[ome-users] Bio-Formats and Omero

Thu Nov 27 19:25:20 GMT 2008

Hi Paulo-

Thanks for this.

On 27 Nov 2008, at 18:56, Paulo Almeida wrote:

> Hi Jason,
>
> Thanks for the lengthy reply. When a user asked me about QuickTime  
> movies, I
> wasn't even thinking of metadata, but of course your concern is
> understandable.
>

It's really just a matter of priorities and resources.

> Just a thought: depending on the focus of Omero (strictly "serious"  
> microscopy
> data, or something broader encompassing science communication, for  
> instance),
> it might be worth relaxing the metadata completeness for a few  
> formats that
> are widely used in areas other than microscopy (png, jpeg, mov,  
> etc). Some
> researchers may want to take advantage of Omero's organization and  
> annotation
> features for their poster and paper images, where the original  
> metadata would
> not be so important.
>

Actually, we agree.  Right now, we are doing metadata, because that  
has to be right.  We recognise the flexibility people want, which is  
why you see JPEG, etc supported.  MOV, AVI, etc.  will come.  We'll  
get it scheduled once we get the metadata sorted.

As always, thanks for your support and interest.

Cheers,

Jason

> - Best,
> Paulo
>
> On Wednesday 26 November 2008 21:08, Jason Swedlow wrote:
>> Hi All-
>>
>> Apologies for the delayed response-- we've been pretty busy.
>>
>> Ok, it all seems so simple.....if only.
>>
>> As Paulo and Sriram highlighted, the support for images in Bio-
>> Formats is much broader than in OMERO.  There are many reasons for
>> this, but ultimately it comes down to metadata and testing-- we only
>> turn on support for a specific file format in OMERO if we have a good
>> set of test data and if we have a home for as much metadata as
>> possible coming from Bio-Formats.  This rather picky approach is very
>> laborious, so we have turned on file formats slowly.
>>
>> HOWEVER, there is another question-- "metadata completeness".  Have
>> we found a home for every element of metadata in a proprietary file
>> format in Bio-Formats and also OMERO?  This has been our focus
>> (really, obsession) for the last few weeks-- see for example:
>>
>> http://trac.openmicroscopy.org.uk/omero/query?
>> status=assigned&status=new&status=reopened&group=status&component=Imp 
>> ort
>> &milestone=OMERO-Beta4
>> http://trac.openmicroscopy.org.uk/omero/query?
>> status=assigned&status=new&status=reopened&group=status&component=Mod 
>> el&
>> order=priority&milestone=OMERO-Beta4
>>
>> Some of you who use the Leica fie formats know how important this
>> work is:
>>
>> http://trac.openmicroscopy.org.uk/omero/ticket/1124
>>
>> Having supported some 30+ file formats in OMERO, and 60+ in Bio-
>> Formats, we have turned our attention to metadata completion.   This
>> is slow, painful work, requiring alot of updates to the OME Data
>> Model (http://ome-xml.org/query?
>> status=closed&group=resolution&milestone=September+2008+Schema
>> +Release), Bio-Formats, and OMERO.  But we are making headway-- that
>> is the good news.  The bad news is that we have just a few file
>> formats fully supported.  The amount it takes to fully support more
>> gets smaller and smaller, but this will still be slow.  "Completion"
>> is synonomous with "perfection", and we are quite good at being
>> imperfect. Think of this as an asymptotic approach to a Holy Grail.
>>
>> (Just to toot our horn-- we have a saying on the OME project: "we eat
>> our own dog food".  That means we don't just issue specifications, we
>> write and release software based on these specifications, so we find
>> many of  the mistakes, limitations, etc.  Honestly, we really are
>> intimately familiar with our spec, and are working very hard to make
>> it better-- more accurate, more usable-- and release software based
>> on it.  Not many format and specification projects do this, and it is
>> one of the reasons we have been, dare I say it,  marginally  
>> successful.)
>>
>> Sooooooooooooo, uh, no, the release of Beta4 most likely won't
>> include a large number of new file formats.  What you will see is a
>> big change in the amount of metadata supported and visible in our
>> clients, and slowly, the existing file formats more fully supported
>> (hopefully completely).  For anyone going to ASCB, we are hoping to
>> show examples of this at the OME Booth-- so please come by and tell
>> us what metadata you must have.
>>
>> HOWEVER, please do keep those file format requests coming, and if at
>> all possible, write to us and let us have some samples of the files
>> you'd like to have supported-- testing helps us be sure we are
>> releasing useful software.   We'll start adding more formats soon,
>> probably in the next couple of months.
>>
>> Cheers,
>>
>> Jason
>>
>> On 26 Nov 2008, at 16:35, Paulo Almeida wrote:
>>> Hi,
>>>
>>> Regarding a recent question about .svs images, does Omero intend to
>>> support
>>> everything in Bio-Formats? That question arose because one of our
>>> users
>>> wanted to upload a QuickTime movie, which is listed in Bio-Formats
>>> but not in
>>> the Omero ImporterFormats that Sriram pointed to (
>>> http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats ).
>>>
>>> Best,
>>> Paulo
>>> Instituto Gulbenkian de Ciência
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
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>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> phone (01382) 385819
>> Intl phone:  44 1382 385819
>> FAX   (01382) 388072
>> email: jason at lifesci.dundee.ac.uk
>>
>> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
>> Open Microscopy Environment: http://openmicroscopy.org
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**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.