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July 2010

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Subject:
From:
George McNamara <[log in to unmask]>
Reply To:
Confocal Microscopy List <[log in to unmask]>
Date:
Mon, 5 Jul 2010 14:09:09 -0400
Content-Type:
text/plain
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Hi Dan,

Read the article - page 2 says the next update will enable users to 
download data.

Dear listservites (or at least those interested in this thread),

Most journal's don't care how long the supplemental pdf is - see 
http://diabetes.diabetesjournals.org/content/59/4/947/suppl/DC1 for a 
recent paper whose supplemental file has 37 figures - about 32 of them images.

Sincerely,

George

At 05:26 AM 7/2/2010, you wrote:
>Dear Jason and All,
>
>
> >
> > Date:    Thu, 1 Jul 2010 17:19:28 +0100
> > From:    Jason Swedlow <[log in to unmask]>
> > Subject: Re: Preparing figures for publication --PPI vs DPI
> >
> > --0016363b9c82b21672048a55d56d
> > Content-Type: text/plain; charset=windows-1252
> > Content-Transfer-Encoding: quoted-printable
> >
> > ****COMPLETELY CONFLICTED RESPONSE******
> >
> > Dear All-
> >
> > Rants are fine, and necessary sometimes.  But it's worth considering real
> > work and activity in the directions you are discussing.
> >
> > We've posted previously to these lists, on just these issues.  The Journal
> > of Cell Biology, in collaboration with Glencoe Software, Inc. and the Open
> > Microscopy Environment, has started to build exactly the kind of
> > applications you are discussing.  Some links:
> >
> > The JCB DataViewer:  http://jcb-dataviewer.rupress.org/
> >
> > The original editorial:  http://jcb.rupress.org/content/183/6/969.full
> >
> > A recent commentary, that includes some info on where the DataViewer is
> > going, and some thoughts on standardized file formats:
> > http://jcb.rupress.org/content/189/5/777.full
> >
> > The JCB DataViewer is built on Bio-Formats and OMERO, open source resources
> > from the Open Microscopy Environment well known to this list.  For more
> > info:  http://www.openmicroscopy.org/
> >
> > Cheers,
> >
> > Jason
> > Cheers,
> >
> > Jason
>
>OME and Jason's group to the rescue!
>This is getting very close to what we need!
>
>A couple of comments:
>
>1) This is a great effort, but its only JCB.. right?
>What we really need is a public database using this kind of technology,
>where all publishes images go. Same model as the PDB or genbank etc.
>EuroBioImaging project needs to make this happen.... I hope we can 
>all support that.
>OME technology used there would be a great way to go I think.
>
>2) While one can browse the images on line in the viewer,
>one can not take the original images and inspect the metadata,
>and analyse the images however you like.
>Or can you also download the original images from there to your own computer?
>This is what PDB and genbank allow, and we also need that I strongly believe.
>I hope we can get the infrastructure together through the 
>EuroBioimaging Project.
>
>Great work JCB and Jason et al!
>
>cheers
>
>Dan
>
>
>
>
>Dr. Daniel James White BSc. (Hons.) PhD
>Senior Microscopist / Image Visualisation, Processing and Analysis
>Light Microscopy and Image Processing Facilities
>Max Planck Institute of Molecular Cell Biology and Genetics
>Pfotenhauerstrasse 108
>01307 DRESDEN
>Germany
>
>+49 (0)15114966933 (German Mobile)
>+49 (0)351 210 2627 (Work phone at MPI-CBG)
>+49 (0)351 210 1078 (Fax MPI-CBG LMF)
>
>http://www.bioimagexd.net       BioImageXD
>http://pacific.mpi-cbg.de               Fiji -  is just ImageJ 
>(Batteries Included)
>http://www.chalkie.org.uk               Dan's Homepages
>https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
>dan (at) chalkie.org.uk
>( white (at) mpi-cbg.de )







George McNamara, Ph.D.
Image Core Manager
Analytical Imaging Core Facility
University of Miami, Miller School of Medicine
Miami, FL 33136
[log in to unmask]
[log in to unmask]
305-243-8436 office
http://www.sylvester.org/AICF (Analytical Imaging Core Facility)
http://www.sylvester.org/AICF/pubspectra.zip (the entire 2000+ 
spectra .xlsx file is in the zip file)
http://home.earthlink.net/~geomcnamara

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