Fig. 2: Characteristic markers and cell type assignments for clusters of nuclei detected in IMC.

a Heatmap showing relative mean intensities of marker expression (columns) in each identified cluster (rows). Markers were grouped based on their cell-type specificities (see top of plot, “cell type marker”). Their relative intensities in each cluster were used to assign clusters to cell types (see left of plot, “assigned cell type”). b Final assignment of neuronal and glial cell types to each cluster, with main markers expressed by each cluster indicated on the right. c Observed and expected proportions of astrocytes, oligodendrocytes, and microglia relative to the total glia population (left) and of excitatory (which include unclassified neurons) or inhibitory neurons to the total neuronal population (right) in the CtrlCV samples (sections from n = 6 brains). d Distributions of cells from each cluster within the 6 cortical layers (CtrlCV samples only), normalised by total numbers of nuclei per layer. Cell type and layer assigned to clusters are indicated in the coloured “Assigned cell type” and grey “Assigned layer” boxes above, respectively. Quantification was performed on three ROIs acquired from a single section of each sample and pooled together. Boxplots in (c) show median (middle line), interquartile range (box), and variability outside of first and third quartiles (lines extending from box). Source data are provided as a Source Data file. Scale bars in (d) represent 100 μm.