<div dir="ltr">Hi Curtis,<div><br></div><div>I have wrapped the Bioformats tools and am using it for now. I'll let you know and e-mail the ome-users list if the problem recurs.</div><div><br></div><div>Thanks,</div><div>
<br></div><div>-Kedar</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 19, 2014 at 3:48 PM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</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">Hi Kedar,<div><br></div><div><div>> I have made montages of the same image in three instances where tiles</div>
<div>> were scrambled and once when it worked.</div></div><div><br></div><div>When you have file-format-specific problems like this, it is very important to understand at what layer the problem is occurring. Please test with Bio-Formats 5.0.2 -- e.g., with the command line tools, or in an up-to-date version of Fiji -- and verify whether you see the same faulty behavior. Then test with an older version of Bio-Formats [1], too. If the problem occurs with 5.0.2 on its own, that rules out the SCIFIO-ITK bridge layer as the culprit, meaning the bug should be reported to the ome-users list [2] so that the Bio-Formats developers can address it.</div>
<div><br></div><div>Or if the problem truly is with the ITK bridge, then Mark is the best person to investigate, when he returns from vacation.</div><div><br></div><div>Regards,</div><div>Curtis</div><div><br></div><div>
[1] <a href="http://downloads.openmicroscopy.org/bio-formats/" target="_blank">http://downloads.openmicroscopy.org/bio-formats/</a><br>
</div><div>[2] <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/</a></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Thu, Jun 19, 2014 at 9:20 AM, Kedar Grama <span dir="ltr"><<a href="mailto:gbkedar@gmail.com" target="_blank">gbkedar@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">Hi Mark,<div><br></div><div>I have filed an issue on the github site scifio-itk-bridge. We will work around the issue for now.</div><div><br></div><div>Thanks,</div><div><br></div><div>-Kedar</div></div><div>
<div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Thu, Jun 19, 2014 at 8:34 AM, 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 Kedar,<br><br> Just wanted to let you know that I'll be out of the country for two weeks starting tomorrow, and all of my time right now is being spent on the <a href="http://developer.imagej.net/2014/06/04/imagej-200-release-candidate" target="_blank">ImageJ2 release</a>.<br>
<br></div> Would you mind filing this as an issue on the scifio-itk-bridge github site: <a href="https://github.com/scifio/scifio-itk-bridge" target="_blank">https://github.com/scifio/scifio-itk-bridge</a> ? That way it won't get lost in my e-mail and I can investigate when I get back.<br>
<br>Thanks!<span><font color="#888888"><br></font></span></div><span><font color="#888888">- Mark<br></font></span><div><br><br><div><div class="gmail_extra"><div class="gmail_quote"><div>
On Wed, Jun 18, 2014 at 2:39 PM, Kedar Grama <span dir="ltr"><<a href="mailto:gbkedar@gmail.com" target="_blank">gbkedar@gmail.com</a>></span> wrote:<br>
</div><div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Mark,<br><br>I used SCIFIO to write czi as a 3d stack of either nrrd or tiffs. I get tiles that are scrambled and this happens at random. My code to convert the files is here:<br>
<a href="https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp" target="_blank">https://github.com/gbkedar/farsight/blob/IlluminationGraphCuts/IlluminationCorrection/readCziWriteCorrectedTiles.cpp</a><br>
<div><br></div><div>I have made montages of the same image in three instances where tiles were scrambled and once when it worked. The czi file is similar to the one I sent you in June or July last year. Please let me know if you need the file that I'm using right now and I'll upload it.</div>
<div><br></div><div>Thanks,</div><div><br></div><div>-Kedar</div></div>
</blockquote></div></div></div><br></div></div></div></div>
</blockquote></div><br></div>
</div></div></blockquote></div><br></div>
</blockquote></div><br></div>