Workflow to incorporate H&E image (post-Xenium) info SFE?

[dpcook]

Hi there,

I'm wondering if you have any advice on incorporating H&E images into SpatialFeatureExperiments objects--specifically images with an alignment matrix as exported by Xenium Explorer, where pixel/micron conversion and to deal with flipped y-axis coordinates.

I managed to get the aligned image in:

bbox1 <- c(xmin = 7500, xmax = 8500, ymin = -5500, ymax = -4500)

bboxes_sf <- st_as_sfc(st_bbox(bbox1))
p1 <- plotImage(sfe, image_id = "morphology_focus", channel = 3:1, show_axes = TRUE,
          dark = TRUE, normalize_channels = TRUE) +
    geom_sf(data = bboxes_sf, fill = NA, color = "white", linewidth = 0.5)

p2 <- plotImage(sfe, image_id = "HE", channel = 1:3, show_axes = TRUE,
          normalize_channels = TRUE) +
    geom_sf(data = bboxes_sf, fill = NA, color = "white", linewidth = 0.5)

cowplot::plot_grid(p1, p2, align="h")

But any functions that use a bbox to view a subset of the image fail.

> plotImage(sfe, image_id = "HE", channel = 1:3,
+           bbox = bbox1, normalize_channels = TRUE)
Error in .jcall("RBioFormats", "Ljava/lang/Object;", "readPixels", i,  : 
  java.lang.IllegalArgumentException: Invalid array size: 0 x 0 x 1 x 3

Though standard Xenium bundle images work fine:

plotImage(sfe, image_id = "morphology_focus", channel = 3:1,
          bbox = bbox1, normalize_channels = TRUE)

If you have a workflow that has worked for you, it would be greatly appreciated!