[ome-users] Having trouble opening .nd2 file in Bio-formats cppwrap

[Melissa Linkert]

Hi Joe,

> I am using Bio-formats 5.1.2, and I have trouble opening a .nd2 file from
> my program and from "showinf". The .nd2 file has been uploaded. The weird
> thing is Fiji can open the file fine. The error message I got was:
> 
> 11:35:54.179 [main] DEBUG loci.common.NIOByteBufferProvider - Using mapped
> byte buffer? false
> loci.formats.UnknownFormatException: Unknown file format:
> /common1/phsiao/build/vst/sample_vid/samplet01xy1.nd2
>     at loci.formats.ImageReader.getReader(ImageReader.java:190)
>     at loci.formats.ImageReader.setId(ImageReader.java:832)

This is currently expected; at the moment, the cppwrap builds only contain
BSD-licensed readers.  The final column in the list of supported
formats indicates which formats this includes:

http://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html

There is a ticket on our issue tracking system to add all remaining
readers:

https://trac.openmicroscopy.org/ome/ticket/11896

If you would like to be CC'd on the ticket, please let us know.

Regards,
-Melissa

On Thu, Aug 13, 2015 at 03:21:24PM -0400, Joe Ping-Lin Hsiao wrote:
> Hi,
> 
> I am using Bio-formats 5.1.2, and I have trouble opening a .nd2 file from
> my program and from "showinf". The .nd2 file has been uploaded. The weird
> thing is Fiji can open the file fine. The error message I got was:
> 
> 11:35:54.179 [main] DEBUG loci.common.NIOByteBufferProvider - Using mapped
> byte buffer? false
> loci.formats.UnknownFormatException: Unknown file format:
> /common1/phsiao/build/vst/sample_vid/samplet01xy1.nd2
>     at loci.formats.ImageReader.getReader(ImageReader.java:190)
>     at loci.formats.ImageReader.setId(ImageReader.java:832)

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