[ome-users] NIA Image Tables and Images.

[Ilya Goldberg]

On Jan 25, 2008, at 4:47 PM, Kasthuri Srinivasan Kannan wrote:

> Thanks. One more question, sorry two more...
>
> 1. In the README file it says "visit http://localhost/perl2/ 
> serve.pl?Page=OME::Web::TableBrowse&Template=GeneManipulationTable"  
> and try playing with stuffs. I tried getting into this server (with  
> our local host name and even with the given name "localhost") and  
> its not  getting through. Do I need to do anything ? FYI, I did add  
> the 'thomasmp' user and installed the templates and the semantic  
> types.
>
> 2. Does "parseES-BankAnnotations.pl" should be  
> "parseDGASannotations.pl" as well ?

Yes, you are obviously correct.  I hide my face in shame...
Once your run the correct script, the images will be imported and  
annotated, and you should be able to see them.
Thanks for picking this out!
-Ilya


>
> Thanks.
> Kasthuri
>
> ----- 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: Friday, January 25, 2008 12:32:07 PM
> Subject: Re: [ome-users] NIA Image Tables and Images.
>
>
> 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?
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>>
>>
> ______________________________________________________________________
>>>
>>
> ______________
>>>
>>
> Never
>>
> miss
>>
> a
>>
> thing.
>>
> Make
>>
> Yahoo
>>
> your
>>
> home
>>
> page.
>>>
>>
> http://www.yahoo.com/r/
>>>
>>
> hs_______________________________________________
>>>
>>
> ome-users
>>
> mailing
>>
> list
>>>
>>
> ome-users at lists.openmicroscopy.org.uk
>>>
>>
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>>
>>
>>
>>
>>
>
>
>
>>
> ______________________________________________________________________
>>
> ______________
>>
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