[ome-users] ome-users Digest, Vol 49, Issue 21 - Large Images and APERIO

Wed Apr 15 09:43:16 BST 2009

Hi All,

We also have the need to work with very large (tiled, mosaic) image
sizes
and the aperio format.

OMERO support for this would be very welcome!

Best regards,
Frans cornelissen
JnJ Pharma R&D IT
------------------------------

Message: 2
Date: Tue, 14 Apr 2009 16:48:19 -0400
From: "Nandakumar, Sriramkumar" <sriramkumar at uky.edu>
Subject: Re: [ome-users] Regarding Handling of Large Size Images.
To: Jason Swedlow <jason at lifesci.dundee.ac.uk>
Cc: "ome-users at lists.openmicroscopy.org.uk"
	<ome-users at lists.openmicroscopy.org.uk>
Message-ID:
	<EDC22492BE5CAF409A4166B67B1F2E9AA0B5D7E6 at EX7SM01.ad.uky.edu>
Content-Type: text/plain; charset="iso-8859-1"

Hi Jason,
Thanks for your email. I can help you out in providing use cases. And
also I shall provide you test datas (Images with different dimensions)
for your development.
We are dealing with scan scope images  (.svs files) in our lab. Scan
scope images are not supported in Omero as of now.
Do you have any idea about the support for Bio formats in future Omero
releases?

________________________________
From: Jason Swedlow [jason at lifesci.dundee.ac.uk]
Sent: Tuesday, April 14, 2009 6:10 AM
To: Nandakumar, Sriramkumar
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: Regarding Handling of Large Size Images.

Hi Sriram-

Thanks much for your email.

Indeed, those large images aren't well-handled.  Import might work, but
might not, visualization will be very very slow.

For large images, it is important to distinguish between X and Y
dimensions and Z, C, T.  OMERO handles large Z, C, and T well.  Very
large X, Y (larger than 2k x 2k) is not so great.

You will see this targetted under Beta4.2:

http://trac.openmicroscopy.org.uk/omero/milestone/OMERO-Beta4.2

We are still gathering detailed use cases for this-- any help would be
most appreciated.  If you can let us know exactly what you are thinking
and will require, would be great.

Cheers,

Jason

On 13 Apr 2009, at 23:23, Nandakumar, Sriramkumar wrote:

Hi Jason,
Thanks for your email.
I have a doubt regarding Image sizes.
We have image sizes of dimension 40000x40000.
Is it possible to upload large size images irrespective of the dimension
in latest Omero?
Could you please clarify this?

Thanks in Advance.

Thanks & Regards,
Sriram.
________________________________________
From: Jason Swedlow
[jason at lifesci.dundee.ac.uk<mailto:jason at lifesci.dundee.ac.uk>]
Sent: Friday, April 10, 2009 7:58 PM
To: Nandakumar, Sriramkumar
Cc: Joshua Moore
Subject: Re: [ome-users] Doubt regarding OMERO Server Installation.

Hi Sriram-

Our lists are down-- the UK registration agent messed us up pretty
badly.

We routinely import images of 2- 10 GB into OMERO-Beta4.

Please let us know if you have problems.

Cheers,

Jason

On 9 Apr 2009, at 16:22, Nandakumar, Sriramkumar wrote:

Hi Josh,
Thanks for your email. Now I could able to install Omero Server.

We are having large size scan scope images >500 MB
Will it be possible to upload those images in Omero Beta Version 4 ??

Thanks & Regards,
Sriram.
________________________________________
From: josh.moore at gmx.de<mailto:josh.moore at gmx.de>
[josh.moore at gmx.de<mailto:josh.moore at gmx.de>]
Sent: Wednesday, April 08, 2009 2:49 PM
To: Nandakumar, Sriramkumar
Cc:
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicrosc
opy.org.uk>
Subject: [ome-users] Doubt regarding OMERO Server Installation.

Nandakumar, Sriramkumar writes:
Hi,

Hello Sriram,

I have a doubt in OMERO Server installation. Is it mandatory to use
postgreSQL for OMERO?  Will it work for other databases like mysql?

At the moment it is necessary to use Postgres, yes. Porting it to
mysql is possible, but would require a significant effort at this
point. Hopefully that's not an undue burden.

Thanks & Regards,
Sriram.

Best wishes,
~Josh.
_______________________________________________
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ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicrosc
opy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk<mailto:jason at lifesci.dundee.ac.uk>

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.

**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk<mailto:jason at lifesci.dundee.ac.uk>

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.

------------------------------

Message: 3
Date: Wed, 15 Apr 2009 08:38:34 +0100
From: Aleksandra Tarkowska <aleksandrat at lifesci.dundee.ac.uk>
Subject: Re: [ome-users] Initialize the OMERO database
To: "Smith, Stuart C" <Stuart.C.Smith at pfizer.com>
Cc: ome-users at lists.openmicroscopy.org.uk
Message-ID:
	<F44590BD-ABAC-46DD-8355-24F37F6A5F08 at lifesci.dundee.ac.uk>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Hi Stuart

On 14 Apr 2009, at 16:47, Smith, Stuart C wrote:

> Hi, it fell at the first fence.  Upon entering "server enable web", I
> get the error "Error: couldn't find server 'web'".
>
> Have I have missed something really simple here?
>
> Stuart

If you have a problem with running web server on Windows, please try  
to do it by hand.

