<div dir="ltr">Hi Hermann-Josef and Michael,<div><br><div>Michael wrote:</div><div><div>> Would you please tell me how to send you sample files</div></div><div><br></div><div>Files up to 2GB can be sent to the Bio-Formats team using the OME QA system:</div><div><br></div><div><a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a><br></div><div><br></div><div>Please also follow up with a mail explaining what you uploaded and why.</div><div><br></div><div>Hermann-Josef wrote:</div><div><div>> Once it is fixed, will this automatically mean that the fix will be</div><div>> implemented into bio-formats?</div></div><div><br></div><div>Not automatically, although the SCIFIO developers will communicate details of the fix to the Bio-Formats team, to facilitate a similar bug-fix on that end.</div><div><br></div><div>That said, I doubt we will have time to pursue a fix for this issue within the next six months, unfortunately. But in the meantime, a PR from a motivated developer would be very welcome.</div><div><br></div><div>Regards,</div><div>Curtis</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 24, 2015 at 12:41 PM, Cammer, Michael <span dir="ltr"><<a href="mailto:Michael.Cammer@med.nyu.edu" target="_blank">Michael.Cammer@med.nyu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Would you please tell me how to send you sample files to check for:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">1. ND2 files not being opened completely.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">2. CZI files having various issues.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">3. TIFF files exported from Zeiss Blue opening in Photoshop but not with IJ.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thank you!<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">=========================================================================<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> Cell: <a href="tel:914-309-3270" value="+19143093270" target="_blank">914-309-3270</a> **
</span><b><span style="font-size:10.0pt;font-family:"Adobe Fan Heiti Std B","sans-serif";color:#1f497d">MY OFFICE HAS MOVED TO SKIRBALL 2<sup>nd</sup> FLOOR, Back right **</span></b><i><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u><u></u></span></i></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1f497d">
<a href="http://ocs.med.nyu.edu/microscopy" target="_blank">http://ocs.med.nyu.edu/microscopy</a> &
<a href="http://microscopynotes.com/" target="_blank">http://microscopynotes.com/</a><u></u><u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> ome-users [mailto:<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a>]
<b>On Behalf Of </b>Curtis Rueden<br>
<b>Sent:</b> Thursday, September 24, 2015 1:20 PM<br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] Problem importing multi-page tif<u></u><u></u></span></p><div><div>
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<p class="MsoNormal">Hi Hermann-Josef,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Thanks for the sample. I added it to our collection for SCIFIO, where we already have an issue filed for this problem:<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"> <a href="https://github.com/scifio/scifio/issues/159" target="_blank">https://github.com/scifio/scifio/issues/159</a><u></u><u></u></p>
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<p class="MsoNormal">In your case, it's a different bit depths rather than different dimensions, but the problem is the effectively the same.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Sorry to say I don't have a timeline for fixing this, but it's on our radar.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On the Bio-Formats side, I'm not sure whether there is an issue tracking this limitation yet.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Regards,<u></u><u></u></p>
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<p class="MsoNormal">Curtis<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Thu, Sep 24, 2015 at 10:08 AM, <<a href="mailto:posts@roeser-reichartshausen.de" target="_blank">posts@roeser-reichartshausen.de</a>> wrote:<u></u><u></u></p>
<p class="MsoNormal">Hi Curtis,<br>
<br>
a sample image is on my server: <a href="http://www.roeser-reichartshausen.de/Scans/Test.tif" target="_blank">
http://www.roeser-reichartshausen.de/Scans/Test.tif</a> (250 MB)<br>
<br>
Thank you for looking into this.<br>
<br>
Hermann-Josef<br>
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<br>
Zitat von Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>>:<u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Hermann-Josef,<br>
<br>
Can you share a sample image?<br>
<br>
Regards,<br>
Curtis<br>
<br>
On Thu, Sep 24, 2015 at 3:42 AM, <<a href="mailto:posts@roeser-reichartshausen.de" target="_blank">posts@roeser-reichartshausen.de</a>> wrote:<u></u><u></u></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
Hello,<br>
<br>
my multi-page tif image, created with imagemagick, contains a 3x16bit RGB<br>
image on page 1 and a 1x16bit B&W image on page 2. This image is not<br>
correctly imported with bio-formats 5.1.4 into imageJ. However, it is<br>
correctly opened in GIMP2 and IrfanView. So I suspect, there is a problem<br>
with bio-formats input. However, other images with the same structure but<br>
from a source different to imagemagick are imported correctly.<br>
<br>
Does anybody know this problem and a possible solution?<br>
<br>
Hermann-Josef<br>
<br>
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