Fig. 1: The four-dimension spatiotemporal transcriptomic cell atlas of planarian Schmidtea mediterranea. | Nature Communications

Fig. 1: The four-dimension spatiotemporal transcriptomic cell atlas of planarian Schmidtea mediterranea.

From: Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration

Fig. 1

a Overview of the study design for multi-omics atlas of planarian regeneration. b Workflow depicting processing and content of analysis. c ST spots clustering using STAGATE according to spatial expression similarity and named by distribution characteristics. d Overlay of hematoxylin and eosin (H&E) staining of tissue sections and ST spots of each major cell type predicted by cell2location, in comparison to whole-mount in situ hybridization (WISH) staining of each cell marker. Scale bar, 500 µm. e High-resolution ST spots imputed by the deep learning procedure-based cell annotation, overlaying with H&E staining, and stacked to form a three-dimensional atlas. f Spatial distribution of major cell types with tiled spots from 20 consecutive sections. g Planarian virtual model illustrating major cell types reconstructed by Imaris. See also Supplementary Figs. 1–4.

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