1) Re-configure the Web server in C:\OMERO4.0.0\etc\grid\default.xml  
to be on-demand:
      <server-instance template="ShellTemplate" id="Web" act="on- 
demand"/>

and restart:

bin\omero admin stop
bin\omero admin start

2) Please follow the instruction on http://www.openmicroscopy.org/ 
site/documents/data-management/omero4/server/troubleshooting on the  
section "I cannot access page http://localhost:8000/webclient/"

3) Please look at "Web server start up error on WINDOWS (for 4.0.0)"  
and "I can access OMERO.web but every request produce error page" as  
well.

If you still have any problems please let me know.

Thanks
Aleksandra

------------------------------

Message: 4
Date: Wed, 15 Apr 2009 09:29:48 +0100
From: Jason Swedlow <jason at lifesci.dundee.ac.uk>
Subject: Re: [ome-users] Regarding Handling of Large Size Images.
To: "Nandakumar, Sriramkumar" <sriramkumar at uky.edu>
Cc: "ome-users at lists.openmicroscopy.org.uk"
	<ome-users at lists.openmicroscopy.org.uk>
Message-ID:
	<FA2AB867-9892-4109-B0DA-0F408411CDC7 at lifesci.dundee.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Hi Sriram-

On 14 Apr 2009, at 21:48, Nandakumar, Sriramkumar wrote:

> Hi Jason,
> Thanks for your email. I can help you out in providing use cases.  
> And also I shall provide you test datas (Images with different  
> dimensions) for your development.

That's great-- contact us off-line for details for upload.

>
> We are dealing with scan scope images  (.svs files) in our lab. Scan  
> scope images are not supported in Omero as of now.

I assume you mean the Aperio format?  Aperio's format is not yet  
turned on within OMERO, as we don't yet have a very good mechanism for  
supporting images with large X,Y dimensions.

>
> Do you have any idea about the support for Bio formats in future  
> Omero releases?

OMERO uses Bio-Formats for its image import.  We turn on files  
supported by Bio-Formats within OMERO once we know the file format  
works well, i.e.,  we have test data, have verified that metadata is  
properly handled, and that images are properly displayed.  We have  
some Aperio sets, but more would help.

Thanks again.

Cheers,

Jason

>
>
> ________________________________
> From: Jason Swedlow [jason at lifesci.dundee.ac.uk]
> Sent: Tuesday, April 14, 2009 6:10 AM
> To: Nandakumar, Sriramkumar
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: Regarding Handling of Large Size Images.
>
> Hi Sriram-
>
> Thanks much for your email.
>
> Indeed, those large images aren't well-handled.  Import might work,  
> but might not, visualization will be very very slow.
>
> For large images, it is important to distinguish between X and Y  
> dimensions and Z, C, T.  OMERO handles large Z, C, and T well.  Very  
> large X, Y (larger than 2k x 2k) is not so great.
>
> You will see this targetted under Beta4.2:
>
> http://trac.openmicroscopy.org.uk/omero/milestone/OMERO-Beta4.2
>
> We are still gathering detailed use cases for this-- any help would  
> be most appreciated.  If you can let us know exactly what you are  
> thinking and will require, would be great.
>
> Cheers,
>
> Jason
>
> On 13 Apr 2009, at 23:23, Nandakumar, Sriramkumar wrote:
>
> Hi Jason,
> Thanks for your email.
> I have a doubt regarding Image sizes.
> We have image sizes of dimension 40000x40000.
> Is it possible to upload large size images irrespective of the  
> dimension in latest Omero?
> Could you please clarify this?
>
> Thanks in Advance.
>
> Thanks & Regards,
> Sriram.
> ________________________________________
> Jason
>
> On 9 Apr 2009, at 16:22, Nandakumar, Sriramkumar wrote:
>
> Hi Josh,
> Thanks for your email. Now I could able to install Omero Server.
>
> We are having large size scan scope images >500 MB
> Will it be possible to upload those images in Omero Beta Version 4 ??
>
> Thanks & Regards,
> Sriram.
> ________________________________________
> From: josh.moore at gmx.de<mailto:josh.moore at gmx.de>
[josh.moore at gmx.de<mailto:josh.moore at gmx.de 
> >]
> Sent: Wednesday, April 08, 2009 2:49 PM
> To: Nandakumar, Sriramkumar
> Cc:
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicrosc
opy.org.uk 
> >
> Subject: [ome-users] Doubt regarding OMERO Server Installation.
>
> Nandakumar, Sriramkumar writes:
> Hi,
>
> Hello Sriram,
>
> I have a doubt in OMERO Server installation. Is it mandatory to use
> postgreSQL for OMERO?  Will it work for other databases like mysql?
>
> At the moment it is necessary to use Postgres, yes. Porting it to
> mysql is possible, but would require a significant effort at this
> point. Hopefully that's not an undue burden.
>
> Thanks & Regards,
> Sriram.
>
> Best wishes,
> ~Josh.
> _______________________________________________