[ome-users] NIA Image Tables and Images.

[Ilya Goldberg]

Always useful to have another pair of eyes looking over this stuff...
The name of the file is DGAS_annotations.txt.
I'll patch the README.
Thanks,
Ilya

On Jan 24, 2008, at 5:48 PM, Kasthuri Srinivasan Kannan wrote:

> Hi Ilya:
>
> I sincerely thank you for the immediate response. I went through  
> the 'README' file that you had suggested and there it says I may  
> need to modify "ES_Bank_images.txt"  to have my username instead of  
> 'thomasmp'. I tried finding this file and I couldn't trace it. Can  
> you tell me where to look for this ? And by IDL, I meant the data  
> visualization tool which can be found at: http://www.ittvis.com/idl/
>
> Thanks.
> Kasthuri Kannan
>
> ----- Original Message ----
> From: Ilya Goldberg <igg at nih.gov>
> To: Kasthuri Srinivasan Kannan <kasthurisrinivasan at yahoo.com>
> Cc: ome-users at lists.openmicroscopy.org.uk
> Sent: Thursday, January 24, 2008 4:19:00 PM
> Subject: Re: [ome-users] NIA Image Tables and Images.
>
>
> Hi
> Kasthuri
> Harry
> Hochheiser
> and
> I
> are
> largely
> responsible
> for
> this
> example.
> The
> "How
> To"
> is
> a
> little
> bit
> out
> of
> date
> with
> regard
> to
> what
> was
> actually
> shipped
> in
> OME
> 2.6.1
> A
> bunch
> of
> the
> nomenclature
> (and
> filenames
> -
> sorry!)
> changed
> since
> the
> How
> To
> was
> written.
> The
> good
> news
> is
> that
> the
> capabilities
> and
> flexibility
> in
> 2.6.1
> is
> quite
> a
> bit
> more
> than
> what
> was
> described
> in
> the
> How
> To.
>
> I
> would
> recommend
> reading
> this
> file:
> OME/custom/DGAS-Annotations/README
> There
> are
> a
> handful
> of
> simple
> steps
> to
> take
> to
> import
> and
> annotate
> a
> set
> of
> images
> that
> come
> with
> the
> software
> distribution.
> The
> images
> are
> primarily
> annotated
> by
> manipulated
> gene
> (up
> or
> down-
> regulated),
> stain,
> antibody+gene,
> or
> in-situ-probe+gene.
> The
> gene
> annotations
> link
> out
> to
> entries
> in
> the
> NIA
> Mouse
> Gene
> Index.
> The
> images
> are
> screen-shots
> of
> text
> listing
> the
> annotations
> (just
> placeholders
> for
> real
> images).
>
> The
> viewer
> (which
> I
> think
> is
> the
> coolest
> part
> of
> all
> this)
> lets
> you
> compare
> groups
> of
> images
> based
> on
> the
> various
> annotation
> hierarchies
> in
> this
> example.
> The
> entire
> example/demo
> is
> self-contained
> so
> it
> is
> relatively
> straight-forward
> to
> extend
> it
> to
> more
> closely
> meet
> your
> needs.
> It
> should
> be
> very
> easy
> to
> set
> up,
> and
> I
> will
> be
> happy
> to
> help
> you
> if
> you
> run
> into
> trouble.
>
> Sorry,
> not
> sure
> what
> you
> mean
> by
> IDL
> -
> Corba's
> IDL?
> OME's
> design
> is
> somewhat
> informed
> by
> Corba,
> but
> is
> a
> vast
> simplification
> of
> all
> that
> it
> entails.
> -Ilya
>
>
> On
> Jan
> 24,
> 2008,
> at
> 4:28
> PM,
> Kasthuri
> Srinivasan
> Kannan
> wrote:
>
>>
> Hi:
>>
>>
> I
> thank
> the
> developers
> of
> OME.
> Its
> a
> nice
> tool.
> We
> are
> trying
> to
>>
> use
> OME
> for
> the
> microscopy
> data
> obtained
> in
> our
> institute.
> I
> went
>>
> through
> the
> "The
> Use,
> Configuration
> and
> Implementation
> of
> the
> OME
>>
> Image
> Table
> Tools"
> documentation
> in
> the
> "How
> To
> &
> User
> Guides"
> in
>>
> the
> OME
> page
> which
> I
> found
> pertinant
> to
> the
> kind
> of
> application
>>
> that
> we
> are
> working
> on.
> In
> the
> documentation,
> I
> found
> NIA
> mouse
>>
> development
> images
> and
> data
> model
> were
> taken
> as
> an
> example
> to
>>
> illiustrate
> the
> configuration
> and
> implementation
> of
> OME
> image
> table
>>
> tools.
> However,
> I
> was
> not
> able
> to
> see
> the
> NIA
> images
> or
> the
> tables
>>
> when
> I
> logged
> into
> the
> OME
> using
> the
> username
> and
> the
> password
>>
> assigned
> to
> me
> by
> my
> admin.
> Are
> those
> images
> availabe
> only
> using
>>
> the
> guest
> access
> mode?
> If
> not,
> what
> changes
> do
> the
> admin
> has
> to
>>
> make
> to
> view
> those
> NIA
> tables
> other
> than
> re-installing
> OME
> and
>>
> validating
> the
> guest
> user
> account?
> And
> where
> can
> I
> find
> the
>>
> "MouseAnnotations.ome"
> file?
> Also,
> it
> will
> be
> of
> help
> to
> know
> how
>>
> one
> can
> make
> changes
> (like
> defining
> a
> new
> semantic
> type)
> to
> the
>>
> already
> existing
> NIA
> templates
> and
> view
> the
> corresponding
> images
> in
>>
> the
> web
> based
> interface.
>>
>>
> Thanks.
>>
> Kasthuri
> Kannan.
>>
>>
> P.S:
> On
> a
> different
> note
> though,
> has
> anybody
> tried
> working
> with
> the
>>
> IDL
> and
> the
> OME?
>>
>>
>>
>>
>>
>
>
>
>>
> ______________________________________________________________________
>>
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>>
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> miss
> a
> thing.
> Make
> Yahoo
> your
> home
> page.
>>
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>>
> hs_______________________________________________
>>
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>>
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>>
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>
>
>
>
>
>
>
>        
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