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Hi <span class="">Marjolein,</span>
<div class=""><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class=""><br class="">
</span></font></div>
<div class="">
<div>thanks for uploading the file and some minimal code. Unfortunately, I was</div>
<div>not able to reproduce either with MATLAB or Fiji and Bio-Formats 5.5.3, e.g.</div>
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</div>
<div>>> [~,v]=bfCheckJavaPath</div>
<div><br class="">
</div>
<div>v =</div>
<div><br class="">
</div>
<div>5.5.3</div>
<div><br class="">
</div>
<div>>> Reader = bfGetReader('BugReport_MM.lif');</div>
<div>Reader.setSeries(0);</div>
<div>omeMeta = Reader.getMetadataStore();</div>
<div>deltaT = omeMeta.getPlaneDeltaT(0,0)</div>
<div><br class="">
</div>
<div>deltaT =</div>
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</div>
<div>ome.units.quantity.Time: value[0.0], unit[s] stored as java.lang.Double</div>
<div><br class="">
</div>
<div>>> deltaT2 = omeMeta.getPlaneDeltaT(0,1)</div>
<div><br class="">
</div>
<div>deltaT2 =</div>
<div><br class="">
</div>
<div>ome.units.quantity.Time: value[16.53299903869629], unit[s] stored as java.lang.Double</div>
<div class=""><br class="">
</div>
<div class="">Support for recent LIF timestamps has been added in Bio-Format 5.3.3 [1]. Can you confirm</div>
<div class="">the version and the revision of Bio-Formats used (as given by</div>
<div class="">loci.formats.FormatTools.VCS_REVISION in MATLAB or the About Plugins > Bio-Formats Plugins…</div>
<div class="">menu in Fiji)?</div>
<div><br class="">
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br class="">
</div>
[1] <a href="https://github.com/openmicroscopy/bioformats/pull/2728" class="">https://github.com/openmicroscopy/bioformats/pull/2728</a> </div>
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<div>
<blockquote type="cite" class="">
<div class="">On 18 Jul 2017, at 22:13, Marjolein Meddens <<a href="mailto:marjolein@unm.edu" class="">marjolein@unm.edu</a>> wrote:</div>
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Hello.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
I think I found a bug in Bio-Formats.<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
The issue is that I’m not able to load time stamps from my Leica .lif files. I ran into the problem while using Matlab toolbox, but I checked whether I could get the time stamps in Fiji and I also couldn’t get them there.</div>
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<o:p class=""></o:p></div>
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One thing to note is that my data was acquired using “Live Data Mode” which allows you to acquire different ‘jobs’ in the Leica software.<o:p class=""></o:p></div>
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I can see the timestamps in the LASX software (see screenshot) so they’re saved in the lif file.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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I have uploaded my file on the QA system. (BugReport_MM.lif).<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Code that reproduces problem in Matlab:<o:p class=""></o:p></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">Reader = bfGetReader(</span><span style="font-size: 10pt; font-family: 'Courier New'; color: rgb(160, 32, 240);" class="">'BugReport_MM.lif'</span><span style="font-size: 10pt; font-family: 'Courier New';" class="">);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: 'Courier New';" class="">Reader.setSeries(0);</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 10pt; font-family: 'Courier New';" class="">omeMeta = Reader.getMetadataStore();</span><span style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="NL" style="font-size: 10pt; font-family: 'Courier New';" class="">deltaT = omeMeta.getPlaneDeltaT(0,0); %deltaT is empty</span><span lang="NL" style="font-size: 12pt; font-family: 'Courier New';" class=""><o:p class=""></o:p></span></div>
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<br class="">
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Code that reproduces problem in Fiji<o:p class=""></o:p></div>
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run("Bio-Formats Macro Extensions");<o:p class=""></o:p></div>
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Ext.setId("Y:\\Marjolein\\OME bug report\\BugReport_MM.lif")<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="NL" class="">Ext.getPlaneTimingDeltaT(deltaT, 1)<o:p class=""></o:p></span></div>
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<span lang="NL" class="">print(deltaT); // deltaT is NaN<o:p class=""></o:p></span></div>
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<span lang="NL" class=""><o:p class=""> </o:p></span></div>
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System info:<o:p class=""></o:p></div>
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Windows 8.1 Enterprise 64-bit<o:p class=""></o:p></div>
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Java 1.8.0_111<o:p class=""></o:p></div>
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BioFormats 5.5.3<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Thank you,<o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Marjolein<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span style="color: rgb(131, 60, 11);" class="">Marjolein Meddens PhD</span></b><span style="font-size: 9pt;" class=""><span class="Apple-converted-space"> </span>| Postdoc</span><o:p class=""></o:p></div>
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<span style="font-size: 3pt;" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 9pt;" class="">Department of Physics and Astronomy</span><o:p class=""></o:p></div>
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<span style="font-size: 9pt;" class="">Department of Pathology</span><o:p class=""></o:p></div>
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<span style="font-size: 9pt;" class="">University of New Mexico</span><o:p class=""></o:p></div>
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<span style="font-size: 9pt;" class="">Albuquerque, USA</span><span lang="NL" class=""><o:p class=""></o:p></span></div>
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<span lang="NL" class=""><o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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<span id="cid:DEC8E910-FE31-488C-A3EA-88805EDCEAC8"><LASX screenshot.jpg></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></div>
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