Open Microscopy Environment

I have been using the bioformats package to load nd2 files through MATLAB for image processing. This has worked without any issues until I received some nd2s from a collaborator. These nd2s are taken in high content mode and each well of the imaging plate is a separate nd2 file.

I can initialize a reader using bfGetReader - loci.formats.ChannelSeparator@3e8f9a77
When I try and initialize this reader on the file I get the following error:

Java exception occurred:
java.lang.NoClassDefFoundError: loci/formats/codec/JPEG2000BoxType

at
loci.formats.in.JPEG2000Reader.isThisType(JPEG2000Reader.java:96)

at loci.formats.FormatReader.isThisType(FormatReader.java:615)

at loci.formats.ImageReader.getReader(ImageReader.java:185)

at loci.formats.ImageReader.setId(ImageReader.java:836)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at
loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)

at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)

at loci.formats.Memoizer.setId(Memoizer.java:677)

Hi,

This error is likely caused by a conflict between the JPEG2000 library which Bio-Formats uses and other installed libraries which also provide JPEG2000 decoding in MATLAB.

What all toolboxes do you currently have installed? You can view a list of the installed toolboxes using the 'ver' command:
http://www.mathworks.com/help/matlab/ref/ver.html

David Gault