[ome-devel] Loading electron microscopy MRC float-point images

[Andrii Iudin]

Dear Jean-Marie and Sebastian,

Thank you for the prompt reply! We are currently using the development 
version and for now our service will remain in development. Checks were 
made on both the downloaded pre-build 5.1.0 and on the one built locally 
from Github source.

The problem we have is that EM images are often very large, even greater 
than 4096x4096 and often float. Please could you point me to the code 
where one can turn the pyramid generation off for such images? Is it, 
perhaps, possible to render only a part of a large image, say 1024x1024 
slice out of 4096x4096?

Best regards,
Andrii


On 01/12/2014 14:05, Sebastien Besson wrote:
> Dear Andrii,
>
> as a side-note, OMERO 5.1.0 is not released yet as the OME team is 
> actively working
> on it. As a matter of fact, it is still in development and should not 
> be used in production.
> Just to make sure we are not shipping non-production versions, was 
> your sever built
> from the source code?
>
> Best regards,
> Sebastien
>
> On 1 Dec 2014, at 13:46, Jean-Marie Burel <j.burel at dundee.ac.uk 
> <mailto:j.burel at dundee.ac.uk>> wrote:
>
>> Dear Andrii
>>
>> When the size of plane is greater than 4kx4k, a pyramid is generated.
>> The fact that you end up with a black square is a result of JPEG-2000 not
>> supporting floating point images at all.
>> We are investigating options, no candidate library found yet, we might
>> have to turn the pyramid generation off
>> for such images.
>> Unfortunately in the current implementation not a parameter you can 
>> switch
>> off.
>> An alternative could be to increase the limit of the plane size before
>> generating a pyramid.
>> The image will be slower to load but you will be able to view it.
>>
>> Regards
>>
>> Jmarie
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk 
>> <mailto:ome-devel at lists.openmicroscopy.org.uk>
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
> Dr Sébastien Besson
> Open Microscopy Environment / Harvard Medical School
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096 

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