<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">When I try to run the script "perl dgas-templates.pl" after creating a user name I get this error:<br><br>--------------------------------------------------<br>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<br>Compilation failed
in require at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Image/LocalPixels.pm line 50.<br>BEGIN failed--compilation aborted at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Image/LocalPixels.pm line 50.<br>Compilation failed in require at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/PixelsManager.pm line 56.<br>BEGIN failed--compilation aborted at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/PixelsManager.pm line 56.<br>Compilation failed in require at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/ImageTasks.pm line 45.<br>BEGIN failed--compilation aborted at /n/site/inst/shared/sys/lib/perl5/site_perl/5.8.6/OME/Tasks/ImageTasks.pm line 45.<br>Compilation failed in require at dgas-templates.pl line 9.<br>BEGIN failed--compilation aborted at dgas-templates.pl line 9.<br>----------------------------------------------------<br><br>Can somebody help me out here ? Our OME is running in
CentOS release 5.<br><br>Thanks.<br>Kasthuri<br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Ilya Goldberg <igg@nih.gov><br>To: Kasthuri Srinivasan Kannan <kasthurisrinivasan@yahoo.com><br>Cc: ome-users@lists.openmicroscopy.org.uk<br>Sent: Friday, January 25, 2008 4:00:07 PM<br>Subject: Re: [ome-users] NIA Image Tables and Images.<br><br>
<br>On
Jan
25,
2008,
at
4:47
PM,
Kasthuri
Srinivasan
Kannan
wrote:<br><br>>
Thanks.
One
more
question,
sorry
two
more...<br>><br>>
1.
In
the
README
file
it
says
"visit
<a href="http://localhost/perl2/" target="_blank">http://localhost/perl2/</a> <br>>
<a target="_blank" href="http://serve.pl">serve.pl</a>?Page=OME::Web::TableBrowse&Template=GeneManipulationTable" <br>>
and
try
playing
with
stuffs.
I
tried
getting
into
this
server
(with <br>>
our
local
host
name
and
even
with
the
given
name
"localhost")
and <br>>
its
not
getting
through.
Do
I
need
to
do
anything
?
FYI,
I
did
add <br>>
the
'thomasmp'
user
and
installed
the
templates
and
the
semantic <br>>
types.<br>><br>>
2.
Does
"<a target="_blank" href="http://parseES-BankAnnotations.pl">parseES-BankAnnotations.pl</a>"
should
be <br>>
"<a target="_blank" href="http://parseDGASannotations.pl">parseDGASannotations.pl</a>"
as
well
?<br><br>Yes,
you
are
obviously
correct.
I
hide
my
face
in
shame...<br>Once
your
run
the
correct
script,
the
images
will
be
imported
and <br>annotated,
and
you
should
be
able
to
see
them.<br>Thanks
for
picking
this
out!<br>-Ilya<br><br><br>><br>>
Thanks.<br>>
Kasthuri<br>><br>>
-----
Original
Message
----<br>>
From:
Ilya
Goldberg
<<a ymailto="mailto:igg@nih.gov" href="mailto:igg@nih.gov">igg@nih.gov</a>><br>>
To:
Kasthuri
Srinivasan
Kannan
<<a ymailto="mailto:kasthurisrinivasan@yahoo.com" href="mailto:kasthurisrinivasan@yahoo.com">kasthurisrinivasan@yahoo.com</a>><br>>
