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<p>Hi David,</p>
<p><br>
</p>
<p>I just uploaded it. Thank you very much <br>
</p>
<p>for looking at this.</p>
<p><br>
</p>
<p>Incidentally, depending on the particular set of files</p>
<p>I sometimes get a different error message, namely:</p>
<p><br>
</p>
<p></p>
<div>Error using bfGetReader (line 85)<br>
Java exception occurred:<br>
java.util.NoSuchElementException<br>
<br>
at java.util.StringTokenizer.nextToken(Unknown Source)<br>
<br>
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:870)<br>
<br>
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:429)<br>
<br>
at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)<br>
<br>
at loci.formats.FormatReader.setId(FormatReader.java:1397)<br>
<br>
at loci.formats.ImageReader.setId(ImageReader.java:839)<br>
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br>
<br>
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br>
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br>
<br>
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)</div>
<br>
<p></p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Von:</b> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk> im Auftrag von David Gault (Staff) <d.gault@dundee.ac.uk><br>
<b>Gesendet:</b> Mittwoch, 18. April 2018 11:36:25<br>
<b>An:</b> OME User Support List<br>
<b>Betreff:</b> Re: [ome-users] problem loading multiple ome.tiff files in Matlab</font>
<div> </div>
</div>
<div>Hi Pablo,
<div class=""><br class="">
</div>
<div class="">Have your files have been saved with a companion metadata file? </div>
<div class="">If so then uploading it to the link below should provide us with the information required to debug this problem further:</div>
<div class=""><a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a></div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 17 Apr 2018, at 15:45, Fernandez, Pablo <<a href="mailto:pablo.fernandez@tum.de" class="">pablo.fernandez@tum.de</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi ome-users,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I am having an issue loading a set of multiple<span class="Apple-converted-space"> </span><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">ome.tiff files in Matlab. The files were created</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">by<span class="Apple-converted-space"> </span><span class="">micro-manager</span><span class="Apple-converted-space"> </span>running a long multidimensional<span class="Apple-converted-space"> </span><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">acquisition, saving the data as a series of 4 GB ome.tiff files,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">appending to the filename "_1", "_2" and so on.<br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Now, I intend to analyze the data in Matlab, so I have</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">installed bfmatlab.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">To my surprise I am able to open all files - except for the first one.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">With bfGetReader I get the following error:</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div class="">Error using bfGetReader (line 85)<br class="">
Java exception occurred:<br class="">
java.lang.StringIndexOutOfBoundsException: String index out of range: -2<br class="">
<br class="">
at java.lang.String.substring(Unknown Source)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:810)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:429)<br class="">
<br class="">
at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:297)<br class="">
<br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1397)<br class="">
<br class="">
at loci.formats.ImageReader.setId(ImageReader.java:839)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br class="">
<br class="">
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)<br class="">
<br class="">
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)</div>
<br class="">
<p style="margin-top: 0px; margin-bottom: 0px;" class=""></p>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I am using Windows 10, Java 8u40, Bioformats 5.8.1.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Incidentally, although the images correspond to stacks at different positions and timepoints µManager stores all frames along the</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">time direction, as a stack with many timepoints and only one Z</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">value.<br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">The file is 4 GB large; I will be glad to upload it if that<br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">helps solve the issue.<br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">I would greatly appreciate any help...We are generating</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">tons of data and really need to analyze it as soon</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">as possible, before our servers explode<span class="Apple-converted-space"> </span><span class="">😊</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class=""><br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">Keep up the great work!</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">Cheers,</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">Pablo<br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Tel +49-(0)89-289-12490<br class="">
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