[ome-users] Request for volunteers interested in integration with CellProfiler 2

[Adam Fraser]

This is wonderful news! I'm running your module now and I'm happy to say it
works as expected. :)

I hope you don't mind, but I have a handful of questions:

Would you mind if we included this module in CP2.0?

I noticed some #TODOs in the code. Perhaps we could help to check these off
of your list. Are there any features that would be particularly useful?

Are there any other CP-OMERO modules that you'd like to see written? eg:
Writing data back to the server?

Do you use CellProfiler Analyst for downstream analysis, and if so, do you
think you would benefit from a CPA-OMERO interface?

Do you are anyone in your group have some time to answer questions about how
you are using OMERO and CellProfiler? A 15 minute chat on Skype would be
greatly appreciated!

Thanks so much,
Adam

On Thu, Feb 10, 2011 at 2:21 AM, <b.gerritsen at nki.nl> wrote:

> Dear Adam Fraser,
>
> At the NKI we have been successfully using cellprofiler 2.0 and omero in an
> image analysis pipeline for some time now. In case you might be interested,
> attached is the latest version of the module we use to import plates,
> images, or datasets from omero into cellprofiler 2.0.
>
> Please let me know if it helps.
>
> Kind Regards,
> Bram Gerritsen
>
> PS: I have cc-ed this e-mail to the omero mailing list because there might
> be others interested as well.
>
> ________________________________________
> From: ome-users-bounces at lists.openmicroscopy.org.uk [
> ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Adam Fraser [
> afraser at broadinstitute.org]
> Sent: Wednesday, February 09, 2011 10:54 PM
> To: Josh Moore
> Cc: OME Users
> Subject: Re: [ome-users] Request for volunteers interested in integration
> with CellProfiler 2
>
> Thanks to Josh for sending this out, I guess I'll chime in briefly.
>
> First of all, this is a great opportunity for people who:
>
>  *   are using OMERO to organize and access your HCS data, and you would
> like an easier way to get your data into CellProfiler 2.0 for analysis.
>  *   are using CellProfiler for HCS image analysis and you'd benefit from a
> centralized data repository with easy-to-use tools for browsing and
> annotating your data.
>
> I've been a software engineer working in Anne Carpenter's group<
> http://www.broadinstitute.org/~anne/people.html> at the Broad Institute in
> Cambridge, MA for the past 3 years. I'm currently working to bridge the gap
> between OMERO and our current version of CellProfiler<
> http://cellprofiler.org/>, but unfortunately I have yet to find anyone who
> is using both tools or at least would like to. If this is something that
> interests you (anyone!), I'd love to hear your thoughts and ideas.
>
> I'm currently getting started by porting the existing OMERO CP modules<
> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroCellProfiler> from CP1.0
> to CP2.0. I've gotten the impression that this is something useful that
> people have been meaning to do, but once again, I'd love to hear from people
> with real use cases.
>
> Thanks,
> Adam Fraser
>
> On Fri, Feb 4, 2011 at 4:23 AM, Josh Moore <josh at glencoesoftware.com
> <mailto:josh at glencoesoftware.com>> wrote:
> Hi list,
>
> Adam Fraser from Broad Institue (CC'd) has started investigating the
> interface between CellProfiler / CellProfiler Analyst 2.0 and OMERO. We are
> certainly willing (and hopefully able!) to help him on the technical side of
> the integration, but were wondering if anyone could make suggestions on how
> to most quickly and effectively bring CP & CPA into a real OMERO user's
> workflow. "How is your data laid out?", "How has it been tagged &
> classified?", "How do you want to visualize and interact with your
> results?", "How should results be stored?" are among the questions which it
> might be good to have answers to. If you have time and are interested,
> either contact Adam directly or email the list.
>
> As always, thanks for your support.
> ~Josh
>
>
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