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<p><font face="Karla">Hello,</font></p>
<p><font face="Karla">I am having trouble with several random .nd2
files which will not open with Bio-Formats plugin either in
ImageJ or Matlab. When I call bfGetReader on the file, I get
this error message:</font></p>
<p><font face="Karla">Error using bfGetReader (line 85)<br>
Java exception occurred:<br>
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<br>
<br>
at java.util.ArrayList.rangeCheck(ArrayList.java:653)<br>
<br>
at java.util.ArrayList.get(ArrayList.java:429)<br>
<br>
at loci.formats.FormatReader.getSizeC(FormatReader.java:689)<br>
<br>
at
loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1348)<br>
<br>
at loci.formats.FormatReader.setId(FormatReader.java:1401)<br>
<br>
at
loci.formats.DelegateReader.setId(DelegateReader.java:291)<br>
<br>
at loci.formats.ImageReader.setId(ImageReader.java:835)<br>
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)<br>
<br>
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)<br>
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)<br>
<br>
at
loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)<br>
</font></p>
<p><font face="Karla">The original file is quite big (10Gb), so I
can only upload it through FTP. When I crop the file in NIS, interestingly,
it works, so for now my workaround is to crop the image itself
because apparently NIS re-encodes channels and timepoints
during cropping so I can open it with Bio-Formats. <br>
</font></p>
<p><font face="Karla">Moreover, these problematic files open fine
with the ImageJ ND2 Reader plugin
(<a class="moz-txt-link-freetext" href="https://imagej.nih.gov/ij/plugins/nd2-reader.html">https://imagej.nih.gov/ij/plugins/nd2-reader.html</a>). <br>
</font></p>
<p><font face="Karla">Thank you for your time.</font></p>
<p><font face="Karla">Best regards,</font><br>
</p>
<div class="moz-signature">-- <br>
Guilhem CHENON <br>
LCMD - ESPCI Paris</div>
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