Nanostring-Biostats / SpatialOmicsOverlay

Tools for analyzing data on the image from NanoString GeoMx Digital Spatial Profiler (DSP).
MIT License
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Error for readSpatialOverlay() - Error in .jcall #59

Open ybaeus opened 1 month ago

ybaeus commented 1 month ago

readSpatialOverlay() throws me an error for one of the TIFFs while another TIFF I was successfully called in R. Do you have any idea how to fix the issue? (I am not familiar with TIFF files and any information would be really appreciated)

muHepat_slide1 <- readSpatialOverlay(ometiff = "/active/minkah_n/Aditi/Nanostring_DSP/OME_TIFF/slide1_correct_7_31_24.ome.tiff", 
+                               annots = muHepat_LW, 
+                               slideName = "slide1_", image = FALSE,  
+                               saveFile = FALSE, outline = FALSE))
**Extracting XML
Error in .jcall(.jcall("RBioFormats", "Lloci/formats/meta/MetadataStore;",  : 
  java.lang.NullPointerException: Cannot invoke "loci.formats.tiff.IFD.getImageWidth()" because "subifd" is null**
github-actions[bot] commented 1 month ago

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