[ome-users] hdf5 format huygens

[Josh Moore]

Hi Glyn & Andreas,


On Mon, Sep 25, 2017 at 1:16 PM, Glyn Nelson
<glyn.nelson at newcastle.ac.uk> wrote:
> Hi Vita, and other Huygens users,
>
> I would like to ask when BioFormats plan to start supporting h5 file which
> are generated by the Huygens software? We just recently had a course with 16
> participants, where they learned how to use Huygens and after that the
> participants wanted to open their images in Fiji/ImageJ, but unfortunately
> Fiji/ImageJ does not support h5 format. I was told by SVI, that I can
> contact you about this issue.
...
>
> Best wishes,
> Glyn

It’s a very fair question. The Huygens format was brought to our
attention years ago [1] and has seen a reasonable amount of interest
from the community. We owe everyone a general update on supporting
file formats, and we’re working on the blog post now, but much of last
year’s message [2] still holds:

The open source OME team does not have the resources to commit to the
full development of new file format readers probably in the upcoming
months given the ongoing academic deliverables. Bio-Formats
development is currently funded by academic grants, with specific
deliverables for development of new binary vessels, support for object
stores etc. These necessarily have to be our first priority. We are of
course trying to fix bugs, update readers, etc., but alone, without
contributions from the community, we can’t support the continuing and
seemingly eternal list of new formats developed by the hundreds of
vendors in the imaging community.

That being said, the OME team will review any external contribution to
Bio-Formats including new reader additions and consider their
inclusion in a minor release of Bio-Formats. If you are interested in
having this support delivered within specific deadlines, you could
engage a partnership with Glencoe Software or contribute directly to
the development of the new reader (see [3] for examples where this has
worked well recently).


[1] https://trac.openmicroscopy.org/ome/ticket/4104 (Huygens ticket)

[2] http://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/

[3] http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/



On Mon, Sep 25, 2017 at 1:42 PM, Bruckbauer, Andreas
<a.bruckbauer at imperial.ac.uk> wrote:
> Huygens Core, part of the Huygens Software, is a full compute engine
> intended to run image processing and deconvolution jobs on large 64 bit
> multiprocessor servers. It has no specific graphical interface by itself.
> Huygens Remote Manager (HRM) is an open source web task manager for servers
> that can acts as an interface to Huygens Core to handle multi-user batch
> processing. HRM has an optimized interface connection to the open source
> OMERO server. Click here to try out HRM/Huygens Core on our online demo
> server.
>
> https://svi.nl/Huygens-Core

Thanks for pointing to this. Having others involved in the integration
effort is very welcome.

All the best,
~Josh


> Best wishes
> Andreas