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

[Jean-Marie Burel (Staff)]

Dear Andrii

You can modify the plane size in the omero.properties file
The rendering engine allows to render only region of the image so that will be an option too.
We are hoping to have our viewer adjusted for 5.1.0 to handle large images I.e. Images that do not qualify for pyramid generation but with large planes

Regards
Jmarie

From: Andrii Iudin <andrii at ebi.ac.uk<mailto:andrii at ebi.ac.uk>>
Date: Monday, 1 December 2014 17:18
To: Sebastien Besson <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
Cc: OME-devel OME <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>, Ardan Patwardhan <ardan at ebi.ac.uk<mailto:ardan at ebi.ac.uk>>, jburel burel <j.burel at dundee.ac.uk<mailto:j.burel at dundee.ac.uk>>
Subject: Re: [ome-devel] Loading electron microscopy MRC float-point images

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


The University of Dundee is a registered Scottish Charity, No: SC015096
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20141202/28d2dee6/attachment.html>