Issue with image path using readXenium()

[NJNataren]

Hi guys,

Thanks for your essential package!
I am trying to read in some very recent Xenium data using readXenium(), but am getting the following error:

`sfe <- readXenium(s1, add_molecules = TRUE) #s1 is just the path to my data

Error in .get_imgData(img_fn[1], sample_id = sample_id, image_id = "morphology_focus", :
img is not a valid file path.`

Below is the traceback():

traceback()
6: stop("img is not a valid file path.") at image.R#900
5: .get_imgData(img_fn[1], sample_id = sample_id, image_id = "morphology_focus",
flip = (flip == "image")) at read.R#1118
4: .get_xenium_images(data_dir, image, major_version, flip, max_flip,
sample_id) at read.R#1213
3: force(value) at operator.R#127
2: c(img_df, flip) %<-% .get_xenium_images(data_dir, image, major_version,
flip, max_flip, sample_id) at read.R#1213
1: readXenium(s1, add_molecules = TRUE)

How would one get around this?

Would this be related to the latest XOA v4 as this user suggested?

Thanks in advance.

[NJNataren]

Looking into this further, and with help from the clue provided by Issue #82, for now I have worked around this very crudely by creating symlinks for the new channel names with the syntax that your package expects:

ch0000_dapi.ome.tif --> morphology_focus_0000.ome.tif
ch0001_atp1a1_cd45_e-cadherin.ome.tif --> morphology_focus_0001.ome.tif
ch0002_18s.ome.tif --> morphology_focus_0002.ome.tif
ch0003_alphasma_vimentin.ome.tif --> morphology_focus_0003.ome.tif

I was able to create the object:

sfe <- readXenium(

• s1,
• row.names = "symbol",
• add_molecules = TRUE)

Must use gene symbols as row names when adding transcript spots.
Preprocessed sf segmentations found
Reading cell and nucleus segmentations
Reading cell metadata -> cells.parquet
Reading h5 gene count matrix
filtering cellSeg geometries to match 26396 cells with counts > 0
filtering nucSeg geometries to match 25344 cells with counts > 0
Reading transcript coordinates
Converting transcript spots to geometry
Writing reformatted transcript spots to disk
Total of 3 features/genes with no transcript detected or min_phred < 20 are removed from SFE object
To keep all features -> set min_phred = NULL