[ome-users] NIA Image Tables and Images.
Kasthuri Srinivasan Kannan
kasthurisrinivasan at yahoo.com
Fri Jan 25 22:14:20 GMT 2008
Dear Ilya:
Thanks for your immediate response. Once I added the user and ran the script I was able to see the images. However, I am not able to connect to the "http://localhost/perl2/serve.pl?Page=OME::Web::TableBrowse&Template=GeneManipulationTable".
I get this error:
Error serving OME::Web::TableBrowse: Malformed class name at /usr/lib/perl5/site_perl/5.8.8/OME/Web/ImageAnnotationTable.pm line 863Is there a problem with my installation/sematic type import ?
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 4:00:07 PM
Subject: Re: [ome-users] NIA Image Tables and Images.
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
>>
>>
>>
>>
>>
>>
>>
>>
>
>
>
>>
>
______________________________________________________________________
>>
>
______________
>>
>
Looking
>
for
>
last
>
minute
>
shopping
>
deals?
>>
>
Find
>
them
>
fast
>
with
>
Yahoo!
>
Search.
>
http://tools.search.yahoo.com/
>>
>
newsearch/category.php?category=shopping
>
>
>
>
>
>
>
>
>
______________________________________________________________________
>
______________
>
Looking
for
last
minute
shopping
deals?
>
Find
them
fast
with
Yahoo!
Search.
http://tools.search.yahoo.com/
>
newsearch/category.php?category=shopping
____________________________________________________________________________________
Never miss a thing. Make Yahoo your home page.
http://www.yahoo.com/r/hs
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