<div dir="ltr"><div><div><div>Hi Sebastien,<br></div>the 5.0.2-DEV version you pointed me to works and bfopen returns a correctly cropped image.<br></div>Best wishes,<br></div>Enno<br></div><div class="gmail_extra"><br><br>
<div class="gmail_quote">On Mon, Jul 28, 2014 at 2:19 PM, Sebastien Besson <span dir="ltr"><<a href="mailto:seb.besson@gmail.com" target="_blank">seb.besson@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 style="word-wrap:break-word">Hi Enno,<div><br></div><div>thanks for the quick upload. I have been able to reproduce the bug you saw using MATLAB</div><div>and Bio-Formats 5.0.2 and I can confirm the 5.0.3 release candidate should fix this issue with</div>
<div>the tile correctly loaded.</div><div><br></div><div>You can either wait for the imminent 5.0.3 release of try out one of the non-release</div><div>quality continuous integration artifacts from:</div><div><a href="http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-latest/lastSuccessfulBuild/artifact/artifacts/" target="_blank">http://ci.openmicroscopy.org/job/BIOFORMATS-5.0-latest/lastSuccessfulBuild/artifact/artifacts/</a></div>
<div><br></div><div>Best regards,</div><div>Sebastien</div><div><div class="h5"><div><br><div><div>On 28 Jul 2014, at 13:10, Enno R. Oldewurtel <<a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a>> wrote:</div>
<br><blockquote type="cite"><div dir="ltr"><div><div><div>Hey Sebastien,<br><br></div>I used the 5.0.2 release. I uploaded a nd2 file as requested<br><a href="http://qa.openmicroscopy.org.uk/qa/feedback/9422/?token=f74e8565db4a90d1b876660e6b2e3e21" target="_blank">http://qa.openmicroscopy.org.uk/qa/feedback/9422/?token=f74e8565db4a90d1b876660e6b2e3e21</a><br>
</div><br></div>Thanks for the quick reply,<br>Enno<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jul 28, 2014 at 1:44 PM, Sebastien Besson <span dir="ltr"><<a href="mailto:seb.besson@gmail.com" target="_blank">seb.besson@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 style="word-wrap:break-word">Hi Enno,<div><br></div><div>which version of Bio-Formats are you using? The upcoming 5.0.3 release of Bio-Formats</div>
<div>will include a large set of bug fixes for the ND2 format.</div><div>Could you upload a sample file to <a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a> for us to check</div>
<div>this release also addresses your issues?</div><div><br></div><div>Best regards,</div><div>Sebastien</div><div><br><div><div><div>On 28 Jul 2014, at 12:19, Enno R. Oldewurtel <<a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a>> wrote:</div>
<br></div><blockquote type="cite"><div dir="ltr"><div><div>Dear all,<br><br></div><div>I just tried to read in ND2 files via matlab (either using r.openBytes directly or bfopen.m). However, when specifying a sub-image with x-origin>=2, the resulting image is skewed along a diagonal with slope depending on the x-origin, i.e. slope=1 for x-origin=2. The y-origin works with all values.<br>
<br>This is the command I use:<br>test=bfopen(f,2,1,400,300);<br><br></div><div>Using bfopen on a tif-file returns a correctly cropped image. Thus this might be a nd2 specific problem.<br><br></div><div>Has anyone experienced the same problem?<br>
<br></div></div><div>These are images obtained with x-origin=1 and x-origin=2:<span><x-originEquals1.png></span><span><x-originEquals2.png></span><br>
</div><div><div><br></div><div>Thanks,<br>Enno<br></div><div><br></div><br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>
50674 Koeln<br>
<br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br><a href="http://www.biophysics.uni-koeln.de/" target="_blank">http://www.biophysics.uni-koeln.de/</a>
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</blockquote></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>50674 Koeln<br>
<br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br>Tel: <a href="tel:%2B49-221-470-8048" value="+492214708048" target="_blank">+49-221-470-8048</a><br>Fax: <a href="tel:%2B49-221-470-6230" value="+492214706230" target="_blank">+49-221-470-6230</a><br>
<a href="http://www.biophysics.uni-koeln.de/" target="_blank">http://www.biophysics.uni-koeln.de/</a>
</div>
</blockquote></div><br></div></div></div></div></blockquote></div><br><br clear="all"><br>-- <br>Enno R. Oldewurtel<br>AG Prof. B. Maier / Biophysics Group<br>Biozentrum<br>Universitaet zu Koeln<br>Zuelpicher Str. 47b<br>
50674 Koeln<br><br><a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a><br>Tel: +49-221-470-8048<br>Fax: +49-221-470-6230<br><a href="http://www.biophysics.uni-koeln.de/" target="_blank">http://www.biophysics.uni-koeln.de/</a>
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