<p>Hi,</p><p>Lately I have been troubled with the problem that some nd2 images cannot be opened in either a matlab program that calls Bio-formats or Fiji with LOCI plugin. Both my Bio-Formats package and fiji have been updated to the newest version. My system information is Win7 64-bit and Java 1.6.0_24[64-bit]. The image is 1024 x 1024, with 3 channels and 7 z-stacks, and no timepoint.</p><p>the error message in Fiji is as followed:</p><p>Fiji/ImageJ 1.47m; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 15MB of 5983MB (<1%)<br> <br>java.lang.StringIndexOutOfBoundsException: String index out of range: -409<br> at java.lang.String.substring(String.java:1937)<br> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:493)<br> at loci.formats.FormatReader.setId(FormatReader.java:1322)<br> at loci.formats.DelegateReader.setId(DelegateReader.java:267)<br> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)<br> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br> at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br> at loci.plugins.in.Importer.run(Importer.java:79)<br> at loci.plugins.LociImporter.run(LociImporter.java:81)<br> at ij.IJ.runUserPlugIn(IJ.java:193)<br> at ij.IJ.runPlugIn(IJ.java:160)<br> at ij.IJ.runPlugIn(IJ.java:149)<br> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:405)<br> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)<br> at ij.IJ.runUserPlugIn(IJ.java:193)<br> at ij.IJ.runPlugIn(IJ.java:160)<br> at ij.IJ.runPlugIn(IJ.java:149)<br> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:434)<br> at ij.io.Opener.openImage(Opener.java:306)<br> at ij.io.Opener.openImage(Opener.java:329)<br> at ij.io.Opener.open(Opener.java:142)<br> at ij.io.Opener.openAndAddToRecent(Opener.java:242)<br> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)<br> at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)<br> at java.lang.Thread.run(Thread.java:662)<br></p><p>the error information in the matlab is as followed:</p><p>??? Java exception occurred:<br>java.lang.StringIndexOutOfBoundsException: String index out of range: -409</p><p> at java.lang.String.substring(Unknown Source)</p><p> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:493)</p><p> at loci.formats.FormatReader.setId(FormatReader.java:1333)</p><p> at loci.formats.DelegateReader.setId(DelegateReader.java:267)</p><p> at loci.formats.ImageReader.setId(ImageReader.java:757)</p><p> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:563)</p><p> at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)</p><p><br>Error in ==> imreadBFmeta at 56<br>r.setId(datname);</p><p>Error in ==> infoget at 9<br>info = imreadBFmeta(filename);</p><p>Error in ==> oibread3d at 27<br>info=infoget(filename);</p><p>Error in ==> bwj at 12<br>fig=oibread3d(fn{j});</p><p>A non-working image is enclosed (556_t2) as well as a working image (521_t1), because the problem I met only popped out when opening SOME nd2 images, others worked just fine.  The non-working can be successfully opened in NIS-elements viewer (3.jpg enclosed).</p><p>I would really appreciate any help to fix this problem.</p><p>Thanks<br><br>W. J.<br><span><br>--<br>边文杰<br>Wenjie Bian<br>Laboratory of Dendritic Development and Neural Circuit formation<br>Institute of Neuroscience(ION), Shanghai Institutes for Biological Sciences(SIBS), Chinese Academy of Sciences(CAS)<br>Office Tel: 86-21-5492-1803<br>E-mail: <a href="mailto:wjbian@ion.ac.cn" target="_blank">wjbian@ion.ac.cn</a><br>Address: 320 Yue-yang Rd, Shanghai, 200031, China</span></p><br><br><div style="padding: 4px; width: auto; font-family: Verdana,Arial,Tahoma; font-size: 14px; margin-bottom: 15px; background-color: rgb(227, 227, 227);" id="largeAttachmentsBox"><hr style="display: none;"><div style="padding: 6px 0pt 10px 6px; text-align: left;"><b style="font-size: 14px;">从ion.ac.cn发来的超大附件</b></div><div style="background: rgb(255, 255, 255); padding: 0pt 8px 6px 12px; -moz-background-clip: border; -moz-background-origin: padding; -moz-background-inline-policy: continuous;"> <div style="clear: both;"><div style="clear: both;"><div style="padding: 10px 0pt; font-size: 12px;"> <div style="margin-top: 2px; margin-right: 8px; float: left;"><b class="bico bfMSWORD"></b></div><div class="bigatt_bt" title=""><div class="name_big"><span><a style="color: rgb(0, 0, 0); text-decoration: none;" href="https://mail.cstnet.cn/coremail/viewDownloadFile.jsp?key=1U31Ssvkjqju-9Ym3sKU-sELo90yo9FLUu2kTD3iSstESZmg-s0Lon2LzsvpTgKq3XKyTgGka1AXF1fdTuxEOnEXaWCmTZtL3srL3ZtMfeYpzsFWSnKvSbKyTgk8Ss2maUrUUUU8jnCgTuDn0ka6r4rGw48Kr4DAr1DurXF6SZmg-s81Tsvk1q3Ur7jAUn5U-7jjUnfUaJj7U87U27jNUe3USDUuU8tUF7jqU08U77jjUntUrD0mUAofPMU=&code=ramuz4m5" target="_blank">556_t2.nd2</a> <span style="color: rgb(160, 160, 160);"> (44MB, 2013年03月26日 20:05 到期)</span></span><div class="down_big"><a href="https://mail.cstnet.cn/coremail/viewDownloadFile.jsp?key=1U31Ssvkjqju-9Ym3sKU-sELo90yo9FLUu2kTD3iSstESZmg-s0Lon2Lz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