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

Wed Apr 15 09:29:48 BST 2009

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.
> ________________________________________
> 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.
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk 
> >
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> **************************
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>
> phone (01382) 385819
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>
> 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.
>
>
>

**************************
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

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.

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