[ome-users] Regarding Handling of Large Size Images.

Wed Apr 15 18:57:00 BST 2009

Hi Jason,
Yes it is aperio format. Do you have any idea of support for scan scope images in future omero releases?

Thanks & Regards,
Sriram.
________________________________
From: Jason Swedlow [jason at lifesci.dundee.ac.uk]
Sent: Wednesday, April 15, 2009 4:29 AM
To: Nandakumar, Sriramkumar
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: Regarding Handling of Large Size Images.

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<mailto: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<mailto: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.openmicroscopy.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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**************************
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.