Bfconvert of SVS files - unexpected result

Hi OME team,
I’m trying to use bfconvert (version 6.5.0) to convert Aperio .svs files into ome.tif (so we can distribute them in a standard format and so I can stick additional metadata into the OME-XML header). These are regular H&E SVS images in RGB just like the public test image at ( with a label and a macro image.
bfconvert yields a correct “main” image with pyramid levels but the label and macro image in the output ome.tif file are actually additional copies of the main image (without pyramid levels). Thus the output file is unexpectedly large and there is no label or macro image.

Just FYI: I was trying the bioformats2raw/raw2ometiff tools as well and those have an entirely different set of issues with these same SVS files as I reported via their github site


This is very likely a bug that was introduced in BF Tools 6.4.0, we have an open PR ( which will hopefully lead to it being resolved in the next release. As a work around using the command line tools from 6.3.1 ( should enable you to convert without this problem.