[ome-users] 12k x 12k limits for ROI extraction/manipulation - are there fixes in the pipeline?

[Jean-Marie Burel (Staff)]

Dear Jake

We currently have a limit on the size of the image that can downloaded.
By ROI extraction, are you thinking of creating ROI on some of those large images and "cropping" to generate a new image then download that image?

A new script is available in OMERO 5.3, https://github.com/ome/scripts/pull/115 to generate tiles images from ROIs

We are considering a 5.2.7 release to add support for ice 3.6.3
So we could certainly back port the script  mentioned above if it solved some of the issues.


Cheers

Jmarie

From: Jake Carroll <jake.carroll at uq.edu.au<mailto:jake.carroll at uq.edu.au>>
Date: Tuesday, 25 October 2016 03:50
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Cc: jmarie burel <j.burel at dundee.ac.uk<mailto:j.burel at dundee.ac.uk>>, "Sebastien Besson (Staff)" <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>>
Subject: 12k x 12k limits for ROI extraction/manipulation - are there fixes in the pipeline?

Hi all.

I was just wondering if there had been any consideration given to the 12k x 12k pixel limit on certain ROI Extraction/manipulation semantics in OMERO 5.3 for your road map? From what I can tell, in OMERO 5.2.x series code, there still exists limitations on how large an extraction of an ROI can be, and the ability to manipulate data beyond 12k x 12k pixel wide dimensions.

We're now on a daily basis, getting significant requests/complaints from people ingesting very big things (100k x 100k pixel style stuff) who'd dearly love to work with their data - but can't ROI extract, nor work with it anymore, due to the fact that there seems to be a 12k x 12k limit on file format transforms (I assume it is a BIOFormats thing/BIgTIFF thing/OMETIFF limitation).

Would like to know if any progress had been made with this limitation - it'd kind of liberate OMERO for us in an amazing way/really make a lot of scientists smile...

Thank you.

-jc

The University of Dundee is a registered Scottish Charity, No: SC015096
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