[ome-users] NIA Image Tables and Images.

Sat Jan 26 01:15:56 GMT 2008

When I try to run the script "perl dgas-templates.pl" after creating a user name I get this error:

--------------------------------------------------
Can't locate loadable object for module OME::Image::Pix in @INC (@INC contains: /n/site/inst/Linux-i686/bioinfo/seals/lib/perl /n/site/inst/shared/sys/lib/perl5/5.8.8/i686-linux-thread-multi-ld /n/site/inst/shared/sys/lib/perl5/5.8.8 /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.8/i686-linux-thread-multi-ld /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.8 /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6 /n/site/inst/shared/sys/lib/perl5/site_perl .) at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Image/LocalPixels.pm line 50
Compilation failed in require at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Image/LocalPixels.pm line 50.
BEGIN failed--compilation aborted at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Image/LocalPixels.pm line 50.
Compilation failed in require at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/PixelsManager.pm line 56.
BEGIN failed--compilation aborted at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/PixelsManager.pm line 56.
Compilation failed in require at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/ImageTasks.pm line 45.
BEGIN failed--compilation aborted at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/ImageTasks.pm line 45.
Compilation failed in require at dgas-templates.pl line 9.
BEGIN failed--compilation aborted at dgas-templates.pl line 9.
----------------------------------------------------

Can somebody help me out here ?  Our OME is running in CentOS release 5.

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

      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping
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