[ome-users] Nikon Elements 4.0 and Bio-Formats

[Melissa Linkert]

Dear users of Nikon Elements and Bio-Formats,

As some of you have already noticed, upgrading to Nikon Elements 4.0
causes Elements to produce .nd2 files that cannot be read by
Bio-Formats.  (For those who haven't seen this, the error message that
you can expect is pasted at the bottom of this email.)

The reason for this is that .nd2 files written by Elements 4.0 are not
backwards compatible with .nd2 files written by previous versions; those of
you with access to older versions of Elements will notice that it is also
not possible to read the new files in pre-4.0 versions.  We are very
much aware of this problem, and have collected example files from a
number of people already.  We do have a proposed patch:

https://github.com/melissalinkert/bioformats/commit/4dbd0092e0230f5b832620ff057500f6454c78d6

...which is currently under review for inclusion in the trunk builds of
Bio-Formats.  As this has been a widely reported problem, I will send an
announcement to these mailing lists once the fix is included in the
trunk builds.

Regards,
-Melissa

The exception that you can expect to see is:

Exception in thread "main" java.lang.IllegalArgumentException: 0 must not be null and positive.
  at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:41)
  at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:208)
  at loci.formats.MetadataTools.populatePixels(MetadataTools.java:121)
  at loci.formats.MetadataTools.populatePixels(MetadataTools.java:96)
  at loci.formats.in.NativeND2Reader.populateMetadataStore(NativeND2Reader.java:968)
  at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:725)
  at loci.formats.FormatReader.setId(FormatReader.java:1087)
  at loci.formats.DelegateReader.setId(DelegateReader.java:232)
  at loci.formats.ImageReader.setId(ImageReader.java:682)
  at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:492)
  at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:956)
  at loci.formats.tools.ImageInfo.main(ImageInfo.java:989)