Cc:
<a ymailto="mailto:ome-users@lists.openmicroscopy.org.uk" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>>
Sent:
Friday,
January
25,
2008
12:32:07
PM<br>>
Subject:
Re:
[ome-users]
NIA
Image
Tables
and
Images.<br>><br>><br>>
Always<br>>
useful<br>>
to<br>>
have<br>>
another<br>>
pair<br>>
of<br>>
eyes<br>>
looking<br>>
over<br>>
this<br>>
stuff...<br>>
The<br>>
name<br>>
of<br>>
the<br>>
file<br>>
is<br>>
DGAS_annotations.txt.<br>>
I'll<br>>
patch<br>>
the<br>>
README.<br>>
Thanks,<br>>
Ilya<br>><br>>
On<br>>
Jan<br>>
24,<br>>
2008,<br>>
at<br>>
5:48<br>>
PM,<br>>
Kasthuri<br>>
Srinivasan<br>>
Kannan<br>>
wrote:<br>><br>>><br>>
Hi<br>>
Ilya:<br>>><br>>><br>>
I<br>>
sincerely<br>>
thank<br>>
you<br>>
for<br>>
the<br>>
immediate<br>>
response.<br>>
I<br>>
went<br>>
through<br>>><br>>
the<br>>
'README'<br>>
file<br>>
that<br>>
you<br>>
had<br>>
suggested<br>>
and<br>>
there<br>>
it<br>>
says<br>>
I<br>>
may<br>>><br>>
need<br>>
to<br>>
modify<br>>
"ES_Bank_images.txt"<br>>
to<br>>
have<br>>
my<br>>
username<br>>
instead<br>>
of<br>>><br>>
'thomasmp'.<br>>
I<br>>
tried<br>>
finding<br>>
this<br>>
file<br>>
and<br>>
I<br>>
couldn't<br>>
trace<br>>
it.<br>>
Can<br>>><br>>
you<br>>
tell<br>>
me<br>>
where<br>>
to<br>>
look<br>>
for<br>>
this<br>>
?<br>>
And<br>>
by<br>>
IDL,<br>>
I<br>>
meant<br>>
the<br>>
data<br>>><br>>
visualization<br>>
tool<br>>
which<br>>
can<br>>
be<br>>
found<br>>
at:<br>>
<a href="http://www.ittvis.com/idl/" target="_blank">http://www.ittvis.com/idl/</a><br>>><br>>><br>>
Thanks.<br>>><br>>
Kasthuri<br>>
Kannan<br>>><br>>><br>>
-----<br>>
Original<br>>
Message<br>>
----<br>>><br>>
From:<br>>
Ilya<br>>
Goldberg<br>>
<<a ymailto="mailto:igg@nih.gov" href="mailto:igg@nih.gov">igg@nih.gov</a>><br>>><br>>
To:<br>>
Kasthuri<br>>
Srinivasan<br>>
Kannan<br>>
<<a ymailto="mailto:kasthurisrinivasan@yahoo.com" href="mailto:kasthurisrinivasan@yahoo.com">kasthurisrinivasan@yahoo.com</a>><br>>><br>>
Cc:<br>>
<a ymailto="mailto:ome-users@lists.openmicroscopy.org.uk" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>>><br>>
Sent:<br>>
Thursday,<br>>
January<br>>
24,<br>>
2008<br>>
4:19:00<br>>
PM<br>>><br>>
Subject:<br>>
Re:<br>>
[ome-users]<br>>
NIA<br>>
Image<br>>
Tables<br>>
and<br>>
Images.<br>>><br>>><br>>><br>>
Hi<br>>><br>>
Kasthuri<br>>><br>>
Harry<br>>><br>>
Hochheiser<br>>><br>>
and<br>>><br>>
I<br>>><br>>
are<br>>><br>>
largely<br>>><br>>
responsible<br>>><br>>
for<br>>><br>>
this<br>>><br>>
example.<br>>><br>>
The<br>>><br>>
"How<br>>><br>>
To"<br>>><br>>
is<br>>><br>>
a<br>>><br>>
little<br>>><br>>
bit<br>>><br>>
out<br>>><br>>
of<br>>><br>>
date<br>>><br>>
with<br>>><br>>
regard<br>>><br>>
to<br>>><br>>
what<br>>><br>>
was<br>>><br>>
actually<br>>><br>>
shipped<br>>><br>>
in<br>>><br>>
OME<br>>><br>>
2.6.1<br>>><br>>
A<br>>><br>>
bunch<br>>><br>>
of<br>>><br>>
the<br>>><br>>
nomenclature<br>>><br>>
(and<br>>><br>>
filenames<br>>><br>>
-<br>>><br>>
sorry!)<br>>><br>>
changed<br>>><br>>
