[ome-users] [ome-devel] What OME Means to You

[Lee Kamentsky]

Hi Jason, hope the meeting went well, sorry about the late reply, but just
getting back from a vacation. I'm somewhat invested in OMERO and
Bio-Formats and if  you want me to write a letter of support detailing how
CellProfiler relies on them, our participation in your effort (e.g. the new
Python-bioformats bridge, CP/OMERO integration and our contributions to the
Bio-formats codebase) and what we hope to gain from the next cycle of
funding, I'd be glad to do that (or to work with Anne if you want it to
come from her hand, assuming she's willing). Regarding future direction,
here are some bullet-points outlining what I would hope from the next
funding cycle, ordered in terms of importance to us:

* Maintenance on Bio-Formats: this is crucial for CP, to have issues in
Bio-Formats addressed, formats added and to have continued infrastructure
improvements such as your recent elimination of Java AWT dependencies.

* Scalability enhancements to OMERO: by far, our most crucial need from
OMERO is that it scale to the size of our experiments and to the demands
required by cloud / server-farm massively parallel access to that data. We
will probably pilot use of OMERO for large-scale experiments (on the order
of 1,000,000 images and simultaneous access by several hundred compute
nodes) in the timeframe of the next grant cycle. OMERO offers a scalable
solution for us when accessing the metadata for such a large-scale
experiment - our current mechanism of parsing metadata from directory
listings is both prone to error and does not scale well to this experiment
size, so OMERO offers a decided advantage.

* CellProfiler / OMERO integration: we are looking forward to features to
be added to OMERO that are specifically designed for integration with
CellProfiler such as export of worklists of images to be processed and
execution of CellProfiler on the server back-end. While these are not
necessary for our internal work, we feel they will be utilized by
CellProfiler users in the community at-large and will lead to increased use
of both CellProfiler and OMERO.

* Feature storage: we welcome the opportunity to add export capabilities to
CellProfiler to upload feature measurements to OMERO based on CellProfiler
analysis of images stored in the OMERO database.

* Standards work: we welcome and depend on maintenance of the OME data
model including standards for storing feature measurements and segmentation
results.

--Lee


On Tue, Jun 3, 2014 at 1:22 PM, Jason Swedlow <j.r.swedlow at dundee.ac.uk>
wrote:

> Dear All
>
> As Helen mentioned, it's time for our annual trek to Paris, for the
> highlight of our year, the OME Annual Users Meeting.  We're excited to
> present what we've been doing and most importantly, hear ideas for future
> priorities and work.  We'll post regular updates and the presentations, as
> always.
>
> However, it's also time for another regular rite-- the funding of OME's
> next steps.  As many of you know, OME is funded by a combination of funding
> from the Wellcome Trust and the BBSRC.  Our main funding comes from a
> Wellcome Trust Strategic Award, which runs through the end of 2014.  We are
> now applying for another Strategic Award, which we have proposed to be
> funded by the Wellcome Trust and the BBSRC.  We're proposing the funding
> run through 2017.
>
> A critical part of this application is feedback from the community-- what
> you like, what you don't, and what you think we should do.
>
> So, we'd ask you to send your thoughts, suggestions and ideas by email to
> me privately, or this list-- whichever you prefer.  Tell us how you use
> OME's tools, how you see the project's work, and anything in particular you
> think we should be doing in the future. Obviously, we have our own ideas,
> but in this exercise, we want to hear yours.  Finally, if you could change
> one thing about OME, what would it be?
>
> Please send feedback through the month of June. Thanks in advance for your
> comments and ideas.
>
> Cheers,
>
> Jason
>
> Centre for Gene Regulation & Expression | Open Microscopy Environment |
> University of Dundee
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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>
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