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

Tue Jan 13 21:23:15 GMT 2009

Hi Ghislain & Frans,

Sorry for delaying so long in replying to this thread.

I agree that multidimensional compression is something we want to reexamine
for use with OMERO in the future. It is on our radar, and something we plan
to explore, but I cannot give a specific timetable. However, please note
that one of our goals for the coming year is better support for big images
-- improving OMERO as a tool for HCS -- including tiling for very high
resolution image planes, as well as handling many thousands of focal planes
and time points efficiently. Exploring things like multidimensional wavelet
compression to improve storage requirements and/or performance over the wire
is something that could certainly be part of that.

I am not an expert on the JAI codebase, so am not sure whether it can handle
3D, but I somehow doubt it. For our investigation a few years ago, LOCI had
a graduate student who implemented a 4D wavelet-based compression scheme in
Java. It was somewhat slow but achieved very high compression rates while
maintaining impressive quality. More recently (but still a few years ago)
LOCI collaborated with professors Sharpley and DeVore at the University of
South Carolina to explore using their most recent wavelet library to perform
a lossless wavelet-based compression. We had some promising results but
ultimately the project was not funded so the work was never completed.

There has been lots of research on efficiently compressing 3D data over time
(movies), but less for data of high dimensionality (e.g., multiple focal
planes). It is an area still ripe for research. I do not think you will find
a library you can just hook up to Bio-Formats out of the box to achieve what
you want -- it's going to take some work. If it is something you decide to
tackle, the OME team will help however we can as our time allows -- just
ask!

-Curtis

On Thu, Dec 11, 2008 at 5:13 PM, Ghislain Bonamy <GBonamy at gnf.org> wrote:

> Frans, Curtis
>
> Thanks for the response. It would be very nice to implement this
> strategy in bioformats directly to avoid having to go through 3rd party
> software to decompress images before reading them into OMERO for
> instance but also imageJ etc.
>
> Since OME is becoming the reference standard for images in microscopy
> and perhaps, biological images as a whole. It would make sense to take
> the time to implement this.
>
> Does JAI or the version incubated at LOCI provide support for 3D
> compression? If so how is this achieved? If not what libraries could we
> use for JP3D? This is a bit over my head, so if you have any old code
> for me to play with and try to implement in the compressor that would be
> great.
>
> 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
>
>
> -----Original Message-----
> From: Cornelissen, Frans [PRDBE] [mailto:FCORNELI at its.jnj.com]
> Sent: Wednesday, December 10, 2008 2:11 AM
> To: Ghislain Bonamy; ome-users at lists.openmicroscopy.org.uk
> Subject: RE: ome-users Digest, Vol 45, Issue 9 - -4. OMERO compression
> and duplicate storage (Ghislain Bonamy)
>
> Ghislain,
>
> We are currently using the MCT (multi component trasnsform) version of
> JPEG 2000 to compress 3D volumes.
> We use the SDK from AWARE
> (http://www.aware.com/imaging/digitalarchives.htm) to do this.
> There also is a refererence implementation of the "real" 3D jpeg 2000
> compression already (X,Y,Z and C(eg RGB) compressed in one "volume"
> file). This will be available within a number of months...
>
> Regards, frans
>
> -----Original Message-----
> From: Ghislain Bonamy [mailto:GBonamy at gnf.org]
> Sent: Sunday, 7 December 2008 11:04 PM
> To: Cornelissen, Frans [PRDBE]; ome-users at lists.openmicroscopy.org.uk
> Subject: RE: ome-users Digest, Vol 45, Issue 9 - -4. OMERO compression
> and duplicate storage (Ghislain Bonamy)
>
> Frans,
>
> Thanks for the answer. Like you I agree that JPEG2000, offers state of
> the art compression when it comes to images. This is why I have
> implemented JPEG2000 compression in bioformats for the TIFF and the OME
> files (readers and writers). This should hopefully be released soon. I
> am also trying to implement a solution to allow for variable rate
> compression. For instance images that are on a 16bit scale but only use
> the first 8 bit, should be saved on 1byte and not 2, this would also
> increase compression by a factor of 2. I also would like to generalize
> this so that images that use 12bit of data be compressed as 12 bit
> images and not 16 (if this is possible, this would certainly save a lot
> of space this would be particularly useful in lossy compression).
> Finally I intend to implement lossy Jpeg2000 compression in this
> variable bit rate format, which should allow 10 fold compression,
> without many artifacts, in particular for images that are dim.
>
> I would be most interested to hear how you compress your 3D data! Do you
> actually compress 1 slice at a time, or do you somehow use compression
> like in JPEG motion where info from multiple slice are pulled together
> to improve the overall compression. If so, how could this be implemented
> for multi stack tiffs etc. and build into bioformats?
>
> For the storage solution  am not quite sure how Castor operates nor how
> expensive it is, but I prompted our IT guys to have a look at it. This
> could ultimately be the solution of choice!
>
> Best,
>
>  Ghislain Bonamy, PhD
> _______________________________
> Genomic Institute of the
> Novartis Research
> Foundation
> Functional Genomics, G214
> +1 (858) 812-1534 (W & F)
> +1 (858) 354-7388 (C)
> www.gnf.org <http://www.gnf.org/>
>
> Hudson Alfa Instiute for Biotechnology
> www.haib.org <http://www.haib.org/>
> <http://www.gnf.org/>
>
> ________________________________
>
> From: Cornelissen, Frans [PRDBE] [mailto:FCORNELI at its.jnj.com]
> Sent: Sat 12/6/2008 4:55 AM
> To: ome-users at lists.openmicroscopy.org.uk; Ghislain Bonamy
> Subject: RE: ome-users Digest, Vol 45, Issue 9 - -4. OMERO compression
> and duplicate storage (Ghislain Bonamy)
>
>
>
>
>   4. OMERO compression and duplicate storage (Ghislain Bonamy)
>
> ----------------------------------------------------------------------
>
> 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
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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>
>
> End of ome-users Digest, Vol 45, Issue 9
> ****************************************
>
>
>
>
>
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