BioFormats DICOM WSI reader problem with nested Pixel Data in private data element and/or offset tables

[dclunie]

One of my tools creates DICOM WSI images that are dual-personality TIFF, but also
contain a "hidden" pyramid of TIFF sub-layers, using a private data element, so
that ordinary TIFF readers have the pyramid they are expecting, even though DICOM
spreads the pyramid over multiple files.

Normal DICOM readers ignore these hidden, and use the PixelData element in the
top level data set.

Unfortunately, adding these seems to confuse the BioFormats reader.

See the samples at:

https://www.dropbox.com/scl/fo/za255deqf1rrmmwqsv5lv/h?rlkey=b3uow8ormdaz0tr4q7g3u5yyl

with screenshots of QuPath (5) using BioFormats and OpenSlide readers.

I am just guessing that the nested Pixel Data in the private data element is the
problem, since if I don't include it, the BioFormats reader works OK. It may be
something else.

These test images also contain both the Basic Offset Table and Extended
Offset Tables with pointers to the actual pixel data frame Items. I am testing including
these to allow faster reading when present. Note that the standard says that only
one or the other should be present, not both, so these are just for testing. Not
sure if BioFormats takes advantage of the presence of either.

[melissalinkert]

Thanks, @dclunie. With 7.2.0 and either showinf -noflat -resolution 2 img_0.dcm or showinf -nogroup img_3.dcm, I can see an image with tiles that are obviously incorrect.

The nested Pixel Data does seem to be the problem, and in particular we'll need to update https://github.com/ome/bioformats/blob/develop/components/formats-bsd/src/loci/formats/dicom/DicomTag.java#L312 and surrounding lines. That's assuming that a Pixel Data isn't nested within a Sequence, so if a Pixel Data is found within the current Sequence we should stop and assume the Sequence ended immediately before the Pixel Data. I don't have a fix quite yet, but am adding this issue to the next milestone so that it gets prioritized.

For internal testing, files here are now in inbox/gh-4165.