[ome-users] SVS file format functionality problem

[Leon Kolchinsky]

Hello Will,

Sorry for a late reply (I've been on the training last week and off I go
for another week from tomorrow ;).

Anyway, I've tested again with:
237M - 3066.svs

I've tested this file on another OMERO server with Insight client.
Import went fine but I can't see the images (see the snapshots).
It's definetely not 8 min ;(

Logs are here -
https://cloudstor.aarnet.edu.au/filesender/?vid=09D4E374-EF48-AF26-D9E6-C49263129BD7

May be it takes a reeeeally long time.

Thanks,
Leon Kolchinsky



On Wed, Nov 16, 2011 at 09:41, Will Moore <will at lifesci.dundee.ac.uk> wrote:

> Hi Kim (& Leon),
>
>  I'm not sure what the "Version 5.0" logging statement means.
> Could you show us that part of the log? Our roadmap for when and what
> OMERO 5.0 is has evolved over time. We probably need to clear that up.
>
> Could you give us some more details on how slow you're finding the import?
> I just tried it again with your sample file, running the server on my
> laptop (Recent Macbook Pro) and it took about 8 minutes to generate image
> pyramids for all the images apart from the largest (which fails).
> Is it taking you longer than this?
>
> I have also noticed incidentally that my laptop seems to be working hard
> at the failing image (fan going etc) until I delete it using Insight.
> Haven't investigated this fully yet. My logs are attached.
>
>
>
>  Cheers,
>
>   Will.
>
>
>
> On 14 Nov 2011, at 03:30, Kim Linton wrote:
>
> Hi Will,
>
> Thanks for looking into this issue for us. So all the functionality is
> there i.e. it will load all the images but it is very slow. It says in the
> log that it will be fixed in Version 5.0. Is there an approximate timeframe
> for this?
>
> Thanks for your help,
>
> Kim Linton
>
> On 11 November 2011 21:13, Will Moore <will at lifesci.dundee.ac.uk> wrote:
>
>> Hi Leon,
>>
>>  The file seems to import OK, except for the largest of the 7 images. 95k
>> x 45k (see screen-shots).
>>
>> The largest image doesn't import - This is a known issue:
>> http://trac.openmicroscopy.org.uk/ome/ticket/6500
>> "SizeX * SizeY exceeds Integer.MAX_VALUE."
>>
>> When we give you the warning "Please try again later", this is when the
>> image pyramids are being built on the server. Just takes time.
>>
>>
>>   Will.
>>
>>
>>
>> On 11 Nov 2011, at 00:54, Leon Kolchinsky wrote:
>>
>> Hello,
>>
>> We're trying to use .svs files with OMERO (latest 4.3.3 version)
>> and experiencing some issues with that.
>>
>> When .svs file uploaded via "Insight" it appears in the client as
>> following -  (checkout the screenshot )
>>  It should look like this - (checkout screenshot svs thumbnail.tiff<https://mail.google.com/mail/?ui=2&ik=c2449854ef&view=att&th=133901bdcecab120&attid=0.1&disp=safe&realattid=f_guugh9y10&zw>
>> ).
>>
>> Can you please test it and tell us how to fix the problem?
>>
>> Sample .svs file provided here -
>> https://cloudstor.aarnet.edu.au/filesender/?vid=99FF5385-A079-29C7-3B5D-90178BFC6ED7
>>
>> Thanks,
>> Leon Kolchinsky
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: Kim Linton <kim.linton at monash.edu>
>> Date: Fri, Nov 11, 2011 at 11:44
>> Subject: OMERO - SVS file format functionality
>> To: Leon Kolchinsky <leon.kolchinsky at monash.edu>
>>
>>
>> he Rendering Engine. Image not ready. Please try again later.' I also get
>> an error message when trying to view the image in Image J via the OMERO
>> plugin. I have tried loading the file including archive and without.
>>
>> Attached is a the thumbnail of the image.
>>
>> <svs thumbnail.tiff><2011-11-11_115031.jpg>
>> _______________________________________________
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>>
>>
>>
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>>
>
>
> --
>   Kim Linton
> Senior Research Systems Facilitator
> Monash e-Research Centre
> Building 75
> Monash University
> Clayton Victoria 3800, Australia
> Ph:      +61 3 99020712
> Fax:    +61 3 9902-0193
> Email:  kim.linton at monash.edu
> Web:    http://www.monash.edu.au/eresearch
> Part time: Mon, Tues, Thurs & Fri
>
>
>
>
>
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