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<p>Hi ome-users,</p>
<p><br>
</p>
<p>I am having an issue loading a set of multiple <br>
</p>
<p>ome.tiff files in Matlab. The files were created</p>
<p>by <span>micro-manager</span> running a long multidimensional <br>
</p>
<p>acquisition, saving the data as a series of 4 GB ome.tiff files,</p>
<p>appending to the filename "_1", "_2" and so on.<br>
</p>
<p><br>
</p>
<p>Now, I intend to analyze the data in Matlab, so I have</p>
<p>installed bfmatlab.</p>
<p><br>
</p>
<p>To my surprise I am able to open all files - except for the first one.</p>
<p>With bfGetReader I get the following error:</p>
<p><br>
</p>
<p></p>
<div>Error using bfGetReader (line 85)<br>
Java exception occurred:<br>
java.lang.StringIndexOutOfBoundsException: String index out of range: -2<br>
<br>
at java.lang.String.substring(Unknown Source)<br>
<br>
at loci.formats.in.MicromanagerReader.parsePosition(MicromanagerReader.java:810)<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>
<p>I am using Windows 10, Java 8u40, Bioformats 5.8.1.</p>
<p><br>
</p>
<p>Incidentally, although the images correspond to stacks at different positions and timepoints µManager stores all frames along the</p>
<p>time direction, as a stack with many timepoints and only one Z</p>
<p>value.<br>
</p>
<p><br>
</p>
<p>The file is 4 GB large; I will be glad to upload it if that<br>
</p>
<p>helps solve the issue.<br>
</p>
<p><br>
</p>
<p>I would greatly appreciate any help...We are generating</p>
<p>tons of data and really need to analyze it as soon</p>
<p>as possible, before our servers explode <span>😊</span></p>
<p><span><br>
</span></p>
<p><span>Keep up the great work!</span></p>
<p><span>Cheers,</span></p>
<p><span>Pablo<br>
</span></p>
<p><br>
</p>
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<div>
<p>-------------------------------------------</p>
<p>Tel +49-(0)89-289-12490<br>
</p>
<p>E27 Zellbiophysik<br>
</p>
<p>Technische Universität München<br>
</p>
<p>James-Franck-Straße 1</p>
D 85748 Garching b. München</div>
<br>
<p></p>
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