[ome-users] OMERO for Electron Microscopy

[Kim Linton]

Hi Jason,

Thank you for all the information, it has been very valuable to getting a
base understanding of how OMERO can support EM.

I should be able to get more of an idea about the type of EM next week when
I meet up with the researcher who asked the initial question.

Thanks again,
Kim

On 25 May 2012 09:20, Jason Swedlow <j.r.swedlow at dundee.ac.uk> wrote:

>  Hi Kim-
>
>
>
> As decribed in our recent paper on OMERO:
>
>
>
> http://www.openmicroscopy.org/site/about/publications
>
>
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> We’ve used OMERO to hold EM data of a variety of types:
>
>
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> http://emdb.openmicroscopy.org.uk/webemdb/
>
>
>
> I‘ve heard anecdotally of people using Columbus, Perkin-Elmer’s commercial
> version of OMERO, to manage EM data.  Obviously, if Bio-Formats supports
> the data, then OMERO (more or less) supports the data.
>
>
>
> OMERO’s data model, as released doesn’t explicitly include support for
> tomographic tilt series.  The data would go in, but the metadata will be
> wrong.  A proposed solution for this is here:
>
>
>
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> http://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/6d-7d-and-8d-storage
>
>
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> The only other issue will be images from very large format cameras—OMERO,
> as released will treat these images as “Big Images”, calculate pyramids etc.
>
>
>
> If you give us more detail about the specific type of electron microscopy
> you are interested in, we can probably tell you more about what you can and
> might do.
>
>
>
> Hope that helps.
>
>
>
> Cheers,
>
>
>
> Jason
>
>
>
> *From:* ome-users-bounces at lists.openmicroscopy.org.uk [mailto:
> ome-users-bounces at lists.openmicroscopy.org.uk] *On Behalf Of *Kim Linton
> *Sent:* Monday, May 21, 2012 7:44 AM
> *To:* ome-users at lists.openmicroscopy.org.uk
> *Subject:* [ome-users] OMERO for Electron Microscopy
>
>
>
> Hi There,
>
>
>
> I am interested to see if anyone has used OMERO for Electron Microscopy?
>
>
>
> From what I can tell the file format are part of bioformats.
>
>
>
> Cheers,
>
>
>
> Kim
>
>
>
> --
>
> Kim Linton
> Senior Research Systems Facilitator
> Monash e-Research Centre
> Building 75
> Monash University
> Clayton Victoria 3800, Australia
> Ph:      +61 3 99020712
>
> Mob:    0408 972 629
> Fax:    +61 3 9902-0193
> Email:  kim.linton at monash.edu
> Web:    http://www.monash.edu.au/eresearch
>
> Part time: Mon, Tues, Thurs & Fri
>
>
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Kim Linton
Senior Research Systems Facilitator/Lead for the e-Research Portfolio
Monash e-Research Centre
Building 75
Monash University
Clayton Victoria 3800, Australia
Ph:      +61 3 99020712
Mob:    0408 972 629
Fax:    +61 3 9902-0193
Email:  kim.linton at monash.edu
Web:    http://www.monash.edu.au/eresearch
Part time: Mon, Tues, Thurs & Fri
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