Fig. 1: Overall outline of study, the regenerating alveolar niche in IPF lungs and its cellular constituents.

a–k overall workflow of study from macroscopic selection of lung biopsy (b) to final analysis (k). l Representative ROIs from lung sections obtained in Early, Intermediate (Intm) and Advanced (Adv) lung regions (see b) showing histopathology features (e.g., collagen deposition, alveolar metaplasia, inflammatory infiltrate and smooth muscle hyperplasia) and matching MCD images stained with metal tagged antibodies—five of 33 markers shown. Lung sections are representative of n = 19 Early, n = 20 Intm and n = 14 Adv ROIs. Staining performed once. m Representative ROI from an H&E-stained IPF lung section showing criteria for ROI selection (presence of AT II metaplasia, immune cell infiltrate and lack of airways). n Metal-tagged antibody panel used for Imaging Mass Cytometry (IMC) staining (o). UMAP (front and back of 3 dimensional projection) of annotated cell clusters derived from 33 plex IMC staining. H&E hematoxylin and eosin, FFPE formalin fixed paraffin embedded, AT II type 2 alveolar epithelial cells, Neut neutrophils, mac macrophages, mono monocytes, SM smooth muscle, ABI aberrant basal intermediates. Hereon, where relevant, Early stage is depicted by green colour, Intm by blue and Adv by red.