[ome-devel] [ome-users] Using 3D JPEG2000 compression in OMERO

Fri Dec 12 16:50:26 GMT 2008

Frans, Curtis, Prof. Schelkens, 

I have added this thread to the Ome-Dev List as it now seems more
suited. Hopefully I have the right address this time around.

It would indeed wonderful if the 4D JP2000 (ie. XY,C,Z) could be
implemented into Bioformats. Prof. Schelkens, would you agree to provide
your source code for the OME open source project, or at least allow the
use of the binaries?

Curtis, how would you fell about using some C code as part of bioformat?
I can imagine the problem being having platform specific compilations
(unless we package many different binaries and use a JNI wrapper to call
the right version). 

Unfortunately, I am not well versed in C programming, and never wrote
any JNI wrappers. Perhaps, someone who shares this interest to provide
greater image compression could jump and try to implement some hooks to
Prof. Schelkens Codec. In addition if the source code is available,
perhaps adding also a pure java code could be useful (to mirror the JAI
project).

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: Friday, December 12, 2008 5:17 AM
To: Ghislain Bonamy; Curtis Rueden; Schelkens Peter
Cc: 
Subject: Using 3D JPEG2000 compression in OMERO
Importance: High

Ghislain,

As far as 3D-JPEG2000 compression (=compression of XYZ with multiple
color channels) is ocncerned, there is one reference implementation
(written in C) from the Free Univerisity of Brussels.

You could ask Prof. Peter Schelkens for permission to use the
(compiled?source?-)code in OMERO (maybe under a kind of NDA about the
source code...)

It would be fantastic to see this embedded in OMERO/Bioformats!

Best regards, frans

-----Original Message-----
From: Ghislain Bonamy [mailto:GBonamy at gnf.org] 
Sent: Friday, 12 December 2008 12:13 AM
To: Cornelissen, Frans [PRDBE]; Curtis Rueden
Cc: 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, 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

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