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

[b.gerritsen at nki.nl]

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

Thanks! We do not mind at all, so feel free to include it.

> 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?

None of the todos contain anything urgent on our end, though it might be different for other users. Currently the module is sufficient for our needs and we have no immediate requests. Thanks for the offer!

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

Not yet.

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

Yes, we would be interested in a CPA-OMERO interface. Currently it's not yet part of the pipeline, but we were intending to integrate it in the near future.

> 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!

That should be possible.


Kind Regards,
Bram

________________________________________
From: adam.n.fraser at gmail.com [adam.n.fraser at gmail.com] On Behalf Of Adam Fraser [afraser at broadinstitute.org]
Sent: Thursday, February 10, 2011 4:57 PM
To: Bram Gerritsen
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Request for volunteers interested in integration with CellProfiler 2

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<mailto: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<mailto:ome-users-bounces at lists.openmicroscopy.org.uk> [ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>] On Behalf Of Adam Fraser [afraser at broadinstitute.org<mailto: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><mailto: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