I am using bftools to convert MetaMorph .STK files to OME.TIFF and OME.XML. Now I would like to skip the conversion to OME.TIFF and just keep the XML file. This doesn’t seem to be possible without dumping the binary data and then removing it from the resulting XML. Here’s what I am using:
bfconvert file.stk file.ome.xml
xmlindent file.ome.xml > file.xml
The resulting xml file has a tag for each z-slice in the original STK file, but it’s incredibly inefficient to do this when I just want the XML.