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

[Kai Schleicher]

Hi Roger,

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?

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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-- 
>> Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) |kai.schleicher at unibas.ch  |www.biozentrum.unibas.ch  |www.microscopynetwork.unibas.ch

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