[ome-users] SVS file format functionality problem

[Will Moore]

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).
>>> 
>>> 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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