since<br>>><br>>
the<br>>><br>>
How<br>>><br>>
To<br>>><br>>
was<br>>><br>>
written.<br>>><br>>
The<br>>><br>>
good<br>>><br>>
news<br>>><br>>
is<br>>><br>>
that<br>>><br>>
the<br>>><br>>
capabilities<br>>><br>>
and<br>>><br>>
flexibility<br>>><br>>
in<br>>><br>>
2.6.1<br>>><br>>
is<br>>><br>>
quite<br>>><br>>
a<br>>><br>>
bit<br>>><br>>
more<br>>><br>>
than<br>>><br>>
what<br>>><br>>
was<br>>><br>>
described<br>>><br>>
in<br>>><br>>
the<br>>><br>>
How<br>>><br>>
To.<br>>><br>>><br>>
I<br>>><br>>
would<br>>><br>>
recommend<br>>><br>>
reading<br>>><br>>
this<br>>><br>>
file:<br>>><br>>
OME/custom/DGAS-Annotations/README<br>>><br>>
There<br>>><br>>
are<br>>><br>>
a<br>>><br>>
handful<br>>><br>>
of<br>>><br>>
simple<br>>><br>>
steps<br>>><br>>
to<br>>><br>>
take<br>>><br>>
to<br>>><br>>
import<br>>><br>>
and<br>>><br>>
annotate<br>>><br>>
a<br>>><br>>
set<br>>><br>>
of<br>>><br>>
images<br>>><br>>
that<br>>><br>>
come<br>>><br>>
with<br>>><br>>
the<br>>><br>>
software<br>>><br>>
distribution.<br>>><br>>
The<br>>><br>>
images<br>>><br>>
are<br>>><br>>
primarily<br>>><br>>
annotated<br>>><br>>
by<br>>><br>>
manipulated<br>>><br>>
gene<br>>><br>>
(up<br>>><br>>
or<br>>><br>>
down-<br>>><br>>
regulated),<br>>><br>>
stain,<br>>><br>>
antibody+gene,<br>>><br>>
or<br>>><br>>
in-situ-probe+gene.<br>>><br>>
The<br>>><br>>
gene<br>>><br>>
annotations<br>>><br>>
link<br>>><br>>
out<br>>><br>>
to<br>>><br>>
entries<br>>><br>>
in<br>>><br>>
the<br>>><br>>
NIA<br>>><br>>
Mouse<br>>><br>>
Gene<br>>><br>>
Index.<br>>><br>>
The<br>>><br>>
images<br>>><br>>
are<br>>><br>>
screen-shots<br>>><br>>
of<br>>><br>>
text<br>>><br>>
listing<br>>><br>>
the<br>>><br>>
annotations<br>>><br>>
(just<br>>><br>>
placeholders<br>>><br>>
for<br>>><br>>
real<br>>><br>>
images).<br>>><br>>><br>>
The<br>>><br>>
viewer<br>>><br>>
(which<br>>><br>>
I<br>>><br>>
think<br>>><br>>
is<br>>><br>>
the<br>>><br>>
coolest<br>>><br>>
part<br>>><br>>
of<br>>><br>>
all<br>>><br>>
this)<br>>><br>>
lets<br>>><br>>
you<br>>><br>>
compare<br>>><br>>
groups<br>>><br>>
of<br>>><br>>
images<br>>><br>>
based<br>>><br>>
on<br>>><br>>
the<br>>><br>>
various<br>>><br>>
annotation<br>>><br>>
hierarchies<br>>><br>>
in<br>>><br>>
this<br>>><br>>
example.<br>>><br>>
The<br>>><br>>
entire<br>>><br>>
example/demo<br>>><br>>
is<br>>><br>>
self-contained<br>>><br>>
so<br>>><br>>
it<br>>><br>>
is<br>>><br>>
relatively<br>>><br>>
straight-forward<br>>><br>>
to<br>>><br>>
extend<br>>><br>>
it<br>>><br>>
to<br>>><br>>
more<br>>><br>>
closely<br>>><br>>
meet<br>>><br>>
your<br>>><br>>
needs.<br>>><br>>
It<br>>><br>>
should<br>>><br>>
be<br>>><br>>
very<br>>><br>>
easy<br>>><br>>
to<br>>><br>>
set<br>>><br>>
up,<br>>><br>>
and<br>>><br>>
I<br>>><br>>
will<br>>><br>>
be<br>>><br>>
happy<br>>><br>>
to<br>>><br>>
help<br>>><br>>
you<br>>><br>>
if<br>>><br>>
you<br>>><br>>
run<br>>><br>>
into<br>>><br>>
trouble.<br>>><br>>><br>>
Sorry,<br>>><br>>
not<br>>><br>>
sure<br>>><br>>
what<br>>><br>>
you<br>>><br>>
mean<br>>><br>>
