[ome-users] NIA Image Tables and Images.
Kasthuri Srinivasan Kannan
kasthurisrinivasan at yahoo.com
Fri Jan 25 21:47:41 GMT 2008
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 ?
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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>
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