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Re: [Imgcif-l] CBF Format

Hi All, particularly Justin,

I agree very strongly with Harry that there should be one imgCIF -
however, if you have enough information in the miniCBF header that one
of Herb's jiffy programs can turn it into a real CBF then I will be
happy enough...

In terms of the information content, basically everything should be in
there to allow correct processing of the images, from simple stuff like
distance / beam centre / wavelength to more subtle things like the
exposure date of the image and detector serial number. If you can write
in the gain then that would be great, though I am not sure how trivial
this is to get right. 

To my mind, the measure of success for something like this is if you can
perform a pretty much optimal processing of the data with no additional
information beyond the frames then we are there... If you need to
scratch around in log files for anything then we have work to do.

As with Nick, if you could make a full data set of say cubic insulin or
trypsin or lysozyme available that would be great. If this is successful
will it be retrofitted to already installed Mar CCD systems?

Cheers,

Graeme 

-----Original Message-----
From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
Behalf Of Harry Powell
Sent: 12 September 2007 22:31
To: The Crystallographic Binary File and its imgCIF application to image
data
Subject: Re: [Imgcif-l] CBF Format

Hi

I'd like to concur with Nick. As far as Mosflm is concerned, the miniCBF
is not a CBF. In my opinion, it should not be called "anything" CBF. 
Developers of some other integration programs have been rather less
polite
(privately) in their descriptions of the miniCBF.

My understanding is that the miniCBF was developed for the Pilatus
detector for processing with XDS - which does not use image header
information except for the image size and compression algorithm (and it
gets these from the MIME part).

If you include the CIF fields that are present in images from the ADSCs
at Diamond, you will not be going far wrong - see an example header at

 	http://www.mrc-lmb.cam.ac.uk/harry/herb.header

(this is a file I prepared for Herb a little while ago, and not linked
to, so you need to use this URL). Note that it also includes the normal
ADSC header information as a properly-formed CIF comment (i.e. free text
delimited by ";" on lines on their own), but this is not parsed by
Mosflm. 
MarCCD headers, being binary encoded, would probably not be usefully
reproduced in the CBF header!

The beamline and data acquisition staff at Diamond expect all their PX
area detectors to write CBFs in the same form with the same header
information as proper CIF items; the image compression algorithm is up
to the detector manufacturer, as long as it is one of those supported by
CBFlib.

>From a personal point of view, I think it would be really nice if all 
>CBFs
(at least in the same field) conformed to the same format!

> Thanks for working on CBF support for the Mar CCD.  The image 
> processing program LABELIT expects full CBF, not miniCBF.  The MIME 
> area is not parsed.  You are correct in identifying the "non-optional"
data items.
> This is as far as my expertise goes...it would be quite helpful if 
> some Mar datasets written in CBF format were to be made available.  
> The most useful test cases would be those where the direct beam is 
> offset from the detector center, but not at a 45- or 90-degree 
> position angle.  Full datasets would be most useful.
>
> Nick Sauter
>
> Justin Anderson wrote:
>
>> Hello everyone,
>>
>> My name is Justin Anderson with Rayonix (formerly MarUSA).  I have 
>> been given the task of adding CBF format support to the marccd 
>> program.  I was hoping you could help me with a few questions that 
>> have arisen.  I truly appreciate it.
>>
>> Now for the questions...
>>
>> 1)  Are miniCBF files meant to be read by imaging programs such as 
>> marccd or are they expected to be converted to full CBF format first?
>>
>> 2)  What is the minimum set of fields that is necessary for an 
>> official miniCBF and CBF file?  In the "Simple Example Header" in 
>> section 2 of the Draft Format
>> (http://www.iucr.org/iucr-top/cif/cbf/cbf_definition.html) it does 
>> mention at one point that "the above" data items are optional.  Does 
>> that imply that the items below are required?
>>
>> 3)  Some items can exist in both the header area and the MIME area.  
>> One such example is the image size (e.g. fastest and second-fastest 
>> number of pixels).  When reading a CBF file, should I expect to get 
>> that information from the MIME, the CBF header area or would it be
found in both?
>>
>> I appreciate any help you can give me.
>>
>>
>>
>> Justin Anderson                    Rayonix, LLC (Formerly Mar USA)
>> Software Engineer                  justin@rayonix.com
>> 1880 Oak Ave. Ste. 120             Evanston, IL, USA 60201
>> 877.627.9729                       847.869.1548
>>
>> _______________________________________________
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>>
>>
>
> --
> Nicholas K. Sauter, Ph.D.
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road
> Berkeley, CA 94720
>
> nksauter@lbl.gov
> Voice: 510-486-5713
> Fax: 510-486-5909
> _______________________________________________
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>

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

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