[ome-users] NIA Image Tables and Images.

[Kasthuri Srinivasan Kannan]

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out 
of 
date 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?
>
>
>
>
>  
  
  
  
> 
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