[ome-users] SVS file format functionality problem

Thu Nov 24 11:52:53 GMT 2011

Thanks Will,

If you need more logs or those .svs files I can upload them for you.

Have a great day,
Leon Kolchinsky

On Thu, Nov 24, 2011 at 18:31, Will Moore <will at lifesci.dundee.ac.uk> wrote:

> Hi Leon,
>
>  I've created a ticket to look at this.
> http://trac.openmicroscopy.org.uk/ome/ticket/7298
>
> Not sure what is going on just yet, but at least it seems like the
> difference between import on my laptop and your system is that on my
> laptop, the "too big" image is processed last (pyramid generation hangs).
> This means that the other images are processed reasonably quickly first,
> whereas on your system this blocker is encountered before any other images
> are processed??
>
>  Hopefully we can fix this for you soon,
>
>   Will.
>
>
>
> On 21 Nov 2011, at 05:23, Leon Kolchinsky wrote:
>
> 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>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>>
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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
>>
>>
>>
>>
>>
> <import.png><snap1.png>
>
>
>
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