[ome-users] ome-users Digest, Vol 45, Issue 9 - -4. OMERO compression and duplicate storage (Ghislain Bonamy)

Sat Dec 6 12:55:00 GMT 2008

   4. OMERO compression and duplicate storage (Ghislain Bonamy)

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Ghislain,

About: "store lossy images on disk":

We are currently using Jpeg 2000 compression for this.
The advantage of using this would be that you do not even need to store
2 versions of your image files; JP2 allow sto read any size or any
quality
image version out of a single (lossless or lossy) compressed file.

JP2 is currently THE state of the art way to get maximum flexibility AND
Maximum compression ratio; for 2D Biological images lossless, factors of
2.5 to 4 are achievable (depending on the actual image content)
In 3D, quasi lossless compression (PSNR >45) of 20-100 times is possible

About:"slow tape system to store files"

you could have a look at CASTOR from CARINGO (www.caringo.com), a
simple,cheap, but very efficient next-gen Software system for
distributed storage on heterogenous hardware, with very good
performance. 
Scales very well to > 80 PB.
We have been testing it to store JPEG 2000 images for 18 months, worked
withour a flaw! 
Also in use at the The Center of Inherited Disease Research (CIDR) at
Johns Hopkins University

Message: 4
Date: Fri, 5 Dec 2008 10:10:54 -0800
From: "Ghislain Bonamy" <GBonamy at gnf.org>
Subject: [ome-users] OMERO compression and duplicate storage
To: <ome-users at lists.openmicroscopy.org.uk>
Message-ID:
	<F5A26DAD36F60843830631774C95CAE205807A58 at EXCH2.rec.gnf.org>
Content-Type: text/plain; charset="us-ascii"

Dear all,

I was wondering if OMERO has already implement, is thinking or would
consider implementing a mechanism to store images into two different
format while keeping there metadata linked.

I am working in a center were we are generating several TB of data a
month and where keeping all of our images on disk becomes impossible. To
remedy to this, we have a >2 PT tape storage solution, which is however
very slow (takes about 2-4 Minutes to retrieve a file the first time
until it is de-cued) . My idea would be to store lossy images on disk
for people to view and modify metadata, while keeping the full blown
image onto our slow storage solution in case they needed to be
reanalyzed for instance. The metadata for this images would however be
kept identical between images. 

Perhaps, a way to do this would be to store in Omero the file and keep
in the metadata a link to the original image. If there are another and
better solution please let me know.

In addition, does OMERO store the metadata in a compressed way (as well
as the images), or is there a way to have OMERO apply a script (for
instance a gzip compression) when importing images and when an image is
queried?

Thanks a bunch for all your help and answers,

Best,

Ghislain Bonamy, PhD
__________________________________________

Research Investigator I

Genomic Institute of the

Novartis Research

Foundation

Department of Molecular & Cell Biology, room G214

10675 John Jay Hopkins Drive

San Diego CA 92121

USA

+1 (858) 812-1534 (W & F)

+1 (757) 941-4194 (H)

+1 (858) 354-7388 (M)

www.gnf.org

Hudson-Alpha Institute for Biotechnology

www.hudsonalpha.org

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End of ome-users Digest, Vol 45, Issue 9
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