<div dir="ltr"><div><div><div><div>Dear Balaji,<br><br></div>I just upload some nd2 files: QA Bug #11064<br></div>I, also, added txt and xlsx files with the corresponding meta-data exported by NIS-elements.<br></div><br>Hope this helps! It would be great to stay updated on this issue. Many thanks,<br></div>Enno<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 7, 2015 at 12:23 PM, Balaji Ramalingam (Staff) <span dir="ltr"><<a href="mailto:b.ramalingam@dundee.ac.uk" target="_blank">b.ramalingam@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">
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<div>Dear Enno,</div>
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<div>Thank you for reporting the issue.</div>
<div>Unfortunately, we were not able to reproduce the same with the files that we had locally (with Bio-Formats 5.1.1/5.1.2). </div>
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<div>As suggested, it would help us troubleshoot the issue better, if you could submit your file to our QA system.</div>
<div><a href="https://www.openmicroscopy.org/qa2/qa/upload/" target="_blank">https://www.openmicroscopy.org/qa2/qa/upload/</a></div><span class="">
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<div>Best,</div>
<div>Balaji</div>
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<div style="color:rgb(40,40,40)"><span style="background-color:rgb(255,255,255)">__________________</span></div>
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<p style="margin-top:0px;margin-bottom:0px">Mr Balaji Ramalingam</p>
<p style="margin-top:0px;margin-bottom:0px">Software Developer<br>
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<p style="margin-top:0px;margin-bottom:0px">OME Team</p>
<p style="margin-top:0px;margin-bottom:0px">College of Life Sciences</p>
<p style="margin-top:0px;margin-bottom:0px">University of Dundee</p>
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<span style="font-weight:bold">From: </span>"Enno R. Oldewurtel" <<a href="mailto:enno.oldewurtel@uni-koeln.de" target="_blank">enno.oldewurtel@uni-koeln.de</a>><br>
</span><span style="font-weight:bold">Date: </span>Tuesday, 5 May 2015 14:16<br>
<span style="font-weight:bold">To: </span>Balaji Ramalingam <<a href="mailto:b.ramalingam@dundee.ac.uk" target="_blank">b.ramalingam@dundee.ac.uk</a>><br>
<span style="font-weight:bold">Cc: </span>Melissa Linkert <<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>>, "OME-users
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>ND2 position meta data with bioformats 5.1.1<br>
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<div>Dear Balaji and Melissa,<br>
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<div>firstly thanks for your great effort regarding bioformats! Following is a problem, which I believe could be another bug:<br>
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last year I submitted a problem about wrong indexing of x,y data of nd2 files (#<span>12569</span>: BUG: ND2 files - x,y position of the different multi points returned in the wrong order).<br>
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<div>I still use matlab for loading nd2 files and retrieve metadata with commands like:<br>
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r = loci.formats.ChannelFiller();<br>
r = loci.formats.ChannelSeparator(r);<br>
r.setMetadataStore(loci.formats.MetadataTools.createOMEXMLMetadata());<br>
r.setId( FileName);<br>
metadata=r.getMetadataStore();<br>
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<div>i=positionIndex;<br>
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<div>j=loci.formats.FormatTools.getIndex(r, z, channel, time)<br>
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<div>x=double(metadata.getPlanePositionX(i,j).value)<br>
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<div>t=double(metadata.getPlaneDeltaT(i,j).value)<br>
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Position data for x,y,z retrieved with 5.1.1 for the nd2 file I submitted with my previous problem, are correct now. However, time-points retrieved with metadata.getPlaneDeltaT(i,j) in the same manner are in the wrong order.<br>
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Furthermore the position data for nd2 files acquired with several z-slices is wrongly indexed. I have an example nd2 files with T(1) x XY(8) x Z(4) dimensions. Version 5.0.3 shows the correct order of 4 z-steps at the first XY position, which is then repeated
at the remaining 7 positions. Version 5.1.1 shows the x,y,z values jumping about in the wrong order.<br>
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As an aside: I noted that with 5.1.1 the number of the dimensions of nd2 files with all four T, XY, Z and lambda dimensions are correctly identified. Previously I could only use bioformats with 3 different types of dimensions. However, as soon as an nd2 files
is modified and saved in NIS elements, the numbers of the dimensions are not correct anymore.<br>
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I can supply example nd2 files if needed, but will need to upload them via the qa system.<br>
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Hope this helps, and again many thanks for maintaining and developing such a great product!<br>
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Best,<br>
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Enno</div>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature">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></div>
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