[ome-devel] ome-devel Digest, Vol 81, Issue 5

[Rubén Muñoz]

Hi Andrew and list subscribers,  

I have some comments to add regarding the OME.TIFF and OME.XML requirements for changes. The current description of our issue is:
* EMBL Screening (Ruben Muñoz, Jan Ellenberg)
        * Not duplicating XML for each field, _plane_, etc.
I would like to add that our use case, will apply to each user of the OME.TIF multi-file export option. 

We previously pointed out that the number of planes that are stored per OME-TIFF has a big impact in each file's size. For multi-file datasets, the conversion output will be exponentially bigger than the raw data.

At EMBL-Heidelberg HCS Facility, we have used this as internal standard, with the pre-requisite of having one single plane per file. 
The reasons to do that can be summarized:  gives maximum compatibility with software for image processing, online control of the microscope and visualization, even after instrument/power failure. This software includes in-house developments: CellCognition, Micropilot, Cellbase and 3rd-party projects: CellProfiler, Image J/FIJI.

Given this scenario we found OME.TIF convenient because it has the correct conversion tools and an evolving metadata structure, in addition the commercial adoption of the format is growing.

In the practice, a lot of the metadata consist in "<Plate>", "<Image>" and "<Pixel>" elements (describing the SPW, dimensionally and the references to the files in the set). 

That can be prohibitive at the processing and the storage stage.
Some options to simplify the format have ben discussed as follows:

 - The master/slave approach. All files will reference the one that contains the complete headers.
 - "<Plate>", "<Image>" and "<Pixel>" elements could be grouped when similar (e.g. reg. expressions following a pattern)
 - The "<Plate>", "<Image>" and "<Pixel>"  could be extracted to a separate file.

The first alternative was supported by Andrew. I suggested the second, but the project philosophy is opposite to the third. 

Are there other suggestions? I would like to keep this discussion open and to help to define more details if needed.

Best,
Rubén

On Dec 7, 2010, at 4:03 PM, ome-devel-request at lists.openmicroscopy.org.uk wrote:
> 
> Date: Tue, 7 Dec 2010 13:07:49 +0000
> From: Andrew Patterson <ajpatterson at lifesci.dundee.ac.uk>
> To: ome-devel at lists.openmicroscopy.org.uk,
> 	ome-users at lists.openmicroscopy.org.uk
> Subject: [ome-devel] OME-XML Updates
> Message-ID:
> 	<B5B2766B-2357-40C1-B1DD-06CCEC3A62C9 at lifesci.dundee.ac.uk>
> Content-Type: text/plain; charset=us-ascii
> 
> Hello OME-XML & OME-TIFF users and potential users,
> 
> We are in the process of compiling requirements for changes to the way our OME-XML and OME-TIFF formats work. This is in response to the new ways people are wanting to use our formats, and drawbacks they have come across when storing datasets in certain circumstances.
> 
> Examples we have so far include:
> * storing large datasets, one plane per OME-TIFF: this is a valid way to want to store data, but one which at the moment causes metadata duplication on disk.
> * creating a 'lite' OME-TIFF for display or to pass to external applications.
> 
> A full list of our current thoughts is on the requirement ticket:
> http://trac.openmicroscopy.org.uk/omero/ticket/3535
> 
> Some of these changes may effect key features of our formats, e.g. our current insistence that all matadata is stored in the same file as the image data. 
> 
> We would really like to have your input on this feature, or any others.
> 
> If you have a use case that you think would help guide out future work we would love to hear from you. If you can reply on either of the mailing lists (OME-USER or OME-DEVEL), it will let others see and join in!
> 
> Thanks again for your help and support.  
> 
> Cheers,
> 
> Andrew
> 
> --
> Andrew Patterson
> ajpatterson at lifesci.dundee.ac.uk
> Software Developer, Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation & Expression, University of Dundee

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