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

[Josh Moore]

On Wed, Nov 29, 2017 at 9:42 AM, Kai Schleicher
<kai.schleicher at unibas.ch> wrote:
> Hi Roger,

Hi Kai,


> thanks for the quick response! And already with the fix :)
>
> Since we don't own a Dragonfly at the moment we don't need an immediate
> resolve, but it might become relevant in the near future. If so, we'd also
> be very keen on OMERO supporting it. Can we use your suggestion to make our
> own instance of OMERO read these images as well?

considering we haven't done the same on our side, I'd suggest you
_not_ do so ( even if we can't really stop you :)  )

The biggest risk is that we have to make further changes on top of
Roger's PR such that the files would then no longer be readable. If
that's an acceptable risk and you want to give it a go, don't hesitate
to let us know how the testing goes. Otherwise, we'll keep you posted
when we've done the same.

~Josh.





> Thanks for your explanation and cheers,
> Kai
>
> On 11/28/2017 10:40 PM, Roger Leigh wrote:
>
> 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
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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