Seeking Ideas for Threshold-Based Molecule Visualization in Seurat’s ImageDimPlot for Spatial Data

[sallyseullee-0821]

Hi Seurat community,

I’m currently working with Nanostring spatial data and am visualizing molecule expression across cell types in each field of view (FOV) using ImageDimPlot. My goal is to highlight only molecules that exceed a specific expression threshold, so that in the resulting plot, the molecule-specific dots (e.g., red dots representing INS) are visible only when their expression is above this threshold, while all cell types remain visible in the background.

Here's a sample of my code:

for(IS in unique([email protected]$slide)) { 
      for(IF in unique([email protected]$fov)) { 
      IF.sub <- subset(IP.sub, subset = fov == IF) 
      Idents(IF.sub) <- factor(IF.sub$celltype) 
      seg.xmin <- min(IF.sub$CenterX_global_px) 
      seg.xmax <- max(IF.sub$CenterX_global_px) 
      seg.ymin <- min(IF.sub$CenterY_global_px) 
      seg.ymax <- max(IF.sub$CenterY_global_px) 
      
      cropped.coords <- Crop(IF.sub[[unique(IF.sub$slide)]], x = c(seg.xmin, seg.xmax), y = c(seg.ymin, seg.ymax), coords = "tissue") 
      IF.sub[["zoom1"]] <- cropped.coords 
      DefaultBoundary(IF.sub[["zoom1"]]) <- "segmentation" 

      i <- "INS"
       f <- ImageDimPlot(IF.sub, fov = "zoom1", cols = col, alpha = 0.3, molecules = i, crop = TRUE, axes = TRUE, dark.background = FALSE, mols.cols = "red", mols.size = 1.5, nmols = 20000, border.color = NA, coord.fixed = TRUE, size = 1, mols.alpha = 1) + 
          theme_bw() + 
          theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank()) + 
          guides(fill = guide_legend(override.aes = list(alpha = 0.3))) + 
          scale_fill_manual(breaks = c("Acinar", "Alpha", "Beta", "Delta", "Ductal", "Endothelial", "Immune", "Mesenchymal"), 
                            values = c("#F8766D", "#CD9600", "#7CAE00", "#00BE67", "#00BFC4", "#00A9FF", "#C77CFF", "#FF61CC"))
   
  }
}

Currently, this code visualizes all cells and places molecule dots on them, regardless of their expression level. However, I’d like the molecule-specific dots to appear only when the expression exceeds a certain threshold, while keeping the full cell type map visible.

Is there a way to achieve this directly within ImageDimPlot? Or would any of you have alternative suggestions for threshold-based molecule visualization in Seurat?

Thanks in advance for your insights!