[ome-devel] TIFF pyramid support in Bio-Formats - reference files for review

[Roger Leigh]

On 27/03/18 23:30, Damir Sudar wrote:
> On 3/27/2018 14:45, Roger Leigh wrote:

>> In theory, all "C" files should work with all tools with or without
>> support for SUBIFDs.  As you say, readers which don't handle SUBIFDS
>> should simply ignore them.
> Indeed, that's exactly what I'm seeing.
>>
>> I had noticed the odd behaviour of Leica-Fluorescence-1, but I haven't
>> yet dug into why this is happening in detail.  It's likely to be
>> something odd in the OME-XML, maybe because the shell script isn't doing
>> the conversion quite right.  Since it's only for the OME-XML, and not
>> the plain TIFF (I think), this is likely bad OME-XML metadata.
> Indeed, that was my observation as well. Would it indeed make sense to
> set as a ground rule (at least for now) that a new-style
> pyramid-OME-TIFF should pass without errors through xmlvalid, showinf,
> and any other current BF tools, readers, etc.?

Absolutely, the new files should work with the existing tools.

Looking more closely at Leica-Fluorescence-1, it contains images with
both JPEG YCbCr and separate colour planes.  The latter aren't handled
by the shell script; it requires more sophisticated parsing of the SCN
metadata, and more complex modifications of the OME-XML to add all the
extra TiffData elements.  It's a limitation of the shell script, so I'd
suggest ignoring this sample for now; once we have bfconvert working
this will be a candidate for checking the conversion works correctly,
preserving the IFD mappings for all the per-resolution channels.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096