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

[Mark Hiner]

Hi all,

>While I'm not entirely sure of the separation of responsibilities between
ITK, SCIFIO and Bio-Formats for this
>particular task

The readme for the SCIFIO-ITK ImageIO (
https://github.com/scifio/scifio-imageio) was out of date. It should now
correctly instruct users to e-mail scifio at scif.io (copied) for ITK imageIO
troubleshooting.

> I found this only occurs when you enable "-w" to use SCIFIO for output.

Note that without the -w flag, the default ITK TIFF writer will be used,
which I thought was limited to 3 dimensions (or at least it was at one
time). If you want to write an .ome.tiff it has to be written with
Bio-Formats, anyway.

> Looks like it's trying to read z plane 60 when there are only 60 planes

I'm assuming the # of planes to read isn't being updated for each series..
I'll look into it when I get a chance.

Thanks for the report,
Mark


On Wed, Aug 20, 2014 at 9:53 AM, Roger Leigh <rleigh at dundee.ac.uk> wrote:

> 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
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