Fig. 1: Distinct regional collagen organisation in the fibrotic lung influences KRT5⁺ BC distribution.

a Lung tissue sections from control (n = 5) and IPF (n = 8) donors were imaged using a ZEISS 880 2-photon microscope with spectral detection, and linear unmixing of autofluorescence and second harmonic generation (SHG) signals. Schematic created with BioRender.com. Representative images of distal lung tissue from b control (n = 5), and c IPF (n = 8) donors with overview (upper panels) and regions quantitively analysed (lower panels). White arrows marking single KRT5⁺ BCs within IPF matrix in c. Regions included alveolar (ALV), honeycomb cyst (HC), fibrotic (FIBRO), airway (AW), peribronchial (PB) and perivascular (PVS). d KRT5⁺ BCs counted per image area; each data point represents the average of 2–6 images per area per control (n = 4) and IPF patient (n = 8 for PB, PVS, ALV, FIBRO and n = 6 for HC). Data plotted as mean ± SEM. e Principal component analysis (PCA) of collagen intensity, density, orientation and GLCM parameters for each region for controls (CTRL) vs. IPF patients. Quantitative image analysis per region showing f collagen density (Control PB vs. Control ALV, P value = 0.0007; IPF PB vs. IPF PVS, P value = 0.0017; IPF PB vs. IPF FIBRO, P value = 0.020; IPF PB vs. IPF ALV, P value < 0.0001; IPF ALV vs. IPF HC P = 0.0295) g coherency (IPF PB vs. IPF FIBRO, P value = 0.0044; IPF PB vs. IPF PVS, P value = 0.0012) and h entropy (Control PVS vs. Control ALV, P value = 0.0011; IPF PVS vs. IPF HC, P value = 0.0386; IPF PVS vs. IPF ALV, P value = 0.0034; IPF ALV vs. IPF FIBRO, P value < 0.0001, IPF FIBRO vs. IPF HC, P value = 0.0018). Each data point represents the average of 2–6 images per area per control (n = 5) and IPF patient (n = 8 for PB, PVS, ALV, FIBRO and n = 6 for HC). Data plotted as mean ± SEM. Ordinary one-way ANOVA with Tukey’s multiple comparisons test ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05. Spearman correlation analysis between i collagen density and KRT5⁺ BC numbers and j collagen coherency and KRT5⁺ BC numbers in distal lung tissue from IPF patients. Each data point represents the average of 2–6 images per area per IPF patient (n = 8 for PB, PVS, ALV, FIBRO and n = 6 for HC). Two-tailed P value reported. Linear regression of correlation analysis with best- fit line and 95% confidence bands shown. Source data are provided as a Source Data file.