Hi
Just to add to this. imgCIF (or CBF, which amounts to pretty well the same
thing) has fast and efficient compression built in, and has been developed
with protein crystallography (particularly) in mind. There are even (a
few) detectors out there which will write these instead of (or as well as)
the manufacturer's native format, saving the user the trouble of
conversion.
If you're looking for a standard format for storing image data in, I
wouldn't look any further, since (in principle) imgCIF/CBF can store all
the image information you (or a fussy^H^H^H^H^H conscientious reviewer who
could be bothered to re-process your dataset) would want about your data
collection and you wouldn't need to come up with inventive tags for data
items that might be required for other (general purpose) image formats.
There are even conversion programs available to convert to imgCIF/CBF
files from some native formats - if your favourite detector isn't one of
these, drop Herb Bernstein a line and ask for support ;-)
I looked at jpeg2000 as a compression for diffraction images for
archiving purposes - it works well but is *SLOW*. It's designed with the
idea in mind of compressing a single image, not the several hundred
typical for our work. There is also no place to put the header.
Bzip2 works pretty much as well and is standard, but again slow. This is
what people mostly seem to use for putting diffraction images on the
web, particularly the JCSG.
The ccp4 "pack" format which has been around for a very long time works
very well and is jolly quick, and is supported in a number of data
processing packages natively (Mosflm, XDS). Likewise there is a new
compression being used for the Pilatus detector which is quicker again.
These two have the advantage of being designed for diffraction images
and with speed in mind.
So there are plenty of good compression schemes out there - and if you
use CBF these can be supported natively in the image standard... So you
don't even need to know or care...
Just my 2c on this one.
Cheers,
Graeme
-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Maneesh Yadav
Sent: 18 August 2007 00:02
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] diffraction images images/jpeg2000
FWIW, I don't agree with storing image data, I don't think they justify
the cost of storage even remotely (some people debate the value of the
structures themselves....)...but if you want to do it anyway, maybe we
should use a format like jpeg2000.
Last time I checked, none of the major image processing suites used it,
but it is a very impressive and mature format that (I think) would be
suitable for diffraction images. If anyone is up for experimenting, you
can get a nice suite of tools from kakadu (just google kakdu +
jpeg2000).
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH
