<div dir="ltr"><div><div><div><div><div>Hi Michael,<br><br></div>I opened <a href="http://review.source.kitware.com/#/c/16967/">a pull request</a> to get the latest SCIFIO-ITK imageIO incorporated into the master ITK branch.<br><br></div>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.<br><br></div>With these updates I was able to fully convert your image as a multi-series image, using the command: <br>SCIFIOTestDriver ko-A.ome.tiff out.ome.tif -w -a -d 5<br><br></div>Thanks for the report, it was very helpful. Please let us know if you run into any more problems.<br><br></div>Regards,<br>Mark<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Aug 20, 2014 at 12:05 PM, Mark Hiner <span dir="ltr"><<a href="mailto:hinerm@gmail.com" target="_blank">hinerm@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Hi all,<span class=""><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></span></div><div>The readme for the SCIFIO-ITK ImageIO (<a href="https://github.com/scifio/scifio-imageio" target="_blank">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) was out of date.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" target="_blank">scifio@scif.io</a> (copied) for ITK imageIO troubleshooting.<br>
</div><span class=""><div><br>> I found this only occurs when you enable "-w" to use SCIFIO for output.<br><br></div></span>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.<span class=""><br>
<br>> Looks like it's trying to read z plane 60 when there are only 60 planes<br><br></span></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="HOEnZb"><div class="h5"><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><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><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>
______________________________<u></u>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.<u></u>openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.<u></u>org.uk/mailman/listinfo/ome-<u></u>users</a><br>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>