[ome-users] bug report with nd2 image

[wjbian at ion.ac.cn]

Hi,

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.

the error message in Fiji is as followed:

Fiji/ImageJ 1.47m; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 15MB of 5983MB (<1%)
 
java.lang.StringIndexOutOfBoundsException: String index out of range: -409
 at java.lang.String.substring(String.java:1937)
 at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:493)
 at loci.formats.FormatReader.setId(FormatReader.java:1322)
 at loci.formats.DelegateReader.setId(DelegateReader.java:267)
 at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
 at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
 at loci.plugins.in.Importer.showDialogs(Importer.java:141)
 at loci.plugins.in.Importer.run(Importer.java:79)
 at loci.plugins.LociImporter.run(LociImporter.java:81)
 at ij.IJ.runUserPlugIn(IJ.java:193)
 at ij.IJ.runPlugIn(IJ.java:160)
 at ij.IJ.runPlugIn(IJ.java:149)
 at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:405)
 at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
 at ij.IJ.runUserPlugIn(IJ.java:193)
 at ij.IJ.runPlugIn(IJ.java:160)
 at ij.IJ.runPlugIn(IJ.java:149)
 at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:434)
 at ij.io.Opener.openImage(Opener.java:306)
 at ij.io.Opener.openImage(Opener.java:329)
 at ij.io.Opener.open(Opener.java:142)
 at ij.io.Opener.openAndAddToRecent(Opener.java:242)
 at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
 at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
 at java.lang.Thread.run(Thread.java:662)


the error information in the matlab is as followed:

??? Java exception occurred:
java.lang.StringIndexOutOfBoundsException: String index out of range: -409

 at java.lang.String.substring(Unknown Source)

 at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:493)

 at loci.formats.FormatReader.setId(FormatReader.java:1333)

 at loci.formats.DelegateReader.setId(DelegateReader.java:267)

 at loci.formats.ImageReader.setId(ImageReader.java:757)

 at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:563)

 at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)


Error in ==> imreadBFmeta at 56
r.setId(datname);

Error in ==> infoget at 9
info = imreadBFmeta(filename);

Error in ==> oibread3d at 27
info=infoget(filename);

Error in ==> bwj at 12
fig=oibread3d(fn{j});

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).

I would really appreciate any help to fix this problem.

Thanks

W. J.

--
边文杰
Wenjie Bian
Laboratory of Dendritic Development and Neural Circuit formation
Institute of Neuroscience(ION), Shanghai Institutes for Biological Sciences(SIBS), Chinese Academy of Sciences(CAS)
Office Tel: 86-21-5492-1803
E-mail: wjbian at ion.ac.cn
Address: 320 Yue-yang Rd, Shanghai, 200031, China




从ion.ac.cn发来的超大附件
556_t2.nd2 (44MB, 2013年03月26日 20:05 到期)
查看下载信息 
521_t1.nd2 (44MB, 2013年03月26日 20:07 到期)
查看下载信息 





从ion.ac.cn发来的超大附件
521_t1.nd2 (44MB, 2013-03-26 到期)
查看下载信息：https://mail.cstnet.cn/coremail/viewDownloadFile.jsp?key=1U31Ssvkjqju-9Ym3sKU-sELo90yo9FLUu2kTD3iSstESZmg-s0Lon2LzsvpTgKq3XKyTgGka1AXF1fdTuxEOnEXaWCmTZtL3srL3ZtMfeYpzsFWSnKvSbKyTgk8Ss2maUrUUUU8jnCgTuDn0ka6r4rGw48Kr4DAr1DurXF6SZmg-s81Tsvk1q3Ur7jAUn5U-7jjUnfU-Jj7U87U27jNUe3USDUuU8tUF7jqUefU77jjUntUr70mUWMTmOd=&code=ish2p4s6
556_t2.nd2 (44MB, 2013-03-26 到期)
查看下载信息：https://mail.cstnet.cn/coremail/viewDownloadFile.jsp?key=1U31Ssvkjqju-9Ym3sKU-sELo90yo9FLUu2kTD3iSstESZmg-s0Lon2LzsvpTgKq3XKyTgGka1AXF1fdTuxEOnEXaWCmTZtL3srL3ZtMfeYpzsFWSnKvSbKyTgk8Ss2maUrUUUU8jnCgTuDn0ka6r4rGw48Kr4DAr1DurXF6SZmg-s81Tsvk1q3Ur7jAUn5U-7jjUnfUaJj7U87U27jNUe3USDUuU8tUF7jqU08U77jbUntUrJ0mUG2Q-zf=&code=tg6pr03a



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