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

[Jake Carroll]

Hi Jean-Marie.

Thanks for getting back to me. Most appreciated.

>> We currently have a limit on the size of the image that can downloaded.

Yes, and this worries people locally a great deal. They feel like their data “becomes trapped”. They can absolutely get the data IN to OMERO, but from a preservation perspective it becomes questionable to them if they can’t get *the same* data back out. From a data-governance and provenance perspective, I’d really like to see this fixed. It would allow us to adhere to several strict federal regulations and laws by doing so – and it’d make the scientists feel a lot more secure in their knowledge that OMERO is an authoritative data sink. If data can only go “one way” it represents a risk to scientists in some respects, from a digital preservation and data governance perspective, as you can appreciate.

>> 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?

Absolutely correct, yes.

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

That could be exceedingly useful to us and I’d welcome it.

>> 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.

You’d absolutely make a lot of progress for us by doing this and we’d be exceedingly appreciative. These things have been long-term niggling issues with complete OMERO adoption and total trust for a very long time. Fixing these things would boost confidence in the researchers and make OMERO a more ubiquitous platform for all.

Regards, and thanks again for your response. It is heartening.

-jc

From: "Jean-Marie Burel (Staff)" <j.burel at dundee.ac.uk>
Date: Wednesday, 26 October 2016 at 07:02
To: Jake Carroll <jake.carroll at uq.edu.au>, "ome-users at lists.openmicroscopy.org.uk" <ome-users at lists.openmicroscopy.org.uk>
Cc: "Sebastien Besson (Staff)" <s.besson at dundee.ac.uk>
Subject: Re: 12k x 12k limits for ROI extraction/manipulation - are there fixes in the pipeline?

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20161025/2899cba1/attachment.html>