Journal: EBioMedicine

Article Title: Distinct lung cell signatures define the temporal evolution of diffuse alveolar damage in fatal COVID-19.

doi: 10.1016/j.ebiom.2023.104945

Figure Lengend Snippet: Fig. 2: OPTIMAL analysis of single cells in COVID19 PM lung tissue reveals a progressive loss of lung air space leading to elevated cellularity due to tissue obliteration rather than a de novo cellular influx. a) PM lung tissue slides were stained with a panel of 40 metal tagged antibodies alongside an additional control TMA slide (1). The pathologist-marked ROIs were then set using an OMERO reference image and ablated using a Hyperion IMC system (2) to produce a set of 41 multispectral images (3) that were segmented to single cell data (4), corrected for spill-over and other factors that could affect clarity (5) and converted to FCS file format with additional key metadata added (6). Batch effect was determined and corrected for using a z-score normalisation approach (7). b) A PacMap dimensionality reduction plot for all 901,602 single cells representing ∼195 mm2 of COVID19 PM lung tissue. c) Cell counts per mm2 of the ablated ROI area for each of the 8 pathology classes. d) A graph showing the % of air space within each ROI as a function of pathology class. e) A graph of the cell counts per mm2

Article Snippet: The H&E-stained primary slide from each serial deck was scanned onto the open-source digital online pathology platform OMERO (‘The Open Microscopy Environment’).

Techniques: Staining, Control