[ome-users] Can't read Andor Dragonfly/Fusion *.ims with Bioformats

[Roger Leigh]

On 28/11/2017 15:47, Kai Schleicher wrote:
> Dear OME team,
>
> we recently had the opportunity to test Andors new Spinning-disk
> confocal ("Dragonfly") together with its new acquisition software "Fusion".
>
> The default file format in which Fusion save the data is *.ims, since
> Andor also owns Bitplane Imaris.
>
> As expected these images
> <https://filesender.switch.ch/filesender/?vid=03e9a405-643f-8229-0aa3-00000e50b3a6>
> open nicely in Imaris - but not when using Fiji with the latest Bio-formats:
>
> "Sorry, there was an I/O problem during import". See console and log
> output at the end of this email.
>
> I received this error both when opening files from a remote or local
> destination.
>
> The "regular" *.ims 5.5 images saved by Imaris still open fine in Fiji.
>
> Do you maybe have an idea whats the problem/difference in the *.ims
> saved by the fusion software?

Dear Kai,

This is a result of us using an older version of NetCDF to read the .ims
HDF5 files.  This PR updates Bio-Formats to use a newer version:

   https://github.com/openmicroscopy/bioformats/pull/2938

With this PR, Bio-Formats can then open new .ims files without any problems.

Unfortunately, its inclusion has been delayed because the NetCDF update
causes problems with building OMERO (due to incompatibilities with how
maven and ivy resolve dependencies).  In the meantime, you can either
build Bio-Formats with this PR included, or you can simply copy an
updated NetCDF cdm jar into your Fiji jar directory to replace the old
version, and that should also work in the interim.


Kind regards,
Roger


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