MCD images is for ROI from n = 10 ROIs for ALV, n = 8 ROIs (DAD), n = 8 ROIs (OP); n = 12 patients. H&E staining performed once per tissue section. 37-plex staining was performed once for each lung sample. c Point when samples were obtained from the first day of symptoms and corresponding histopathology states in lung sections. Mean and S.D. shown, p value calculated using one-way ANOVA test with Tukey’s multiple comparison test; normality tested with d’Agostino & Pearson test. n = 4 patients in each histopathology group (ALV, DAD and OP). d C-reactive protein (CRP) levels closest to the point of sampling and corresponding histopathology state in lung sections. Median and IQR shown, p value calculated using Kruskal-Wallis test with Dunn’s multiple comparison test. n = 4 patients in each histopathology group (ALV, DAD and OP). Source data are provided in the Source Data File.