Overview of the experimental workflow, cell segmentation and QC metrics. (IMAGE)
Caption
Figure 1. Overview of the experimental workflow, cell segmentation and QC metrics. (a) Schematic representation of the technical workflow, from post-mortem lung tissue collection to downstream analyses. All steps were carried out separately for COVID-19 and control samples before pooling of the data during downstream analyses; (b) Representative immunofluorescence images of FOV 16 from COVID-19 slide (left) and FOV 23 from Control slide (right), of nuclear stain DAPI (blue), cytoplasmic stain CD298/B2M (white), CD68+ macrophages (Mac, red) and pan-cytokeratin+ epithelial cells (Epi, green) present alongside the subsequent cellular annotation of FOV; (c) Cell numbers per condition represented by a barplot and cell numbers per FOVs within each condition represented by a boxplot; (d) Violin plots depicting gene and transcript numbers of each sample (width = abundance of cells); (e) UMAP plot of CosMx output. Endo: endothelial cells; Fibro: fibroblasts. FOV: field of view; COVID-19: coronavirus disease 2019; UMAP: Uniform Manifold Approximation and Projection; DAPI: 4’,6-diamidino-2-phenylindole.
Credit
© Thomas Marichal, Coraline Radermecker, et al. 2026. This is an Open Access article licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing, adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
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