by<br>>><br>>
IDL<br>>><br>>
-<br>>><br>>
Corba's<br>>><br>>
IDL?<br>>><br>>
OME's<br>>><br>>
design<br>>><br>>
is<br>>><br>>
somewhat<br>>><br>>
informed<br>>><br>>
by<br>>><br>>
Corba,<br>>><br>>
but<br>>><br>>
is<br>>><br>>
a<br>>><br>>
vast<br>>><br>>
simplification<br>>><br>>
of<br>>><br>>
all<br>>><br>>
that<br>>><br>>
it<br>>><br>>
entails.<br>>><br>>
-Ilya<br>>><br>>><br>>><br>>
On<br>>><br>>
Jan<br>>><br>>
24,<br>>><br>>
2008,<br>>><br>>
at<br>>><br>>
4:28<br>>><br>>
PM,<br>>><br>>
Kasthuri<br>>><br>>
Srinivasan<br>>><br>>
Kannan<br>>><br>>
wrote:<br>>><br>>>><br>>><br>>
Hi:<br>>>><br>>>><br>>><br>>
I<br>>><br>>
thank<br>>><br>>
the<br>>><br>>
developers<br>>><br>>
of<br>>><br>>
OME.<br>>><br>>
Its<br>>><br>>
a<br>>><br>>
nice<br>>><br>>
tool.<br>>><br>>
We<br>>><br>>
are<br>>><br>>
trying<br>>><br>>
to<br>>>><br>>><br>>
use<br>>><br>>
OME<br>>><br>>
for<br>>><br>>
the<br>>><br>>
microscopy<br>>><br>>
data<br>>><br>>
obtained<br>>><br>>
in<br>>><br>>
our<br>>><br>>
institute.<br>>><br>>
I<br>>><br>>
went<br>>>><br>>><br>>
through<br>>><br>>
the<br>>><br>>
"The<br>>><br>>
Use,<br>>><br>>
Configuration<br>>><br>>
and<br>>><br>>
Implementation<br>>><br>>
of<br>>><br>>
the<br>>><br>>
OME<br>>>><br>>><br>>
Image<br>>><br>>
Table<br>>><br>>
Tools"<br>>><br>>
documentation<br>>><br>>
in<br>>><br>>
the<br>>><br>>
"How<br>>><br>>
To<br>>><br>>
&<br>>><br>>
User<br>>><br>>
Guides"<br>>><br>>
in<br>>>><br>>><br>>
the<br>>><br>>
OME<br>>><br>>
page<br>>><br>>
which<br>>><br>>
I<br>>><br>>
found<br>>><br>>
pertinant<br>>><br>>
to<br>>><br>>
the<br>>><br>>
kind<br>>><br>>
of<br>>><br>>
application<br>>>><br>>><br>>
that<br>>><br>>
we<br>>><br>>
are<br>>><br>>
working<br>>><br>>
on.<br>>><br>>
In<br>>><br>>
the<br>>><br>>
documentation,<br>>><br>>
I<br>>><br>>
found<br>>><br>>
NIA<br>>><br>>
mouse<br>>>><br>>><br>>
development<br>>><br>>
images<br>>><br>>
and<br>>><br>>
data<br>>><br>>
model<br>>><br>>
were<br>>><br>>
taken<br>>><br>>
as<br>>><br>>
an<br>>><br>>
example<br>>><br>>
to<br>>>><br>>><br>>
illiustrate<br>>><br>>
the<br>>><br>>
configuration<br>>><br>>
and<br>>><br>>
implementation<br>>><br>>
of<br>>><br>>
OME<br>>><br>>
image<br>>><br>>
table<br>>>><br>>><br>>
tools.<br>>><br>>
However,<br>>><br>>
I<br>>><br>>
was<br>>><br>>
not<br>>><br>>
able<br>>><br>>
to<br>>><br>>
see<br>>><br>>
the<br>>><br>>
NIA<br>>><br>>
images<br>>><br>>
or<br>>><br>>
the<br>>><br>>
tables<br>>>><br>>><br>>
when<br>>><br>>
I<br>>><br>>
logged<br>>><br>>
into<br>>><br>>
the<br>>><br>>
OME<br>>><br>>
using<br>>><br>>
the<br>>><br>>
username<br>>><br>>
and<br>>><br>>
the<br>>><br>>
password<br>>>><br>>><br>>
assigned<br>>><br>>
to<br>>><br>>
me<br>>><br>>
by<br>>><br>>
my<br>>><br>>
admin.<br>>><br>>
Are<br>>><br>>
those<br>>><br>>
images<br>>><br>>
availabe<br>>><br>>
only<br>>><br>>
using<br>>>><br>>><br>>
the<br>>><br>>
guest<br>>><br>>
access<br>>><br>>
mode?<br>>><br>>
If<br>>><br>>
not,<br>>><br>>
what<br>>><br>>
changes<br>>><br>>
do<br>>><br>>
