Error while reading reading 10x Xenium Ranger based "tif" files #3
Description
Very nice tool. !!
I'm working with Xenium-based 10x data and have outputs from Xenium Ranger that I'm trying to read along with Xenium TIFF files. Here's my current approach:
tenX_output_dir <- "10X_Dataset/Rep1_outs/"
tenX_output_tif <- "10X_Dataset/Rep1_outs/morphology.mip.ome.tif"
spe_10x <- readXenium(tenX_output_dir, tiff_path = tenX_output_tif)
It give me error :
Error in readTIFF(tiff_path, as.is = TRUE): unable to open /10X_Dataset/Rep1_outs/morphology.mip.ome.tif
After further investigation, I found that it requires an "output" TIFF file from BIDCell. In my case, I also want to compare the "marker purity metrics" from the 10x-based segmentation results.
Could you please suggest how I can make the TIFF file compatible with the readXenium function in the CellSPA method?