<div dir="ltr"><div><div>Hi all,<br><br>>While I'm not entirely sure of the separation of responsibilities between ITK, SCIFIO and Bio-Formats for this <br>>particular task<br><br></div><div>The readme for the SCIFIO-ITK ImageIO (<a href="https://github.com/scifio/scifio-imageio">https://github.com/scifio/scifio-imageio</a>) was out of date. It should now correctly instruct users to e-mail <a href="mailto:scifio@scif.io">scifio@scif.io</a> (copied) for ITK imageIO troubleshooting.<br>
</div><div><br>> I found this only occurs when you enable "-w" to use SCIFIO for output.<br><br></div>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.<br>
<br>> Looks like it's trying to read z plane 60 when there are only 60 planes<br><br></div>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.<br>
<br>Thanks for the report,<br>Mark<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 20, 2014 at 9:53 AM, Roger Leigh <span dir="ltr"><<a href="mailto:rleigh@dundee.ac.uk" target="_blank">rleigh@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On 19/08/14 19:52, Michael Meuli wrote:<br>
<br>
Dear Michael,<div class=""><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have some problems converting my .lif files to ome-tiff.<br>
I have converted my .lif files originating from a "CLSM Leica SP 8"<br>
with bfconvert of Bio-Formats 5.0.3.<br>
Trying to make it reproducible I took the file "ko-A.ome.tiff" which<br>
can be found here:<br>
"<a href="https://www.dropbox.com/sh/t2z0f4jttcnfh8s/AADq21HNR7EwH1JFxskhXXhea" target="_blank">https://www.dropbox.com/sh/<u></u>t2z0f4jttcnfh8s/<u></u>AADq21HNR7EwH1JFxskhXXhea</a>"<br>
in the ome-tiff-files folder.<br>
</blockquote>
<br></div>
Thanks. I've been able to reproduce the validation problems. I have<br>
opened a ticket for this and CC'd you on it; please see<br>
<a href="https://trac.openmicroscopy.org.uk/ome/ticket/12532" target="_blank">https://trac.openmicroscopy.<u></u>org.uk/ome/ticket/12532</a><br>
<br>
Note however that the above validation error is harmless; it does not<br>
affect bioformats' correct reading of the OME-TIFF and I was able to<br>
read all planes of every series without trouble, and also convert the<br>
file to a new OME-TIFF which strips out the MetadataOnly elements. I<br>
don't think this is in any way related to your other problem, below.<div class=""><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Below you can find the output of bfconvert, xmlvalid and<br>
SCIFIOTestDriver itkSCIFIOImageIOTest with the -a flag.<br>
The output of tiffcomment you can find as attachment.<br>
itkSCIFIOImageIOTest in this example crashes trying to read the third series.<br>
</blockquote>
<br></div>
I built ITK with itkscifio to test this. I found this only occurs when<br>
you enable "-w" to use SCIFIO for output.<br>
<br>
While I'm not entirely sure of the separation of responsibilities<br>
between ITK, SCIFIO and Bio-Formats for this particular task, I don't<br>
think the problem is in Bio-Formats, but in SCIFIO setting the wrong<br>
plane index when reading the image data, as shown by your stacktrace.<br>
Looks like it's trying to read z plane 60 when there are only 60 planes<br>
(0-59), assuming it's series 2; the others all have too different z<br>
sizes. I would suggest reporting this to the SCIFIO developers at<br>
<a href="https://github.com/scifio/scifio" target="_blank">https://github.com/scifio/<u></u>scifio</a><br>
<br>
<br>
Regards,<br>
Roger Leigh<br>
<br>
--<br>
Dr Roger Leigh -- Open Microscopy Environment<br>
Wellcome Trust Centre for Gene Regulation and Expression,<br>
College of Life Sciences, University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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</blockquote></div><br></div>