[ome-users] converting lif files to ome-tiff

[Roger Leigh]

On 19/08/14 19:52, Michael Meuli wrote:

Dear Michael,

> I have some problems converting my .lif files to ome-tiff.
> I have converted my .lif files originating from a "CLSM Leica SP 8"
> with bfconvert of Bio-Formats 5.0.3.
> Trying to make it reproducible I took the file "ko-A.ome.tiff" which
> can be found here:
> "https://www.dropbox.com/sh/t2z0f4jttcnfh8s/AADq21HNR7EwH1JFxskhXXhea"
>    in the ome-tiff-files folder.

Thanks.  I've been able to reproduce the validation problems.  I have
opened a ticket for this and CC'd you on it; please see
https://trac.openmicroscopy.org.uk/ome/ticket/12532

Note however that the above validation error is harmless; it does not
affect bioformats' correct reading of the OME-TIFF and I was able to
read all planes of every series without trouble, and also convert the
file to a new OME-TIFF which strips out the MetadataOnly elements.  I
don't think this is in any way related to your other problem, below.

> Below you can find the output of bfconvert, xmlvalid and
> SCIFIOTestDriver itkSCIFIOImageIOTest with the -a flag.
> The output of tiffcomment you can find as attachment.
> itkSCIFIOImageIOTest in this example crashes trying to read the third series.

I built ITK with itkscifio to test this.  I found this only occurs when
you enable "-w" to use SCIFIO for output.

While I'm not entirely sure of the separation of responsibilities
between ITK, SCIFIO and Bio-Formats for this particular task, I don't
think the problem is in Bio-Formats, but in SCIFIO setting the wrong
plane index when reading the image data, as shown by your stacktrace.
Looks like it's trying to read z plane 60 when there are only 60 planes
(0-59), assuming it's series 2; the others all have too different z
sizes.  I would suggest reporting this to the SCIFIO developers at
https://github.com/scifio/scifio


Regards,
Roger Leigh

--
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