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Subject: ome-users Digest, Vol 76, Issue 37
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Today's Topics:
1. OMERO R interface (Julio Mateos Langerak)
2. Re: OMERO R interface (Gregory Jefferis)
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Message: 1
Date: Fri, 29 Jul 2011 13:27:15 +0200
From: Julio Mateos Langerak <Julio.Mateos-Langerak at igh.cnrs.fr>
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] OMERO R interface
Message-ID: <E1A54123-3EEF-42BA-B633-69FE464EB9E5 at igh.cnrs.fr>
Content-Type: text/plain; charset="iso-8859-1"
Hi everyone,
Is there, or is someone working on a way to interface R with OMERO. The idea is use R to analyze the (meta)data linked to the images. In particular those coming from the high content screenings.
Thanks,
Julio
__________________________________________
Julio Mateos Langerak, PhD.
OMX manager
Arnaud de Villeneuve Campus Imaging Facility
Montpellier RIO Imaging
Montpellier BIOCAMPUS, UMS3426
Institut de G?n?tique Humaine-CNRS
141, rue de la Cardonille
F-34396 Montpellier (France)
e-mail: Julio.Mateos-Langerak at igh.cnrs.fr
phone: +33.4.34.35.99.90
fax: +33.4.34.35.99.01
URL: http://www.mri.cnrs.fr/
__________________________________________
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Message: 2
Date: Fri, 29 Jul 2011 12:46:58 +0100
From: Gregory Jefferis <jefferis at mrc-lmb.cam.ac.uk>
To: Julio Mateos Langerak <Julio.Mateos-Langerak at igh.cnrs.fr>
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] OMERO R interface
Message-ID: <4E329DB2.7080501 at mrc-lmb.cam.ac.uk>
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We are hesitating about whether to switch to OMERO for handling our own
large confocal image collection. We do a lot of post-hoc image analysis
and R is our glue platform for batch processing and final analysis. I
would therefore be interested to hear about this. What I can add is that
there are some existing bridges between R and ImageJ, but I have not got
round to trying these myself:
http://cran.r-project.org/web/packages/RImageJ/index.html
http://bio7.org/
You might then be able to load images from/into R via the ImageJ OMERO
plugins.
There are also RODBC and RpgSQL packages on CRAN that will let you talk
directly to the postgresql database.
Best wishes,
Greg.
> ------------------------------------------------------------------------
>
> Julio Mateos Langerak <mailto:Julio.Mateos-Langerak at igh.cnrs.fr>
> 29 July 2011 12:27
>
>
> Hi everyone,
>
> Is there, or is someone working on a way to interface R with OMERO.
> The idea is use R to analyze the (meta)data linked to the images. In
> particular those coming from the high content screenings.
>
> Thanks,
>
> Julio
> __________________________________________
> */Julio Mateos Langerak, PhD./*
> /OMX manager/
> Arnaud de Villeneuve Campus Imaging Facility
> Montpellier RIO Imaging
> Montpellier BIOCAMPUS, UMS3426
> Institut de G?n?tique Humaine-CNRS
> 141, rue de la Cardonille
> F-34396 Montpellier(France)
> e-mail: Julio.Mateos-Langerak at igh.cnrs.fr
> <mailto:Julio.Mateos-Langerak at igh.cnrs.fr>
> phone: +33.4.34.35.99.90
> fax: +33.4.34.35.99.01
> URL: http://www.mri.cnrs.fr/
> __________________________________________
>
>
>
>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
--
Gregory Jefferis, PhD jefferis at mrc-lmb.cam.ac.uk
Division of Neurobiology LMB Lab: +44 (0)1223 252943
MRC Laboratory of Molecular Biology, LMB Office:+44 (0)1223 252944
Hills Road, LMB Fax: +44 (0)1223 402310
Cambridge, CB2 0QH, UK.
http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://www.neuroscience.cam.ac.uk/directory/profile.php?gsxej2
http://flybrain.stanford.edu
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