(a) UMAP projections of the manifolds reconstructed by SAM, PCA, and Seurat. SIMLR outputs its own 2D projection based on its constructed similarity matrix using a modified version of t-SNE. The schistosome cells are color-coded by the stem cell subpopulations μ, δ’, εɑ, and εβ determined by Louvain clustering. (b) UMAP projections with gene expressions of subpopulation-specific markers (eledh, nanos-2, cabp, astf, bhlh,) and a ubiquitous stem cell marker, ago2-1, overlaid. Insets: magnified views of the expressing populations. (c) FISH of cabp and EdU labeling of dividing stem cells in juvenile parasites at 2.5 weeks post-infection show that μ-cells (cabp+EdU+, arrowheads) are close to the parasite surface and beneath a layer of post-mitotic cabp+ cells. Dashed outline: parasite surface. Right: magnified views of the boxed region. (d) FISH of cabp and a set of canonical muscle markers, troponin, myosin, tropomyosin, and collagen, shows colocalization in post-mitotic cabp+ cells. Images in (c–d) are single confocal slices. (e) FISH of astf and bhlh shows their orthogonal expression in adjacent EdU+ cells (arrowheads). Bottom: magnified views of the boxed region. Image is a maximum intensity projection of a confocal stack with a thickness of 12 µm. (f) UMAP projection of stem cells isolated from juveniles at 2.5 and 3.5 weeks post-infection. Cell subpopulation assignments based on marker gene expressions are specified. Right: a magnified view to show the mapping of εɑ- and εβ-cells. (g) Standardized dispersions as calculated by Seurat plotted vs. the SAM gene weights. (h) SC3 AUROC scores plotted vs. the SAM gene weights. Error bars indicate the standard deviation of SC3 AUROC scores between trials using different chosen numbers of clusters. In (g) and (h), the top 20 genes specific to each subpopulation are colored according to the color scheme used in (a).