I have been recently using bfconvert to convert some of our whole slide images to ome-tiff format for use in QuPath. For the first set of images I have been converting it has worked very well (all greater than 2 gb, native tiff). For a second set (same format, smaller than 2 gb), after conversion that output doesn’t appear to be a true ome-tiff. I first noticed while trying to extract xml using tiffcomment, but can also see this using showinf. I am using bfconvert 6.5.1. I have pasted showinf data below on both input and output images for the image that doesn’t appear to convert to ome-tiff as well as the one that does. I feel like I must be missing some pre-requisite in the one case but not the other, but am not sure what that might be.
I am calling bftools as:
bfconvert -noflat -bigtiff -pyramid-resolutions 4 -pyramid-scale 2 input.tif output.tif
Any help would be greatly appreciated.
Image that is not converting to ome-tiff but instead just as tiff:
Image after conversion (file format shows as TIFF):
Image that is converting properly to ome-tiff:
Image after conversion (file format shows as OME-TIFF)