the<br>>><br>>
admin<br>>><br>>
has<br>>><br>>
to<br>>>><br>>><br>>
make<br>>><br>>
to<br>>><br>>
view<br>>><br>>
those<br>>><br>>
NIA<br>>><br>>
tables<br>>><br>>
other<br>>><br>>
than<br>>><br>>
re-installing<br>>><br>>
OME<br>>><br>>
and<br>>>><br>>><br>>
validating<br>>><br>>
the<br>>><br>>
guest<br>>><br>>
user<br>>><br>>
account?<br>>><br>>
And<br>>><br>>
where<br>>><br>>
can<br>>><br>>
I<br>>><br>>
find<br>>><br>>
the<br>>>><br>>><br>>
"MouseAnnotations.ome"<br>>><br>>
file?<br>>><br>>
Also,<br>>><br>>
it<br>>><br>>
will<br>>><br>>
be<br>>><br>>
of<br>>><br>>
help<br>>><br>>
to<br>>><br>>
know<br>>><br>>
how<br>>>><br>>><br>>
one<br>>><br>>
can<br>>><br>>
make<br>>><br>>
changes<br>>><br>>
(like<br>>><br>>
defining<br>>><br>>
a<br>>><br>>
new<br>>><br>>
semantic<br>>><br>>
type)<br>>><br>>
to<br>>><br>>
the<br>>>><br>>><br>>
already<br>>><br>>
existing<br>>><br>>
NIA<br>>><br>>
templates<br>>><br>>
and<br>>><br>>
view<br>>><br>>
the<br>>><br>>
corresponding<br>>><br>>
images<br>>><br>>
in<br>>>><br>>><br>>
the<br>>><br>>
web<br>>><br>>
based<br>>><br>>
interface.<br>>>><br>>>><br>>><br>>
Thanks.<br>>>><br>>><br>>
Kasthuri<br>>><br>>
Kannan.<br>>>><br>>>><br>>><br>>
P.S:<br>>><br>>
On<br>>><br>>
a<br>>><br>>
different<br>>><br>>
note<br>>><br>>
though,<br>>><br>>
has<br>>><br>>
anybody<br>>><br>>
tried<br>>><br>>
working<br>>><br>>
with<br>>><br>>
the<br>>>><br>>><br>>
IDL<br>>><br>>
and<br>>><br>>
the<br>>><br>>
OME?<br>>>><br>>>><br>>>><br>>>><br>>>><br>>><br>>><br>>><br>>>><br>>><br>>
______________________________________________________________________<br>>>><br>>><br>>
______________<br>>>><br>>><br>>
Never<br>>><br>>
miss<br>>><br>>
a<br>>><br>>
thing.<br>>><br>>
Make<br>>><br>>
Yahoo<br>>><br>>
your<br>>><br>>
home<br>>><br>>
page.<br>>>><br>>><br>>
<a href="http://www.yahoo.com/r/" target="_blank">http://www.yahoo.com/r/</a><br>>>><br>>><br>>
hs_______________________________________________<br>>>><br>>><br>>
ome-users<br>>><br>>
mailing<br>>><br>>
list<br>>>><br>>><br>>
<a ymailto="mailto:ome-users@lists.openmicroscopy.org.uk" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>>>><br>>><br>>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>>><br>>><br>>><br>>><br>>><br>>><br>>><br>>><br>><br>><br>><br>>><br>>
______________________________________________________________________<br>>><br>>
______________<br>>><br>>
Looking<br>>
for<br>>
last<br>>
minute<br>>
shopping<br>>
deals?<br>>><br>>
Find<br>>
them<br>>
fast<br>>
with<br>>
Yahoo!<br>>
Search.<br>>
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newsearch/category.php?category=shopping<br>><br>><br>><br>><br>><br>><br>><br>>
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______________________________________________________________________ <br>>
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for
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shopping
deals?<br>>
Find
them
fast
with
Yahoo!
Search.
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