Error with opening .nd file

bio-formats
Tags: #<Tag:0x00007fd548783b40>

#1

Hi guys,
recently, I experienced an error during opening an .nd file. Using the Plugins -> Bio-Formats -> Bio-Formats Importer I wanted to open set of Pictures taken overnight (151 time Points, 3 channels, 17 Z-stacks, 4 stages) and do a movie out of it. However, I am unable to open the file and there is a window popping up with this message:

Exception

 (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 86MB of 12131MB (<1%)

java.lang.IndexOutOfBoundsException: Index: 4, Size: 2
 at java.util.ArrayList.rangeCheck(ArrayList.java:653)
 at java.util.ArrayList.get(ArrayList.java:429)
 at ome.xml.model.Instrument.getLightSource(Instrument.java:353)
 at ome.xml.meta.OMEXMLMetadataImpl.setLaserID(OMEXMLMetadataImpl.java:9512)
 at ome.xml.meta.FilterMetadata.setLaserID(FilterMetadata.java:1557)
 at loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:970)
 at loci.formats.FormatReader.setId(FormatReader.java:1397)
 at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
 at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
 at loci.plugins.in.Importer.showDialogs(Importer.java:140)
 at loci.plugins.in.Importer.run(Importer.java:76)
 at loci.plugins.LociImporter.run(LociImporter.java:78)
 at ij.IJ.runUserPlugIn(IJ.java:217)
 at ij.IJ.runPlugIn(IJ.java:181)
 at ij.Executer.runCommand(Executer.java:137)
 at ij.Executer.run(Executer.java:66)
 at java.lang.Thread.run(Thread.java:745)

Do you have an idea what is wrong or how can I possibly open the file? Thank you very much for your Responses :slight_smile:


#2

@Tereza

Unless someone else here has a better insight on this… you can always post a bug report on the Bio-Formats page.

On that page - they say before you report … “If you think you have found a bug in Bio-Formats, the first thing to do is update your version of Bio-Formats to the latest version to check if the problem has already been addressed. The Fiji updater will automatically do this for you, while in ImageJ you can select Plugins ‣ Bio-Formats ‣ Update Bio-Formats Plugins.” The newest version - 5.7.1 - was just released (see this forum post). There is also a list of “Common Issues” - just read the whole page and you’ll see how best to proceed.

I hope this helps!

eta :slight_smile: