<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;">Thanks. One more question, sorry two more...<br><br><span>1. In the README file it says "visit <a target="_blank" href="http://localhost/perl2/serve.pl?Page=OME::Web::TableBrowse&Template=GeneManipulationTable">http://localhost/perl2/serve.pl?Page=OME::Web::TableBrowse&Template=GeneManipulationTable</a>" 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.</span><br> <br>2. Does "parseES-BankAnnotations.pl" should be "parseDGASannotations.pl" as well
?<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 12:32:07 PM<br>Subject: Re: [ome-users] NIA Image Tables and Images.<br><br>
Always
useful
to
have
another
pair
of
eyes
looking
over
this
stuff...<br>The
name
of
the
file
is
DGAS_annotations.txt.<br>I'll
patch
the
README.<br>Thanks,<br>Ilya<br><br>On
Jan
24,
2008,
at
5:48
PM,
Kasthuri
Srinivasan
Kannan
wrote:<br><br>>
Hi
Ilya:<br>><br>>
I
sincerely
thank
you
for
the
immediate
response.
I
went
through <br>>
the
'README'
file
that
you
had
suggested
and
there
it
says
I
may <br>>
need
to
modify
"ES_Bank_images.txt"
to
have
my
username
instead
of <br>>
'thomasmp'.
I
tried
finding
this
file
and
I
couldn't
trace
it.
Can <br>>
you
tell
me
where
to
look
for
this
?
And
by
IDL,
I
meant
the
data <br>>
visualization
tool
which
can
be
found
at:
<a href="http://www.ittvis.com/idl/" target="_blank">http://www.ittvis.com/idl/</a><br>><br>>
Thanks.<br>>
Kasthuri
Kannan<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:
Thursday,
January
24,
2008
4:19:00
PM<br>>
Subject:
Re:
[ome-users]
NIA
Image
Tables
and
Images.<br>><br>><br>>
Hi<br>>
Kasthuri<br>>
Harry<br>>
Hochheiser<br>>
and<br>>
I<br>>
are<br>>
largely<br>>
responsible<br>>
for<br>>
this<br>>
example.<br>>
The<br>>
"How<br>>
To"<br>>
is<br>>
a<br>>
little<br>>
bit<br>>
out<br>>
of<br>>
date<br>>
with<br>>
regard<br>>
to<br>>
what<br>>
was<br>>
actually<br>>
shipped<br>>
in<br>>
OME<br>>
2.6.1<br>>
A<br>>
bunch<br>>
of<br>>
the<br>>
nomenclature<br>>
(and<br>>
filenames<br>>
-<br>>
sorry!)<br>>
changed<br>>
since<br>>
the<br>>
How<br>>
To<br>>
was<br>>
written.<br>>
The<br>>
good<br>>
news<br>>
is<br>>
that<br>>
the<br>>
capabilities<br>>
and<br>>
flexibility<br>>
in<br>>
2.6.1<br>>
is<br>>
quite<br>>
a<br>>
bit<br>>
more<br>>
than<br>>
what<br>>
was<br>>
described<br>>
in<br>>
the<br>>
How<br>>
To.<br>><br>>
I<br>>
would<br>>
recommend<br>>
reading<br>>
this<br>>
file:<br>>
OME/custom/DGAS-Annotations/README<br>>
There<br>>
are<br>>
a<br>>
handful<br>>
of<br>>
simple<br>>
steps<br>>
to<br>>
take<br>>
to<br>>
import<br>>
and<br>>
annotate<br>>
a<br>>
set<br>>
of<br>>
images<br>>
that<br>>
come<br>>
with<br>>
the<br>>
software<br>>
distribution.<br>>
The<br>>
images<br>>
are<br>>
primarily<br>>
annotated<br>>
by<br>>
manipulated<br>>
gene<br>>
(up<br>>
or<br>>
down-<br>>
regulated),<br>>
stain,<br>>
antibody+gene,<br>>
or<br>>
in-situ-probe+gene.<br>>
The<br>>
gene<br>>
annotations<br>>
link<br>>
out<br>>
to<br>>
entries<br>>
in<br>>
the<br>>
NIA<br>>
Mouse<br>>
Gene<br>>
Index.<br>>
The<br>>
images<br>>
are<br>>
screen-shots<br>>
of<br>>
text<br>>
listing<br>>
the<br>>
annotations<br>>
(just<br>>
placeholders<br>>
for<br>>
real<br>>
images).<br>><br>>
The<br>>
viewer<br>>
(which<br>>
I<br>>
think<br>>
is<br>>
the<br>>
coolest<br>>
part<br>>
of<br>>
all<br>>
this)<br>>
lets<br>>
you<br>>
compare<br>>
groups<br>>
of<br>>
images<br>>
based<br>>
on<br>>
the<br>>
various<br>>
annotation<br>>
hierarchies<br>>
in<br>>
this<br>>
example.<br>>
The<br>>
entire<br>>
example/demo<br>>
is<br>>
self-contained<br>>
so<br>>
it<br>>
is<br>>
relatively<br>>
straight-forward<br>>
to<br>>
extend<br>>
it<br>>
to<br>>
more<br>>
closely<br>>
meet<br>>
your<br>>
needs.<br>>
It<br>>
should<br>>
be<br>>
very<br>>
easy<br>>
to<br>>
set<br>>
up,<br>>
and<br>>
I<br>>
will<br>>
be<br>>
happy<br>>
to<br>>
help<br>>
you<br>>
if<br>>
you<br>>
run<br>>
into<br>>
trouble.<br>><br>>
Sorry,<br>>
not<br>>
sure<br>>
what<br>>
you<br>>
mean<br>>
by<br>>
IDL<br>>
-<br>>
Corba's<br>>
IDL?<br>>
OME's<br>>
design<br>>
is<br>>
somewhat<br>>
informed<br>>
by<br>>
Corba,<br>>
but<br>>
is<br>>
a<br>>
vast<br>>
simplification<br>>
of<br>>
all<br>>
that<br>>
it<br>>
entails.<br>>
-Ilya<br>><br>><br>>
On<br>>
Jan<br>>
24,<br>>
2008,<br>>
at<br>>
4:28<br>>
PM,<br>>
Kasthuri<br>>
Srinivasan<br>>
Kannan<br>>
wrote:<br>><br>>><br>>
Hi:<br>>><br>>><br>>
I<br>>
thank<br>>
the<br>>
developers<br>>
of<br>>
OME.<br>>
Its<br>>
a<br>>
nice<br>>
tool.<br>>
We<br>>
are<br>>
trying<br>>
to<br>>><br>>
use<br>>
OME<br>>
for<br>>
the<br>>
microscopy<br>>
data<br>>
obtained<br>>
in<br>>
our<br>>
institute.<br>>
I<br>>
went<br>>><br>>
through<br>>
the<br>>
"The<br>>
Use,<br>>
Configuration<br>>
and<br>>
Implementation<br>>
of<br>>
the<br>>
OME<br>>><br>>
Image<br>>
Table<br>>
Tools"<br>>
documentation<br>>
in<br>>
the<br>>
"How<br>>
To<br>>
&<br>>
User<br>>
Guides"<br>>
in<br>>><br>>
the<br>>
OME<br>>
page<br>>
which<br>>
I<br>>
found<br>>
pertinant<br>>
to<br>>
the<br>>
kind<br>>
of<br>>
application<br>>><br>>
that<br>>
we<br>>
are<br>>
working<br>>
on.<br>>
In<br>>
the<br>>
documentation,<br>>
I<br>>
found<br>>
NIA<br>>
mouse<br>>><br>>
development<br>>
images<br>>
and<br>>
data<br>>
model<br>>
were<br>>
taken<br>>
as<br>>
an<br>>
example<br>>
to<br>>><br>>
illiustrate<br>>
the<br>>
configuration<br>>
and<br>>
implementation<br>>
of<br>>
OME<br>>
image<br>>
table<br>>><br>>
tools.<br>>
However,<br>>
I<br>>
was<br>>
not<br>>
able<br>>
to<br>>
see<br>>
the<br>>
NIA<br>>
images<br>>
or<br>>
the<br>>
tables<br>>><br>>
when<br>>
I<br>>
logged<br>>
into<br>>
the<br>>
OME<br>>
using<br>>
the<br>>
username<br>>
and<br>>
the<br>>
password<br>>><br>>
assigned<br>>
to<br>>
me<br>>
by<br>>
my<br>>
admin.<br>>
Are<br>>
those<br>>
images<br>>
availabe<br>>
only<br>>
using<br>>><br>>
the<br>>
guest<br>>
access<br>>
mode?<br>>
If<br>>
not,<br>>
what<br>>
changes<br>>
do<br>>
the<br>>
admin<br>>
has<br>>
to<br>>><br>>
make<br>>
to<br>>
view<br>>
those<br>>
NIA<br>>
tables<br>>
other<br>>
than<br>>
re-installing<br>>
OME<br>>
and<br>>><br>>
validating<br>>
the<br>>
guest<br>>
user<br>>
account?<br>>
And<br>>
where<br>>
can<br>>
I<br>>
find<br>>
the<br>>><br>>
"MouseAnnotations.ome"<br>>
file?<br>>
Also,<br>>
it<br>>
will<br>>
be<br>>
of<br>>
help<br>>
to<br>>
know<br>>
how<br>>><br>>
one<br>>
can<br>>
make<br>>
changes<br>>
(like<br>>
defining<br>>
a<br>>
new<br>>
semantic<br>>
type)<br>>
to<br>>
the<br>>><br>>
already<br>>
existing<br>>
NIA<br>>
templates<br>>
and<br>>
view<br>>
the<br>>
corresponding<br>>
images<br>>
in<br>>><br>>
the<br>>
web<br>>
based<br>>
interface.<br>>><br>>><br>>
Thanks.<br>>><br>>
Kasthuri<br>>
Kannan.<br>>><br>>><br>>
P.S:<br>>
On<br>>
a<br>>
different<br>>
note<br>>
though,<br>>
has<br>>
anybody<br>>
tried<br>>
working<br>>
with<br>>
the<br>>><br>>
IDL<br>>
and<br>>
the<br>>
OME?<br>>><br>>><br>>><br>>><br>>><br>><br>><br>><br>>><br>>
______________________________________________________________________<br>>><br>>
______________<br>>><br>>
Never<br>>
miss<br>>
a<br>>
thing.<br>>
Make<br>>
Yahoo<br>>
your<br>>
home<br>>
page.<br>>><br>>
<a href="http://www.yahoo.com/r/" target="_blank">http://www.yahoo.com/r/</a><br>>><br>>
hs_______________________________________________<br>>><br>>
ome-users<br>>
mailing<br>>
list<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>>
<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>>
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