[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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