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

[Mark Hiner]

Hi Michael,

I opened a pull request <http://review.source.kitware.com/#/c/16967/> to
get the latest SCIFIO-ITK imageIO incorporated into the master ITK branch.

This fixes the metadata bug suspected by Roger (the dimensions of the first
series were always being used, which would crash on encountering a dataset
with smaller dimensions). It also upgrades the ImageIO to use Bio-Formats
5.0.4, and has some other minor fixes and improvements.

With these updates I was able to fully convert your image as a multi-series
image, using the command:
SCIFIOTestDriver ko-A.ome.tiff out.ome.tif -w -a -d 5

Thanks for the report, it was very helpful. Please let us know if you run
into any more problems.

Regards,
Mark

On Wed, Aug 20, 2014 at 12:05 PM, Mark Hiner <hinerm at gmail.com> wrote:

> 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 https://github.com/scifio/scifio-imageio) was out of date.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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>>
>
>
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